diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 00000000..396fa180 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,690 @@ +# Changelog + +All notable changes to `tfscreen` are recorded here. The format follows +[Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and the project uses +[semantic versioning](https://semver.org/). + +Entries cite files and functions rather than commit hashes, so they stay valid +across rebases and amended commits. + +## Provenance + +The contemporaneous log begins on 2026-09-10, at package version 0.4.3; this +file was assembled on 2026-09-22 around the reconstruction made then. Entries +fall into two kinds: + +- **Contemporaneous.** Written at the time of the change, as part of the + change. Every entry from 0.4.4 onward is contemporaneous *except* blocks + explicitly headed "Reconstructed". +- **Reconstructed.** Backfilled on 2026-09-10 from `git diff` between release + tags, commit messages, and the GitHub + [release notes](https://github.com/harmslab/tfscreen/releases). Every + version section from 0.4.3 back to 0.1.0 is reconstructed and opens with a + marker saying so. Those sections describe the net change between tags; a + feature added and removed within one release is not listed. Commit messages + from this period are terse, so bullets were written from the diffs and kept + only where the diff or code confirmed them; they may still be incomplete. + Where a GitHub release note exists, it is quoted verbatim as the author's + own contemporaneous summary, separate from the reconstructed bullets. + +## [Unreleased] + +Nothing yet. + +## [0.4.4] - 2026-09-22 + +A processing and bookkeeping release: two fixes in the read-counting and +`ln_cfu` paths, a library description for `tfs-configure-model`, and a +general cross-run comparison tool. The inference model itself is unchanged -- +this is the groundwork for 0.5.0, which changes how congression and spiked +genotypes are handled. + +### Added + +- **Library description for `tfs-configure-model` (`--library_config`).** The + model now learns which genotypes were spiked into the library from the + library YAML itself -- the same file handed to `tfs-process-fastq` -- instead + of a hand-written list of genotype names. It is required whenever + `--growth_df` is given and refused for a binding-only model. + - `tfscreen.genetics.library_design`: `library_composition_table()` turns a + library config into one row per genotype (`is_wt`, `in_spiked_origin`, + `pool_fraction`, `bulk_fraction`, `origins`), with + `read_library_composition` / `write_library_composition` for the snapshot. + The module also carries `expected_library_composition`, + `scale_library_design` and `estimate_library_mixture` (the last estimates a + realized `library_mixture` from an observed abundance table, e.g. a + pre-split sample). + - `tfs-configure-model` writes `{out_prefix}_library.csv` and records it in + the config as `library_file`, alongside a `library` block holding the + source path and the declared `library_mixture`. `tfs-fit-model` reads the + snapshot CSV, never the YAML, so the table is where a design number can be + overridden -- the same pattern as the priors and guesses CSVs. + - `tfs-configure-model` now **fails** if any genotype in `growth_df`, + `presplit_df` or `base_growth_df` is absent from the library + (`__unknown__` excepted). A residue-numbering or wt-sequence difference + between the library description and the reads it was called against + mismatches most or all genotypes and is caught on the first run. + - `ModelOrchestrator` gains `library_file` and exposes the table as + `orchestrator.library_df`. + - `examples/process_raw/library_config.yaml` gains `library_mixture`. + +### Changed + +- **Breaking: `tfs-configure-model --spiked` is removed**, replaced by + `--library_config` (above). **Action:** pass the experiment's library YAML + instead of listing spiked genotypes. Configs already written with + `spiked_genotypes` still load, and `ModelOrchestrator(spiked_genotypes=...)` + still works, but the two inputs are mutually exclusive. +- **Breaking: `tfs-fit-genotypes` and `tfs-build-empirical --spiked_file` + become `--library_config`.** The congression-free genotypes are read from + the library description rather than a text file of names. +- A spiked genotype named by the library but absent from the growth data is + reported and ignored, rather than raising. The list is derived from the + library design, and real spikes can drop out of a dataset. A hand-supplied + `spiked_genotypes` list still raises, since it is hand-written. +- `counts_to_lncfu` works in log space. It now reads + `sample_ln_cfu`/`sample_ln_cfu_std`, inferring them via `get_scaled_cfu` + from `sample_ln_cfu_var`, or from `sample_cfu` plus + `sample_cfu_std`/`sample_cfu_var` when the log-space columns are absent + (log-space wins). Genotype `ln_cfu`/`ln_cfu_var` are computed directly in + log space and `cfu`/`cfu_var` derived from them. The new helper + `get_sample_ln_cfu` is called early by `tfs-process-counts` and + `tfs-process-presplit`, so a bad sample sheet fails before any counts are + read; `get_scaled_cfu` gains a `prefix` argument. Existing sample sheets + with `sample_cfu`/`sample_cfu_std` keep working and give identical results; + outputs gain `sample_ln_cfu`/`sample_ln_cfu_std`. + +### Known issues + +- **`pool_fraction` and `bulk_fraction` are recorded but not yet used by the + model.** The fit still treats "spiked" as a binary (congression-free plus a + separate `ln_cfu0` prior class), although wt and the spiked single mutants + are in fact mostly bulk cells. `bulk_fraction` is the per-genotype weight an + observable-level congression mixture will need. +- **Nothing cross-checks `library_mixture`.** No upstream artifact ever reads + it, so a stale or wrong mixture cannot be detected -- only recorded. The + genotype-set check covers the genetics keys only. Use one `run_config.yaml` + per experiment for `tfs-process-fastq`, `tfs-simulate` and + `tfs-configure-model`. + +### Reconstructed: changes between v0.4.3 and 2026-09-10 + +> *Reconstructed on 2026-09-10 from `git diff v0.4.3..HEAD` and commit +> messages. These entries were not written when the changes were made. They +> cover commits from before the contemporaneous log began that are not +> described above.* + +#### Added + +- **Pre-fit model accounting in `tfs-configure-model`.** + `tfmodel/model_stats.py` (`count_model_dimensions`, `format_model_stats`, + `write_model_stats`) traces the numpyro model under `jax.eval_shape` and + counts latent parameters (by plate, support and component) against + observations (from `good_mask`). It also records per-genotype coverage and + the anchors that pin the k/dk_geno/k_ref slide. + - `tfs-configure-model` prints a summary and writes + `{out_prefix}_model_stats.csv` and `{out_prefix}_model_stats.json`. + `--skip_model_stats` disables this. +- `tfs-process-fastq` logs at startup whether numba JIT is active. + +#### Changed + +- **Breaking:** `tfs-compare-feature` is replaced by `tfs-compare-runs` + (`analysis/compare_runs.py`, `analysis/scripts/compare_runs_cli.py`). The + new tool is estimate-agnostic: it accepts predicted features + (theta/growth/epistasis) and `tfs-extract-params` parameter tables. + - Keys are configurable: an auto-detected match key, plus `--match_by`, + `--index_by` and `--group_by`. The run count (`n_present`/`n_runs`) is + reported. + - It reports only raw statistics (`rms_sd`, `overdispersion` with p and a + BH q). The graded A–D `tier` column, the `overdispersed` flag, the + crosstabs output, and `--sd_tier_edges`/`--overdispersion_threshold` are + gone. + - Output is sorted in canonical genotype order. + - Estimates are passed as two or more CSV paths or as a single manifest + file. + - The aggregate mixture CSV is written by default (`--no_aggregate` + suppresses it) and resolved settings go to `{out_prefix}_metadata.json`. +- **Faster `tfs-process-fastq`.** The expected-library reconciliation pass + used to walk `pybktree` in Python. It now flattens the BK-tree to CSR + arrays and searches it in a single numba kernel, which is about 4.4× faster + on that pass with identical output. The `FastqToCounts` object is shipped to + each pool worker once, via an initializer, instead of on every submit. + +#### Fixed + +- **`__unknown__` reads were counted as wildtype.** `standardize_genotypes` + (`genetics/genotype_sorting.py`) parsed the reserved `__unknown__` label as + a self-to-self mutation and collapsed it to `wt`. This produced a phantom + second `wt` row carrying all unattributable reads. + - Reserved labels (`UNKNOWN_GENOTYPE`, `RESERVED_GENOTYPES`) now pass + through unchanged. Mutation tokens without an integer site number now + raise instead of being treated as synonymous. + - `counts_to_lncfu` keeps the `__unknown__` bucket in the per-sample + read-depth denominator, drops it from genotype rows, and excludes it from + the pseudocount term. The binomial frequency variance now uses that same + denominator. + - **Action:** regenerate `ln_cfu` tables produced from counts files that + contain an `__unknown__` row. +- `tfs-process-fastq --num_workers` was parsed with the wrong type because it + defaults to `None`. It is now forced to `int`. + +## [0.4.3] - 2026-07-23 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.4.2..v0.4.3`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> This release improves the epistasis and cat response code. One of the major theoretical predictions motivating this work is that epistasis in dG versus log(effector) should exhibit peak-like behavior if the ensemble is redistributed. This implements that, allowing for epistasis estimates using logit(theta) (proportional to dG), improved/numerically stabilized peak calling, and joint estimates of epistasis from the full posterior rather than marginal theta distributions. +> +> - joint estimates of epistasis +> - improved cat response code +> - ability to predict genotype growth on a small subset of genotypes +> - added ability to pool runs with different seeds to generate aggregate posteriors +> - general bug fixes + +**Reconstructed changes:** + +### Added +- **Joint epistasis from the posterior (`tfs-predict-epistasis`).** New CLI (`tfmodel/scripts/predict_epistasis_cli.py`, backed by `extract_theta_epistasis` in `tfmodel/analysis/extraction.py`). It draws θ for every genotype from the same posterior sample, computes mutant-cycle epistasis within each draw, and reports quantiles across draws. The uncertainty therefore includes the posterior covariance between the four cycle corners, which the marginal-θ route drops. Output columns are `genotype`, `titrant_name`, `titrant_conc`, bare `q` columns, and a trailing `in_regime` flag. Flags: `--scale` (`logit` default, `add`, `mult`), `--scale_constant`, `--regime_eps` (default 0.01), `--regime_ci` (default 0.95), plus the usual `--genotypes_file`/`--titrant_names_file`/`--titrant_concs_file`/`--only_files`. Only genotypes seen in training are supported. A MAP `.pkl` gives a single point estimate. +- **`in_regime` flag.** Set to 1 only when all four cycle corners have their θ posterior (central `regime_ci` interval) inside `[regime_eps, 1 - regime_eps]`. Rows with `in_regime == 0` depend on the model's functional form, not directly on the data. +- **Logit-scale epistasis.** `tfscreen.analysis.extract_epistasis` accepts `scale="logit"`: additive epistasis of `logit(Y)`, which is proportional to ΔG for an occupancy. It also gains `scale_constant` (multiplies the transform, e.g. `-RT` to report an interaction free energy; rejected for `mult`) and `logit_eps` (clamp before the logit; warns on inputs outside [0, 1]). The per-scale definitions now live in one helper, `_epistasis_from_corners`, which the posterior path also uses. +- **`tfs-extract-epistasis` CLI** (`analysis/scripts/extract_epistasis_cli.py`). Computes epistasis from any long-form observable table. Flags: `--y_obs`, `--y_std`, `--group_by`, `--scale add|mult|logit`, `--scale_constant`, `--keep_extra`, `--logit_eps`. When no cycles are found, it prints a diagnostic that names the column(s) that probably need to go in `--group_by`. +- **`tfs-compare-feature` CLI** (`analysis/compare_feature.py`, `analysis/scripts/compare_feature_cli.py`). Grades per-genotype agreement of any quantile-summarized feature (θ, growth, epistasis) across N runs, such as different seeds or k-fold dropouts. It scores two axes: reproducibility (`rms_sd` of `q0.5` across runs, graded into tiers A–D by `--sd_tier_edges`) and self-consistency (an `overdispersion` statistic, with a flag set by `--overdispersion_threshold`). It has a symmetric mean mode and a reference mode (`--reference`), plus `--min_coverage`. It writes `{out_prefix}.csv` and `{out_prefix}_crosstabs.txt`. The input is a manifest file that lists the estimate CSVs. +- **Pooled aggregate posteriors across runs.** `tfs-compare-feature --write_aggregate` (`aggregate_feature`) writes `{out_prefix}_aggregate.csv`. Each row pools the N runs as an equal-weight mixture of their per-run marginal posteriors, rebuilt from the `q` ladder. The pooled error covers both per-run width and run-to-run spread, and it does not shrink with N. +- **`tfs-fit-genotypes` CLI** (`tfmodel/scripts/fit_genotypes_cli.py`). Runs the per-genotype MLE fit of the growth model as a standalone step, with optional congression de-attenuation (`--congression_lambda`). Other flags: `--spiked_file`, `--intercept_cols`, `--dk_geno_prior_sd`, `--min_obs`, `--num_workers`, `--save_theta_history`. It writes `_params.csv`, `_theta.csv`, and, with de-attenuation, `_params_deattenuated.csv` and optionally `_theta_history.csv`. +- **Genotype-subset growth prediction.** `tfs-predict-growth --subset_genotypes` (with `--subset_seed`) predicts one memory-sized block of genotypes instead of the whole library, for a quick input/output ln_cfu check. The block always keeps the binding, spiked, and file-specified genotypes and fills the rest with a random sample. If the device runs out of memory, the random part is halved and the prediction retried. +- **Log-concentration curve models** in `mle/curve_models`: `linear_log`, `bell_peak_log`, `bell_dip_log`. Each is a shape in `log10(x)` that takes raw concentration and applies the transform internally (`_to_log10_x`, which floors `x <= 0` to `min(x>0)/100`). New curated model lists `DEFAULT_MODELS` and `SHAPE_MODELS`. +- **Cat-response magnitude assessment** (`analysis/cat_response/cat_assess.py`). Tests each curve against zero on the observed data: a χ² test on `y_obs/y_std` gives `nonzero_p`, then Benjamini–Hochberg across curves gives `nonzero_q`, and together they drive a boolean `fittable`. Per-point `z`/`sig_nonzero` are also reported. The model-based omnibus test (`omnibus_W/df/p/q`) is reported but does not gate anything. An equivalence rollup (`all_equiv_zero`) uses a ROPE (`--rope_cutoff`, or auto `rope_multiplier * median(y_std)`). +- **Cat-response model-selection modes** (`cat_fit.py`, `--select_by`). `shape` is the default: it gates flat vs curvy on the flat fit's weighted residual autocorrelation (`--curvy_cutoff`), then picks the curvy model with the best weighted R². `aicc` picks the lowest-AICc model. `adequacy` keeps the AICc pick but escalates (never demotes) when a runs test flags clustered residuals (`--adequacy_alpha`). Per-model diagnostics are reported for every model: `runs_p`, `autocorr`/`autocorr_p`, and weighted-χ² `gof_p`. New rollup columns: `shape`, `shape_status`, `aicc_best_model`. +- **New cat-response outputs:** `{out_prefix}_assessment.csv` (per-point record with `y_obs`/`y_std`, `y_model`/`y_model_std`, `z`, `sig_nonzero`, `fittable`) and one `{out_prefix}_{model}.csv` parameter table per model. `--write_all_predictions` writes the predicted curves of every model instead of only the best one. +- `tfscreen.util.resolve_obs_columns`: shared default of `y_obs=q0.5` and `y_std=(q0.841 - q0.159)/2`, used by `tfs-cat-response` and `tfs-extract-epistasis`. `tfscreen.util.parallel.resolve_workers` handles joblib-style worker counts (`-1` = `cpu_count - 1`). +- `predict_with_error(..., full_cov=True)` also returns the full prediction covariance. `xfill` gains `min_value` to clamp the padded lower bound (e.g. at 0 for concentrations). +- `simulate/toy_thermo/`: a self-contained four-state thermodynamic toy TF model for building intuition about observables and logit epistasis (basis curves, measurement window, plotting helpers), with the notebook `examples/toy_thermo/toy_thermo.ipynb`. Also new: `examples/simulate-empirical/simulate_config.yaml` and `docs/manuscript/methods.md`. + +### Changed +- **Breaking: `tfs-cat-response` interface rewritten.** The CLI moved to `tfscreen.analysis.scripts.cat_response_cli` (the old `analysis/cat_response/scripts/` module was removed). It is now generic over `data_file x_obs [--y_obs] [--y_std] [--group_by ...]`, and groups are `genotype` plus the `--group_by` columns. It replaces the θ-specific `theta_file` + `--theta_col`/`--sigma_col`, which grouped on `genotype`/`titrant_name` with `titrant_conc` as x. `--workers` became `--num_workers` (default `-1`). Without `--models`, it fits `SHAPE_MODELS` in the default shape mode and `DEFAULT_MODELS` in the other modes; the old default was every model in `MODEL_LIBRARY`. **Action:** update scripts that call `tfs-cat-response`, e.g. `tfs-cat-response theta.csv titrant_conc --group_by titrant_name`. +- **Breaking: cat-response prediction columns renamed.** `y`/`y_std` became `y_model`/`y_model_std` in `{out_prefix}_predictions.csv`. `plot.cat_fits` now expects the new names. By default, predictions hold only the best model. `cat_fit` now returns `(flat_output, pred_df, assess_df)`, and `cat_response` returns `(results_df, predictions_df, assessment_df, rope_cutoff)`. +- **Breaking: `condition_selector` renamed to `group_by`** in `extract_epistasis` and `mutant_cycle_pivot`. `plot.heatmap.epistasis_heatmap` is updated to match. +- `biphasic_dip` bounds on `baseline`/`amplitude` are now unbounded. The old `>= 0` bounds made it unfittable on signed data such as logit epistasis. +- The per-genotype MLE fit and congression de-attenuation moved from `simulate/empirical/` to `tfmodel/genotype_fit/` (`fit.py`, `congression.py`). `simulate.empirical.fit_phenotypes` and `.congression` remain as re-export shims. New helpers: `fits_to_results_df` and `predict_theta`. +- `tfs-build-empirical` keeps `_stage1_fits.csv` as the raw (pre-de-attenuation) fit. When `--congression_lambda` is given, it now also writes the de-attenuated fits that feed Stage 2 to `_stage1p5_fits.csv`. +- The auto-sized `genotype_batch_size` overhead multiplier (`tfmodel/analysis/batch_sizing.py`) changed from 8.0 to 6.5. +- Cat-response fitting is parallelized over chunks of groups. + +### Fixed +- **Parameter covariance on ill-conditioned fits** (`mle/fitters/_util.get_cov`). The covariance is now built from the SVD of the Jacobian, as `scipy.optimize.curve_fit` does, instead of inverting `JᵀJ`. Before, fits that were ill-conditioned but still identifiable could return a spurious all-NaN covariance. Truly rank-deficient Jacobians still return NaN. +- **`linear` curve-model guess swapped slope and intercept.** `guess_linear` built its design matrix as `[1, x]`, so the guess came back as `[b, m]` while the model expects `[m, b]`. It now builds `[x, 1]`. +- **Crash in empirical Stage 2** (`simulate/empirical/population.py`). A numerically singular per-genotype covariance, e.g. from an unidentified Stage-1 parameter, raised `LinAlgError: Singular matrix` and could fail the whole batched inversion. Inversion and the marginal log-likelihood now use a floored eigendecomposition, which always returns finite values. + +## [0.4.2] - 2026-07-12 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.4.1..v0.4.2`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> - Added dk_geno inputs to calibration +> - Added pinning to fit (can pin growth parameters in SVI for example) +> - Improved simulation architecture +> - Added empirical simulations (fit experimental data and use to as an empirical generator for simulated data) +> - Fixed multiple bugs + +**Reconstructed changes:** + +### Added +- **Empirical phenotype simulation (`simulate/empirical/`).** A new pipeline fits real screen data and uses the fit as the phenotype generator for simulated libraries. `fit_phenotypes.py` does per-genotype MLE of the growth model with the calibration frozen (Stage 1, parallelizable via `num_workers`). `population.py` runs a measurement-error EM that deconvolves estimation noise into a `PopulationModel` (Stage 2). `resample.py` draws per-genotype phenotypes and builds `theta_gc_override`/`theta_params_override`/`dk_geno_override` (Stage 3). +- **`tfs-build-empirical` CLI** (`simulate/scripts/build_empirical_cli.py`). A one-command orchestrator that runs `configure_model`, then `run_prefit_calibration`, then Stages 1–2, and writes `_phenotype_model.json` plus a diagnostic `_stage1_fits.csv`. Flags include `--binding_file`, `--spiked_file`, `--base_growth_file`, `--thermo_data`, `--calibration_file` (skips configure+prefit and reuses an existing calibration), `--congression_lambda`, `--dk_geno_prior_sd`, `--min_obs`, `--drop_railed` and `--num_workers`. +- **Optional congression de-attenuation** (`simulate/empirical/congression.py`, enabled by `--congression_lambda`). Corrects bulk genotypes' Stage-1 theta curves for co-transformation with a fixed-point iteration on the inference's own congression operator, then refits Hill. Spiked genotypes are left unchanged. +- **`phenotype_source: empirical` simulate mode.** `library_prediction` resamples every genotype from the model named in an `empirical: {phenotype_model: ...}` block. This forces `theta_component=hill_geno` (with a warning if the config asks for something else) and fixed activity. +- **`dk_geno` component `pinned`** (`generative/components/dk_geno/pinned.py`, registered as `dk_geno: pinned`). Sets `dk_geno` deterministically from caller-supplied per-genotype values and defaults every other genotype to 0. wt is always 0. Values come from a pins CSV passed through `ModelOrchestrator(dk_geno_pins_file=...)`. +- **dk_geno inputs to calibration.** When a `base_growth_df` is configured, `tfs-prefit-calibration` turns its measured rates into per-genotype `dk_geno` pins (`_dk_geno_pins_from_base_growth`), so the calibration MAP uses real `dk_geno` values instead of assuming 0. +- **`tfs-prefit-calibration --pin_m`.** Hard-clamps the `linear` growth slope `m` to its per-condition calibration loc. The new `ModelPriors.m_pinned` makes `m` a deterministic site and drops its guide parameters, so the growth likelihood cannot pull `m` away during the SVI fit. +- **Per-condition growth priors.** The `linear`, `power` and `saturation` `condition_growth` components now accept either a scalar or a per-`condition_rep` array for each prior loc/scale, and declare `get_scale_bounds()`. The priors CSV (`configuration_io.py`) supports indexed per-condition rows that are name-joined to the model's `condition_rep` order. `tfs-prefit-calibration` writes per-condition MAP locs and floored scalar scales into those rows. New floor/ceiling flags: `--k_scale_floor`, `--m_scale_floor`, `--k_scale_ceiling`, `--m_scale_ceiling`; `--hessian_chunk_size` is also new. +- **Base growth-rate calibration data (`base_growth_df`).** Inference now takes direct reference-condition growth-rate measurements that anchor a global `k_ref` latent through the new `observe_base_growth` observer (`generative/observe/base_growth.py`). Added `tfs-configure-model --base_growth_df`; `k_ref` is included in the extracted parameters. +- **`observe_presplit` observer** (`generative/observe/presplit.py`). The presplit likelihood now lives in the observer layer alongside `observe_base_growth`, and each is wired in only when its data is supplied. +- **`tfs-process-presplit` CLI** (`process_raw/scripts/process_presplit_cli.py`). Converts per-sample count CSVs into a presplit `ln_cfu` table for `tfs-configure-model`. Count I/O shared with `tfs-process-counts` moved into `process_raw/_counts_io.py`. +- **`tfs-report-cfu0` CLI** (`simulate/scripts/report_cfu0_cli.py`). Prints the mean `ln_cfu0` and the number of surviving genotypes by class (`wt`/`spiked`/`single`/`double`) across `--num_replicates` simulated transformations. Use it to tune `transform_sizes`/`library_mixture`. +- **Finer control of simulated binding data.** A new `binding_data` schema has two sub-blocks, `spiked_binding` (clean controls drawn from `spiked_seqs`) and `library_binding` (in-library, congression-affected controls). Each takes `choose_by: stratified | random | ` and an optional or required `num`, validated fail-fast in `_validate_binding_config`. `library_binding` genotypes are selected after the growth simulation from the genotypes that survived (`simulate/library_binding_data.py`) and written to `tfs_sim_library_binding.csv`. `sample_theta` gained `select_mode="random"`. +- **New simulation outputs.** + - `base_growth_data` YAML block (`simulate/base_growth_data.py`): writes the `base_growth` CSV and a single-row `k_ref` echo. + - `presplit_data` generation moved to `simulate/presplit_data.py`. + - `tfs_sim_growth_parameters.csv`: per-condition ground truth for `condition_growth` (`simulate/growth_parameters_output.py`). + - Transformation-lambda ground-truth file (`simulate/transformation_lam_output.py`). +- **`tfs-summarize-fit` ground-truth comparison** for condition-growth parameters, `k_ref` and the transformation Poisson lambda. +- **Genotype batching in `tfs-predict-growth`** (`--genotype_batch_size`). When the flag is omitted, the batch size is estimated automatically from available device memory (`tfmodel/analysis/batch_sizing.py`). +- `tfs-setup-grid` rewrites `presplit_df`/`base_growth_df` paths and accepts `growth_noise` as a grid axis. + +### Changed +- **Breaking:** the library-genetics config keys `sub_libraries` and `library_combos` are renamed to `tiles` and `tile_combos` (`LibraryManager`, simulate/process_raw configs). **Action:** rename these keys in existing run configs. +- **Breaking:** the `library` column is now required in `growth_df` and `presplit_df`. It was previously filled with `"default"` when missing, and it is now part of the prediction merge keys. **Action:** add a `library` column to hand-built input tables. +- **Breaking:** `tfs-configure-model`'s default `--transformation_model` changed from `empirical` to `single`. The `empirical` and `logit_norm` models now require `--transformation_lambda MEAN STD` (the measured congression lambda), which anchors the transformation prior. Passing it together with `single` is an error. **Action:** add `--transformation_lambda` to any configure call that uses `empirical`/`logit_norm`. +- **Breaking:** simulated `binding_data` no longer takes a top-level `genotypes` list for choosing binding genotypes. Use `spiked_binding`/`library_binding` instead (see `examples/simulate/simulate_config.yaml`). +- Growth-component priors are now built inside each component instead of in `ModelOrchestrator`, and observer variable naming and prior handling were standardized. +- Binding genotype-params CSVs now ignore extra columns rather than rejecting them, so a `*_stage1_fits.csv` can be used directly as a `choose_by` file. +- `tfs-predict-growth`/`predict()` report parameter sites plated on `condition_rep` at one row per `condition_rep` instead of forcing them onto the growth-row grid. +- The ln_cfu0 components (`hierarchical`, `hierarchical_factored`) and the posterior-sampling path in `run_inference.py` were reworked to reduce memory use when sampling posteriors. + +### Removed +- `tfscreen.mle.parse_patsy`. +- `src/tfscreen/simulate/scripts/example_config.yaml` (use `examples/simulate/simulate_config.yaml`). +- `tfs-summarize-grid` no longer merges `*_calib_stats.json` into its rows. + +### Fixed +- **Tile mixing in simulation:** each transformant pool's weight is now normalized by its number of transformants. Previously `transform_sizes` leaked into the `library_mixture` ratio in `_sim_transform_and_mix`. +- **Congression correction under batching (`empirical` transformation):** the background theta CDF is now built from the full genotype population, not just the genotypes in the current minibatch or prediction subset (`update_thetas(..., population_theta=...)`). +- **Thermodynamic theta models under batching:** the `O2_C4_*`/`O2_C12_*` `thermo.py` models now index genotypes through `data.batch_idx`, so minibatches no longer pick up the wrong genotypes' theta. +- **Growth prediction batching:** each batch now includes the binding genotypes, so the binding tensor is never empty; their duplicate rows are then stripped from the output. +- Out-of-memory failures in the new posterior-sampling path. +- Presplit data simulated by `tfs-simulate` now carries and groups by the `library` column. +- The prefit calibration model no longer receives the production `transformation_lambda` after its transformation is forced to `single`. +- `base_growth_data` is now a recognized simulate config key. +- `tfs-fit-model`'s pre-MAP stage now honors `convergence_tolerance`, `convergence_window` and `patience`. + +## [0.4.1] - 2026-06-22 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.4.0..v0.4.1`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> Release contains bug-fixes, improved tools for evaluating fit results (`tfs-summarize-fit`) and improved documentation and examples. + +**Reconstructed changes:** + +### Added +- **Expanded `tfs-summarize-fit`.** It now writes a `summary/` directory containing `{out_prefix}_fit_summary.json` (loss, parameter count, and theta/growth prediction statistics), training and test theta correlation CSVs and a PDF (`_theta_corr.pdf`), a growth correlation plot (`_growth_corr.pdf`), a training-loss curve (`_losses.pdf`), per-genotype theta-fit plots and per-genotype growth-trajectory plots. When a `*_sim_parameters.csv` ground-truth file is present in the run directory, it annotates each `*_params_*.csv` (direct, `_params_d_*` per-mutation and `_params_epi_*` epistasis files) with a `ref` column and plots ref against median. `--ref_theta_file` supplies ground-truth theta explicitly; otherwise a `*_sim_genotype_theta.csv` in the run directory is used. +- **Posterior calibration diagnostics** in the new `tfmodel/analysis/error_calibration.py`: + - PIT from samples or from stored quantiles (`pit_from_samples`, `pit_from_quantiles`) + - `calibration_curve` and `pit_uniformity_test` + - PIT-histogram and calibration-curve plots + - `calibration_summary` for single runs + - SBC rank statistics (`compute_sbc_ranks`, `summarize_sbc`) + + `tfs-summarize-fit` uses `calibration_summary` when ground truth is available. +- **Pre-split observations.** An optional `presplit_df` holds the sequencing aliquot taken at t = −t_pre, with columns `replicate, condition_pre, genotype, ln_cfu, ln_cfu_std`. It enters the model as a `presplit_obs` Normal likelihood directly on `ln_cfu0` (`PreSplitData` in `data_class.py`). Pass it with `tfs-configure-model --presplit_df`; the path is recorded under `data: presplit` in the config. Genotypes absent from the growth data are dropped with a message. +- **Simulated pre-split data.** `tfs-simulate` writes a presplit CSV when a `presplit_data` block (optional `noise`) is present in the simulate config. The CSV includes an `ln_cfu_0_true` ground-truth column. +- **Perturbation-based theta simulation for `hill_geno` and `hill_mut`.** These components gain `simulate()`, a `SimPriors` class and `get_sim_hyperparameters()`, configured by the new `theta_sim_priors` simulate-config block: + - a wild-type reference curve + - per-genotype or per-mutation perturbation widths + - `hill_geno` mixture fractions for stuck-bound, never-binds and inverted phenotypes + - `hill_mut` pairwise epistasis drawn from a regularized horseshoe; `epi_tau_scale: 0.0` disables epistasis +- **Measured Hill parameters for binding genotypes.** The new `simulate/binding_params.py` reads a per-genotype CSV (`genotype, theta_low, theta_high, log_hill_K, hill_n`) set by `binding_data.genotype_params_file`. The measured curves are injected into the growth simulation (`build_theta_gc_override_hill_geno`, `build_theta_gc_override_hill_mut`). For `hill_mut`, singles are converted to per-mutation deltas and the curves are assembled for the whole library. This is only supported for Hill-based theta components. +- **Stratified binding-genotype sampling.** Binding genotypes can be chosen by greedy-maximin selection over a pool of prior-predictive theta curves (`sample_theta_stratified` in `simulate/sample_theta.py`), so their curves are diverse and span the binding concentrations. Pool size is set by `binding_stratify_pool_size` (default 500). +- **`dk_geno_zero`** simulate-config key pins every genotype's `dk_geno` to 0. When it is set, the `dk_geno_hyper_*` keys become optional. +- **Unknown-key validation.** Simulate and tfmodel YAML configs now fail on unrecognized top-level keys (`check_unknown_keys`, `SIMULATE_KNOWN_KEYS`, `TFMODEL_KNOWN_KEYS`). +- **Pre-fit scale bounds.** `tfs-prefit-calibration` gains `--k_scale_floor`, `--m_scale_floor`, `--k_scale_ceiling` and `--m_scale_ceiling`. The calibrated k and m prior scales are now derived from the Hessian and clamped to these bounds (`_build_hessian_scale_updates`). +- **Trajectory plotting module.** `tfscreen.plot.geno_trajectory` now holds `plot_geno_trajectory` (plots from a prediction DataFrame), `predict_geno_trajectory_df` and `predict_and_plot_geno_trajectory`. Trajectory plotting was previously embedded in the pre-fit calibration script. +- **Library spec shorthand.** `LibraryManager` now strips internal whitespace from `wt_seq`, `degen_sites` and `sub_libraries`, and accepts `.` in `degen_sites` and `spiked_seqs` to mean "wild-type base at this position". +- **Documentation and examples.** + - New `docs/source/quickstart.rst`. + - New `docs/source/summarize-fit.rst`, a guide to every `tfs-summarize-fit` output. + - `analysis.rst` expanded with the pre-fit output files, the parameter CSVs and the quantile-column convention. + - New `examples/simulate-and-analyze/` (`simulate_config.yaml`, `hill_params.csv`, `run.sh`, `README.md`) running the full simulate → configure → prefit → fit → sample → extract → predict → summarize pipeline. + - `examples/simulate/simulate_config.yaml` now documents the thermo and Hill theta components, `theta_sim_priors`, `dk_geno_zero` and `presplit_data`. + +### Changed +- **Breaking: quantile columns renamed.** `tfs-extract-params`, `tfs-predict-theta` and `tfs-predict-growth` now write 17 quantile columns named `q` (`q0.001` … `q0.5` … `q0.999`, including `q0.159` and `q0.841` for ±1σ). The previous named columns (`min`, `lower_95`, `lower_std`, `lower_quartile`, `median`, `upper_quartile`, `upper_std`, `upper_95`, `max`) are gone. MAP-checkpoint input now yields a single `q0.5` column instead of `point_est`. `tfs-cat-response` now reads `q0.5` by default and derives sigma from `(q0.841 − q0.159)/2`. **Action:** update any downstream scripts that read the old column names. +- **Breaking: posterior sampling removed from `tfs-fit-model`.** The `num_posterior_samples`, `sampling_batch_size` and `always_get_posterior` options are gone. Run `tfs-sample-posterior` after fitting. `tfs-sample-posterior` now restores the SVI state directly from the checkpoint (`RunInference.restore_svi_from_checkpoint`) instead of re-entering the optimizer with zero epochs. `run_optimization` also writes a checkpoint when a run stops before converging. +- **Breaking: simulate-config seed keys unified.** `random_seed` and `theta_rng_seed` are replaced by a single `seed` key, and `tfs-simulate` gains `--seed`. Because of the new unknown-key validation, a config that still uses the old keys now errors. **Action:** rename these keys in existing simulate configs. +- **Breaking: `final_cfu_pct_err` removed** from the simulate config. Simulated `sample_cfu_std` is now 0. +- **Default output prefixes.** `tfs-predict-theta` now defaults to `tfs_pred_theta` (was `tfs_theta_pred`) and `tfs-predict-growth` to `tfs_pred_growth` (was `tfs_growth_pred`). The default `tfs-simulate` output prefix is now `tfs_sim_`. +- **Selection vs. control priors on the slope `m` (`linear` growth).** Each condition's name is checked for `+` (selection) or `-` (control). Control conditions get a tight `m_scale_minus` (0.001) prior on `m` and selection conditions get `m_scale_plus` (0.01). This keeps the optimizer from moving selection-phase theta signal into control conditions, a cause of theta undershoot. `ModelOrchestrator` passes `condition_labels` to any component whose `get_priors` accepts them. A condition name containing both `+` and `-`, or neither, raises a `ValueError`. +- **Growth prior defaults.** + - `linear` and `power`: `k_loc` 0.025 → 0.020. + - `linear`: `m_scale` 0.05 → 0.01. + - `saturation`: `min_loc` 0.025 → 0.020 and `max_loc` 0.025 → 0.030; the initial guesses change to match. +- **Per-genotype curves in the pre-fit calibration.** The `_simple` theta component used by the pre-fit now accepts per-genotype `(T, C, G)` theta values, so each calibration genotype keeps its own observed binding curve instead of a population average. `_simple` is now registered in `model_registry["theta"]` (calibration-only). +- **Binding/growth mismatch is no longer fatal.** `binding_df` genotype/titrant pairs that are missing from `growth_df` are now dropped with a per-titrant message; previously this raised an error. +- **Clearer stale-guesses error.** A guesses CSV whose parameter sizes no longer match the model now raises a `ValueError` telling you to regenerate it. +- **Module moves and renames.** Console-script names are unchanged. + - `run_prefit_calibration_cli.py` → `prefit_calibration_cli.py` + - `prior_predictive_cli.py` → `sample_prior_cli.py` + - `simulate/scripts/run_simulation_cli.py` → `simulate_cli.py` + - `analysis/cat_response/cat_response_cli.py` → `analysis/cat_response/scripts/cat_response_cli.py` + - `mle/stats_test_suite.py` → `analysis/stats_test_suite.py`, now exported from `tfscreen.analysis` +- **Internal renames.** Code that took a `gm` model object now uses `orchestrator` throughout (e.g. `write_configuration(orchestrator=...)`, `predict(orchestrator=...)`). The test tree now mirrors `tfmodel/generative/components/`. + +### Removed +- `analysis/cat_response/fit_response_cli.py`, which was not registered as a console script; use `tfs-cat-response`. +- `tfmodel/analysis/sbc.py`; its SBC functions now live in `tfmodel/analysis/error_calibration.py`. + +### Fixed +- **Genotypes scrambled in growth predictions.** `predict` used the static binding-first `batch_idx`, which misaligned posterior values (stored in canonical genotype order) with per-genotype masks and offsets. Prediction now builds a canonical-order batch with `get_batch(data, arange(num_genotype))`. `_setup_batching` also fills the non-binding positions of the static index with valid genotype indices instead of zeros. +- **MAP predictions corrupted by a double transform.** MAP (`AutoDelta`) parameters are already stored in constrained space, but `predict` applied the support bijection again, corrupting positive-constrained sites such as `ln_cfu0_hyper_scale`. The extra transform is removed. +- **Misplaced values for non-tail-aligned prediction sites.** Sites whose dimensions are not tail-aligned with the tensor layout (e.g. `ln_cfu0`, shape `(rep, condition_pre, genotype)`) were assigned to the wrong rows. The new `_align_site_to_tm_dims` maps them correctly. +- **Pinned hyperpriors ignored at prediction.** `predict` now uses the original orchestrator's priors, so calibrated hyperpriors stay pinned; previously a rebuilt orchestrator with default priors was used. +- **Empty `condition_rep` groups.** The `linear` growth component and the `memory` growth-transition component no longer fail extraction when the `condition_rep` map group is absent. +- **`theta_sim_priors` rejected by the simulator.** The key was missing from the recognized simulate-config keys and is now accepted. +- **Integer time columns.** `t_pre` and `t_sel` are cast to float on load, avoiding dtype problems when merging with float prediction grids. + +## [0.4.0] - 2026-05-31 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff 99b77e0..v0.4.0` (i.e. changes after the untagged 0.3.1 bump), and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> Reorganized code around three core functions: running the hierarchical model, simulating an experiment, and processing raw experimental data. Standardized command line interface, yaml inputs, and model naming conventions. Lots of bug fixes throughout. + +**Reconstructed changes:** + +### Added +- **Thermodynamic theta models.** Lac-dimer and MWC-dimer partition-function theta components, with and without an unfolded state, each in three parameterizations: per-mutation lnK (`PK`), structure-based neural-net prior (`PnnC`), and ddG prior (`PddG`). They are registered under standardized names such as `thermo.O2_C4_K3_U0_a.PK` and `thermo.O2_C12_K5_U1_a.PddG`. Supporting pieces are `scripts/generate_struct_ensemble.py` and a sparse `mut_geno_matrix`. +- **New model components:** + - `activity`: `horseshoe_mut` (horseshoe epistasis prior). + - `ln_cfu0`: `hierarchical_factored`. + - `theta_rescale` (new category): `passthrough`, `logit`. + - `theta_growth_noise`: `logit_normal`. + - `growth_noise` (new category): `zero`, `normal_kt`. + - `sample_offset` (new category): `zero`, `normal`. + - `growth_transition`: `baranyi_k`, `baranyi_tau`, `two_pop`. +- **Two-stage calibration.** `tfs-prefit-calibration` pre-fits the growth linking function by MAP and pins the hyperpriors (empirical Bayes) for the production fit. +- **Empirical initial guesses** for `ln_cfu0`, `dk_geno`, the growth components and the Hill components. `ln_cfu0` also accepts spiked-genotype priors and more than one prior class. +- **Inference options:** + - NUTS is available from the command line (`tfs-fit-model --analysis_method nuts`, with `--nuts_*` options). + - MAP fits can produce Hessian-based Laplace posteriors (`tfs-sample-posterior`, chunked through `hessian_chunk_size`). + - Models can be fit on binding data alone (`binding_only`). + - Checks for exploding NaNs were added, along with the `tfs-diagnose-nan` script. +- **Prior predictive and simulation-based calibration.** Adds `tfmodel/analysis/prior_predictive.py` (`tfs-sample-prior`) and `tfmodel/analysis/sbc.py` (`tfs-summarize-sbc`). +- **Prediction and extraction:** + - `tfs-predict-growth` and `tfs-predict-theta` take over from `tfs-predict`. `tfs-predict-theta` supports categorical theta models and predicts unmeasured genotypes (`tfmodel/analysis/predict_unmeasured.py`). + - `tfs-extract-params` reads parameters directly from a checkpoint `.pkl` without sampling, and uses a point-estimate/median output contract. + - Individual posterior samples can be pulled during prediction and extraction. +- **Grid and summary tooling:** + - `tfs-setup-grid` and `tfs-summarize-grid` handle grids of model configs; `tfs-setup-sim-grid` handles grids of simulations. Both rely on the shared helpers in `util/grid_utils.py` (Jinja2 templates, which adds `jinja2` as a new dependency). + - `tfs-summarize-fit` summarizes a fit, including a fit-summary plot. + - `tfs-subset-genotypes` subsets genotype data. + - `tfs-cat-response` is registered as a CLI. +- **Simulation:** + - The `tfs-simulate` CLI (`simulate/scripts/run_simulation_cli.py`). + - Prior-predictive theta sampling (`simulate/sample_theta.py`). + - A `SimData` container (`simulate/sim_data_class.py`). + - Simulation activity, `dk_geno`, growth-transition and thermodynamic theta are now shared with or synchronized to the `tfmodel` components. +- `genetics/count_mutation_backgrounds.py` (mutation background counter) and `plot/plot_theta_fits.py`. +- `examples/` gained reference configs and templates: `simulate/`, `tfmodel/` and `process_raw/`. +- New docs pages (`grid.rst`, `process-raw.rst`, `ligandmpnn-features.rst`) and a GitHub Actions test workflow (`.github/workflows/tests.yml`). + +### Changed +- **Breaking: package reorganized** around three core functions: the hierarchical model, simulation and raw-data processing. + - `analysis/hierarchical/growth_model/` → `tfmodel/`: + - `model.py`, `registry.py`, `components/` and `observe/` → `tfmodel/generative/`. + - `model_class.py` → `tfmodel/model_orchestrator.py`. + - `configuration_io.py` and `data_class.py` → `tfmodel/`. + - `prediction.py` and `extraction.py` → `tfmodel/analysis/`. + - Scripts → `tfmodel/scripts/*_cli.py`. + - `analysis/hierarchical/{run_inference,posteriors}.py` → `tfmodel/inference/`, plus a new `checkpoint_io.py`. + - `analysis/hierarchical/{tensor_manager,populate_dataclass}.py` and `growth_model/batch.py` → `tfmodel/tensors/`. + - `fitting/` → `mle/`; `models/generic/` → `mle/curve_models/`. + - `models/growth_linkage.py` and `models/transition_linkage.py` → `simulate/growth/`. + - `data.py` → `genetics/data.py`. + - `process_raw/{process_fastq,process_counts}.py` → `process_raw/scripts/*_cli.py`. +- **Breaking: CLI renamed and standardized.** Every entry point now lives in a `_cli.py` file and is built with `generalized_main`. + - `tfs-configure-growth-analysis` → `tfs-configure-model`. + - `tfs-growth-analysis` → `tfs-fit-model`. + - `tfs-predict` → `tfs-predict-growth` / `tfs-predict-theta`. + - `tfs-summarize-posteriors` → `tfs-summarize-fit`, `tfs-extract-params` and `tfs-sample-posterior`. +- **Breaking: component names standardized** on a `_geno`/`_mut`/`thermo.*` scheme: + - `activity`: `hierarchical` → `hierarchical_geno`, `horseshoe` → `horseshoe_geno`. + - `dk_geno`: `hierarchical` → `hierarchical_geno`. + - `theta`: `hill` → `hill_geno`, `categorical` → `categorical_geno`. +- **Breaking: YAML inputs standardized.** + - `read_yaml` no longer converts whole-number floats to ints; only quoted scientific-notation strings are converted. + - `read_yaml` `override_keys` rejects unknown keys. + - `read_yaml` validates that the `growth` and `condition_blocks` sections agree. +- **Breaking:** `sample_df` uses `sample_cfu` instead of OD600, and `process_raw/od600_to_cfu.py` is removed. +- `tfs-configure-model` uses a default batch size of 1024. +- Epistasis is represented with a sparse matrix, and epistasis prediction runs in batches to avoid running out of memory. +- `read_dataframe` converts `genotype` columns to categoricals automatically. +- Hierarchical-model parameter names are standardized. +- The convergence criteria were updated. +- All positive constraints get a small numerical floor. +- Requires Python >= 3.11 and `numpyro>=0.19.0`. `patsy` was dropped from the dependencies. + +### Removed +- **Breaking:** the independent (non-hierarchical) analysis (`analysis/independent/`) and the MLE calibration package (`calibration/`). +- **Breaking:** the `models/` package, which held the old growth regressions (`ols`, `wls`, `gls`, `glm`, `gee`, `nls`, `kf`, `ukf`), `lac_model/` and `eee_model.py`. The rest of it moved (see above). +- **Breaking:** these components: + - `condition_growth`: `linear_independent`, `linear_fixed`. + - `dk_geno`: `hierarchical_mut`. +- `fitting/fitters/ols_2D.py`, `wls_2D.py`, `simulate/setup_observable.py` and `util/design.py`. +- The `notebooks/` directory. + +### Fixed +- Genotype labels in the binding data were being swapped during fits. +- `tfs-prefit-calibration` was upweighting the binding data. +- Posterior writing overran its buffer. +- Hessian computation ran out of memory on GPUs. +- MAP "posteriors" were wrong, and posterior generation required a seed. +- Indexing bugs, including growth data with discontinuous indexes (`get_scaled_cfu`) and indexing in `run_inference`. +- The `epistasis` setting was dropped from the config. +- Guide bug in the `growth_transition` components; NaN in the memory-model term (now clamped). +- Batching bugs in the `_mut` components; collapse in the `horseshoe_mut` activity prior. +- Guesses for some MWC-dimer models under `binding_only`. +- Out-of-memory errors in the lac-dimer mutation and NN-prior theta models. + +## [0.3.1] - 2026-03-31 (untagged) + +> *Reconstructed on 2026-09-10 from `git diff v0.3.0..99b77e0`, the untagged commit that bumped `__version__` to 0.3.1 ("version bump; ready for pyro port"), and commit messages. These entries were not written at release time and may be incomplete.* +> +> *This version was never tagged or released on GitHub; it is recorded because `__version__` reported 0.3.1 between 2026-03-31 and 2026-05-31.* + +**Reconstructed changes:** + +### Added +- **Mutation-level and epistasis inference:** + - `theta`: `hill_mut`. + - `activity`: `hierarchical_mut`. + - `dk_geno`: `hierarchical_mut`. +- **Growth-transition components** (`instant`, `memory`, `baranyi`) under a new `growth_transition` category. +- **Nonlinear condition-growth models:** `power` and `saturation`. +- **New `transformation` components:** `empirical` (empirical transformation correction) and `logit_norm`. +- **New CLIs:** + - `tfs-configure-growth-analysis` (config writing and reading through `configuration_io.py`). + - `tfs-predict`, which predicts `ln_cfu` from parameter samples (`prediction.py`). + - Parameter extraction split out into `extraction.py`. +- A MAP optimization can run before SVI, and checkpoints are protected from being overwritten by accident. +- Growth parameters can be shared across replicates. +- Base documentation. +- Growth-linkage modules (`models/growth_linkage.py`, `transition_linkage.py`, `occupancy_growth_model.py`), plus `genetics/build_mut_geno_matrix.py`. + +### Changed +- **Breaking: CLIs replaced.** + - `tfs-hier-theta` → `tfs-growth-analysis`. + - `tfs-summarize-posteriors` moved to `growth_model/scripts/`. + - `tfs-indep-theta` was removed from the entry points. +- **Breaking: components reorganized** into per-category subpackages (`components//.py`), with these registry renames: + - `condition_growth`: `hierarchical` / `independent` / `fixed` → `linear` / `linear_independent` / `linear_fixed`. + - Noise: `none` → `zero`. + - `transformation`: `congression` replaced by `empirical` / `logit_norm`. +- **Breaking:** the `condition` plate and mapper are renamed to `condition_rep`. +- The categorical theta component was modernized. +- The MLE calibration routine and FASTQ parsing were improved. + +### Removed +- **Breaking:** `.npz` posterior files; posteriors are `.h5` only. + +### Fixed +- Overflow in long inference runs. +- `.h5` posterior file sync on clusters. +- Indexing bugs in prediction. + +## [0.3.0] - 2026-01-02 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.2.2..v0.3.0`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> This release includes updates to the posterior sampling and summarization code. It also switches to a more consistent run interface, switching from number of iterations to number of epochs for SVI and MAP inference. + +**Reconstructed changes:** + +### Added +- **Posterior summarization CLI** `tfs-summarize-posteriors` (`analysis/hierarchical/summarize_posteriors.py`): reads a posterior file plus the run's `{out_root}_config.yaml` and writes per-parameter CSVs, `{out_root}_growth_pred.csv`, and (for the `hill` theta model) `{out_root}_theta_curves.csv`. `tfs-hier-theta` now calls it automatically after posterior sampling. +- New `GrowthModel` methods `extract_growth_predictions` and `extract_theta_curves`, plus `write_config`/`load_config` for a YAML record of the run's data and model settings. +- `tfs-hier-theta` flag `--config_file`: re-runs from a saved config. `growth_df`, `binding_df`, and `seed` are now optional (`seed` is required unless resuming from a checkpoint). +- `tfs-hier-theta` flag `--transformation_model` (`congression` (default) | `single`) exposes the transformation component on the command line. +- Epoch-based convergence controls `--patience` (consecutive passing checks required) and `--convergence_check_interval` (in epochs). +- End-to-end smoke tests (`tests/smoke-tests/`) and unit tests for batch consistency, posterior mapping, and posterior extraction. + +### Changed +- **Breaking:** **Epoch-based run interface for SVI and MAP.** `--num_steps` was replaced by `--max_num_epochs`. `--convergence_window` and `--checkpoint_interval` are now counted in epochs (one epoch is `ceil(num_genotypes / batch_size)` iterations), and the defaults changed (`convergence_tolerance` 1e-6 → 0.01, `convergence_window` 10000 → 10, `checkpoint_interval` 10000 → 10). The learning-rate decay now spans the full run. +- **Breaking:** Posterior samples are now written to HDF5 (`{out_root}_posterior.h5`, via `h5py`) instead of `.npz`. The summarization code still reads `.npz`. +- **Breaking:** `RunInference.setup_map` was removed. MAP now uses `setup_svi(guide_type="delta")` (`AutoDelta`), and SVI uses `guide_type="component"`. +- Default theta noise models are now `none` for both `--theta_growth_noise_model` and `--theta_binding_noise_model` (previously `beta`). +- Posterior prediction now uses better batching and has a progress bar. The congression correction reuses its grid integration across genotypes (`n_grid` 512 → 256), and the default `lam_scale` prior changed from 1.0 to 0.5. +- `pyproject.toml` now lists the inference stack as dependencies (`jax`, `jaxlib`, `numpyro`, `optax`, `flax`, `dill`, `h5py`, `scipy`). + +### Fixed +- Fixed genotype indexing errors in posterior sampling, including when reading from a checkpoint, and added guards so indexing is consistent in batched and full-batch modes. +- Fixed an out-of-memory error in `run_inference`. +- Fixed an overflow error in `model_class`. +- `fitting.fitters.least_squares` now warns and returns NaN when SVD fails to converge instead of raising. `ols_2D` and `stats_test_suite` now handle zero-variance and constant inputs. + +## [0.2.2] - 2025-12-18 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.2.1..v0.2.2`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> - Added correction to inferred theta values accounting for the fact cells can pick up more than one plasmid +> - Refactored the util submodule from flat to hierarchical +> - Tweaks to increase speed of inference +> - Updated command line interface to analyze_theta to interface with the model changes +> - Lots of docstring clean up +> - Added a bunch of unit tests +> - Various bug fixes + +**Reconstructed changes:** + +### Added +- **Multi-plasmid (congression) correction of theta.** A new `transformation` category was added to the hierarchical model registry, with components `congression` (`transformation_congression.py`) and `single` (`transformation_single.py`). `congression` corrects inferred theta for cells carrying more than one plasmid by integrating over a logit-normal background theta distribution with co-transformation rate `lam`. `GrowthModel` uses `transformation="congression"` by default. +- `tfs-hier-theta --spiked [...]` (`spiked_genotypes` in `GrowthModel`): lists genotypes that are excluded from the congression correction. Unknown genotypes raise an error. +- `--adam_final_step_size` for `tfs-hier-theta`. The Adam step size now decays exponentially from `--adam_step_size` to this value. +- A human-readable `{out_root}_losses.txt` loss log. +- A large set of unit tests, covering `util/` and the hierarchical model among others. + +### Changed +- **Breaking:** **`tfscreen.util` restructured from flat modules into subpackages:** + - `util/cli/`: `generalized_main` + - `util/dataframe/`: `add_group_columns`, `check_columns`, `chunk_by_group`, `df_to_arrays`, `expand_on_conditions`, `get_group_mean_std`, `get_scaled_cfu` + - `util/io/`: `read_dataframe`, `read_yaml` + - `util/numerical/`: `array_search`, `broadcast_args`, `xfill`, `zero_truncated_poisson`, plus `padding.py` (was `vstack_padded.py`) and `transform.py` (was `numerical.py`) + - `util/validation/`: `check` (was `check.py`) + - Top-level re-exports from `tfscreen.util` are preserved. Direct imports of old module paths, such as `tfscreen.util.generalized_main`, must be updated. +- **Faster inference.** Optimization steps now run in `jax.lax.scan` blocks of `checkpoint_interval` steps with vmapped batch extraction, replacing the per-step Python loop. +- New `tfs-hier-theta` defaults: `--adam_step_size` 1e-6 → 1e-3, `--elbo_num_particles` 10 → 2. +- `analysis_method=posterior` now disables batching. +- Docstrings were cleaned up throughout the hierarchical model. + +### Removed +- **Breaking:** `tfscreen.analysis.growth_to_theta` and `tfscreen.fitting.fitters.map` (`run_map`) were removed. + +### Fixed +- Fixed posterior-sampling indexing: latents are now sampled against a full-genotype batch, and batch outputs are concatenated on the last axis. `not_binding_idx` is now a pytree array. +- Fixed `fitting.fit_manager` scale-parameter masking, error-message propagation, and robustness in the `stats_test_suite` Breusch-Pagan test. Other small fixes found by the new tests in `fitting/`, `models/growth/`, `calibration/io.py`, `cat_response`, and `plot/cat_fits.py`. + +## [0.2.1] - 2025-12-15 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.2.0..v0.2.1`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> + Hierarchical modeling analysis now complete. +> + Cleaned up analysis and demo notebooks. + +**Reconstructed changes:** + +### Added +- **Hand-written variational guides for every hierarchical model component.** Each module in `analysis/hierarchical/growth_model/components/` (`growth_independent`, `growth_hierarchical`, `growth_fixed`, `ln_cfu0`, `dk_geno_fixed`, `dk_geno_hierarchical`, `activity_fixed`, `activity_hierarchical`, `activity_horseshoe`, `theta_cat`, `theta_hill`, `no_noise`, `beta_noise`) and both observers (`observe/binding.py`, `observe/growth.py`) now define a `guide()` function alongside `define_model()`. Hyperparameter scales use LogNormal guides with positive-constrained `pyro.param` sites. The growth observer's guide learns the Student-t degrees of freedom `nu`, and `beta_noise` learns `kappa` with an amortized Beta guide. +- **Component registry** (`growth_model/registry.py`): a `model_registry` dict that maps each category (`condition_growth`, `ln_cfu0`, `dk_geno`, `activity`, `theta`, `theta_growth_noise`, `theta_binding_noise`) to its component modules, plus `observe_binding`/`observe_growth`. +- **GPU-resident mini-batching with likelihood rescaling.** `GrowthModel` takes a `batch_size` argument. Binding genotypes are always included in each batch, and the remaining slots are filled with random non-binding genotypes. A per-genotype `scale_vector` (applied via `pyro.handlers.scale`) reweights the sampled genotypes so the batch stands in for the full library. `GrowthData`/`BindingData` gained `batch_size`, `batch_idx`, `scale_vector` and `geno_theta_idx` fields. `RunInference` moves the data to the device once with `jax.device_put` and slices each batch there with a jitted `get_batch`. +- `GrowthModel.jax_model_guide`, `GrowthModel.get_batch` and `GrowthModel.get_random_idx`. `RunInference` now requires the model to provide `jax_model_guide`. +- Validation in `_read_binding_df`: it raises `ValueError` if `binding_df` contains genotype/titrant_name pairs that are not in `growth_df`. +- Unit tests for `run_inference` and `analyze_theta` (`tests/tfscreen/analysis/hierarchical/test_run_inference.py`, `test_analyze_theta.py`). Hierarchical-model tests were updated to match the new structure. +- New notebooks: `notebooks/monoculture-calibration/` (growth calibration from control experiments), `notebooks/development-tools/` (`distributions`, `run-nuts_single`, `check-for-int-in-svi`), `notebooks/create-test-data/`, `notebooks/tune-ensemble-parameters/` (lac model behavior, with AlphaFold/experimental structures), and several `notebooks/dev/` notebooks. Test and coverage badges were added under `docs/badges/`. + +### Changed +- **Hierarchical model restructured around the registry.** `jax_model` (`growth_model/model.py`) no longer dispatches through integer flags and `if/elif` chains. It receives the selected component modules as keyword arguments plus an `is_guide` flag, and `GrowthModel` binds these with `functools.partial` to build both the model and the guide from the same function. +- **SVI and MAP use the component guide instead of numpyro autoguides.** `RunInference.setup_map`/`setup_svi` now pass `model.jax_model_guide` to `SVI`, replacing `AutoDelta` and `AutoLowRankMultivariateNormal`. As a result, the `guide_rank` argument was removed from `setup_svi`, `_run_svi` and `analyze_theta`. +- `batch_size` moved from `RunInference.run_optimization`/`_run_map`/`_run_svi` to the `GrowthModel` constructor. `analyze_theta` passes it through. +- **Growth tensor layout.** The combined `treatment` axis was split into separate `condition_pre`, `condition_sel`, `titrant_name` and `titrant_conc` axes, giving a 7-D tensor with genotype last. `condition_sel` is re-indexed within each `condition_pre` (`condition_sel_reduced`). The separate growth-theta TensorManager and the `map_ln_cfu0`/`map_genotype`/`map_theta`/`map_theta_group` tensors are gone, and `titrant_conc`/`log_titrant_conc` are now 1-D arrays taken from the tensor axis labels. The growth observer's plates were updated to match, and `ln_cfu0` is sampled over replicate × condition_pre × genotype plates. +- The wild-type location changed from `wt_index`/`not_wt_mask`/`num_not_wt` to a `wt_indexes` array. +- Posterior sampling (`RunInference.get_posteriors`) slices the genotype-indexed latent samples to each forward-prediction batch before running `Predictive`, instead of running the forward pass on unsliced latents. +- `analyze_theta` defaults: `activity_model` changed from `"fixed"` to `"horseshoe"`, and the default `convergence_tolerance` in `_run_svi` changed from `1e-7` to `1e-4`. +- `populate_dataclass` converts numpy arrays to JAX arrays, and `TensorManager` builds `good_mask` with an explicit `bool` dtype. + +### Removed +- `ControlClass` (from `growth_model/data_class.py`), together with the `MODEL_COMPONENT_NAMES` table and the integer component constants in `growth_model/model.py`. The registry replaces them. +- `sample_batch` and `deterministic_batch` in `growth_model/batch.py`. Both are replaced by `get_batch(full_data, idx)`. + +### Fixed +- `simulate/selection_experiment.py`: the growth-rate noise standard deviation is now `abs(mean * growth_rate_noise)`, so a negative mean growth rate no longer produces an invalid (negative) noise scale. +- `calibration/plot.py`: fixed a broken import of `get_indiv_growth` by importing it from `tfscreen.analysis.independent.get_indiv_growth`. + +## [0.2.0] - 2025-11-26 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, `git diff v0.1.0..v0.2.0`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> Code now does: +> +> - Simulation of experiments +> - Processing raw reads (fastq through ln_cfu/condition) +> - Independent modeling (extract that for each genotype independently) +> - Hierarchical modeling (Bayesian analysis of theta together) +> - Epistasis analysis +> - Epistasis vs. [titrant] categorization analysis +> - Various helpful plotting utilities. +> +> Additionally, the API is now (roughly) stable. I antiquate no major changes to the simulation, raw-processing, or independent modeling code base. I expect to build out the hierarchical modeling codebase and clean up the utilities functions. None of these will be architectural changes, however, just minor refactors. + +**Reconstructed changes:** + +### Added +- **Hierarchical Bayesian theta inference** (`tfscreen.analysis.hierarchical`): a JAX/NumPyro/Flax joint growth + binding model (`growth_model/model.py`) that infers per-genotype operator occupancy (theta) together with condition growth, `ln_cfu0`, and pleiotropic `dk_geno` effects. Components in `growth_model/components/` are selectable per axis: condition growth (`hierarchical`, `independent`, `fixed`), `dk_geno` (`hierarchical`, `fixed`), activity (`fixed`, `hierarchical`, `horseshoe`), theta (`hill`, categorical `theta_cat`), and theta noise (`beta`, none). Separate observation layers for growth and binding data live in `growth_model/observe/`. +- **`RunInference`** (`analysis/hierarchical/run_inference.py`): SVI (low-rank autoguide, `ClippedAdam`) and MAP optimization with mini-batching, convergence detection over a loss window, checkpoint write/restore, loss logging, posterior sampling, and prediction. `TensorManager` (`tensor_manager.py`) and `populate_dataclass.py` pack ragged per-genotype data into JAX tensors. +- **`tfs-hier-theta`** CLI: wraps `analysis.hierarchical.analyze_theta` (growth + binding DataFrames, component choices, `analysis_method` `svi`/`map`, checkpoint restart). +- **Independent per-genotype analysis** (`tfscreen.analysis.independent`) with the **`tfs-indep-theta`** CLI: per-genotype growth-rate estimation (`get_indiv_growth`), pre-growth modeling (`model_pre_growth`), and direct counts-to-theta fitting (`cfu_to_theta`); plus `analysis/growth_to_theta.py`. +- **Raw read processing** (`tfscreen.process_raw`): paired FASTQ to genotype counts (`FastqToCounts`, `process_fastq`, multiprocess chunked; uses `pyfastx` and `pybktree`), counts to `ln_cfu` (`counts_to_lncfu`, `process_counts`), and OD600-to-CFU/mL conversion (`od600_to_cfu`). CLIs **`tfs-process-fastq`** and **`tfs-process-counts`**. +- **Genetics utilities** (`tfscreen.genetics`): `LibraryManager` (library definition from wt sequence, degenerate sites, tiles), genotype standardization/sorting (`standardize_genotypes`, `argsort_genotypes`, `set_categorical_genotype`), mutant-cycle construction (`build_cycles`), and `combine_mutation_effects`. +- **Epistasis analysis**: `analysis/extract_epistasis.py` (`extract_epistasis`, `mutant_cycle_pivot`). +- **Categorical response fitting** (`analysis/cat_response/`): `cat_response`/`cat_fit` fit a library of empirical curve shapes (flat, linear, polynomial, Hill repressor/inducer, bell, biphasic peak/dip) defined in `models/generic/` (`MODEL_LIBRARY`). +- **Plotting subpackage** (`tfscreen.plot`): heatmaps (amino acid vs residue, amino acid vs titrant, epistasis), corner plots, Hill and categorical fit plots, error/uncertainty-calibration plots, and x-y correlation plots. +- **General fitting framework** (`tfscreen.fitting`): `FitManager`, patsy formula parsing (`parse_patsy`), `predict_with_error`, and fitters in `fitting/fitters/` (least squares, MAP with configurable priors, matrix NLS/WLS, vectorized 2D OLS/WLS). +- **Shared utilities** in `tfscreen.util`, including `generalized_main` (builds a CLI from a function signature), `read_yaml`, DataFrame/column validation, and `zero_truncated_poisson`. + +### Changed +- **Simulation rewritten** around `library_prediction` (thermodynamics to per-genotype theta and growth, `thermo_to_growth.py`) and `selection_experiment` (transformation, mixing, index hopping, growth, and sequencing); the simulation uses `LibraryManager` to generate libraries. The old step modules (`generate_libraries`, `initialize_population`, `transform_and_mix`, `simulate_growth`, `sequence_samples`, `load_simulation_config`, `cell_growth_moves`) were removed. +- `tfscreen.analyze` renamed to `tfscreen.analysis`; phenotype models moved from `simulate/generate_phenotypes/` to `tfscreen.models` (`lac_model/`, `eee_model.py`), and time-series growth estimators (OLS/WLS/GLS/GEE/GLM/NLS/Kalman/UKF) moved from `fitting/` to `models/growth/`. +- Calibration rebuilt (`calibration/`): separate wt growth-rate, wt theta, background, and k-vs-theta steps (`get_wt_k`, `get_wt_theta`, `get_background`, `get_k_vs_theta`) plus calibration plotting. +- Dependencies: `eee` and `dataprob` dropped; `numba`, `patsy`, `pybktree`, `pyfastx`, `corner`, and `statsmodels` added. + +## [0.1.0] - 2025-09-02 + +> *Reconstructed on 2026-09-10 from the GitHub release notes, the source tree at tag `v0.1.0`, and commit messages. These entries were not written at release time and may be incomplete.* + +**Release notes (contemporaneous, by the author):** + +> This is a first draft of the code that allows simulation and analysis of a transcription factor high-throughput screen. Expect large changes to the API. + +**Reconstructed changes:** + +### Added +- Initial release of `tfscreen`, a library for simulating and analyzing high-throughput screens of transcription factor libraries. No command-line entry points; use is through the Python API and example notebooks. +- **Simulation** (`tfscreen.simulate`, `run_simulation` driven by a YAML config): library generation, population initialization, transformation and mixing, growth under selection conditions, and sequencing of samples. +- **Phenotype models** (`simulate/generate_phenotypes/`): lac repressor thermodynamic models (`lac_model/`: MWC dimer, microscopic dimer, linkage dimer and dimer-tetramer) and an `eee`-based ensemble model for mapping mutational effects to operator occupancy. +- **Analysis** (`tfscreen.analyze`): growth-rate estimation from time series (`estimate_growth_rates`) and per-genotype theta estimation (`estimate_theta`). +- **Growth calibration** (`tfscreen.calibration`): fitting of condition growth rates versus theta, with calibration read/write. +- **Fitting routines** (`tfscreen.fitting`): OLS, WLS, GLS, GEE, GLM, NLS, matrix NLS/WLS, and Kalman / unscented Kalman filter estimators. +- Walkthrough notebook (`notebooks/tfscreen-walkthrough/`). + +[Unreleased]: https://github.com/harmslab/tfscreen/compare/v0.4.4...HEAD +[0.4.4]: https://github.com/harmslab/tfscreen/compare/v0.4.3...v0.4.4 +[0.4.3]: https://github.com/harmslab/tfscreen/compare/v0.4.2...v0.4.3 +[0.4.2]: https://github.com/harmslab/tfscreen/compare/v0.4.1...v0.4.2 +[0.4.1]: https://github.com/harmslab/tfscreen/compare/v0.4.0...v0.4.1 +[0.4.0]: https://github.com/harmslab/tfscreen/compare/v0.3.0...v0.4.0 +[0.3.0]: https://github.com/harmslab/tfscreen/compare/v0.2.2...v0.3.0 +[0.2.2]: https://github.com/harmslab/tfscreen/compare/v0.2.1...v0.2.2 +[0.2.1]: https://github.com/harmslab/tfscreen/compare/v0.2.0...v0.2.1 +[0.2.0]: https://github.com/harmslab/tfscreen/compare/v0.1.0...v0.2.0 +[0.1.0]: https://github.com/harmslab/tfscreen/releases/tag/v0.1.0 diff --git a/CLAUDE.md b/CLAUDE.md index 16d71d84..29637e29 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -43,10 +43,10 @@ flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 tfs-process-fastq # FASTQ → read counts tfs-process-counts # counts → ln_cfu DataFrames tfs-process-presplit # Process pre-split count files -tfs-configure-model # Generate YAML config template +tfs-configure-model # Generate YAML config template (+ library composition snapshot) tfs-prefit-calibration # Pre-fit linking function via MAP tfs-fit-model # Main hierarchical Bayesian inference -tfs-fit-genotypes # Per-genotype MLE fits of the growth model (+ optional congression de-attenuation) +tfs-fit-genotypes # Per-genotype MLE fits of the growth model (+ optional congression de-attenuation; spiked genotypes come from --library_config) tfs-sample-posterior # Draw posterior samples from fitted model tfs-sample-prior # Draw prior predictive samples tfs-extract-params # Extract parameters from checkpoint @@ -166,7 +166,21 @@ Net flow: `configure` (scalar) → `prefit` (per-condition `k_loc` indexed rows ### Configuration (YAML) -See **YAML Standards** below for the full conventions. The tfmodel config (`tfs_configure_config.yaml`) is generated by `tfs-configure-model` and drives `tfs-fit-model`. It contains `data`, `components`, `priors_file`, and `guesses_file` sections. Do not hand-edit it. +See **YAML Standards** below for the full conventions. The tfmodel config (`tfs_configure_config.yaml`) is generated by `tfs-configure-model` and drives `tfs-fit-model`. It contains `data`, `components`, `priors_file`, `guesses_file` and — for a growth model — `library_file` plus a `library` provenance block. Do not hand-edit it. + +### Library description (`--library_config`) + +`tfs-configure-model` takes `--library_config`, the library YAML that describes the screened library — **the same file handed to `tfs-process-fastq`**. It is required whenever `growth_df` is given (a binding-only model has no congression correction and no ln_cfu0 latents, so it refuses one). It replaced the old `--spiked` list, which could not express the central fact that the spiked controls are *also* encoded in the bulk sub-libraries: wt and each spiked single mutant arrive both as a monoclonal spike and as bulk library members, and they cannot be told apart by sequence. + +Keys read (via `LibraryManager`): `reading_frame`, `first_amplicon_residue`, `wt_seq`, `degen_sites`, `tiles`, `tile_combos`, `spiked_seqs`, plus `library_mixture`. Everything else (a full simulate config, say) is ignored. + +Flow: `genetics.library_composition_table(library_config)` (`genetics/library_design.py`) → one row per genotype with `is_wt`, `in_spiked_origin`, `pool_fraction` and `bulk_fraction` → written to `{out_prefix}_library.csv`. The **snapshot CSV is what `tfs-fit-model` reads**, never the YAML; this mirrors the priors/guesses CSV pattern and makes the table the place to override the design's numbers. `ModelOrchestrator(library_file=...)` derives today's `spiked_genotypes` from `in_spiked_origin` and exposes the full table as `orchestrator.library_df`. `spiked_genotypes` is still accepted directly (and is what `tfs-prefit-calibration` uses when it clears both keys for its calibration-subset model), but the two are mutually exclusive, and a config carrying `spiked_genotypes` is the legacy path. + +**Two checks, two different guarantees.** The *genetics* keys are attestable: they determine the genotype names, so `tfs-configure-model` fails fast if any genotype in `growth_df`/`presplit_df`/`base_growth_df` is absent from the library (`check_genotypes_in_library`; `__unknown__` excepted). A residue-numbering shift mismatches essentially every mutant and is caught immediately. `library_mixture` is **declared-only**: no upstream artifact ever saw it, so nothing can cross-check it. It is recorded verbatim in the config's `library` block, and that is the whole defense — the values should be the best available estimate of the realized pool, not just the intended design. + +A library-derived spiked genotype that has no growth data is **reported, not fatal** (spikes can drop out of a real dataset), unlike the hand-supplied `spiked_genotypes` list, which still raises. + +`pool_fraction`/`bulk_fraction` are computed and snapshotted but **not yet consumed by the model** — `bulk_fraction` is the `f_g` the observable-level congression mixture will use (see `future/congression-physics-plan.md`), and the current backend still treats spiked as a binary via `congression_mask`/`ln_cfu0_spiked_mask`. ### Pre-fit model accounting (`tfmodel/model_stats.py`) @@ -457,13 +471,13 @@ Both grid CLIs import from `tfscreen.util.grid_utils` for run-name generation, J | `simulate-and-analyze/run.sh` | Jinja2 shell template for simulate-and-analyze runs | | `tfmodel/grid.yaml` | Example tfmodel grid for `tfs-setup-grid` | | `tfmodel/run.srun` | Jinja2 SLURM template rendered into each tfmodel grid run subdir | -| `process_raw/library_config.yaml` | Minimal library genetics config for `tfs-process-fastq` | +| `process_raw/library_config.yaml` | Minimal library config for `tfs-process-fastq` and `tfs-configure-model --library_config` (genetics keys + `library_mixture`) | ### `process_raw` YAML `tfs-process-fastq` accepts a `run_config` argument that is passed to `LibraryManager`. It reads only the library genetics keys: `reading_frame`, `wt_seq`, `degen_sites`, `tiles`, `expected_5p`, `expected_3p`, `tile_combos`, `spiked_seqs`. All other keys are ignored. -**Recommended practice**: maintain one `run_config.yaml` per experiment and pass it to both `tfs-simulate` and `tfs-process-fastq` — no need for a separate file. Use `examples/process_raw/library_config.yaml` only when you need a minimal standalone library config (e.g. for processing real data without a matching simulation). +**Required practice**: maintain **one** `run_config.yaml` per experiment and pass that same file to `tfs-simulate`, `tfs-process-fastq` and `tfs-configure-model --library_config`. Nothing in the pipeline checks that the three saw the same file: the genotype-set check in `tfs-configure-model` catches a genetics mismatch, but `library_mixture` (which only `tfs-configure-model` and `tfs-simulate` read) can silently drift. Use `examples/process_raw/library_config.yaml` only when you need a minimal standalone library config (e.g. for processing real data without a matching simulation); note it carries `library_mixture` as well as the genetics keys. ### Terminology @@ -502,6 +516,10 @@ Positional argument order (use only what the script needs): 3. `data_file` — path to a long-form observable CSV (e.g. `tfs-cat-response` takes `data_file x_obs y_obs`; `tfs-extract-epistasis` takes `data_file y_obs`) +### `--library_config` + +`tfs-configure-model`, `tfs-fit-genotypes` and `tfs-build-empirical` take the library YAML as `--library_config`. It is an exception to the positional-if-required rule: `tfs-configure-model` requires it only when `growth_df` is given, and `growth_df` is itself a flag, so a positional would be wrong for the binding-only call. Validate it in the function body instead. + ### Output flag Always `--out_prefix` (never `--out_root`, `--out`, or `--output_file`). The function parameter must also be named `out_prefix`. diff --git a/docs/badges/tests-badge.svg b/docs/badges/tests-badge.svg index 402edbd0..934192a8 100644 --- a/docs/badges/tests-badge.svg +++ b/docs/badges/tests-badge.svg @@ -1 +1 @@ -tests: 4408tests4408 \ No newline at end of file +tests: 4420tests4420 \ No newline at end of file diff --git a/docs/source/analysis.rst b/docs/source/analysis.rst index a18d84c5..1d8b32e4 100644 --- a/docs/source/analysis.rst +++ b/docs/source/analysis.rst @@ -19,11 +19,13 @@ Step 1: Configure Model (``tfs-configure-model``) -------------------------------------------------- Validates the input data, maps categorical labels to numerical indices, selects -model components, and writes three configuration files: +model components, and writes the configuration files: * ``{out_prefix}_config.yaml`` — main configuration read by all downstream steps * ``{out_prefix}_priors.csv`` — prior distribution settings for all parameters * ``{out_prefix}_guesses.csv`` — initial-value guesses for array parameters +* ``{out_prefix}_library.csv`` — per-genotype library composition resolved from + ``--library_config`` (growth models only) ``binding_df`` (direct binding measurements) is the only required argument. ``growth_df`` is optional; omitting it configures a binding-only model. See @@ -35,8 +37,20 @@ data is useful, and the exact file format for ``binding_df``, ``growth_df``, tfs-configure-model binding.csv \ --growth_df growth.csv \ + --library_config run_config.yaml \ --out_prefix tfs_configure +``--library_config`` is the library YAML describing the screened library — the +**same file** passed to ``tfs-process-fastq``. It is required whenever +``--growth_df`` is given. It tells the model which genotypes came in as +monoclonal spikes (and so are congression-free), replacing the older +hand-written ``--spiked`` list; because a spiked control is usually also +encoded in the bulk sub-libraries, the resolved table records each genotype's +expected ``pool_fraction`` and ``bulk_fraction`` rather than a yes/no flag. +``tfs-configure-model`` fails if any genotype in the data is absent from the +library, which catches a residue-numbering or wt-sequence mismatch between the +library description and the reads it was called against. + Key component flags (see :ref:`model-components` for the full list): * ``--condition_growth_model`` — how growth rate depends on TF occupancy (default: ``linear``) diff --git a/docs/source/grid.rst b/docs/source/grid.rst index 95bf0187..1c7e8f23 100644 --- a/docs/source/grid.rst +++ b/docs/source/grid.rst @@ -77,6 +77,7 @@ Grid YAML format variants: - binding_df: ../data/binding.csv growth_df: ../data/growth.csv + library_config: ../data/run_config.yaml # 'auto' enumerates every registered component for an axis. # Incompatible combinations are skipped automatically. @@ -120,8 +121,8 @@ Key rules: component axes; e.g. ``condition_growth`` rather than ``--condition_growth_model``). * Relative paths in ``configure_model`` blocks (``binding_df``, ``growth_df``, - ``thermo_data``) are resolved relative to the grid YAML and re-expressed - relative to each subdirectory in the written config. + ``library_config``, ``thermo_data``) are resolved relative to the grid YAML + and re-expressed relative to each subdirectory in the written config. * The ``auto`` form enumerates every registered component for the given axis. Incompatible combinations (e.g. ``power`` growth + ``logit`` theta_rescale) are caught by ``tfs-configure-model``, skipped, and logged in diff --git a/docs/source/process-raw.rst b/docs/source/process-raw.rst index 10591f0b..768dfb19 100644 --- a/docs/source/process-raw.rst +++ b/docs/source/process-raw.rst @@ -113,8 +113,14 @@ genotype across all samples, ready for hierarchical modelling. to match this row to a counts CSV file. * ``library`` — name of the physical library this sample belongs to. Genotypes are filtered and frequency-normalised within each library. - * ``sample_cfu`` — total colony-forming units (CFU) measured for this tube. - * ``sample_cfu_std`` — standard deviation of ``sample_cfu``. + * ``sample_ln_cfu`` — natural log of the total colony-forming units (CFU) + measured for this tube. + * ``sample_ln_cfu_std`` — standard deviation of ``sample_ln_cfu``. + + Instead of ``sample_ln_cfu``/``sample_ln_cfu_std``, you may supply + ``sample_ln_cfu_var``, or the linear-space ``sample_cfu`` with + ``sample_cfu_std`` (or ``sample_cfu_var``); the log-space columns are then + inferred. Log-space columns are used when both are present. The following columns are not used by ``tfs-process-counts`` itself but are carried through into the ``ln_cfu`` output and are **required by the growth @@ -179,8 +185,12 @@ can be matched to the correct growth conditions. * ``replicate`` — replicate index; matched to the growth data. * ``condition_pre`` — pre-selection condition name; matched to the growth data. - * ``sample_cfu`` — total CFU for this tube. - * ``sample_cfu_std`` — standard deviation of ``sample_cfu``. + * ``sample_ln_cfu`` — natural log of the total CFU for this tube. + * ``sample_ln_cfu_std`` — standard deviation of ``sample_ln_cfu``. + + As for ``tfs-process-counts``, these may instead be inferred from + ``sample_ln_cfu_var`` or from ``sample_cfu`` with ``sample_cfu_std`` (or + ``sample_cfu_var``). * ``counts_csv_path``: Directory containing the per-sample count CSV files. * ``output_file``: Path for the output presplit CSV. diff --git a/examples/process_raw/library_config.yaml b/examples/process_raw/library_config.yaml index c31bd62f..00e38435 100644 --- a/examples/process_raw/library_config.yaml +++ b/examples/process_raw/library_config.yaml @@ -42,3 +42,23 @@ tile_combos: ["single-1", "single-2", "double-1-2"] spiked_seqs: - gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctggcggcgccgtcgcaaattgtcgcggcgattctgtctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg # k84l - gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgattgcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattctgtctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg # m42i/k84l + +# --------------------------------------------------------------------------- +# Library composition (for tfs-configure-model) +# +# Relative amount of each transformed sub-library in the pooled library. Only +# ratios matter. Keys must be exactly the tile_combos above, plus 'spiked' +# when spiked_seqs is defined. +# +# tfs-configure-model uses these -- with the genetics keys above -- to work out +# each genotype's expected share of the pool and what fraction of its cells +# come from the bulk (congression-affected) sub-libraries rather than from the +# monoclonal spike. Nothing cross-checks these numbers against the data, so +# they should be the best available estimate of what actually went into the +# pool, not just the intended design. +# --------------------------------------------------------------------------- +library_mixture: + single-1: 100 + single-2: 100 + double-1-2: 1_000 + spiked: 1 diff --git a/examples/simulate-and-analyze/run.sh b/examples/simulate-and-analyze/run.sh index 65d9b4fb..09ff0d9b 100644 --- a/examples/simulate-and-analyze/run.sh +++ b/examples/simulate-and-analyze/run.sh @@ -42,6 +42,11 @@ fi echo ">>> Simulate library" tfs-simulate "${config_file}" "${run_dir}" --seed "${seed}" +# The simulate config also describes the library (genetics keys + +# library_mixture), so tfs-configure-model reads the same file. Resolve it to +# an absolute path before changing directory. +library_config="$(cd "$(dirname "${config_file}")" && pwd)/$(basename "${config_file}")" + cd "${run_dir}" # --------------------------------------------------------------------------- @@ -66,7 +71,7 @@ tfs-configure-model \ --theta_growth_noise_model logit_normal \ --theta_binding_noise_model zero \ --growth_noise_model normal_kt \ - --spiked wt M42I H74A K84L M42I/H74A M42I/K84L H74A/K84L D88A \ + --library_config "${library_config}" \ --growth_shares_replicates \ --epistasis diff --git a/examples/simulate-empirical/simulate_config.yaml b/examples/simulate-empirical/simulate_config.yaml index 72c95306..8b8afb02 100644 --- a/examples/simulate-empirical/simulate_config.yaml +++ b/examples/simulate-empirical/simulate_config.yaml @@ -11,7 +11,8 @@ # Workflow: # # 1. real data -> empirical generating distribution (writes emp_phenotype_model.json) # tfs-build-empirical growth.csv 42 \ -# --binding_file binding.csv --spiked_file spiked.txt --out_prefix emp +# --binding_file binding.csv --library_config library_config.yaml \ +# --out_prefix emp # # 2. simulate from it # tfs-simulate simulate_config.yaml out_dir/ # diff --git a/examples/tfmodel/grid.yaml b/examples/tfmodel/grid.yaml index b1cbe049..21775e41 100644 --- a/examples/tfmodel/grid.yaml +++ b/examples/tfmodel/grid.yaml @@ -35,6 +35,9 @@ configure_model: variants: - binding_df: ../data/binding.csv growth_df: ../data/growth.csv + # The library description -- the same YAML used for tfs-process-fastq. + # Required whenever growth_df is given. + library_config: ../data/run_config.yaml - name: fixed_components variants: diff --git a/reports/flake.txt b/reports/flake.txt index ec42ab09..5d19625b 100644 --- a/reports/flake.txt +++ b/reports/flake.txt @@ -1,14901 +1,3 @@ -./.claude/worktrees/compassionate-curran-92f7bd/scripts/generate_struct_ensemble.py:266:11: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/data.py:44:23: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/data.py:45:23: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/data.py:46:23: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/data.py:46:28: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:16:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:79:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:95:41: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:96:31: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/expand_genotype_columns.py:105:14: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:31:1: C901 '_standardize_one' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:180:8: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:181:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:230:14: E111 indentation is not a multiple of 4 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:230:14: E117 over-indented -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:265:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:268:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:268:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:268:50: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:287:40: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:320:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:321:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:339:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/genotype_sorting.py:345:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:46:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:55:59: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:58:38: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:59:38: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:60:39: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:63:11: E124 closing bracket does not match visual indentation -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:65:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:66:52: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:78:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:80:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:87:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:90:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:93:37: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:94:61: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/get_single_with_wt.py:107:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:57:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:159:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:169:22: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:180:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:181:5: C901 'LibraryManager._parse_and_validate' is too complex (12) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:219:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:226:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:235:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:244:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:250:9: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:251:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:254:27: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:254:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:258:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:258:46: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:288:51: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:288:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:288:70: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:300:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:300:94: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:307:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:309:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:310:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:311:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:313:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:316:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:316:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:318:30: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:321:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:324:18: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:373:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:378:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:380:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:386:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:415:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:421:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:427:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:466:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:467:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:471:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:476:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:478:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:478:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:479:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:482:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:488:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:493:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:526:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:527:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:528:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:555:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:560:73: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:560:82: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:561:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:562:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:562:55: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:562:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:563:39: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:563:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:564:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:564:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:566:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:568:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:605:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:611:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:613:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:616:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:617:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:648:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:650:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:656:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:657:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:661:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:663:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:665:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:695:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:698:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:703:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:708:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:710:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:712:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:713:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:721:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:740:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:740:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:748:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:776:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:781:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:787:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:790:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:791:39: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:794:72: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:795:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:798:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:806:9: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:807:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:810:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:811:15: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/genetics/library_manager.py:825:1: 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:382:21: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:396:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:396:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:399:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:399:21: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:402:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:413:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:413:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/guesses.py:415:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:80:26: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:82:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:141:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:143:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:148:25: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:161:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:164:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:203:27: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:203:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:203:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:203:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:205:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:279:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:279:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:280:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:280:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:283:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:284:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:286:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:286:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:287:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:375:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:375:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:376:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:378:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:378:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:379:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:383:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:386:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:428:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:440:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:450:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/curve_models/models.py:454:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:26:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:29:56: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:34:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:36:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:123:5: E301 expected 1 blank line, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:186:62: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:219:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:223:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:225:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:227:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:247:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:250:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:269:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:272:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:291:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:294:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:320:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:337:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:340:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:342:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:344:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:344:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fit_manager.py:473:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/__init__.py:7:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:44:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:44:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:47:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:118:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:119:18: F541 f-string is missing placeholders -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/least_squares.py:128:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:13:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:43:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:43:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:43:39: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:56:52: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_nls.py:67:54: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:27:81: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:52:40: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/fitters/matrix_wls.py:55:52: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/predict_with_error.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/predict_with_error.py:50:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/predict_with_error.py:68:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/predict_with_error.py:72:45: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/mle/predict_with_error.py:89:32: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/__init__.py:36:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:13:1: C901 'cat_fits' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:13:15: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:13:17: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:99:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:99:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:113:80: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:120:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:121:14: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:123:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:123:44: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:128:22: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:128:24: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:131:23: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:131:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:131:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:137:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:147:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:147:54: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:163:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:163:54: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:171:26: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:172:26: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:173:12: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:174:12: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:175:12: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:176:12: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/cat_fits.py:187:5: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:11:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:12:23: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:17:66: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:19:80: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:38:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:39:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:47:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:51:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:51:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:51:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/corner.py:51:63: E231 missing whitespace after ',' 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after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:28:16: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:29:16: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:33:9: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:34:12: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:38:8: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:39:16: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:40:16: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:44:12: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:45:9: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:46:17: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:47:14: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:54:9: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:55:12: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:56:13: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:56:16: E261 at least two spaces before inline comment 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whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:65:20: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:66:33: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:70:18: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:71:17: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:72:22: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:73:20: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:74:33: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:79:18: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:79:21: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:80:17: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:81:22: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:82:20: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:83:33: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/default_styles.py:84:2: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:18:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:20:34: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:33:55: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:43:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:44:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:49:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:49:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:55:5: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_vs_mag.py:57:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/err_zscore.py:79:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:24:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:54:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:57:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:72:5: E303 too many blank lines (2) 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/est_v_real_summary.py:106:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/geno_trajectory.py:29:1: C901 'plot_geno_trajectory' is too complex (14) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:15:53: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:16:53: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:17:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:26:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:27:25: E211 whitespace before '(' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:39:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:41:19: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:15:53: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:16:53: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:19:21: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:20:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:21:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:25:17: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:33:25: E211 whitespace before '(' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:50:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/epistasis_heatmap.py:52:19: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:6:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:28:1: C901 '_build_heatmap_collection' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:88:38: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:90:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:93:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:107:55: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:110:55: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:126:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:129:68: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:142:33: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:143:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:149:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:149:28: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:151:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:154:33: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:155:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:156:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:157:34: E203 whitespace before ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:157:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:158:34: E203 whitespace before ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:158:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:158:41: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:159:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:159:41: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:160:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:162:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:162:66: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:172:1: C901 '_build_color_mapper' is too complex (13) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:172:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:217:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:241:39: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:241:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:243:26: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:280:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:281:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:338:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:373:40: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:375:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:382:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:388:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:443:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:448:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:457:1: C901 'heatmap' is too complex (13) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:509:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:528:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:531:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:561:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:569:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:570:5: F841 local variable 'e' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:580:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:589:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:590:39: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:592:37: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:592:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:592:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:593:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:596:29: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:612:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:615:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:620:20: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:621:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:622:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:625:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:629:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:636:35: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:637:34: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:638:32: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:639:37: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:643:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:644:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:645:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:647:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:661:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:661:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:661:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:661:56: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:662:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:662:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:662:45: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:662:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:666:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:666:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:671:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:672:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:679:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/heatmap/heatmap_core.py:680:19: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:28:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:29:40: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:31:55: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:51:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:60:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:62:71: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:64:61: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:69:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:70:26: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:84:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:93:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/helper.py:100:17: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/hill_fit.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:84:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:84:50: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:88:73: E225 missing whitespace around operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:89:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:92:52: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:98:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:98:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:102:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:102:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:105:40: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:108:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:108:46: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:115:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:121:21: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:124:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:130:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:133:25: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:139:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:144:22: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/plot_theta_fits.py:153:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/uncertainty_calibration.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/uncertainty_calibration.py:21:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/uncertainty_calibration.py:24:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/plot/uncertainty_calibration.py:65:36: E231 missing whitespace after ',' 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:405:29: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:412:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:413:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:414:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:415:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:416:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:417:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:419:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:422:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:423:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:426:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:427:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:429:37: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:433:39: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:434:33: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:436:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_fastq_cli.py:437:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_presplit_cli.py:77:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_presplit_cli.py:78:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_presplit_cli.py:79:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/process_raw/scripts/process_presplit_cli.py:86:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/__init__.py:29:2: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:222:1: C901 'build_theta_gc_override_hill_mut' is too complex (15) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:286:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:287:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:289:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:290:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:293:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:295:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:296:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:314:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:315:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:318:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:318:43: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:320:23: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:321:23: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:327:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:329:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:330:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:333:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:347:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:347:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:349:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:349:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:350:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:350:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:380:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:382:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:383:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:386:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/binding_params.py:388:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/build_sample_dataframes.py:95:21: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/library_prediction.py:76:1: C901 '_validate_binding_config' is too complex (13) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/library_prediction.py:212:43: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/library_prediction.py:212:44: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:55:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:56:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:57:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:58:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:62:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:63:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:64:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:83:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:84:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:85:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:90:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:103:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:106:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:107:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:108:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:111:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:113:25: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:115:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/presplit_data.py:129:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:18:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:21:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:22:23: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:22:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:22:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:22:62: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:24:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:25:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:50:38: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:50:39: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:51:39: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:51:40: E252 missing whitespace around parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:53:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:56:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:71:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:72:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:82:46: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:88:51: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:88:62: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:91:26: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:92:29: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:93:33: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:94:25: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:95:25: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:100:50: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/run_simulation.py:107:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:170:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:171:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:172:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:173:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:174:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:175:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:176:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:177:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:178:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/sample_theta.py:271:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/scripts/setup_sim_grid_cli.py:101:1: C901 'setup_sim_grid' is too complex (17) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/scripts/simulate_cli.py:18:1: C901 'run_simulation_from_config' is too complex (15) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/scripts/simulate_cli.py:153:128: E501 line too long (153 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:42:38: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:43:37: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:44:36: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:45:36: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:46:36: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:74:1: C901 '_check_dict_number' is too complex (13) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:160:1: C901 '_check_cf' is too complex (25) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:182:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:201:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:225:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:226:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:292:1: C901 '_check_lib_spec' is too complex (12) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:292:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:344:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:349:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:371:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:424:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:440:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:448:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:448:44: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:458:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:468:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:511:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:515:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:516:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:526:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:529:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:575:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:586:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:587:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:590:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:594:55: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:600:32: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:605:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:606:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:610:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:652:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:658:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:663:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:687:43: E231 missing whitespace after ',' 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:761:79: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:767:29: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:809:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:815:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:816:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:822:79: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:824:33: E231 missing whitespace after ',' 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1041:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1050:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1051:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1053:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1059:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1061:51: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1068:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1070:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1071:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1078:79: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1083:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1084:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1086:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1088:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1092:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1098:128: E501 line too long (145 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1099:128: E501 line too long (145 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1104:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1108:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1115:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1161:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1196:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1217:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1218:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1221:28: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1221:39: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/simulate/selection_experiment.py:1226:1: W293 blank line contains whitespace 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indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/batch_sizing.py:35:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/batch_sizing.py:119:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/batch_sizing.py:120:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/batch_sizing.py:121:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/batch_sizing.py:122:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/error_calibration.py:474:32: E127 continuation line over-indented for visual indent 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spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:41:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:45:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:99:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:120:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:165:1: C901 'copy_orchestrator' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:292:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:399:1: C901 'predict' is too complex (29) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:542:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:545:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:550:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:570:31: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:572:31: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:604:58: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:607:26: E111 indentation is not a multiple of 4 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:607:26: E117 over-indented -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:610:25: E122 continuation line missing indentation or outdented -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prediction.py:616:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/analysis/prior_predictive.py:104:33: E203 whitespace before ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:37:1: E302 expected 2 blank lines, found 1 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under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:471:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:477:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:502:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/configuration_io.py:507:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/data_class.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/data_class.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/data_class.py:28:5: E303 too many blank lines (2) 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of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:16:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:17:35: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:48:46: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/activity/fixed.py:51:45: W291 trailing whitespace 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W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/beta.py:185:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/beta.py:194:48: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/zero.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/zero.py:18:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/zero.py:19:39: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/noise/zero.py:46:1: E302 expected 2 blank lines, found 1 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E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:504:29: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:505:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:516:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:518:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:519:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:556:25: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: E305 expected 2 blank lines after class or function definition, found 1 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before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:102:6: E201 whitespace after '[' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:102:38: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:103:6: E201 whitespace after '[' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:103:38: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:104:6: E201 whitespace after '[' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:104:38: E202 whitespace before ']' 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:362:30: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:363:29: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:364:30: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:365:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:366:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:375:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:376:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:377:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:378:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:379:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:382:29: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:383:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:384:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:385:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:437:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:438:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:442:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:446:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:449:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:454:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:457:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:461:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:480:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:483:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:115:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:116:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:121:6: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:126:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:127:6: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:144:7: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:211:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:212:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:215:7: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:216:6: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:221:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:227:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:228:6: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:249:40: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:309:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:323:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:324:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:328:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:329:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:99:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:110:40: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:111:48: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:112:49: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:76:7: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:91:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:102:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:86:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:115:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:171:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:181:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/theta/thermo/nn.py:62:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:131:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:164:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:169:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:177:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:179:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:191:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:194:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:196:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:199:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:206:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:209:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:213:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:234:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:243:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:309:35: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:333:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:354:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:366:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:369:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:369:21: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:370:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:393:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:416:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:423:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:523:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:536:1: E302 expected 2 blank lines, found 1 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lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/logit_norm.py:58:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/single.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/single.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/single.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/single.py:14:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/generative/components/transformation/single.py:15:35: W291 trailing 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contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/inference/run_inference.py:1355:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/inference/run_inference.py:1359:30: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/inference/run_inference.py:1362:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/inference/run_inference.py:1366:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/inference/run_inference.py:1372:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/model_orchestrator.py:38:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/model_orchestrator.py:72:1: W293 blank line contains whitespace 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':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:276:59: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:277:63: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:278:70: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:279:55: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:280:70: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/configure_model_cli.py:282:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:97:6: 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whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:251:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:514:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:516:60: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:517:53: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:518:64: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:519:66: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/fit_model_cli.py:520:66: E231 missing whitespace after ':' 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complex (16) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/predict_growth_cli.py:193:27: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/predict_theta_cli.py:12:1: C901 'predict_theta' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:129:23: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:130:23: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:221:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:222:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:227:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:405:1: C901 '_inject_calibration_priors' is too complex (21) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:664:1: C901 '_build_csv_updates' is too complex (12) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:733:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:734:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:735:35: E127 continuation line over-indented for visual indent 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/subset_genotypes_cli.py:93:5: F841 local variable 'all_genotypes' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:154:1: C901 '_read_all_losses' is too complex (11) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:413:1: C901 '_summarize_params' is too complex (23) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:528:1: C901 '_summarize_condition_growth_params' is too complex (14) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:723:1: C901 'summarize_fit' is too complex (59) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/tfmodel/scripts/summarize_grid_cli.py:47:30: E127 continuation line over-indented for visual indent 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/__init__.py:16:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:1:11: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:5:1: C901 'generalized_main' is too complex (15) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:13:78: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:14:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:24:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:27:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:30:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:57:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:58:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:69:30: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:75:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:85:58: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:87:34: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:87:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:92:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:94:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:97:39: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:104:45: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:104:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:104:75: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/cli/generalized_main.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/__init__.py:32:2: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:8:79: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:10:82: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:12:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:13:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:25:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:42:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:43:12: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:47:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:52:29: E211 whitespace before '(' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:65:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:73:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:80:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:81:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/add_group_columns.py:90:21: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/check_columns.py:4:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/check_columns.py:4:21: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/check_columns.py:35:30: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/chunk_by_group.py:3:1: F811 redefinition of unused 'np' from line 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/chunk_by_group.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/chunk_by_group.py:74:44: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:65:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:68:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:84:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:89:74: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:90:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:91:22: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:105:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/df_to_arrays.py:112:24: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/expand_on_conditions.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/expand_on_conditions.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/expand_on_conditions.py:62:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_group_mean_std.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_group_mean_std.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_group_mean_std.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_group_mean_std.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_group_mean_std.py:95:37: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:9:14: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: C901 'get_scaled_cfu' is too complex (17) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:130:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/dataframe/get_scaled_cfu.py:131:14: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:7:1: C901 'read_dataframe' is too complex (16) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:84:27: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_dataframe.py:102:14: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/io/read_yaml.py:31:1: C901 'read_yaml' is too complex (12) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:48:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:82:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/array_search.py:97:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:43:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:44:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:50:30: E203 whitespace before ':' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/padding.py:53:21: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/transform.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/transform.py:189:36: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:65:14: E111 indentation is not a multiple of 4 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:65:14: E117 over-indented -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:65:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/xfill.py:88:20: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:57:22: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:70:71: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:71:34: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/numerical/zero_truncated_poisson.py:74:23: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/validation/check.py:37:1: C901 'check_number' is too complex (12) -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/validation/check.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/validation/check.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/src/tfscreen/util/validation/check.py:118:18: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:40:63: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:54:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:60:9: F841 local variable 'patterns' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:65:68: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:70:64: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:70:65: F541 f-string is missing placeholders -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:77:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:81:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:85:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:94:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:100:1: E266 too many leading '#' for block comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/conftest.py:107:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_nuts_reference.py:37:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_nuts_reference.py:38:9: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:28:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:29:8: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:30:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:34:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:35:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:37:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/fixtures/generate_reference_posteriors.py:42:5: E221 multiple spaces before operator 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whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:143:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:151:52: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:152:28: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:156:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:159:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:162:76: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:163:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:168:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:175:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:177:90: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:189:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:191:88: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:191:100: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:196:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:199:50: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:204:91: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:210:77: E231 missing whitespace after ',' 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expression, use a def -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_extract_epistasis.py:411:79: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:9:52: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:20:41: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:23:39: W291 trailing whitespace 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import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:87:1: E302 expected 2 blank lines, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:96:10: E111 indentation is not a multiple of 4 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:96:10: E117 over-indented -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/analysis/test_stats_test_suite.py:99:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:21:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:23:28: E124 closing bracket does not match visual indentation -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:47:38: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_cycles.py:61:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_build_mut_geno_matrix.py:1:1: F401 'pytest' imported but unused 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_combine_mutation_effects.py:101:17: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_combine_mutation_effects.py:108:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_combine_mutation_effects.py:111:39: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_data.py:8:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_expand_genotype_columns.py:4:1: F401 'pandas.testing.assert_frame_equal' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_expand_genotype_columns.py:11:1: E302 expected 2 blank lines, found 1 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blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_expand_genotype_columns.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_expand_genotype_columns.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_expand_genotype_columns.py:99:29: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_argsort_genotypes.py:38:30: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_argsort_genotypes.py:84:72: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:8:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:53:1: E303 too many blank lines (4) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:120:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:145:27: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:22:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:31:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:40:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:51:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:84:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:86:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:92:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:94:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:101:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:103:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:107:52: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:115:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:117:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:127:26: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:138:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:157:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:163:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:167:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:176:48: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:4:1: F401 'pandas.testing.assert_frame_equal' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:13:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:15:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:74:80: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:109:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:129:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:132:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:142:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_get_single_with_wt.py:145:31: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:94:25: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:117:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:124:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:127:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:144:45: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:173:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:186:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:191:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:193:26: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:198:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:206:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:211:39: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:215:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:223:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:236:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:241:47: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:245:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:257:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:293:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:312:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:319:14: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:319:39: E202 whitespace before ')' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:320:14: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:320:55: E202 whitespace before ')' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:335:22: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:336:23: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:356:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:360:26: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:361:21: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:367:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:371:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:377:26: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:378:21: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:384:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:385:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:387:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:390:28: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:391:26: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:392:21: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:400:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:403:30: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:404:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:404:36: E116 unexpected indentation (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:405:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:405:36: E116 unexpected indentation (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:406:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:406:36: E116 unexpected indentation (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:407:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:408:26: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:409:21: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:417:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:421:26: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:421:37: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:422:21: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:475:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:491:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:493:32: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:526:19: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:527:58: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:528:18: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:534:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:539:51: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:540:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:551:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:556:19: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:557:67: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:558:18: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:562:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:566:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:579:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:586:19: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:588:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:597:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:599:24: E201 whitespace after '{' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:599:75: E202 whitespace before '}' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:601:24: E201 whitespace after '{' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:601:75: E202 whitespace before '}' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:603:24: E201 whitespace after '{' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:603:75: E202 whitespace before '}' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:610:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:625:19: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:627:18: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:648:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:654:19: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:656:18: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:656:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:665:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:680:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:684:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:694:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:702:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:704:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:707:48: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:708:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:720:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:734:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:747:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:751:42: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:759:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:764:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:768:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:774:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:779:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:811:22: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:815:35: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:815:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/genetics/test_library_manager.py:840:34: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:27:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:81:32: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:112:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:120:45: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:121:45: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:127:45: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:128:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_guesses.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:29:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:36:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:44:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:58:52: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:91:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:98:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/curve_models/test_models.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:18:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:22:38: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:43:22: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:43:24: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:81:54: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:83:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:97:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_least_squares.py:108:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_nls.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:15:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:35:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:40:43: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_matrix_wls.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:29:32: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_svd_error.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:14:34: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:15:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:24:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:26:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:44:18: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/fitters/test_util.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:6:1: F401 'scipy.special.expit' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:38:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:39:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:45:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:63:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:65:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:81:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:83:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:106:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:109:20: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:121:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:128:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:147:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:155:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:156:33: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:157:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:161:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:163:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:172:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:173:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:174:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:176:60: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:180:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:182:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:185:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_fit_manager.py:189:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:51:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/mle/test_predict_with_error.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:25:1: F401 'tfscreen.plot.default_styles.DEFAULT_HMAP_PATCH_KWARGS' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:31:1: F401 'tfscreen.plot.helper.get_ax_limits' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:31:47: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:50:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:96:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:138:48: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:144:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:145:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:148:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:166:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:177:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:180:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:184:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:203:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:208:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:211:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:213:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:234:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:239:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:240:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:260:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:272:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:274:9: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:292:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:295:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:299:40: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:304:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:305:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:314:43: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:318:57: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:319:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:320:41: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:331:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:351:50: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:352:59: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:353:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:356:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:370:48: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:381:49: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:392:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:415:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:428:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:455:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:460:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:475:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:476:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:480:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:484:71: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:499:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:512:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:514:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:525:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:535:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:538:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:543:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:547:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:570:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:572:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:587:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:590:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:593:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:602:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:632:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:682:21: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:694:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:698:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:701:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:704:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:717:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:720:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:724:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:727:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:729:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:741:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:744:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:750:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:754:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:760:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:782:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:785:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:791:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:800:10: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:801:10: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:802:10: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:803:10: E201 whitespace after '(' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:814:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmap_core.py:817:30: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:4:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:17:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:36:57: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:37:36: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:98:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:102:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:110:47: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:113:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:121:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:123:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/heatmap/test_heatmaps.py:136:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:32:27: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:34:40: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:37:34: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:38:26: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:59:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_cat_fits.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:6:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:9:5: F401 'corner' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:78:41: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_corner.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_default_styles.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_default_styles.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_default_styles.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_err_plots.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_est_v_real_summary.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:18:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:20:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:159:25: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:304:31: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:305:42: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:320:31: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:321:42: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:488:19: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:516:19: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_geno_trajectory.py:544:19: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:31:16: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:33:59: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_helper.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_hill_fit.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_hill_fit.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_hill_fit.py:118:34: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_plot_theta_fits.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_plot_theta_fits.py:301:26: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:18:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:22:5: F841 local variable 'ylim' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:32:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:35:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:42:53: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:43:72: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:49:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:53:5: F841 local variable 'ax' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/plot/test_xy_corr.py:149:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:101:53: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:110:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:130:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:131:47: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:142:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:147:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:204:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:213:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:221:73: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:30: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:239:53: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:240:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:247:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:249:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:250:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:256:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_counts_to_lncfu.py:261:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:63:25: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:73:25: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:107:1: E265 block comment should start with '# ' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:109:1: E265 block comment should start with '# ' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:111:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:121:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:123:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:137:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:142:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:147:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:155:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:170:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:191:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:217:59: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:274:9: E116 unexpected indentation (comment) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:278:67: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:287:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:296:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:347:5: F841 local variable 'f3' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:361:5: F841 local variable 'f1_as_rev_read' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:374:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:392:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:396:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:429:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:466:48: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:515:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:583:37: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:584:37: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:621:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:707:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:708:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:718:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:728:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:737:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:751:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:754:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:755:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:761:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:771:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:785:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:789:71: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:795:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:805:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:809:69: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:819:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:874:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:878:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:883:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:884:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:908:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:909:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:920:1: E302 expected 2 blank lines, found 1 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contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:986:52: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1001:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1004:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1005:27: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1019:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1040:1: W293 blank line contains whitespace 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contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_fastq_to_counts.py:1104:45: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:2:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:26: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:33: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:40: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:47: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:54: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:61: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:68: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:75: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:82: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:39:89: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:84:1: E302 expected 2 blank lines, found 1 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whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:153:62: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:154:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:177:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:193:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:200:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:209:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:215:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:218:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:233:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:240:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:250:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:253:1: E302 expected 2 blank lines, found 1 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blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:298:38: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:300:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:313:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:345:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:349:128: E501 line too long (132 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_fastq_cli.py:360:1: W293 blank line contains whitespace 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'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_presplit_cli.py:80:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_presplit_cli.py:88:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/process_raw/test_process_presplit_cli.py:113:37: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:33:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:94:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:95:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:169:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_fit_phenotypes.py:173:57: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_library_prediction_empirical.py:9:1: F401 'tfscreen.util' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/empirical/test_population.py:4:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_growth_linkage.py:50:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_growth_linkage.py:95:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_growth_linkage.py:154:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:60:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:70:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:83:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:90:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:92:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:100:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:101:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:108:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:129:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:145:32: E127 continuation line over-indented for visual indent 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over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:456:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:459:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:474:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:480:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:482:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:492:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:497:53: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:564:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:565:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:566:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:567:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/growth/test_transition_linkage.py:568:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:5:1: F401 'io' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:8:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:11:1: F401 'tfscreen.simulate.binding_params._logit' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:83:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:85:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:86:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:87:25: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:89:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:90:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:91:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:93:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:206:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:208:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:218:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:220:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:232:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:240:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:305:38: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:307:37: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:316:5: F811 redefinition of unused 'pd' from line 8 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:319:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:320:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:425:43: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:445:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:446:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:466:46: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:487:38: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:488:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:490:37: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:508:45: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_binding_params.py:587:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:83:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:94:18: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:95:8: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:104:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:115:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_build_sample_dataframes.py:128:55: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_growth_parameters_output.py:4:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_library_prediction.py:47:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_library_prediction.py:293:5: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_library_prediction.py:441:16: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:71:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:83:42: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:84:42: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:86:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:94:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:102:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:120:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:121:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:137:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:138:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:139:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:140:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:142:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:155:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:157:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_presplit_data.py:159:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_report_cfu0_cli.py:5:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_report_cfu0_cli.py:131:26: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:3:1: F401 'os' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:5:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:7:1: F401 'tfscreen.util' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:47:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:70:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:82:128: E501 line too long (150 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:110:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:113:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:116:5: F841 local variable 'results' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_run_simulation.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_sample_theta.py:260:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_sample_theta.py:277:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_sample_theta.py:282:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_sample_theta.py:297:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_sample_theta.py:338:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:4:1: F401 'numpy.ma' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:6:1: F401 'scipy.stats.gmean' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:9:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:141:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:175:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:185:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:194:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:203:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:221:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:227:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:236:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:237:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:249:16: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:251:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:251:57: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:252:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:272:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:280:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:283:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:286:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:289:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:293:52: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:294:64: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:303:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:306:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:314:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:320:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:322:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:326:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:332:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:335:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:337:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:338:61: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:343:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:345:31: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:345:32: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:368:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:373:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:380:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:383:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:390:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:400:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:406:1: E303 too many blank lines (3) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:410:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:416:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:418:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:421:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:428:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:436:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:444:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:448:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:452:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:456:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:460:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:464:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:470:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:485:22: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:486:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:488:70: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:497:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:500:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:514:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:517:25: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:528:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:581:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:584:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:585:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:586:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:600:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:607:47: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:613:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:614:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:615:20: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:623:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:626:9: F811 redefinition of unused 'gmean' from line 6 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:634:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:638:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:645:1: E302 expected 2 blank lines, found 1 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contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:724:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:732:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:743:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:744:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:745:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:751:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:754:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:762:43: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:777:31: E201 whitespace after '[' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:778:54: E202 whitespace before ']' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:779:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:783:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:785:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:786:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:795:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:797:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:801:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:809:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:810:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:811:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:820:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:825:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:828:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:834:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:839:25: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:845:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:849:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:851:45: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:852:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:853:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:856:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:864:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:869:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:873:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:879:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:883:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:886:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:889:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:893:37: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:914:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:919:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:922:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:927:41: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:947:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1178:12: F841 local variable 'k_sel' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1193:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1195:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1217:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1232:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1235:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1273:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1285:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1296:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1300:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1303:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_selection_experiment.py:1353:18: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:401:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:405:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:448:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:453:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:455:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:457:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_simulate_cli.py:513:5: F401 'tfscreen.simulate.scripts.simulate_cli as cli_mod' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:41:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:229:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:1437:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/simulate/test_thermo_to_growth.py:1525:9: F841 local variable 'G_out' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_batch_sizing.py:123:40: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_batch_sizing.py:136:40: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_error_calibration.py:313:9: F401 'matplotlib.axes.Axes' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_error_calibration.py:355:9: F401 'matplotlib.axes.Axes' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:50:47: E261 at least two spaces before inline comment 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:30:128: E501 line too long (130 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:50:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:10:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:35: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:42: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:50: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:56: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:62: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:88:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:176:9: F841 local variable 'q_min' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:373:9: F841 local variable 'rng' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:4:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:38:71: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:46:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:93:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:101:57: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:102:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:103:10: E111 indentation is not a multiple of 4 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:103:10: E117 over-indented -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:105:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:115:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:36: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:50: E231 missing whitespace after ',' 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:6:1: F401 'unittest.mock.patch' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:9:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:13:1: F401 'tfscreen.tfmodel.inference.posteriors.get_posterior_samples' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_extraction_robustness.py:52:128: E501 line too long (130 > 127 characters) 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lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:82:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:93:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/analysis/test_prediction.py:103:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:23:1: E302 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:66:45: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:67:50: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:72:19: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:73:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:76:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_fixed.py:113:42: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:23:17: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:27:18: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:28:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:54:29: E261 at least two spaces before inline comment 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whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:142:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:147:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:153:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_geno.py:356:6: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_hierarchical_mut.py:36:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:26:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:27:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:53:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:81:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:97:1: W293 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:126:50: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:127:55: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:132:19: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:133:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:136:1: W293 blank line contains whitespace 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contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_geno.py:176:42: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/activity/test_horseshoe_mut.py:36:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:49:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:66:44: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:67:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:72:19: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:73:24: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:94:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_fixed.py:113:41: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:4:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:78:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:82:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:120:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:121:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:183:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:197:34: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:282:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:283:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:314:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:352:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:353:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:370:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:383:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:386:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:389:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:393:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:409:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:410:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:411:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:412:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:415:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/dk_geno/test_hierarchical_geno.py:426:9: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_linear.py:7:1: F401 'tfscreen.tfmodel.generative.components.growth.linear.LinearParams' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_linear.py:34:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_linear.py:70:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_linear.py:152:28: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_linear.py:154:28: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_power.py:4:1: F401 'numpyro.handlers.substitute' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_power.py:7:1: F401 'tfscreen.tfmodel.generative.components.growth.power.PowerParams' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_power.py:31:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_power.py:38:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_saturation.py:7:1: F401 'tfscreen.tfmodel.generative.components.growth.saturation.SaturationParams' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_saturation.py:31:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth/test_saturation.py:38:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_noise/test_normal_kt.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_noise/test_normal_kt.py:3:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_noise/test_normal_kt.py:4:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_noise/test_normal_kt.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_noise/test_zero.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:38:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/growth_transition/test_instant.py:47:1: W293 blank line contains whitespace 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whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:190:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:193:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:200:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:220:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:379:44: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:4:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:5:1: F401 'numpyro.handlers.trace' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:176:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:179:36: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:180:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:205:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:248:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:252:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:253:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:278:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:279:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:285:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:285:64: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:304:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:320:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:329:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:331:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:355:38: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:357:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:358:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:477:51: E222 multiple spaces after operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:492:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:537:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:540:36: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:541:26: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:12:1: F401 'tfscreen.tfmodel.generative.components.theta.hill_mut._population_moments' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:55:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:125:15: F841 local variable 'G' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:136:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:140:15: F841 local variable 'G' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:140:18: F841 local variable 'P' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:246:9: F841 local variable 'M' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:254:62: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:453:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:480:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:482:33: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:492:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:494:26: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:509:43: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:512:40: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:513:30: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:528:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:530:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:530:52: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:719:34: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:722:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:730:36: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:730:70: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:25:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:155:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:156:33: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:157:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:158:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:159:30: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:160:32: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:161:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:162:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:164:36: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:166:37: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:167:37: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:204:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:205:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:301:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:41:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:58:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:198:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:251:6: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:283:37: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:318:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:335:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:336:44: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:349:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:350:44: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:427:39: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:428:44: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:429:45: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:430:35: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:431:34: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:432:47: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:308:28: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:327:31: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:391:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:473:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:478:22: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:586:17: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:586:29: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:586:40: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:587:29: E701 multiple statements on one line (colon) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:588:18: E272 multiple spaces before keyword 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:49:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:121:45: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:163:23: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:230:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:232:14: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_features.py:177:33: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_features.py:178:33: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_features.py:179:33: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:6:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:7:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:30:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:37:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:38:31: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:39:30: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:43:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_horseshoe.py:49:17: E221 multiple spaces before operator 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operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:41:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:130:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:147:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:166:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:167:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:172:31: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:229:49: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:236:49: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:241:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:244:55: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:272:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:377:49: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:3:1: F401 'jax' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:7:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:9:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.nn._DEFAULT_HIDDEN_SIZE' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:24:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:26:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:39:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:41:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:54:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:72:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:74:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:77:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:95:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:97:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:6:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:7:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:29:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:36:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:43:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:51:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:75:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:84:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:91:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/theta_rescale/test_logit.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:6:1: F401 'unittest.mock.patch' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:29:1: E302 expected 2 blank lines, found 1 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W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:71:26: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:75:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:313:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:329:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:7:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:54:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_empirical.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_logit_norm.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_logit_norm.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:4:1: F401 'collections.namedtuple' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:7:1: F401 'tfscreen.tfmodel.data_class.GrowthData' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:21:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:25:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:32:22: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:36:51: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:38:26: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:75:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:297:62: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:16:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:18:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:21:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:58:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:65:15: E251 unexpected spaces around keyword / parameter equals 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:85:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:86:18: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:86:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:86:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:87:18: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:87:18: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:134:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:140:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:145:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:154:15: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:155:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:182:15: E221 multiple spaces before operator 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:235:10: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:239:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:244:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:4:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.DataClass' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.PriorsClass' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.GrowthData' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.BindingData' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.GrowthPriors' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.BindingPriors' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:11:53: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:18:1: E302 expected 2 blank lines, found 1 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inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:100:61: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:101:49: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:102:48: E261 at least two 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line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:166:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:169:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:174:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:177:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:180:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:188:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:194:25: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:198:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:204:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:206:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:208:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:211:31: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:221:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:224:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:233:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:236:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:242:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model.py:332:61: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model_math.py:16:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_model_math.py:130:27: E128 continuation line 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equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:26: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:25: E251 unexpected spaces around keyword / parameter equals 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operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:163:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:175:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:180:23: E251 unexpected spaces around keyword / parameter equals 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equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:186:38: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:197:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:197:25: E251 unexpected spaces around keyword / parameter equals 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equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:218:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:218:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:27: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:220:29: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:220:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:26: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:225:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:225:22: E221 multiple spaces before operator 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keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:228:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:228:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:232:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:27: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:27: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:250:29: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:250:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:26: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:22: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:255:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:255:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:256:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:256:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:19: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:320:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:354:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:410:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:411:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:412:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:422:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:429:11: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/generative/test_reference_math.py:432:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:5:1: F401 'numpyro.handlers' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.SVI' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.Trace_ELBO' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.Predictive' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:11:1: F401 'jax' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:85:50: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:86:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:86:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:87:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:87:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:88:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:92:48: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:94:53: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:106:63: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:107:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:107:49: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:108:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:108:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:109:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:110:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:118:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:126:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:176:5: F841 local variable 'num_titrants' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:179:5: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:184:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:190:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:193:50: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:194:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:194:48: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:195:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:195:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:196:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:197:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:199:54: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:201:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:205:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:210:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:217:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:223:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:225:5: F841 local variable 'svi' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:226:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:230:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:235:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:237:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:239:59: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:240:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:240:52: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:241:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:241:50: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:242:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:243:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:247:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:32:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:37:14: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:86:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:95:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:108:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_posteriors.py:138:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:2:1: F401 'jax' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:5:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:12:1: F401 'optax' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:13:1: F401 'numpyro.infer.autoguide.AutoLaplaceApproximation' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:16:1: F811 redefinition of unused 'SVIState' from line 14 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:82:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:83:27: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:97:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:108:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:112:128: E501 line too long (139 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:115:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:123:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:139:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:144:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:146:18: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:147:28: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:154:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:158:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:161:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:164:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:168:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:185:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:421:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:426:5: E722 do not use bare 'except' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:428:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:431:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:434:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:439:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:441:128: E501 line too long (131 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:443:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:451:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:492:32: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:594:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:597:5: F841 local variable 'mock_seed' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:598:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/inference/test_run_inference.py:606:1: W293 blank line contains whitespace 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:1814:128: E501 line too long (136 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:1828:128: E501 line too long (136 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:1842:128: E501 line too long (136 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:1854:128: E501 line too long (136 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:2037:14: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:2056:14: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:2071:14: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_sample_posterior_cli.py:5:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_sample_prior_cli.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_subset_genotypes_cli.py:84:31: E741 ambiguous variable name 'l' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_subset_genotypes_cli.py:598:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:16:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:17:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:18:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:19:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:21:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:31:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:969:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:972:17: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1237:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1419:14: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1681:1: E402 module level import not at top of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:2061:21: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_grid_cli.py:78:9: F841 local variable 'data' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/scripts/test_summarize_grid_cli.py:182:91: E712 comparison to True should be 'if cond is True:' or 'if cond:' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:4:1: F401 'collections.namedtuple' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:37:16: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:80:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:109:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:111:73: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:113:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:127:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:133:71: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:140:5: F841 local variable 'full_array' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:140:52: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch.py:142:46: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:6:1: F401 'tfscreen.tfmodel.data_class.BindingData' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:10:1: F401 'tfscreen.tfmodel.model_orchestrator.ModelOrchestrator' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:17:5: F841 local variable 'batch_size' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:82:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:120:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:143:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:149:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:189:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:8:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:57:56: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:25:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:62:28: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:79:38: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:83:46: F541 f-string is missing placeholders -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:137:44: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:17:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:46:37: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:49:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:56:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:76:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:84:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:108:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:119:69: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:125:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:137:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:141:44: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:145:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:18:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:19:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:80:51: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:108:52: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:118:26: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:126:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:127:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:140:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:151:59: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:152:59: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:165:64: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:166:64: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:194:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:195:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_base_growth.py:196:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class.py:11:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:5:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:24:54: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_data_class_jit.py:109:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:6:1: F401 'yaml' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:8:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:8:1: F401 'unittest.mock.ANY' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:119:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:154:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:171:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:300:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:323:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:329:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:331:76: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:354:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:362:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:363:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:373:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:48: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:50: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:52: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:54: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:56: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:58: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:379:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:387:112: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:387:128: E501 line too long (191 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:392:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:395:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:399:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:406:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:425:128: E501 line too long (198 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:430:128: E501 line too long (167 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:477:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:502:18: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:503:18: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:804:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:955:79: E712 comparison to False should be 'if cond is False:' or 'if not cond:' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:956:64: E712 comparison to True should be 'if cond is True:' or 'if cond:' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:960:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:968:51: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:77: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:98: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:125: E231 missing whitespace after ':' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:128: E501 line too long (131 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:975:128: E501 line too long (138 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:977:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:979:86: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:991:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:996:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1004:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1012:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1023:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1026:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1033:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1040:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1048:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1053:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1058:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1064:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1073:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1077:26: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1087:30: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1088:25: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1090:34: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1091:33: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:43: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:45: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:47: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:49: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:51: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:53: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:55: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1118:26: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1119:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1122:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1125:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1388:9: F401 'inspect' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:1785:34: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:2029:18: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_model_orchestrator.py:2043:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:30:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:30:31: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:31:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:32:32: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:33:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:33:31: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:34:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:35:32: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:115:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:12:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:15:1: F401 'numpyro' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:24:1: F401 'tfscreen.tfmodel.data_class.DataClass' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:25:1: F401 'tfscreen.tfmodel.tensors.populate_dataclass.populate_dataclass' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:95:52: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:98:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:127:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:140:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:174:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:200:28: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:218:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_presplit.py:230:28: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:36:78: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_share_replicates.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:5:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:7:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:7:1: F401 'unittest.mock.patch' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:66:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_spiked_genotypes.py:79:28: E261 at least two spaces before inline comment 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-./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:162:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:176:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:195:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:197:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:226:9: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:233:71: E272 multiple spaces before keyword -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:247:20: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:249:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:283:5: F401 'os' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:287:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:289:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:318:16: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:320:12: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:389:20: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:390:20: E128 continuation line under-indented for visual indent -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:401:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/tfmodel/test_struct_wiring.py:448:13: E221 multiple spaces before operator -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:1:1: F401 'argparse' imported but unused -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:10:9: F841 local variable 'mock_fcn' is assigned to but never used -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:14:75: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:16:83: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:21:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:25:30: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:28:1: W293 blank line contains whitespace 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W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:68:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:76:38: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:77:45: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:82:35: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:86:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:92:38: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:93:44: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:113:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:125:9: F401 'sys' imported but unused 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trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:151:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:154:39: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:155:53: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:157:46: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/cli/test_generalized_main.py:159:1: E305 expected 2 blank lines after class or function definition, found 1 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blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:55:65: E231 missing whitespace after ',' -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:67:46: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:74:32: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:76:49: W291 trailing whitespace 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line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:117:41: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:118:42: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:119:42: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:129:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:131:41: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:132:42: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:133:42: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_add_group_columns.py:134:47: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:66:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_check_columns.py:73:54: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_chunk_by_group.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_chunk_by_group.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_chunk_by_group.py:67:60: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:83:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:146:77: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:154:37: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:157:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:160:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:162:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_df_to_arrays.py:166:37: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:7:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:41:5: E303 too many blank lines (2) -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:78:1: W391 blank line at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:105:43: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:84:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:143:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:146:49: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:63:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:68:49: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:124:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:139:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:150:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:151:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:162:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:171:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:179:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:192:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:200:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:207:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/io/test_read_dataframe.py:215:67: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_array_search.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_array_search.py:143:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_array_search.py:167:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_array_search.py:190:37: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:47:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_broadcast_args.py:68:59: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:35:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:42:34: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:84:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:87:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:90:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_padding.py:93:44: W292 no newline at end of file -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_transform.py:18:31: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_transform.py:93:31: W291 trailing whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:13:36: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:32:34: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:58:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:76:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:84:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:101:29: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:110:1: E302 expected 2 blank lines, found 0 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_xfill.py:125:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:44:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:78:26: E261 at least two spaces before inline comment -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/validation/test_check.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/validation/test_check.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/compassionate-curran-92f7bd/tests/tfscreen/util/validation/test_check.py:75:70: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/scripts/generate_struct_ensemble.py:266:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/scripts/generate_struct_ensemble.py:272:24: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/scripts/generate_struct_ensemble.py:433:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/__init__.py:19:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/__version__.py:5:16: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/__init__.py:13:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/__init__.py:2:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/__init__.py:3:55: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:148:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:188:1: C901 'cat_fit' is too complex (28) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:365:72: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:365:74: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:471:55: E712 comparison to True should be 'if cond is True:' or 'if cond:' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_fit.py:473:57: E712 comparison to False should be 'if cond is False:' or 'if not cond:' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/cat_response/cat_response.py:65:1: C901 'cat_response' is too complex (16) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/compare_runs.py:626:1: C901 'compare_runs' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:9:1: C901 'mutant_cycle_pivot' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:79:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:203:1: C901 'extract_epistasis' is too complex (16) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:207:37: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:207:38: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:285:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:285:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:303:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:326:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:326:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:326:65: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:328:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:334:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/extract_epistasis.py:341:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:8:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:8:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:55:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:66:52: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:104:33: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:143:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:144:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:148:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:149:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:150:15: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:151:26: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:155:21: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:156:24: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:157:24: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:158:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:159:21: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:161:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/analysis/stats_test_suite.py:163:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/build_cycles.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/build_cycles.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/build_cycles.py:69:26: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/build_cycles.py:78:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/build_mut_geno_matrix.py:5:1: C901 'build_mut_geno_matrix' is too complex (17) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:11:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:32:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:34:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:35:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:73:27: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:74:10: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:74:10: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/combine_mutation_effects.py:104:25: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/count_mutation_backgrounds.py:8:1: C901 'count_mutation_backgrounds' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:25:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:26:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:27:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:28:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:29:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:30:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:31:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:32:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:33:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:34:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:35:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:36:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:37:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:38:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:41:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:42:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:43:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:44:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:45:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:46:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/data.py:46:28: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:16:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:79:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:95:41: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:96:31: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/expand_genotype_columns.py:105:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:31:1: C901 '_standardize_one' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:180:8: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:181:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:230:14: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:230:14: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:265:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:268:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:268:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:268:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:287:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:320:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:321:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:339:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/genotype_sorting.py:345:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:46:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:55:59: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:58:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:59:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:60:39: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:63:11: E124 closing bracket does not match visual indentation -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:65:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:66:52: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:78:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:80:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:87:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:90:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:93:37: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:94:61: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/get_single_with_wt.py:107:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:57:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:91:1: W293 blank line contains 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line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:568:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:605:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:611:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:613:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:616:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:617:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:648:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:650:1: W293 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',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:748:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:776:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:781:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:787:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:790:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:791:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:794:72: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/genetics/library_manager.py:795:1: W293 blank line contains whitespace 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:105:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:106:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:107:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:108:27: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:109:30: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:112:30: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:113:30: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:114:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:115:26: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:116:29: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:119:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:120:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:121:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:123:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:124:34: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:127:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:128:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:129:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:131:30: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:132:33: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:135:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:136:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:137:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:138:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:139:34: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:145:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:146:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:147:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:148:30: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/__init__.py:149:33: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:3:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:27:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:27:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:53:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:56:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:76:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:96:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:100:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:120:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:140:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:141:24: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:145:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:159:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:160:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:161:24: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:165:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:181:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:186:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:196:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:212:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:217:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:227:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:257:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:287:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:303:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:306:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:308:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:313:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:316:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:334:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:338:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:341:26: E225 missing whitespace around operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:343:10: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:348:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:348:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:351:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:362:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:362:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:365:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:365:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:368:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:379:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:379:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:382:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:382:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:396:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:396:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:399:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:399:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:402:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:413:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:413:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/guesses.py:415:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:80:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:82:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:141:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:143:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:148:25: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:161:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:164:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:203:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:203:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:203:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:203:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:205:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:279:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:279:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:280:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:280:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:283:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:284:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:286:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:286:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:287:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:375:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:375:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:376:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:378:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:378:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:379:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:383:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:386:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:428:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:440:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:450:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/curve_models/models.py:454:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:26:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:29:56: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:34:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:36:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:123:5: E301 expected 1 blank line, found 0 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:186:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:219:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:223:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:225:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:227:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:247:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:250:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:269:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:272:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:291:24: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:294:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:320:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:337:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:340:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:342:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:344:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:344:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fit_manager.py:473:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/__init__.py:7:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:44:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:44:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:47:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:118:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:119:18: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/least_squares.py:128:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:13:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:43:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:43:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:43:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:56:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_nls.py:67:54: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:27:81: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:52:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/fitters/matrix_wls.py:55:52: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/predict_with_error.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/predict_with_error.py:50:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/predict_with_error.py:68:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/predict_with_error.py:72:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/mle/predict_with_error.py:89:32: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/__init__.py:36:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:13:1: C901 'cat_fits' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:13:15: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:13:17: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:99:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:99:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:113:80: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:120:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:121:14: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:123:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:123:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:128:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:128:24: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:131:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:131:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:131:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:137:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:147:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:147:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:163:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:163:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:171:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:172:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:173:12: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:174:12: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:175:12: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:176:12: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/cat_fits.py:187:5: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:11:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:12:23: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:17:66: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:19:80: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:38:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:39:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:47:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:51:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:51:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:51:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:51:63: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:51:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:54:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/corner.py:64:15: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:17:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:17:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:17:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:18:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:18:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:18:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:19:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:19:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:19:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:19:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:27:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:28:16: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:29:16: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:33:9: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:34:12: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:38:8: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:39:16: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:40:16: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:44:12: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:45:9: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:46:17: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:47:14: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:54:9: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:55:12: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:56:13: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:56:16: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:58:41: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:59:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:59:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:59:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:62:18: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:63:17: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:63:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:64:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:65:20: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:66:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:70:18: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:71:17: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:72:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:73:20: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:74:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:79:18: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:79:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:80:17: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:81:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:82:20: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:83:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/default_styles.py:84:2: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:18:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:20:34: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:33:55: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:43:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:44:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:49:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:49:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:55:5: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:19: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:62:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:63:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:64:24: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_vs_mag.py:70:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:18:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:21:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:22:37: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:52:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:52:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:54:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:54:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:57:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:73:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:73:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:73:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:74:19: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:74:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:74:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:79:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:79:24: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:79:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/err_zscore.py:79:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:24:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:54:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:57:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:72:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:72:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:72:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:72:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:102:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/est_v_real_summary.py:106:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/geno_trajectory.py:29:1: C901 'plot_geno_trajectory' is too complex (14) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:15:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:16:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:19:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:26:25: E211 whitespace before '(' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:32:37: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:33:37: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:36:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:42:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_res_heatmap.py:44:19: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:16:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:17:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:18:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:20:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:26:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:27:25: E211 whitespace before '(' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:39:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/aa_v_titrant_heatmap.py:41:19: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:6:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:15:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:16:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:19:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:20:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:21:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:25:17: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:33:25: E211 whitespace before '(' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:50:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/epistasis_heatmap.py:52:19: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:6:18: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:28:1: C901 '_build_heatmap_collection' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:88:38: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:90:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:93:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:107:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:110:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:126:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:129:68: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:142:33: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:143:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:149:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:149:28: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:151:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:154:33: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:155:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:156:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:157:34: E203 whitespace before ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:157:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:158:34: E203 whitespace before ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:158:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:158:41: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:159:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:159:41: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:160:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:162:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:162:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:172:1: C901 '_build_color_mapper' is too complex (13) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:172:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:217:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:241:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:241:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:243:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:280:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:281:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:338:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:373:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:375:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:382:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:388:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:443:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:448:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:457:1: C901 'heatmap' is too complex (13) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:509:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:528:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:531:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:561:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:569:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:570:5: F841 local variable 'e' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:580:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:589:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:590:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:592:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:592:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:592:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:593:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:596:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:612:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:615:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:620:20: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:621:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:622:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:625:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:629:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:636:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:637:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:638:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:639:37: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:643:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:644:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:645:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:647:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:661:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:661:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:661:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:661:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:662:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:662:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:662:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:662:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:666:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:666:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:671:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:672:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:679:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/heatmap/heatmap_core.py:680:19: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:28:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:29:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:31:55: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:51:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:60:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:62:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:64:61: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:69:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:70:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:84:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:93:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/helper.py:100:17: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/hill_fit.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:84:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:84:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:88:73: E225 missing whitespace around operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:89:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:92:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:98:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:98:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:102:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:102:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:105:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:108:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:108:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:115:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:121:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:124:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:130:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:133:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:139:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:144:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/plot_theta_fits.py:153:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:21:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:24:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:65:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:71:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:71:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:84:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:84:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:15: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:18: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:87:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:89:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:19: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:90:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:91:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:93:24: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:94:18: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/uncertainty_calibration.py:97:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:24:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:63:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:64:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:69:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:69:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:88:17: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:89:17: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:91:67: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:93:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:94:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/plot/xy_corr.py:97:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/_counts_io.py:110:16: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:31:69: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:38:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:111:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:162:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:206:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:208:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:209:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:212:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:215:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:218:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:259:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:268:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:268:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:269:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/counts_to_lncfu.py:272:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:21:14: E401 multiple imports on one line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:191:44: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:226:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:235:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:258:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:259:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:260:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:261:70: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:266:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:271:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:278:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:308:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:310:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:316:15: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:328:42: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:331:42: E127 continuation line over-indented for visual indent 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:373:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:384:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:500:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:506:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:507:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:507:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:512:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:513:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:514:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:515:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:516:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:528:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:529:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:532:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:534:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:536:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:538:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:538:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:542:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:544:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:545:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:545:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:546:57: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:548:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:552:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:557:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:558:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:559:9: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:559:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:567:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:567:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:567:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:571:15: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:574:79: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:575:79: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:577:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:578:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:581:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:587:54: E231 missing whitespace after ',' 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:650:65: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:661:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:668:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:669:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:670:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:674:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:677:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:677:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:733:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:733:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:737:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:738:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:747:68: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:752:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:753:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:753:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:757:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:767:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:770:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:778:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:778:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:778:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:778:67: E231 missing whitespace after ',' 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missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:809:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:812:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:815:22: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:817:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:820:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:821:67: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:822:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:825:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:827:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:835:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:836:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:837:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:841:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:843:67: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:844:70: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:845:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:846:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:851:27: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:853:70: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:854:26: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:855:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:859:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:862:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:862:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:864:62: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:865:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:866:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:893:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:894:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/fastq_to_counts.py:905:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:15:28: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:15:29: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:16:26: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:16:27: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:17:21: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:17:22: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:18:5: E125 continuation line with same indent as next logical line -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:75:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_counts_cli.py:79:44: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:74:87: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:75:87: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:84:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:93:78: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:123:70: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:124:70: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:134:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:143:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:180:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:203:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:215:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:244:25: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:244:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:247:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:277:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:297:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:298:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:299:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:300:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:336:10: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:336:10: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:341:27: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:342:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:346:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:347:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:348:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:349:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:350:54: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:364:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:369:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:369:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:387:67: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:398:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:404:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:407:80: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:411:70: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:424:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:444:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:451:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:452:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:453:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:454:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:455:23: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:458:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:461:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:462:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:465:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:466:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:468:37: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:472:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:473:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:475:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_fastq_cli.py:476:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_presplit_cli.py:77:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_presplit_cli.py:78:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_presplit_cli.py:79:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/process_raw/scripts/process_presplit_cli.py:86:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/__init__.py:29:2: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:222:1: C901 'build_theta_gc_override_hill_mut' is too complex (15) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:286:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:287:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:289:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:290:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:293:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:295:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:296:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:314:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:315:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:318:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:318:43: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:320:23: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:321:23: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:327:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:329:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:330:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:333:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:347:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:347:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:349:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:349:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:350:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:350:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:380:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:382:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:383:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:386:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/binding_params.py:388:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/build_sample_dataframes.py:95:21: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/library_prediction.py:76:1: C901 '_validate_binding_config' is too complex (13) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/library_prediction.py:212:43: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/library_prediction.py:212:44: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:55:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:56:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:57:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:58:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:62:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:63:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:64:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:83:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:84:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:85:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:90:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:103:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:106:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:107:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:108:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:111:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:113:25: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:115:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/presplit_data.py:129:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:18:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:21:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:22:23: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:22:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:22:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:22:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:24:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:25:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:50:38: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:50:39: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:51:39: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:51:40: E252 missing whitespace around parameter equals -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:53:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:56:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:71:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:72:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:82:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:88:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:88:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:91:26: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:92:29: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:93:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:94:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:95:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:100:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/run_simulation.py:107:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:170:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:171:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:172:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:173:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:174:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:175:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:176:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:177:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:178:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sample_theta.py:271:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/scripts/setup_sim_grid_cli.py:101:1: C901 'setup_sim_grid' is too complex (17) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/scripts/simulate_cli.py:18:1: C901 'run_simulation_from_config' is too complex (15) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/scripts/simulate_cli.py:153:128: E501 line too long (153 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:42:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:43:37: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:44:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:45:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:46:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:74:1: C901 '_check_dict_number' is too complex (13) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:160:1: C901 '_check_cf' is too complex (25) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:182:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:201:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:225:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:226:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:292:1: C901 '_check_lib_spec' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:292:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:344:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:349:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:371:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:424:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:440:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:448:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:448:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:458:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:468:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:511:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:515:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:516:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:526:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:529:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:575:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:586:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:587:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:590:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:594:55: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:600:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:605:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:606:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:610:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:652:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:658:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:663:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:687:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:687:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:689:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:691:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:692:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:693:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:694:67: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:744:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:761:79: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:767:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:809:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:815:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:816:18: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:822:79: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:824:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:829:80: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:834:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:840:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:851:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:894:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:899:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:916:25: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1024:26: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1024:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1024:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1024:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1024:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1032:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1033:32: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1041:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1050:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1051:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1053:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1059:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1061:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1068:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1070:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1071:24: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1078:79: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1083:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1084:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1086:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1088:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1092:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1098:128: E501 line too long (145 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1099:128: E501 line too long (145 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1104:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1108:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1117:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1117:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1118:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1120:32: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1121:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1133:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1141:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1148:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1150:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1155:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1156:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1156:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1156:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1156:61: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1161:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1196:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1217:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1218:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1221:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1221:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1226:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1232:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1235:19: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1243:33: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1244:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1245:37: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1247:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1248:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1250:19: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1252:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1260:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1261:43: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1265:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1268:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1292:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1300:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1301:76: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1306:11: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1311:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1328:6: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1335:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1336:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1337:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1338:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/selection_experiment.py:1341:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/sim_data_class.py:97:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/thermo_to_growth.py:102:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/thermo_to_growth.py:103:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/thermo_to_growth.py:289:1: C901 'thermo_to_growth' is too complex (21) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/simulate/thermo_to_growth.py:644:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:2:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:3:20: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:18:65: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:22:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:23:19: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:26:66: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:30:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:33:26: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:37:37: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:40:9: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:41:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:43:56: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/__init__.py:46:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:33:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:34:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:35:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:119:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:120:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:121:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/batch_sizing.py:122:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/error_calibration.py:474:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/error_calibration.py:511:1: C901 'summarize_sbc' is too complex (16) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:103:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:196:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:274:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:462:29: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:463:29: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:518:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:570:1: C901 'extract_growth_predictions' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:669:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:688:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:690:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/extraction.py:691:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:41:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:45:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:99:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/predict_unmeasured.py:120:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:165:1: C901 'copy_orchestrator' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:292:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:399:1: C901 'predict' is too complex (29) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:542:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:545:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:550:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:570:31: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:572:31: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:604:58: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:607:26: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:607:26: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:610:25: E122 continuation line missing indentation or outdented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prediction.py:616:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/analysis/prior_predictive.py:104:33: E203 whitespace before ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:68:1: C901 '_update_dataclass' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:123:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:252:1: C901 'write_configuration' is too complex (37) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:334:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:337:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:339:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:340:40: E713 test for membership should be 'not in' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:346:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:347:31: E713 test for membership should be 'not in' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:353:18: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:369:33: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:381:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:417:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:417:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:419:1: C901 'read_configuration' is too complex (18) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:419:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:456:128: E501 line too long (139 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:467:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:468:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:469:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:470:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:471:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:477:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:502:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/configuration_io.py:507:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:28:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:42:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/data_class.py:133:49: W291 trailing whitespace 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lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:46:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:46:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:47:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:100:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:104:83: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/activity/hierarchical_geno.py:108:1: W293 blank line contains whitespace 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trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:19:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:42:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:45:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:48:65: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:52:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:53:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/fixed.py:63:53: E231 missing whitespace after ',' 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whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:42:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:43:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:49:20: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:96:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/dk_geno/hierarchical_geno.py:100:83: W291 trailing whitespace 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:107:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:280:40: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:304:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:318:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:324:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:326:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:327:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:328:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:329:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:330:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:331:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/growth/linear.py:332:11: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:462:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:463:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:465:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:490:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:493:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical.py:510:13: E221 multiple spaces before operator 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before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:399:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:400:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:411:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:415:24: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:417:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/ln_cfu0/hierarchical_factored.py:418:21: E128 continuation line under-indented for 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E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:610:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:614:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:633:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:634:30: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:635:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:643:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:644:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:645:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:646:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:647:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:648:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:649:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:650:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:651:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:652:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:653:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:654:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:655:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:656:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:657:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:660:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:661:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:662:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:663:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:664:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:665:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:666:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:667:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:668:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:669:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:670:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:671:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:797:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:798:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:799:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:801:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:880:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:880:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:880:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PK.py:880:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:67:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:67:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:81:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:81:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:82:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:82:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:83:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:83:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:84:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:84:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:85:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:222:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:223:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:228:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:229:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:233:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:234:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:260:14: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:487:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:496:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:497:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:498:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:499:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:500:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:501:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:504:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:505:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:516:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:518:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:519:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:556:25: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PddG.py:698:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:80:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:80:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:101:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:101:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:102:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:102:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:103:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:103:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:104:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:104:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:105:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:259:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:264:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:267:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:270:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:271:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:305:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:320:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:363:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:383:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:388:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:389:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:392:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:395:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:396:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:400:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:402:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:404:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:406:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:408:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:423:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:461:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:465:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:467:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:468:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:469:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:470:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:471:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:473:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:477:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:490:24: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:493:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:494:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:515:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:536:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:539:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:542:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:546:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:550:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:563:30: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:565:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:566:30: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:567:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:568:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:577:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:578:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:579:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:580:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:581:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:582:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:585:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:586:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:717:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:720:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:757:25: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:781:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:781:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/PnnC.py:781:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/thermo.py:181:7: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/thermo.py:269:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/thermo.py:299:40: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/thermo.py:367:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:37:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:37:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:175:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:183:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:184:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:185:20: E221 multiple spaces before operator 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characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:523:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:524:128: E501 line too long (138 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:526:128: E501 line too long (128 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:530:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:531:128: E501 line too long (138 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:532:27: E221 multiple spaces 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PK.py:910:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:84:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:84:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:98:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:98:38: E202 whitespace before ']' 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:466:24: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:469:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:470:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:507:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:509:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:511:31: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:746:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PddG.py:746:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:85:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:85:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:100:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:100:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:101:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:101:38: E202 whitespace before ']' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:102:6: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:102:38: E202 whitespace before ']' 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'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U1_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/PnnC.py:786:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/thermo.py:104:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/thermo.py:155:7: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/thermo.py:230:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/thermo.py:246:10: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PK.py:704:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PK.py:808:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PK.py:808:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PK.py:808:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:64:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:64:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:164:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:168:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:173:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:173:25: E221 multiple spaces 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operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:290:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:296:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:301:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:304:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:306:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:308:19: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:558:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:613:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:613:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PddG.py:613:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:75:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:75:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:182:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:190:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:222:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:231:11: E221 multiple spaces 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to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:622:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:622:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U0_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/PnnC.py:622:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/thermo.py:133:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/thermo.py:137:6: E221 multiple spaces 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:442:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:446:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:465:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:467:5: F841 local variable 'titrant_dim' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:519:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:519:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PddG.py:519:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:50:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.run_model' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:50:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.get_population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:124:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:132:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:165:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:174:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:176:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:195:20: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:449:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:454:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:457:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:461:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:480:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:483:5: F841 local variable 'titrant_names' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.build_calc_df' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C4_K3_U1_a.thermo.compute_theta_samples' imported but unused -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/PnnC.py:533:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:115:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:116:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:121:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:126:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:127:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:144:7: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:211:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:212:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:215:7: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:216:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:221:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:227:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:228:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:249:40: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:309:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:323:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:324:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:328:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U1_a/thermo.py:329:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:99:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:110:40: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:111:48: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/features.py:112:49: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:76:7: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:91:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py:102:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:86:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:115:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:171:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/io.py:181:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/theta/thermo/nn.py:62:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:131:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:164:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:169:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:177:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:179:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:191:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:194:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:196:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:199:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:206:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:209:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:213:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:234:1: W293 blank line contains whitespace 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:308:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:309:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:333:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:354:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:366:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:369:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:369:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:370:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:393:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:416:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:423:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:523:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/_congression.py:536:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/empirical.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/empirical.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/empirical.py:32:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/logit_norm.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/logit_norm.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/logit_norm.py:33:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/logit_norm.py:58:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:14:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:15:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:21:25: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:23:21: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:24:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:51:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/components/transformation/single.py:57:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:113:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:114:24: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:114:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:143:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:144:24: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:144:44: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:284:28: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:285:28: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/model.py:292:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:42:71: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:43:75: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:44:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:44:74: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:57:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/binding.py:67:11: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:66:68: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:66:89: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:79:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:104:5: F841 local variable 'nu' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/generative/observe/growth.py:123:52: W292 no newline at end of file 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1347:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1355:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1359:30: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1362:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1366:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/inference/run_inference.py:1372:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:38:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:75:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:79:25: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:79:37: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:79:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:80:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:84:65: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:84:88: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:104:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:104:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:104:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:104:63: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:105:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:119:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:123:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:124:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:126:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:209:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:212:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:212:73: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:214:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:215:61: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:216:61: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:217:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:218:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:220:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:221:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:222:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:223:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:226:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:227:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:228:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:238:63: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:243:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:243:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:243:68: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:244:29: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:245:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:246:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:246:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:246:72: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:287:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:296:33: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:296:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:297:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:300:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:306:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:335:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:367:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:368:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:369:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:371:23: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:372:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:373:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:377:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:456:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:530:66: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:657:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:660:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:665:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:666:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:673:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:677:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:773:82: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:778:87: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:781:84: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:913:5: C901 'ModelOrchestrator._initialize_data' is too complex (19) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:913:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:938:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:939:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:941:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:942:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:942:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:942:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:943:46: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:943:66: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:944:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:948:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:949:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:954:67: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:961:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:963:10: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:963:10: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:965:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:968:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:970:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:972:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:984:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:992:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1014:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1015:41: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1015:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1016:44: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1016:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1017:40: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1017:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1018:46: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1018:71: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1020:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1027:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1047:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1047:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1047:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1054:40: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1100:25: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1101:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1102:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1103:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1143:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1146:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1147:32: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1148:60: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1152:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1153:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1154:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1155:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1157:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1168:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1168:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1171:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1172:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1177:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1178:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1179:58: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1181:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1186:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1190:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1194:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1197:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1203:86: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1205:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1212:77: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1273:57: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1282:25: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1294:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1295:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1296:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1297:38: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1298:39: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1305:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1306:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1307:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1383:25: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1384:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1386:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1459:5: C901 'ModelOrchestrator._initialize_classes' is too complex (25) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1479:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1481:67: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1482:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1484:68: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1485:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1486:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1487:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1504:42: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1505:43: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1506:40: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1506:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1506:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1506:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1506:64: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1595:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1598:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1619:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1621:9: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1705:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1710:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1724:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1734:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1744:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1758:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1761:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1790:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1802:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1814:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1820:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1821:27: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1822:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1823:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1824:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1825:22: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1826:32: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1827:23: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1828:20: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1829:29: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1830:36: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1831:28: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1832:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1833:34: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1834:27: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1835:28: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/model_orchestrator.py:1836:31: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:225:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:226:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:227:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:228:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:229:22: E128 continuation line under-indented for visual indent 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:236:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:237:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:238:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:239:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:240:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:241:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:242:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:243:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:244:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:245:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:246:22: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:260:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:262:59: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:263:58: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:264:60: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:265:63: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:266:55: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:267:60: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:268:59: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:269:63: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:270:70: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:271:55: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:272:70: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/configure_model_cli.py:274:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:97:6: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:97:6: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:120:27: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:124:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:126:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:130:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:245:39: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:247:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:251:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:514:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:516:60: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:517:53: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:518:64: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:519:66: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:520:66: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:521:64: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:522:65: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:523:64: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:524:72: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:525:74: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/fit_model_cli.py:527:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/predict_growth_cli.py:65:1: C901 'predict_growth' is too complex (16) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/predict_growth_cli.py:193:27: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/predict_theta_cli.py:12:1: C901 'predict_theta' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:129:23: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:130:23: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:221:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:222:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:227:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:405:1: C901 '_inject_calibration_priors' is too complex (21) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:664:1: C901 '_build_csv_updates' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:733:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:734:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:735:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:911:1: C901 '_apply_priors_updates' is too complex (13) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:997:1: C901 '_apply_guesses_updates' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:1149:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py:1153:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/setup_grid_cli.py:163:1: C901 'setup_grid' is too complex (17) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/subset_genotypes_cli.py:40:1: C901 'subset_genotypes' is too complex (23) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/subset_genotypes_cli.py:93:5: F841 local variable 'all_genotypes' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:154:1: C901 '_read_all_losses' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:413:1: C901 '_summarize_params' is too complex (23) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:528:1: C901 '_summarize_condition_growth_params' is too complex (14) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_fit_cli.py:723:1: C901 'summarize_fit' is too complex (59) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_grid_cli.py:47:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/scripts/summarize_grid_cli.py:57:1: C901 'summarize_grid' is too complex (11) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:44:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:46:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:47:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:48:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:49:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:50:69: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:51:69: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:52:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/batch.py:53:67: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/populate_dataclass.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/populate_dataclass.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/populate_dataclass.py:86:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/populate_dataclass.py:95:28: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/populate_dataclass.py:101:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:52:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:52:27: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:80:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:107:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:111:54: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:113:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:118:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:119:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:148:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:161:79: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:179:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:183:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:184:67: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:186:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:200:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:204:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:236:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:238:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:244:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:256:29: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:256:34: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:282:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:295:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:302:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:308:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:314:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:315:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:320:84: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:321:55: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:322:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:330:1: W293 blank line contains whitespace 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W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:429:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:435:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:451:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:452:43: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:458:66: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:460:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:466:78: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:467:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:469:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:476:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:477:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:487:40: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:493:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:502:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:512:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:517:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/tfmodel/tensors/tensor_manager.py:528:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/__init__.py:79:2: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/cli/__init__.py:16:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/cli/generalized_main.py:1:11: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/cli/generalized_main.py:5:1: C901 'generalized_main' is too complex (15) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/cli/generalized_main.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/cli/generalized_main.py:13:78: W291 trailing whitespace 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whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:10:82: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:12:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:13:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:25:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:42:74: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:43:12: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:47:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/add_group_columns.py:52:29: E211 whitespace before '(' 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lines (3) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/check_columns.py:4:21: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/check_columns.py:35:30: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/chunk_by_group.py:3:1: F811 redefinition of unused 'np' from line 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/chunk_by_group.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/chunk_by_group.py:74:44: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:63:1: W293 blank line contains whitespace 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-./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:105:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/df_to_arrays.py:112:24: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/expand_on_conditions.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/expand_on_conditions.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/expand_on_conditions.py:62:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_group_mean_std.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_group_mean_std.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_group_mean_std.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_group_mean_std.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_group_mean_std.py:95:37: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:9:14: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: C901 'get_scaled_cfu' is too complex (17) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:130:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/dataframe/get_scaled_cfu.py:131:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:7:1: C901 'read_dataframe' is too complex (16) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:84:27: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_dataframe.py:102:14: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/io/read_yaml.py:31:1: C901 'read_yaml' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:48:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:82:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/array_search.py:98:37: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/broadcast_args.py:4:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/broadcast_args.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/broadcast_args.py:90:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:43:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:44:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:50:30: E203 whitespace before ':' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/padding.py:53:21: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/transform.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/transform.py:189:36: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:3:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:65:14: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:65:14: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:65:29: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/xfill.py:88:20: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:57:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:70:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:71:34: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/numerical/zero_truncated_poisson.py:74:23: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/validation/check.py:37:1: C901 'check_number' is too complex (12) -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/validation/check.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/validation/check.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/src/tfscreen/util/validation/check.py:118:18: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:40:63: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:54:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:60:9: F841 local variable 'patterns' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:65:68: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:70:64: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:70:65: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:77:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:81:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:85:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:94:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:100:1: E266 too many leading '#' for block comment -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/conftest.py:107:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:37:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:38:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:42:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:46:5: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:47:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:48:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:49:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:69:5: F401 'jax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_nuts_reference.py:78:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:28:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:29:8: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:30:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:34:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:35:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:37:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:42:5: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:43:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:44:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:103:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:104:38: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:105:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/fixtures/generate_reference_posteriors.py:106:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:10:1: F401 'math' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:26:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:28:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:29:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:30:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:128:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:129:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:136:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:141:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:223:9: F841 local variable 'logP_raw' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:223:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:225:9: F841 local variable 'nums_raw' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/scripts/test_generate_struct_ensemble.py:225:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/conftest.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/conftest.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/conftest.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/conftest.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:33:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:34:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:102:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:103:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_configure_run_smoke.py:177:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:3:1: F401 'shutil' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:4:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:11:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:12:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:13:42: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:17:27: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:18:25: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:19:16: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:20:28: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:21:18: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:22:19: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:23:18: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:24:29: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:25:30: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/smoke-tests/test_model_smoke.py:29:27: E231 missing whitespace after ':' 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1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:92:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:107:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:108:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:112:52: E261 at least two spaces before inline comment 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:152:28: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:156:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:159:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:162:76: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:163:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:168:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:175:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:177:90: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:189:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:191:88: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:191:100: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:196:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:199:50: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:204:91: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:210:77: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:211:59: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:212:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:219:85: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:220:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:226:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:228:74: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:287:9: E731 do not assign a lambda expression, use a def -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_extract_epistasis.py:411:79: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:9:52: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:20:41: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:23:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:45:49: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:86:1: F401 'warnings' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:86:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:86:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:87:1: E302 expected 2 blank lines, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:96:10: E111 indentation is not a multiple of 4 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:96:10: E117 over-indented -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/analysis/test_stats_test_suite.py:99:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:21:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:23:28: E124 closing bracket does not match visual indentation -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:47:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_cycles.py:61:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_mut_geno_matrix.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_build_mut_geno_matrix.py:77:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:17:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:45:25: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:50:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:63:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:68:5: E731 do not assign a lambda expression, use a def -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:76:24: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:81:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:100:13: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:101:17: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:108:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_combine_mutation_effects.py:111:39: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_data.py:8:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:4:1: F401 'pandas.testing.assert_frame_equal' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:84:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_expand_genotype_columns.py:99:29: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_argsort_genotypes.py:38:30: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_argsort_genotypes.py:84:72: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:48:38: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:53:1: E303 too many blank lines (4) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:68:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:104:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:120:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_set_categorical_genotype.py:145:27: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:22:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:31:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:40:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:51:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:84:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:86:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:92:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:94:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:101:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:103:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:107:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:115:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:117:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:127:26: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:138:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:157:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:163:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:167:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_genotype_sorting_standardize_genotypes.py:176:48: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:4:1: F401 'pandas.testing.assert_frame_equal' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:13:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:15:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:74:80: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:94:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:109:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:129:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:132:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:142:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_get_single_with_wt.py:145:31: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:94:25: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:117:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:124:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:127:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:144:45: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:173:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:186:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:191:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:193:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:198:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:206:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:211:39: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:215:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:223:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:236:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:241:47: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:245:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:257:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:293:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:312:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:319:14: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:319:39: E202 whitespace before ')' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:320:14: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:320:55: E202 whitespace before ')' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:335:22: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:336:23: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:356:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:360:26: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:361:21: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:367:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:371:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:377:26: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:378:21: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:384:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:385:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:387:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:390:28: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:391:26: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:392:21: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:400:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:403:30: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:404:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:404:36: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:405:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:405:36: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:406:36: E114 indentation is not a multiple of 4 (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:406:36: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:407:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:408:26: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:409:21: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:417:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:421:26: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:421:37: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:422:21: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:475:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:491:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:493:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:526:19: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:527:58: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:528:18: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:534:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:539:51: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:540:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:551:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:556:19: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:557:67: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:558:18: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:562:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:566:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:579:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:586:19: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:588:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:597:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:599:24: E201 whitespace after '{' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:599:75: E202 whitespace before '}' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:601:24: E201 whitespace after '{' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:601:75: E202 whitespace before '}' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:603:24: E201 whitespace after '{' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:603:75: E202 whitespace before '}' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:610:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:625:19: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:627:18: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:648:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:654:19: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:656:18: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:656:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:665:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:680:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:684:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:694:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:702:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:704:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:707:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:708:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:720:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:734:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:747:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:751:42: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:759:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:764:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:768:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:774:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:779:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:811:22: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:815:35: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:815:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/genetics/test_library_manager.py:840:34: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:27:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:81:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:96:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:112:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:114:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:120:45: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:121:45: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:127:45: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:128:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_guesses.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:29:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:36:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:44:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:58:52: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:91:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:98:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/curve_models/test_models.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:18:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:22:38: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:43:22: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:43:24: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:81:54: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:83:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:97:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_least_squares.py:108:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_nls.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:15:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:35:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:40:43: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_matrix_wls.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:29:32: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:50:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_svd_error.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:14:34: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:15:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:24:29: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:26:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:44:18: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:52:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/fitters/test_util.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:6:1: F401 'scipy.special.expit' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:38:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:39:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:45:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:63:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:65:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:81:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:83:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:93:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:99:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:106:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:109:20: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:121:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:128:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:147:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:155:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:156:33: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:157:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:161:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:163:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:172:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:173:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:174:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:176:60: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:180:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:182:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:185:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_fit_manager.py:189:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:51:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/mle/test_predict_with_error.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:25:1: F401 'tfscreen.plot.default_styles.DEFAULT_HMAP_PATCH_KWARGS' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:31:1: F401 'tfscreen.plot.helper.get_ax_limits' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:31:47: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:50:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:96:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:138:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:144:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:145:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:148:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:166:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:177:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:180:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:184:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:203:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:208:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:211:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:213:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:234:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:239:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:240:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:260:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:272:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:274:9: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:292:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:295:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:299:40: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:304:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:305:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:314:43: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:318:57: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:319:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:320:41: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:331:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:351:50: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:352:59: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:353:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:356:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:370:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:381:49: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:392:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:415:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:425:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:428:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:455:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:456:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:460:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:475:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:476:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:480:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:484:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:499:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:512:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:514:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:525:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:535:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:538:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:543:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:547:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:570:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:572:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:587:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:590:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:593:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:602:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:632:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:682:21: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:694:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:698:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:701:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:704:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:717:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:720:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:724:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:727:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:729:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:741:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:744:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:750:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:754:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:760:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:782:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:785:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:791:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:800:10: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:801:10: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:802:10: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:803:10: E201 whitespace after '(' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:814:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmap_core.py:817:30: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:4:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:17:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:36:57: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:37:36: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:98:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:102:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:110:47: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:113:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:121:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:123:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/heatmap/test_heatmaps.py:136:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:32:27: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:34:40: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:37:34: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:38:26: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:59:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_cat_fits.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:6:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:9:5: F401 'corner' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:35:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:67:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:78:41: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_corner.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_default_styles.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_default_styles.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_default_styles.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_err_plots.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_est_v_real_summary.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:18:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:20:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:159:25: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:304:31: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:305:42: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:320:31: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:321:42: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:488:19: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:516:19: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_geno_trajectory.py:544:19: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:9:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:31:16: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:33:59: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_helper.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_hill_fit.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_hill_fit.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_hill_fit.py:118:34: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_plot_theta_fits.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_plot_theta_fits.py:301:26: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:16:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:18:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:22:5: F841 local variable 'ylim' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:23:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:32:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:35:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:42:53: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:43:72: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:49:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:53:5: F841 local variable 'ax' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/plot/test_xy_corr.py:149:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:101:53: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:106:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:110:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:130:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:131:47: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:142:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:147:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:204:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:213:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:221:73: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:30: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:231:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:239:53: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:240:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:247:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:249:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:250:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:256:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_counts_to_lncfu.py:261:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:9:1: F401 'tfscreen.process_raw.fastq_to_counts._bktree_find' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:70:25: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:80:25: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:114:1: E265 block comment should start with '# ' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:116:1: E265 block comment should start with '# ' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:118:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:128:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:130:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:144:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:149:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:154:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:162:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:177:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:198:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:224:59: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:281:9: E116 unexpected indentation (comment) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:285:67: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:294:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:303:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:354:5: F841 local variable 'f3' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:368:5: F841 local variable 'f1_as_rev_read' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:381:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:399:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:403:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:436:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:473:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:522:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:590:37: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:591:37: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:628:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:714:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:715:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:725:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:735:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:744:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:758:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:761:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:762:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:768:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:778:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:792:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:796:71: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:802:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:812:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:816:69: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:826:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:881:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:885:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:890:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:891:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:915:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:916:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:927:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:934:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:937:27: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:947:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:960:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:963:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:970:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:982:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:993:52: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1008:29: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1011:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1012:27: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1026:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1047:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1051:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1065:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1068:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1078:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1089:27: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1098:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1106:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_fastq_to_counts.py:1274:35: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:2:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:26: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:33: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:40: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:47: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:54: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:61: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:68: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:75: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:82: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:41:89: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:57:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:86:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:119:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:136:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:196:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:198:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:200:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:201:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:224:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:230:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:240:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:247:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:256:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:262:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:265:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:280:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:287:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:297:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:300:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:304:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:307:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:314:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:320:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:327:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:331:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:335:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:345:38: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:347:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:360:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:392:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:396:128: E501 line too long (132 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:407:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:418:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:423:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:425:26: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:432:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:435:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_fastq_cli.py:443:78: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_presplit_cli.py:5:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_presplit_cli.py:80:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_presplit_cli.py:88:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/process_raw/test_process_presplit_cli.py:113:37: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:33:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:94:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:95:30: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py:169:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_fit_phenotypes.py:173:57: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_library_prediction_empirical.py:9:1: F401 'tfscreen.util' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/empirical/test_population.py:4:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_growth_linkage.py:50:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_growth_linkage.py:95:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_growth_linkage.py:154:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:60:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:70:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:83:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:90:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:92:31: E127 continuation line over-indented for visual indent 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:564:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:565:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:566:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:567:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/growth/test_transition_linkage.py:568:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:5:1: F401 'io' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:8:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:11:1: F401 'tfscreen.simulate.binding_params._logit' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:83:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:85:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:86:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:87:25: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:89:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:90:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:91:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:93:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:206:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:208:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:218:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:220:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:232:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:240:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:305:38: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:307:37: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:316:5: F811 redefinition of unused 'pd' from line 8 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:319:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:320:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:425:43: E127 continuation line over-indented for visual indent 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_binding_params.py:587:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:52:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:83:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:94:18: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:95:8: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:104:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:115:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_build_sample_dataframes.py:128:55: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_growth_parameters_output.py:4:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_library_prediction.py:47:41: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_library_prediction.py:293:5: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_library_prediction.py:441:16: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:71:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:83:42: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:84:42: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:86:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:94:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:102:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:120:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:121:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:137:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:138:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:139:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:140:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:142:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:155:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:157:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_presplit_data.py:159:36: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_report_cfu0_cli.py:5:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_report_cfu0_cli.py:131:26: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:3:1: F401 'os' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:5:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:7:1: F401 'tfscreen.util' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:47:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:70:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:82:128: E501 line too long (150 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:110:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:113:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:116:5: F841 local variable 'results' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_run_simulation.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_sample_theta.py:260:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_sample_theta.py:277:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_sample_theta.py:282:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_sample_theta.py:297:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_sample_theta.py:338:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:4:1: F401 'numpy.ma' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:6:1: F401 'scipy.stats.gmean' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:9:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:77:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:141:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:175:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:178:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:185:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:194:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:203:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:221:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:227:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:236:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:237:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:249:16: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:251:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:251:57: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:252:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:272:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:276:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:280:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:283:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:286:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:289:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:293:52: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:294:64: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:303:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:306:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:314:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:320:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:322:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:326:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:332:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:335:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:337:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:338:61: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:343:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:345:31: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:345:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:368:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:373:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:380:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:383:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:385:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:390:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:400:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:406:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:410:1: E302 expected 2 blank lines, found 3 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:416:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:418:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:421:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:428:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:436:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:444:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:448:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:452:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:456:31: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:460:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:464:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:470:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:485:22: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:486:24: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:488:70: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:497:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:500:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:514:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:517:25: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:528:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:581:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:584:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:585:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:586:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:600:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:607:47: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:613:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:614:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:615:20: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:623:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:626:9: F811 redefinition of unused 'gmean' from line 6 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:634:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:638:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:645:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:652:59: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:654:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:671:41: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:685:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:693:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:709:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:717:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:724:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:732:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:743:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:744:48: W291 trailing whitespace 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:845:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:849:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:851:45: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:852:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:853:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:856:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:864:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:869:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:873:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:879:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:883:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:886:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:889:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:893:37: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:914:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:919:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:922:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:927:41: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:947:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1178:12: F841 local variable 'k_sel' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1193:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1195:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1217:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1232:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1235:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1273:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1285:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1296:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1300:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1303:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_selection_experiment.py:1353:18: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:401:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:405:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:448:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:453:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:455:31: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:457:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_simulate_cli.py:513:5: F401 'tfscreen.simulate.scripts.simulate_cli as cli_mod' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:96:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:98:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:104:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:106:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:195:14: E131 continuation line unaligned for hanging indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:222:44: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:229:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:1437:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/simulate/test_thermo_to_growth.py:1525:9: F841 local variable 'G_out' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_batch_sizing.py:123:40: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_batch_sizing.py:136:40: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_error_calibration.py:313:9: F401 'matplotlib.axes.Axes' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_error_calibration.py:355:9: F401 'matplotlib.axes.Axes' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:50:47: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:51:1: W293 blank line contains whitespace 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_growth_predictions.py:117:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:30:128: E501 line too long (130 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:50:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_parameters_congression.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:10:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:35: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:42: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:36:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:62:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:88:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:176:9: F841 local variable 'q_min' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_samples.py:373:9: F841 local variable 'rng' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:4:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:11:1: E302 expected 2 blank lines, found 1 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blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:79:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:93:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extract_theta_curves.py:99:1: E302 expected 2 blank lines, found 1 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W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:36: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:45:62: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/analysis/test_extraction_new_models.py:54:28: E231 missing whitespace after ':' 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E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:183:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:197:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:201:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:206:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:211:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:215:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_beta.py:217:58: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_logit_normal.py:4:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:5:1: F401 'collections.namedtuple' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:19:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:82:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:87:35: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:88:44: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/noise/test_zero.py:93:46: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/sample_offset/test_normal.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/sample_offset/test_normal.py:5:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/sample_offset/test_normal.py:6:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/sample_offset/test_zero.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/sample_offset/test_zero.py:2:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/test_pinning.py:4:1: F401 'numpyro as pyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test__simple.py:6:1: F401 'tfscreen.tfmodel.generative.components.theta._simple._THETA_EPS' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test__simple.py:447:34: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:6:1: F401 'numpyro.handlers.trace' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:10:1: F401 'tfscreen.tfmodel.generative.components.theta.categorical_geno.ThetaParam' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:38:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:69:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:96:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:102:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:107:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:119:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:130:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:146:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:158:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:167:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:188:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:190:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:193:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:200:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:220:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_categorical_geno.py:379:44: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:4:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:5:1: F401 'numpyro.handlers.trace' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:176:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:179:36: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:180:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:205:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:248:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:252:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:253:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:278:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:279:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:285:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:285:64: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:304:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:320:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:329:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:331:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:355:38: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:357:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:358:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:477:51: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:492:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:537:39: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:540:36: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_geno.py:541:26: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:12:1: F401 'tfscreen.tfmodel.generative.components.theta.hill_mut._population_moments' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:55:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:125:15: F841 local variable 'G' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:136:32: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:140:15: F841 local variable 'G' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:140:18: F841 local variable 'P' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:246:9: F841 local variable 'M' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:254:62: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:453:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:480:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:482:33: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:492:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:494:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:509:43: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:512:40: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:513:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:528:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:530:32: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:530:52: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:719:34: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:722:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:730:36: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_hill_mut.py:730:70: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:25:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:30:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:155:31: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:162:31: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:164:36: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:166:37: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:167:37: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:204:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:205:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/test_predict_unmeasured.py:301:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:41:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:58:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:198:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:251:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:283:37: 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multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:433:47: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:446:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:488:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:599:30: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PK.py:618:17: E272 multiple spaces before keyword 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E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:528:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:528:40: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:529:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:530:18: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:530:29: E701 multiple statements on one line (colon) 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:591:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:595:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:599:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:602:15: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U0_a/test_PddG.py:754:37: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:659:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:662:15: E222 multiple spaces after operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:667:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:694:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:695:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:696:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:697:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:698:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:699:29: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PddG.py:820:35: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:49:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:121:45: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:163:23: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:230:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:232:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:263:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:287:33: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:288:34: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:298:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:299:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:320:42: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:329:5: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:340:5: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:386:28: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:427:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:430:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:447:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:453:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:454:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:544:39: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:546:39: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:572:30: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:591:17: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:591:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:591:40: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:592:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:593:18: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:593:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:593:41: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:594:19: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:594:29: E701 multiple statements on one line (colon) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:594:42: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_PnnC.py:621:24: E272 multiple spaces before keyword 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C12_K5_U1_a/test_thermo.py:563:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:48:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:49:25: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:69:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:69:6: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:285:38: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:286:43: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:287:44: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:346:38: E221 multiple spaces before operator 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spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:364:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:365:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:366:42: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:367:42: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:368:42: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:369:41: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PK.py:379:34: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PddG.py:47:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PddG.py:98:45: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PddG.py:123:5: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PddG.py:134:5: E306 expected 1 blank line before a nested definition, found 0 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multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PnnC.py:280:33: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PnnC.py:281:32: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PnnC.py:282:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PnnC.py:283:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/O2_C4_K3_U0_a/test_PnnC.py:284:30: E272 multiple spaces before keyword 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_io.py:377:49: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:3:1: F401 'jax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:7:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:9:1: F401 'tfscreen.tfmodel.generative.components.theta.thermo.nn._DEFAULT_HIDDEN_SIZE' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:24:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:26:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:39:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:41:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:54:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:72:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:74:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:77:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:95:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_nn.py:97:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:6:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:7:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:29:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:36:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:43:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:51:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:75:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:84:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta/thermo/test_prior.py:91:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/theta_rescale/test_logit.py:2:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:6:1: F401 'unittest.mock.patch' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:29:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:39:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:40:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:41:47: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:53:26: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:56:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:58:24: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:63:1: W293 blank line contains whitespace 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spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:104:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:109:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:279:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:285:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:292:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:305:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:310:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:313:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test__congression.py:329:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:7:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:21:1: W293 blank line contains whitespace 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contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_congression_mask.py:54:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_empirical.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_logit_norm.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_logit_norm.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:4:1: F401 'collections.namedtuple' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:7:1: F401 'tfscreen.tfmodel.data_class.GrowthData' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:15:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:21:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:31:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/components/transformation/test_single.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:3:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:25:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:73:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:79:1: W293 blank line contains whitespace 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:108:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_binding.py:117:41: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:28:20: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:48:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:53:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/observe/test_observe_growth.py:64:31: E231 missing whitespace after ',' 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'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:21:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:58:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:65:15: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:65:15: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:65:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:66:19: E251 unexpected spaces around keyword / parameter equals 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:86:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:87:18: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:87:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:87:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:88:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:108:15: E221 multiple spaces before operator 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:234:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:235:10: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:239:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_loglikelihood.py:244:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:4:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.DataClass' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.PriorsClass' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.GrowthData' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.BindingData' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.GrowthPriors' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:10:1: F401 'tfscreen.tfmodel.data_class.BindingPriors' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:11:53: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:18:1: E302 expected 2 blank lines, found 1 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:224:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:233:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:236:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:242:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model.py:332:61: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model_math.py:16:1: F401 'numpyro.handlers.seed' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model_math.py:130:27: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_model_math.py:131:27: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:29:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:32:9: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:75:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:76:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:77:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:78:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:79:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:80:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:81:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:148:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:148:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:148:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:149:27: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:149:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:149:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:150:29: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:150:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:151:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:160:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:161:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:161:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:162:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:162:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:163:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:163:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:163:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:175:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:179:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:180:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:180:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:181:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:181:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:182:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:182:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:182:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:186:38: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:196:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:197:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:197:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:198:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:198:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:199:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:199:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:199:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:218:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:218:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:218:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:27: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:219:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:220:29: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:220:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:221:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:225:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:225:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:225:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:226:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:226:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:227:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:227:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:228:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:228:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:228:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:232:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:248:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:27: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:27: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:249:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:250:29: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:250:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:26: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:26: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:251:31: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:22: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:22: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:254:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:255:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:255:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:256:23: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:256:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:19: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:19: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:257:25: E251 unexpected spaces around keyword / parameter equals -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:320:29: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:354:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:410:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:411:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:412:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:422:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:429:11: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/generative/test_reference_math.py:432:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:5:1: F401 'numpyro.handlers' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.SVI' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.Trace_ELBO' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:7:1: F401 'numpyro.infer.Predictive' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:11:1: F401 'jax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:20:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:26:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:34:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:37:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:85:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:86:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:86:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:87:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:87:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:88:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:92:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:94:53: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:106:63: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:107:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:107:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:108:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:108:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:109:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:110:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:118:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:126:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:176:5: F841 local variable 'num_titrants' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:179:5: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:184:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:187:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:190:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:193:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:194:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:194:48: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:195:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:195:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:196:24: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:197:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:199:54: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:201:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:205:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:210:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:217:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:223:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:225:5: F841 local variable 'svi' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:226:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:230:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:235:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:237:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:239:59: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:240:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:240:52: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:241:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:241:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:242:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:243:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_get_posteriors_mapping.py:247:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:32:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:37:14: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:54:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:78:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:86:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:95:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:101:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:108:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_posteriors.py:138:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:2:1: F401 'jax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:5:1: F401 'pandas as pd' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:12:1: F401 'optax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:13:1: F401 'numpyro.infer.autoguide.AutoLaplaceApproximation' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:16:1: F811 redefinition of unused 'SVIState' from line 14 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:19:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:39:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:44:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:67:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:82:18: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:83:27: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:97:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:108:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:112:128: E501 line too long (139 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:115:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:123:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:139:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:144:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:146:18: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:147:28: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:154:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:158:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:161:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:164:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:168:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:185:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:421:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:426:5: E722 do not use bare 'except' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:428:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:431:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:434:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:439:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:441:128: E501 line too long (131 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:443:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:451:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:492:32: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:594:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:597:5: F841 local variable 'mock_seed' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:598:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:606:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:611:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:615:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:619:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:623:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:627:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:630:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:638:1: E303 too many blank lines (3) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:647:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:654:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:727:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:1110:25: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:1110:26: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/inference/test_run_inference.py:1111:26: E201 whitespace after '[' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:2:1: F401 'os' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:18:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:25:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_checkpoint_protection.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:21:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:56:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:70:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:79:39: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:80:40: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:81:42: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:92:45: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:93:48: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py:94:44: E261 at least two spaces before inline comment 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'numpyro.infer.svi.SVIState' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_cli.py:5:1: F401 'dill' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_cli.py:6:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:88:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:100:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_fit_model_helpers.py:135:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_growth_cli.py:4:1: F401 'os' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_growth_cli.py:11:1: F401 'tfscreen.tfmodel.inference.checkpoint_io.resolve_param_file' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_growth_cli.py:299:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_theta_cli.py:4:1: F401 'os' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_theta_cli.py:7:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_predict_theta_cli.py:8:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:11:1: F401 'dataclasses' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:13:1: F401 'shutil' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:14:1: F401 'sys' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:22:1: F401 'jax' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:1034:29: E128 continuation line under-indented for visual indent 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-./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_prefit_calibration_cli.py:2071:14: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_sample_posterior_cli.py:5:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_sample_prior_cli.py:3:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_subset_genotypes_cli.py:84:31: E741 ambiguous variable name 'l' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_subset_genotypes_cli.py:598:28: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:16:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:17:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:18:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:19:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:21:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:31:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:969:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:972:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1237:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1419:14: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:1681:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_fit_cli.py:2061:21: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_grid_cli.py:78:9: F841 local variable 'data' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/scripts/test_summarize_grid_cli.py:182:91: E712 comparison to True should be 'if cond is True:' or 'if cond:' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:4:1: F401 'collections.namedtuple' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:27:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:33:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:37:16: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:42:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:61:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:80:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:85:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:97:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:101:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:109:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:111:73: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:113:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:122:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:124:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:127:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:133:71: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:140:5: F841 local variable 'full_array' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:140:52: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:141:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch.py:142:46: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:5:1: F401 'numpyro.distributions as dist' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:6:1: F401 'tfscreen.tfmodel.data_class.BindingData' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:10:1: F401 'tfscreen.tfmodel.model_orchestrator.ModelOrchestrator' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:17:5: F841 local variable 'batch_size' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:25:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:30:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:82:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:120:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:138:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:143:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:149:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:189:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_consistency.py:192:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:8:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:14:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:17:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:57:56: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_batch_fix.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:11:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:25:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:32:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:41:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:62:28: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:79:38: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:83:46: F541 f-string is missing placeholders -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:133:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_populate_dataclass.py:137:44: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:17:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:46:37: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:49:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:56:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:65:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:76:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:84:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:90:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:108:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:119:69: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:125:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:137:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:141:44: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/tensors/test_tensor_manager.py:145:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:18:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:19:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:80:51: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:108:52: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:118:26: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:126:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:127:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:140:56: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:151:59: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:152:59: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:165:64: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:166:64: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:194:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:195:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_base_growth.py:196:60: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class.py:11:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:5:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:24:54: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:87:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_data_class_jit.py:109:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:6:1: F401 'yaml' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:8:1: F401 'unittest.mock.call' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:8:1: F401 'unittest.mock.ANY' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:62:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:86:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:119:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:131:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:154:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:171:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:300:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:323:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:329:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:331:76: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:354:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:362:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:363:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:373:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:48: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:50: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:52: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:54: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:56: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:378:58: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:379:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:387:112: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:387:128: E501 line too long (191 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:392:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:395:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:399:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:406:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:425:128: E501 line too long (198 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:430:128: E501 line too long (167 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:477:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:502:18: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:503:18: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:804:128: E501 line too long (184 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:955:79: E712 comparison to False should be 'if cond is False:' or 'if not cond:' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:956:64: E712 comparison to True should be 'if cond is True:' or 'if cond:' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:960:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:968:51: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:77: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:98: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:125: E231 missing whitespace after ':' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:974:128: E501 line too long (131 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:975:128: E501 line too long (138 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:977:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:979:86: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:991:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:996:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1004:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1012:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1023:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1026:128: E501 line too long (129 > 127 characters) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1033:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1040:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1048:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1053:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1058:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1064:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1073:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1077:26: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1087:30: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1088:25: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1090:34: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1091:33: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:43: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:45: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:47: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:49: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:51: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:53: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1105:55: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1118:26: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1119:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1122:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1125:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1388:9: F401 'inspect' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:1785:34: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:2029:18: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_model_orchestrator.py:2043:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:30:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:30:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:31:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:32:32: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:33:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:33:31: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:34:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:35:32: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_needs_mut_wiring.py:115:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:12:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:15:1: F401 'numpyro' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:24:1: F401 'tfscreen.tfmodel.data_class.DataClass' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:25:1: F401 'tfscreen.tfmodel.tensors.populate_dataclass.populate_dataclass' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:95:52: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:98:33: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:127:35: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:140:48: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:174:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:200:28: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:218:47: E127 continuation line over-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_presplit.py:230:28: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:1:1: F401 'pytest' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:33:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:36:78: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:41:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:58:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_share_replicates.py:66:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:5:1: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:7:1: F401 'unittest.mock.MagicMock' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:7:1: F401 'unittest.mock.patch' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:47:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:53:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:66:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:76:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:79:28: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:83:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:88:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:92:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_spiked_genotypes.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:40:17: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:58:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:59:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:60:32: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:61:30: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:62:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:63:32: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:146:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:148:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:162:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:176:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:195:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:197:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:226:9: F401 'jax.numpy as jnp' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:233:71: E272 multiple spaces before keyword -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:247:20: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:249:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:283:5: F401 'os' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:287:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:289:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:318:16: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:320:12: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:389:20: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:390:20: E128 continuation line under-indented for visual indent -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:401:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/tfmodel/test_struct_wiring.py:448:13: E221 multiple spaces before operator -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:1:1: F401 'argparse' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:10:9: F841 local variable 'mock_fcn' is assigned to but never used -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:13:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:14:75: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:16:83: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:19:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:21:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:24:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:25:30: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:35:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:38:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:52:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:55:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:68:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:71:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:76:38: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:77:45: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:82:35: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:86:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:92:38: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:93:44: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:95:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:100:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:103:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:111:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:113:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:119:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:125:9: F401 'sys' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:128:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:134:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:140:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:142:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:144:38: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:145:53: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:151:9: E306 expected 1 blank line before a nested definition, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:153:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:154:39: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:155:53: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:157:46: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:159:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:159:1: E402 module level import not at top of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/cli/test_generalized_main.py:161:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:3:1: F401 'numpy as np' imported but unused -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:12:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:34:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:40:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:43:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:55:65: E231 missing whitespace after ',' -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:67:46: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:74:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:75:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:76:49: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:77:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:78:50: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:89:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:98:32: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:102:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:105:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:112:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:115:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:117:41: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:118:42: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:119:42: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:126:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:129:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:131:41: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:132:42: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:133:42: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_add_group_columns.py:134:47: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:10:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:23:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:28:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:46:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:66:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_check_columns.py:73:54: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_chunk_by_group.py:13:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_chunk_by_group.py:64:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_chunk_by_group.py:67:60: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:83:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:146:77: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:154:37: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:157:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:160:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:162:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_df_to_arrays.py:166:37: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:7:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:41:5: E303 too many blank lines (2) -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_expand_on_conditions.py:78:1: W391 blank line at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:9:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_group_mean_std.py:105:43: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:65:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:74:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:77:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:84:1: E305 expected 2 blank lines after class or function definition, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:143:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:146:49: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:16:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:43:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:49:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:59:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:63:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:68:49: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:69:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:74:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:85:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:109:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:116:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:124:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:133:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:139:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:144:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:150:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:151:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:162:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:171:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:179:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:192:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:200:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:207:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/io/test_read_dataframe.py:215:67: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_array_search.py:78:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_array_search.py:143:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_array_search.py:167:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_array_search.py:190:37: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:6:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:28:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:42:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:47:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:64:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_broadcast_args.py:68:59: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:7:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:12:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:20:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:24:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:29:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:35:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:39:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:40:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:42:34: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:45:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:55:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:60:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:63:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:72:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:84:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:87:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:90:29: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:91:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_padding.py:93:44: W292 no newline at end of file -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_transform.py:18:31: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_transform.py:93:31: W291 trailing whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:11:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:13:36: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:18:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:22:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:27:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:31:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:32:34: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:36:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:45:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:53:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:58:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:62:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:72:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:76:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:80:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:84:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:88:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:92:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:99:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:101:29: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:110:1: E302 expected 2 blank lines, found 0 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_xfill.py:125:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:5:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:10:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:14:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:22:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:37:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:44:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:51:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:54:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:57:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:61:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:68:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:75:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:78:26: E261 at least two spaces before inline comment -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:79:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/numerical/test_zero_truncated_poisson.py:81:1: W293 blank line contains whitespace -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/validation/test_check.py:8:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/validation/test_check.py:26:1: E302 expected 2 blank lines, found 1 -./.claude/worktrees/quirky-kepler-505215/tests/tfscreen/util/validation/test_check.py:75:70: W292 no newline at end of file -./notebooks/thermo_corr/.ipynb_checkpoints/plots-checkpoint.py:12:1: F401 'pandas as pd' imported but unused -./notebooks/thermo_corr/.ipynb_checkpoints/plots-checkpoint.py:69:84: E261 at least two spaces before inline comment -./notebooks/thermo_corr/.ipynb_checkpoints/plots-checkpoint.py:69:85: E262 inline comment should start with '# ' -./notebooks/thermo_corr/assemble.py:26:1: F401 'glob' imported but unused -./notebooks/thermo_corr/plots.py:12:1: F401 'pandas as pd' imported but unused -./notebooks/thermo_corr/plots.py:69:84: E261 at least two spaces before inline comment -./notebooks/thermo_corr/plots.py:69:85: E262 inline comment should start with '# ' -./notebooks/thermo_corr/test_confound.py:14:1: F401 'thermo_corr as tc' imported but unused -./notebooks/thermo_corr/test_confound.py:41:22: E228 missing whitespace around modulo operator -./notebooks/thermo_corr/test_core.py:8:1: F401 'numpy as np' imported but unused -./notebooks/thermo_corr/tiers.py:25:1: F401 'dataclasses.field' imported but unused -./notebooks/thermo_corr/tiers.py:33:1: F401 '.confound.between_group_corr' imported but unused ./scripts/generate_struct_ensemble.py:266:11: E221 multiple spaces before operator ./scripts/generate_struct_ensemble.py:272:24: E221 multiple spaces before operator ./scripts/generate_struct_ensemble.py:433:18: E221 multiple spaces before operator @@ -15771,24 +873,25 @@ ./src/tfscreen/plot/xy_corr.py:94:23: E231 missing whitespace after ',' ./src/tfscreen/plot/xy_corr.py:97:14: W292 no newline at end of file ./src/tfscreen/process_raw/_counts_io.py:110:16: F541 f-string is missing placeholders -./src/tfscreen/process_raw/counts_to_lncfu.py:12:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/process_raw/counts_to_lncfu.py:31:69: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:38:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/process_raw/counts_to_lncfu.py:75:1: W293 blank line contains whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:78:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/process_raw/counts_to_lncfu.py:111:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/process_raw/counts_to_lncfu.py:162:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/process_raw/counts_to_lncfu.py:206:1: W293 blank line contains whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:208:41: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:209:28: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:212:1: W293 blank line contains whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:215:28: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:218:1: W293 blank line contains whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:259:49: W291 trailing whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:268:49: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:268:66: E231 missing whitespace after ',' -./src/tfscreen/process_raw/counts_to_lncfu.py:269:1: W293 blank line contains whitespace -./src/tfscreen/process_raw/counts_to_lncfu.py:272:52: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:15:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:42:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:61:69: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:68:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:105:1: W293 blank line contains whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:108:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:141:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:190:1: E302 expected 2 blank lines, found 1 +./src/tfscreen/process_raw/counts_to_lncfu.py:240:1: W293 blank line contains whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:242:41: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:243:28: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:246:1: W293 blank line contains whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:249:28: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:252:1: W293 blank line contains whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:293:49: W291 trailing whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:302:49: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:302:66: E231 missing whitespace after ',' +./src/tfscreen/process_raw/counts_to_lncfu.py:303:1: W293 blank line contains whitespace +./src/tfscreen/process_raw/counts_to_lncfu.py:306:52: E231 missing whitespace after ',' ./src/tfscreen/process_raw/fastq_to_counts.py:21:14: E401 multiple imports on one line ./src/tfscreen/process_raw/fastq_to_counts.py:23:1: E302 expected 2 blank lines, found 1 ./src/tfscreen/process_raw/fastq_to_counts.py:191:44: W291 trailing whitespace @@ -15929,8 +1032,8 @@ ./src/tfscreen/process_raw/scripts/process_counts_cli.py:17:21: E252 missing whitespace around parameter equals ./src/tfscreen/process_raw/scripts/process_counts_cli.py:17:22: E252 missing whitespace around parameter equals ./src/tfscreen/process_raw/scripts/process_counts_cli.py:18:5: E125 continuation line with same indent as next logical line -./src/tfscreen/process_raw/scripts/process_counts_cli.py:75:33: E231 missing whitespace after ',' -./src/tfscreen/process_raw/scripts/process_counts_cli.py:79:44: W292 no newline at end of file +./src/tfscreen/process_raw/scripts/process_counts_cli.py:76:33: E231 missing whitespace after ',' +./src/tfscreen/process_raw/scripts/process_counts_cli.py:80:44: W292 no newline at end of file ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:74:87: E231 missing whitespace after ',' ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:75:87: E231 missing whitespace after ',' ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:76:1: W293 blank line contains whitespace @@ -15988,10 +1091,10 @@ ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:473:33: E231 missing whitespace after ',' ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:475:1: E302 expected 2 blank lines, found 1 ./src/tfscreen/process_raw/scripts/process_fastq_cli.py:476:42: E231 missing whitespace after ',' -./src/tfscreen/process_raw/scripts/process_presplit_cli.py:77:34: E127 continuation line over-indented for visual indent -./src/tfscreen/process_raw/scripts/process_presplit_cli.py:78:34: E127 continuation line over-indented for visual indent -./src/tfscreen/process_raw/scripts/process_presplit_cli.py:79:34: E127 continuation line over-indented for visual indent -./src/tfscreen/process_raw/scripts/process_presplit_cli.py:86:31: E127 continuation line over-indented for visual indent +./src/tfscreen/process_raw/scripts/process_presplit_cli.py:82:34: E127 continuation line over-indented for visual indent +./src/tfscreen/process_raw/scripts/process_presplit_cli.py:83:34: E127 continuation line over-indented for visual indent +./src/tfscreen/process_raw/scripts/process_presplit_cli.py:84:34: E127 continuation line over-indented for visual indent +./src/tfscreen/process_raw/scripts/process_presplit_cli.py:91:31: E127 continuation line over-indented for visual indent ./src/tfscreen/simulate/__init__.py:29:2: W292 no newline at end of file ./src/tfscreen/simulate/binding_params.py:222:1: C901 'build_theta_gc_override_hill_mut' is too complex (15) ./src/tfscreen/simulate/binding_params.py:286:17: E221 multiple spaces before operator @@ -18595,13 +3698,13 @@ ./src/tfscreen/util/dataframe/get_group_mean_std.py:80:1: W293 blank line contains whitespace ./src/tfscreen/util/dataframe/get_group_mean_std.py:95:37: W292 no newline at end of file ./src/tfscreen/util/dataframe/get_scaled_cfu.py:9:14: W291 trailing whitespace -./src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: C901 'get_scaled_cfu' is too complex (17) +./src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: C901 'get_scaled_cfu' is too complex (21) ./src/tfscreen/util/dataframe/get_scaled_cfu.py:13:1: E302 expected 2 blank lines, found 1 -./src/tfscreen/util/dataframe/get_scaled_cfu.py:62:1: W293 blank line contains whitespace -./src/tfscreen/util/dataframe/get_scaled_cfu.py:67:1: W293 blank line contains whitespace -./src/tfscreen/util/dataframe/get_scaled_cfu.py:76:1: W293 blank line contains whitespace -./src/tfscreen/util/dataframe/get_scaled_cfu.py:130:1: W293 blank line contains whitespace -./src/tfscreen/util/dataframe/get_scaled_cfu.py:131:14: W292 no newline at end of file +./src/tfscreen/util/dataframe/get_scaled_cfu.py:70:1: W293 blank line contains whitespace +./src/tfscreen/util/dataframe/get_scaled_cfu.py:75:1: W293 blank line contains whitespace +./src/tfscreen/util/dataframe/get_scaled_cfu.py:102:1: W293 blank line contains whitespace +./src/tfscreen/util/dataframe/get_scaled_cfu.py:156:1: W293 blank line contains whitespace +./src/tfscreen/util/dataframe/get_scaled_cfu.py:157:14: W292 no newline at end of file ./src/tfscreen/util/io/read_dataframe.py:7:1: C901 'read_dataframe' is too complex (16) ./src/tfscreen/util/io/read_dataframe.py:7:1: E302 expected 2 blank lines, found 1 ./src/tfscreen/util/io/read_dataframe.py:79:1: W293 blank line contains whitespace @@ -19583,37 +4686,37 @@ ./tests/tfscreen/plot/test_xy_corr.py:49:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/plot/test_xy_corr.py:53:5: F841 local variable 'ax' is assigned to but never used ./tests/tfscreen/plot/test_xy_corr.py:149:1: W391 blank line at end of file -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:18:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:30:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:45:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:61:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:65:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:72:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:89:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:91:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:101:53: E261 at least two spaces before inline comment -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:106:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:110:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:116:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:125:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:130:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:131:47: W291 trailing whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:138:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:142:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:147:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:204:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:213:1: E302 expected 2 blank lines, found 1 -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:221:73: W291 trailing whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:30: E231 missing whitespace after ',' -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:222:42: E231 missing whitespace after ',' -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:231:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:239:53: E261 at least two spaces before inline comment -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:240:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:247:49: W291 trailing whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:249:46: W291 trailing whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:250:1: W293 blank line contains whitespace -./tests/tfscreen/process_raw/test_counts_to_lncfu.py:256:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:19:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:31:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:46:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:62:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:66:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:73:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:90:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:92:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:102:53: E261 at least two spaces before inline comment +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:107:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:111:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:117:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:126:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:131:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:132:47: W291 trailing whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:139:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:143:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:148:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:209:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:218:1: E302 expected 2 blank lines, found 1 +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:226:73: W291 trailing whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:227:30: E231 missing whitespace after ',' +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:227:42: E231 missing whitespace after ',' +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:236:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:244:53: E261 at least two spaces before inline comment +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:245:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:252:49: W291 trailing whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:254:46: W291 trailing whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:255:1: W293 blank line contains whitespace ./tests/tfscreen/process_raw/test_counts_to_lncfu.py:261:1: W293 blank line contains whitespace +./tests/tfscreen/process_raw/test_counts_to_lncfu.py:266:1: W293 blank line contains whitespace ./tests/tfscreen/process_raw/test_fastq_to_counts.py:9:1: F401 'tfscreen.process_raw.fastq_to_counts._bktree_find' imported but unused ./tests/tfscreen/process_raw/test_fastq_to_counts.py:70:25: E128 continuation line under-indented for visual indent ./tests/tfscreen/process_raw/test_fastq_to_counts.py:80:25: E128 continuation line under-indented for visual indent @@ -22223,7 +7326,7 @@ ./tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:84:1: E305 expected 2 blank lines after class or function definition, found 1 ./tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:92:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:143:1: W293 blank line contains whitespace -./tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:146:49: W292 no newline at end of file +./tests/tfscreen/util/dataframe/test_get_scaled_cfu.py:148:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/io/test_read_dataframe.py:8:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/io/test_read_dataframe.py:16:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/io/test_read_dataframe.py:27:1: E302 expected 2 blank lines, found 1 @@ -22330,53 +7433,51 @@ ./tests/tfscreen/util/validation/test_check.py:8:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/validation/test_check.py:26:1: E302 expected 2 blank lines, found 1 ./tests/tfscreen/util/validation/test_check.py:75:70: W292 no newline at end of file -163 C901 'cat_fit' is too complex (28) -30 E111 indentation is not a multiple of 4 -18 E114 indentation is not a multiple of 4 (comment) -18 E116 unexpected indentation (comment) -30 E117 over-indented -3 E122 continuation line missing indentation or outdented -6 E124 closing bracket does not match visual indentation -18 E125 continuation line with same indent as next logical line -639 E127 continuation line over-indented for visual indent -277 E128 continuation line under-indented for visual indent -9 E131 continuation line unaligned for hanging indent -138 E201 whitespace after '[' -84 E202 whitespace before ']' -18 E203 whitespace before ',' -12 E211 whitespace before '(' -5517 E221 multiple spaces before operator -78 E222 multiple spaces after operator -21 E225 missing whitespace around operator -1 E228 missing whitespace around modulo operator -3280 E231 missing whitespace after ',' -309 E251 unexpected spaces around keyword / parameter equals -42 E252 missing whitespace around parameter equals -623 E261 at least two spaces before inline comment -2 E262 inline comment should start with '# ' -6 E265 block comment should start with '# ' -6 E266 too many leading '#' for block comment -447 E272 multiple spaces before keyword -3 E301 expected 1 blank line, found 0 -2308 E302 expected 2 blank lines, found 1 -142 E303 too many blank lines (2) -60 E305 expected 2 blank lines after class or function definition, found 1 -87 E306 expected 1 blank line before a nested definition, found 0 -3 E401 multiple imports on one line -114 E402 module level import not at top of file -261 E501 line too long (153 > 127 characters) -129 E701 multiple statements on one line (colon) -15 E712 comparison to True should be 'if cond is True:' or 'if cond:' -6 E713 test for membership should be 'not in' -3 E722 do not use bare 'except' -6 E731 do not assign a lambda expression, use a def -63 E741 ambiguous variable name 'l' -699 F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.run_model' imported but unused -33 F541 f-string is missing placeholders -12 F811 redefinition of unused 'np' from line 1 -120 F841 local variable 'e' is assigned to but never used -1680 W291 trailing whitespace -243 W292 no newline at end of file -4466 W293 blank line contains whitespace -84 W391 blank line at end of file -22332 +55 C901 'cat_fit' is too complex (28) +10 E111 indentation is not a multiple of 4 +6 E114 indentation is not a multiple of 4 (comment) +6 E116 unexpected indentation (comment) +10 E117 over-indented +1 E122 continuation line missing indentation or outdented +2 E124 closing bracket does not match visual indentation +6 E125 continuation line with same indent as next logical line +213 E127 continuation line over-indented for visual indent +92 E128 continuation line under-indented for visual indent +3 E131 continuation line unaligned for hanging indent +46 E201 whitespace after '[' +28 E202 whitespace before ']' +6 E203 whitespace before ',' +4 E211 whitespace before '(' +1839 E221 multiple spaces before operator +26 E222 multiple spaces after operator +7 E225 missing whitespace around operator +1093 E231 missing whitespace after ',' +103 E251 unexpected spaces around keyword / parameter equals +14 E252 missing whitespace around parameter equals +207 E261 at least two spaces before inline comment +2 E265 block comment should start with '# ' +2 E266 too many leading '#' for block comment +149 E272 multiple spaces before keyword +1 E301 expected 1 blank line, found 0 +771 E302 expected 2 blank lines, found 1 +47 E303 too many blank lines (2) +20 E305 expected 2 blank lines after class or function definition, found 1 +29 E306 expected 1 blank line before a nested definition, found 0 +1 E401 multiple imports on one line +38 E402 module level import not at top of file +87 E501 line too long (153 > 127 characters) +43 E701 multiple statements on one line (colon) +5 E712 comparison to True should be 'if cond is True:' or 'if cond:' +2 E713 test for membership should be 'not in' +1 E722 do not use bare 'except' +2 E731 do not assign a lambda expression, use a def +21 E741 ambiguous variable name 'l' +231 F401 'tfscreen.tfmodel.generative.components.theta.thermo.O2_C12_K5_U0_a.thermo.run_model' imported but unused +11 F541 f-string is missing placeholders +4 F811 redefinition of unused 'np' from line 1 +40 F841 local variable 'e' is assigned to but never used +556 W291 trailing whitespace +80 W292 no newline at end of file +1487 W293 blank line contains whitespace +28 W391 blank line at end of file +7435 diff --git a/reports/junit/junit.xml b/reports/junit/junit.xml index 46d1d2a7..af0ebd3f 100644 --- a/reports/junit/junit.xml +++ b/reports/junit/junit.xml @@ -1 +1 @@ - \ No newline at end of file + \ No newline at end of file diff --git a/scripts/run_template.srun b/scripts/run_template.srun index 7122b55f..6b27197e 100644 --- a/scripts/run_template.srun +++ b/scripts/run_template.srun @@ -43,7 +43,7 @@ tfs-configure-growth-analysis \ --transformation_model {{ TRANSFORMATION_MODEL }} \ --theta_growth_noise_model {{ THETA_GROWTH_NOISE_MODEL }} \ --theta_binding_noise_model {{ THETA_BINDING_NOISE_MODEL }} \ - --spiked {{ SPIKED }} \ + --library_config {{ LIBRARY_CONFIG }} \ {{ GROWTH_SHARES_REPLICATES }} \ {{ DATA_INPUT_FILE }} \ {{ EPISTASIS }} diff --git a/src/tfscreen/__version__.py b/src/tfscreen/__version__.py index 4509340b..99a34f32 100644 --- a/src/tfscreen/__version__.py +++ b/src/tfscreen/__version__.py @@ -5,5 +5,5 @@ Version string. """ -VERSION = (0, 4, 3) +VERSION = (0, 4, 4) __version__ = '.'.join(map(str, VERSION)) diff --git a/src/tfscreen/genetics/__init__.py b/src/tfscreen/genetics/__init__.py index efa4d879..139a3689 100644 --- a/src/tfscreen/genetics/__init__.py +++ b/src/tfscreen/genetics/__init__.py @@ -32,3 +32,12 @@ from .build_mut_geno_matrix import build_mut_geno_matrix # noqa: F401 from .count_mutation_backgrounds import count_mutation_backgrounds # noqa: F401 + +from .library_design import ( # noqa: F401 + estimate_library_mixture, + expected_library_composition, + library_composition_table, + read_library_composition, + scale_library_design, + write_library_composition, +) diff --git a/src/tfscreen/genetics/library_design.py b/src/tfscreen/genetics/library_design.py new file mode 100644 index 00000000..4b170649 --- /dev/null +++ b/src/tfscreen/genetics/library_design.py @@ -0,0 +1,517 @@ +""" +Expected composition of a pooled library from its design. + +A screen library is pooled from several sub-libraries (``library_origin``: +``single-1``, ``double-1-2``, ``spiked``, ...). Each sub-library is transformed +separately and the transformed cultures are mixed by ``library_mixture``. The +same amino-acid genotype can come from more than one sub-library: wt and the +spiked single mutants are also encoded by codons in the bulk sub-libraries, so +spiked and bulk copies of one genotype can't be told apart by sequence. + +Within a sub-library every codon-level sequence is equally likely (before +assembly skew), so a genotype's share of that sub-library is its codon +``degeneracy`` divided by the sub-library's total number of sequences. That is +the ``weight`` column written by ``LibraryManager.build_library_df``. +""" + +import numpy as np +import pandas as pd + +SPIKED_ORIGIN = "spiked" + + +def _check_origin_keys(library_df, mapping, name): + """Fail fast unless ``mapping`` has exactly the library's origins.""" + origins = set(library_df["library_origin"].astype(str)) + keys = set(mapping) + missing = sorted(origins - keys) + extra = sorted(keys - origins) + if missing or extra: + err = f"{name} keys must match the library origins {sorted(origins)}." + if missing: + err += f" Missing: {missing}." + if extra: + err += f" Not in the library: {extra}." + raise ValueError(err) + + +def _origin_sequence_counts(library_df): + """Number of codon-level sequences in each library origin.""" + if "degeneracy" not in library_df.columns: + raise ValueError( + "library_df needs a 'degeneracy' column (as written by " + "LibraryManager.build_library_df)." + ) + counts = (library_df + .assign(library_origin=library_df["library_origin"].astype(str)) + .groupby("library_origin")["degeneracy"] + .sum()) + return counts.to_dict() + + +def expected_library_composition(library_df, + library_mixture, + spiked_origin=SPIKED_ORIGIN): + """ + Expected pool share and bulk fraction of every genotype. + + Parameters + ---------- + library_df : pandas.DataFrame + One row per (library_origin, genotype) with columns + ``library_origin``, ``genotype`` and ``weight`` (the genotype's share + of its sub-library), as written by + ``LibraryManager.build_library_df``. + library_mixture : dict + Relative amount of each transformed sub-library in the pool, keyed by + library origin. Only ratios matter. Must name every origin in + ``library_df`` and no others. + spiked_origin : str, default "spiked" + The origin holding monoclonal spiked controls. Every other origin is + bulk. + + Returns + ------- + pandas.DataFrame + One row per genotype, with columns: + + - ``genotype`` + - ``pool_fraction``: expected fraction of the pooled cells carrying + the genotype. Sums to 1. + - ``bulk_fraction``: expected fraction of the genotype's cells that + come from bulk sub-libraries (0 = pure spike, 1 = pure bulk). + + Notes + ----- + This is the design expectation. It ignores library assembly skew and the + finite number of transformants, both of which scatter the realized value + around it. It also assumes a cell's plasmid copies are shared among the + variants it carries, so a multi-plasmid cell contributes one cell's worth + of each genotype's observable in total, and the fraction does not depend + on the congression parameter lambda. + + Examples + -------- + >>> import pandas as pd + >>> library_df = pd.DataFrame({ + ... "library_origin": ["single-1", "single-1", "spiked", "spiked"], + ... "genotype": ["wt", "M42I", "wt", "H74A"], + ... "weight": [0.25, 0.75, 0.5, 0.5], + ... }) + >>> expected_library_composition(library_df, + ... {"single-1": 3, "spiked": 1}) + genotype pool_fraction bulk_fraction + 0 wt 0.3125 0.6 + 1 M42I 0.5625 1.0 + 2 H74A 0.1250 0.0 + """ + + for col in ("library_origin", "genotype", "weight"): + if col not in library_df.columns: + raise ValueError(f"library_df needs a '{col}' column.") + _check_origin_keys(library_df, library_mixture, "library_mixture") + + df = library_df[["library_origin", "genotype", "weight"]].copy() + df["library_origin"] = df["library_origin"].astype(str) + df["genotype"] = df["genotype"].astype(str) + + mixture = {k: float(v) for k, v in library_mixture.items()} + if any(v < 0 for v in mixture.values()) or sum(mixture.values()) <= 0: + raise ValueError( + "library_mixture values must be non-negative with a positive sum." + ) + + # Normalize each origin's weights so they are shares even if the caller + # passed an unnormalized weight column. + origin_total = df.groupby("library_origin")["weight"].transform("sum") + df["share"] = np.where(origin_total > 0, df["weight"] / origin_total, 0.0) + df["mass"] = df["library_origin"].map(mixture) * df["share"] + df["is_bulk"] = df["library_origin"] != spiked_origin + df["bulk_mass"] = df["mass"].where(df["is_bulk"], 0.0) + + # Keep genotypes in order of first appearance so output order is stable. + order = pd.unique(df["genotype"]) + per_geno = (df.groupby("genotype", sort=False)[["mass", "bulk_mass"]] + .sum() + .reindex(order)) + + total_mass = per_geno["mass"].sum() + out = pd.DataFrame({ + "genotype": per_geno.index, + "pool_fraction": (per_geno["mass"] / total_mass).to_numpy(), + "bulk_fraction": np.divide(per_geno["bulk_mass"].to_numpy(), + per_geno["mass"].to_numpy(), + out=np.full(len(per_geno), np.nan), + where=per_geno["mass"].to_numpy() > 0), + }) + return out.reset_index(drop=True) + + +def scale_library_design(reference_library_df, + target_library_df, + library_mixture, + transform_sizes, + cfu0=None, + total_num_reads=None): + """ + Scale a library design onto a smaller (or larger) library. + + Simulating a full-size library is expensive, so simulations use libraries + with fewer degenerate sites. Copying the real ``library_mixture`` and + ``transform_sizes`` onto a smaller library changes how abundant each + genotype is and what fraction of a spiked genotype's cells come from the + bulk. This function instead preserves, for every library origin, the + quantities that are defined per codon-level sequence: + + - abundance of each sequence relative to every other sequence, so a + genotype encoded by the same number of sequences in each origin in both + libraries keeps its relative abundance and its bulk fraction, + - transformants per sequence (the transformation bottleneck), + - starting cells per sequence (``cfu0``) and reads per sequence + (``total_num_reads``). + + Parameters + ---------- + reference_library_df : pandas.DataFrame + The library the design was made for (for example the real library), + with ``library_origin`` and ``degeneracy`` columns, as written by + ``LibraryManager.build_library_df``. + target_library_df : pandas.DataFrame + The library to scale onto (for example the simulated library), same + columns and the same set of origins. + library_mixture : dict + Reference ``library_mixture``, keyed by origin. + transform_sizes : dict + Reference ``transform_sizes`` (transformants per origin). + cfu0 : float, optional + Reference starting cells for the whole pool. + total_num_reads : int, optional + Reference total sequencing reads. + + Returns + ------- + dict + Keys ``library_mixture`` (dict of float), ``transform_sizes`` (dict of + int, at least 1), ``cfu0`` (float or None) and ``total_num_reads`` + (int or None), for the target library. + + Notes + ----- + Mixture values keep the reference's units, so an origin with the same + number of sequences in both libraries (typically ``spiked``) keeps its + value. ``cfu0`` and ``total_num_reads`` scale by the ratio of total pool + mass, which holds cells and reads per sequence fixed in every origin at + once. Reads are assumed proportional to cells at the start of the + experiment. + """ + + for name, df in (("reference_library_df", reference_library_df), + ("target_library_df", target_library_df)): + if "library_origin" not in df.columns: + raise ValueError(f"{name} needs a 'library_origin' column.") + + ref_seqs = _origin_sequence_counts(reference_library_df) + tgt_seqs = _origin_sequence_counts(target_library_df) + if set(ref_seqs) != set(tgt_seqs): + raise ValueError( + "Reference and target libraries must have the same origins: " + f"{sorted(ref_seqs)} vs {sorted(tgt_seqs)}." + ) + _check_origin_keys(reference_library_df, library_mixture, "library_mixture") + _check_origin_keys(reference_library_df, transform_sizes, "transform_sizes") + + ratio = {k: tgt_seqs[k] / ref_seqs[k] for k in ref_seqs} + + new_mixture = {k: float(library_mixture[k]) * ratio[k] for k in ref_seqs} + new_transform = {k: max(1, int(round(float(transform_sizes[k]) * ratio[k]))) + for k in ref_seqs} + + mass_ratio = sum(new_mixture.values()) / sum(float(v) for v in library_mixture.values()) + new_cfu0 = None if cfu0 is None else float(cfu0) * mass_ratio + new_reads = (None if total_num_reads is None + else max(1, int(round(float(total_num_reads) * mass_ratio)))) + + return {"library_mixture": new_mixture, + "transform_sizes": new_transform, + "cfu0": new_cfu0, + "total_num_reads": new_reads} + + +def estimate_library_mixture(library_df, + observed, + exclude_genotypes=("wt",)): + """ + Estimate the realized ``library_mixture`` from observed abundances. + + A sample of the pooled library (for example a pre-split sample) gives each + genotype's abundance. Under the design, a genotype's expected abundance is + ``sum_L mixture_L * weight_gL``, which is linear in the unknown mixture. + Genotypes are grouped by the set of origins that encode them (for example + tile-1 singles are encoded by ``single-1`` and ``double-1-2``); summing + within a group averages over assembly skew and sampling noise, and the + mixture is the non-negative least-squares solution over the group sums. + + Parameters + ---------- + library_df : pandas.DataFrame + Columns ``library_origin``, ``genotype`` and ``weight``, as written by + ``LibraryManager.build_library_df``. + observed : pandas.Series or pandas.DataFrame + Observed abundance (cells or reads, not logs) per genotype: a Series + indexed by genotype, or a DataFrame with ``genotype`` and + ``abundance`` columns. Library genotypes that are absent count as + zero. + exclude_genotypes : iterable of str, default ("wt",) + Genotypes left out of the fit. wt is excluded by default because it is + often over-represented for reasons outside the design (for example + unmutated template carried through cloning). + + Returns + ------- + mixture : dict + Estimated mixture, keyed by origin, summing to 1 over the origins. + groups : pandas.DataFrame + One row per group: ``origins`` (tuple), ``n_genotypes``, + ``observed_share`` and ``fitted_share`` (shares of the fitted + abundance). + unexplained_fraction : float + Fraction of the total observed abundance on genotypes that are not in + ``library_df`` (not designed), which the fit ignores. + + Notes + ----- + Origins that no group can distinguish get a mixture of 0 or an arbitrary + split, so check ``groups`` before trusting a value. An origin whose + genotypes are all excluded or absent is estimated at 0. + """ + + from scipy.optimize import nnls + + for col in ("library_origin", "genotype", "weight"): + if col not in library_df.columns: + raise ValueError(f"library_df needs a '{col}' column.") + + if isinstance(observed, pd.DataFrame): + for col in ("genotype", "abundance"): + if col not in observed.columns: + raise ValueError(f"observed needs a '{col}' column.") + observed = observed.set_index(observed["genotype"].astype(str))["abundance"] + observed = pd.Series(observed, dtype=float) + observed.index = observed.index.astype(str) + if observed.index.duplicated().any(): + dups = sorted(set(observed.index[observed.index.duplicated()]))[:5] + raise ValueError(f"observed has duplicate genotypes, e.g. {dups}.") + if (observed < 0).any() or not np.isfinite(observed).all(): + raise ValueError("observed abundances must be finite and non-negative.") + + df = library_df[["library_origin", "genotype", "weight"]].copy() + df["library_origin"] = df["library_origin"].astype(str) + df["genotype"] = df["genotype"].astype(str) + origin_total = df.groupby("library_origin")["weight"].transform("sum") + df["share"] = np.where(origin_total > 0, df["weight"] / origin_total, 0.0) + + origins = sorted(df["library_origin"].unique()) + weights = (df.pivot_table(index="genotype", columns="library_origin", + values="share", aggfunc="sum", fill_value=0.0) + .reindex(columns=origins, fill_value=0.0)) + + total_observed = observed.sum() + if total_observed <= 0: + raise ValueError("observed abundances sum to zero.") + unexplained = observed[~observed.index.isin(weights.index)].sum() / total_observed + + exclude = set(map(str, exclude_genotypes or ())) + weights = weights[~weights.index.isin(exclude)] + obs = observed.reindex(weights.index).fillna(0.0) + + key = weights.gt(0).apply(lambda row: tuple(o for o in origins if row[o]), axis=1) + group_w = weights.groupby(key).sum() + group_obs = obs.groupby(key).sum() + group_n = key.value_counts() + + A = group_w[origins].to_numpy() + b = group_obs.reindex(group_w.index).to_numpy() + scale = b.sum() + if scale <= 0: + raise ValueError("No observed abundance on the included library genotypes.") + m, _ = nnls(A, b / scale) + if m.sum() <= 0: + raise ValueError("Could not estimate a mixture (all components zero).") + + fitted = A @ m + groups = pd.DataFrame({ + "origins": list(group_w.index), + "n_genotypes": group_n.reindex(group_w.index).to_numpy(), + "observed_share": b / scale, + "fitted_share": fitted / fitted.sum(), + }).sort_values("observed_share", ascending=False).reset_index(drop=True) + + mixture = {o: float(v / m.sum()) for o, v in zip(origins, m)} + return mixture, groups, float(unexplained) + + +LIBRARY_COMPOSITION_COLUMNS = ["genotype", + "is_wt", + "in_spiked_origin", + "pool_fraction", + "bulk_fraction", + "origins"] + + +def library_composition_table(library_config, + spiked_origin=SPIKED_ORIGIN): + """ + Build the per-genotype library composition table from a library config. + + This is the bridge between the hand-written library description (the same + YAML handed to ``tfs-process-fastq``) and the model, which never reads the + YAML itself. ``tfs-configure-model`` writes the returned table to + ``{out_prefix}_library.csv``; ``tfs-fit-model`` reads that snapshot. + + Parameters + ---------- + library_config : str or dict + Path to (or parsed contents of) the library YAML. Must carry the keys + ``LibraryManager`` requires (``reading_frame``, + ``first_amplicon_residue``, ``wt_seq``, ``degen_sites``, ``tiles``, + ``tile_combos``), plus ``library_mixture``. ``spiked_seqs`` is + optional but is what makes a genotype congression-free. Any other keys + (a full ``tfs-simulate`` config, say) are ignored. + spiked_origin : str, default "spiked" + Library origin holding the monoclonal spiked controls. + + Returns + ------- + pandas.DataFrame + One row per amino-acid genotype in the library, with columns: + + - ``genotype``: standardized genotype name ("wt", "M42I", ...) + - ``is_wt``: True for the wildtype genotype + - ``in_spiked_origin``: True if the genotype is encoded by a spiked + sequence. Note this is *not* the same as congression-free: wt and + the spiked single mutants are also encoded in the bulk + sub-libraries, which is what ``bulk_fraction`` records. + - ``pool_fraction``: expected fraction of pooled cells carrying the + genotype (sums to 1) + - ``bulk_fraction``: expected fraction of the genotype's cells coming + from bulk sub-libraries (0 = pure spike, 1 = pure bulk) + - ``origins``: "|"-joined sub-libraries encoding the genotype + + Raises + ------ + ValueError + If ``library_mixture`` is missing, or if its keys do not exactly match + the library's origins. + + Notes + ----- + ``pool_fraction`` and ``bulk_fraction`` are *design* expectations. They + ignore library assembly skew and the finite number of transformants, and + nothing downstream checks them against the data. The realized mixture can + depart from the design substantially, so the values in ``library_mixture`` + should be the best available estimate of what actually went into the pool. + """ + + from tfscreen.util import read_yaml + from tfscreen.genetics.library_manager import LibraryManager + + config = read_yaml(library_config) + if "library_mixture" not in config: + raise ValueError( + "The library config must have a 'library_mixture' key giving the " + "relative amount of each sub-library in the pool (keys matching " + "'tile_combos', plus 'spiked' if 'spiked_seqs' is defined)." + ) + + library_df = LibraryManager(config).build_library_df() + composition = expected_library_composition(library_df, + config["library_mixture"], + spiked_origin=spiked_origin) + + library_df = library_df.copy() + library_df["genotype"] = library_df["genotype"].astype(str) + library_df["library_origin"] = library_df["library_origin"].astype(str) + + origins = (library_df + .groupby("genotype", sort=False)["library_origin"] + .apply(lambda v: "|".join(sorted(set(v))))) + in_spiked = (library_df + .assign(_s=library_df["library_origin"] == spiked_origin) + .groupby("genotype", sort=False)["_s"] + .any()) + + composition["genotype"] = composition["genotype"].astype(str) + composition["is_wt"] = composition["genotype"] == "wt" + composition["in_spiked_origin"] = (composition["genotype"] + .map(in_spiked) + .fillna(False) + .astype(bool)) + composition["origins"] = composition["genotype"].map(origins) + + return composition[LIBRARY_COMPOSITION_COLUMNS].reset_index(drop=True) + + +def write_library_composition(composition, path): + """ + Write a library composition table to a CSV snapshot. + + Parameters + ---------- + composition : pandas.DataFrame + Table returned by ``library_composition_table``. + path : str + Output CSV path. + """ + + missing = [c for c in LIBRARY_COMPOSITION_COLUMNS + if c not in composition.columns] + if missing: + raise ValueError(f"composition is missing columns: {missing}.") + + composition[LIBRARY_COMPOSITION_COLUMNS].to_csv(path, index=False) + + +def read_library_composition(path): + """ + Read a library composition table written by ``write_library_composition``. + + Parameters + ---------- + path : str + Path to the CSV snapshot (``{out_prefix}_library.csv``). + + Returns + ------- + pandas.DataFrame + The table, with ``is_wt`` and ``in_spiked_origin`` as bools. + + Raises + ------ + FileNotFoundError + If the file does not exist. + ValueError + If required columns are missing or genotypes are duplicated. + """ + + import os + + if not os.path.exists(path): + raise FileNotFoundError(f"Library composition file not found: {path}") + + df = pd.read_csv(path) + missing = [c for c in LIBRARY_COMPOSITION_COLUMNS if c not in df.columns] + if missing: + raise ValueError( + f"'{path}' is missing columns {missing}. It should be the " + f"{{out_prefix}}_library.csv written by tfs-configure-model." + ) + + df["genotype"] = df["genotype"].astype(str) + if df["genotype"].duplicated().any(): + dups = sorted(set(df["genotype"][df["genotype"].duplicated()]))[:5] + raise ValueError(f"'{path}' has duplicate genotypes, e.g. {dups}.") + + for col in ("is_wt", "in_spiked_origin"): + df[col] = df[col].astype(bool) + + return df diff --git a/src/tfscreen/genetics/library_manager.py b/src/tfscreen/genetics/library_manager.py index 7bd14277..6d925563 100644 --- a/src/tfscreen/genetics/library_manager.py +++ b/src/tfscreen/genetics/library_manager.py @@ -718,20 +718,24 @@ def _get_spiked_seqs(self,list_of_seqs): ---------- list_of_seqs : list list of spiked sequences (DNA letters) - + Returns ------- tuple[list[str], list[str]] A tuple containing two lists: (lib_seqs, aa_muts). - - lib_seqs: A list of all generated DNA sequences. + - lib_seqs: A list of the spiked DNA sequences, one per input + sequence, with '.' positions filled in from wt_seq. - aa_muts: A parallel list of the corresponding formatted amino acid mutation strings. Notes ----- - The generated set is inclusive. For each pair of mutated sites, the - output will contain not only the double mutants but also the two - corresponding single mutants and the wild-type sequence. + The output holds exactly the sequences passed in -- one spiked + sequence per input, in the same order. Nothing is expanded: a spiked + double mutant does not imply its two single mutants or wt. This + matters for library composition (``genetics.library_design``), where + membership in the spiked origin is what makes a genotype + congression-free. """ spiked_seqs = [] diff --git a/src/tfscreen/process_raw/counts_to_lncfu.py b/src/tfscreen/process_raw/counts_to_lncfu.py index b07cd175..5d3b5040 100644 --- a/src/tfscreen/process_raw/counts_to_lncfu.py +++ b/src/tfscreen/process_raw/counts_to_lncfu.py @@ -1,5 +1,8 @@ from tfscreen.util.io import read_dataframe -from tfscreen.util.dataframe import check_columns +from tfscreen.util.dataframe import ( + check_columns, + get_scaled_cfu +) from tfscreen.genetics import ( set_categorical_genotype, @@ -9,6 +12,33 @@ import pandas as pd import numpy as np +def get_sample_ln_cfu(sample_df: pd.DataFrame) -> pd.DataFrame: + """ + Ensure `sample_df` has 'sample_ln_cfu' and 'sample_ln_cfu_std' columns. + + Existing log-space columns are used as-is. Otherwise they are inferred + (via get_scaled_cfu) from 'sample_ln_cfu_var', or from 'sample_cfu' with + 'sample_cfu_std' or 'sample_cfu_var'. + + Raises + ------ + ValueError + If the columns cannot be obtained from what `sample_df` provides. + """ + try: + sample_df = get_scaled_cfu(sample_df, + need_columns=["ln_cfu", "ln_cfu_std"], + prefix="sample_") + except ValueError as e: + raise ValueError( + "sample_df must give each sample's cfu/mL and its uncertainty " + "as 'sample_ln_cfu' with 'sample_ln_cfu_std' (or " + "'sample_ln_cfu_var'), or as 'sample_cfu' with 'sample_cfu_std' " + f"(or 'sample_cfu_var'). ({e})" + ) from e + + return sample_df + def _filter_low_observation_genotypes(df: pd.DataFrame, min_genotype_obs: int) -> pd.DataFrame: """Filter out genotypes with total counts below a threshold for each library. @@ -112,12 +142,18 @@ def _calculate_concentrations_and_variance( df: pd.DataFrame, total_counts_per_sample: pd.Series) -> pd.DataFrame: """ - Calculate the cfu/mL for each genotype and propagate the variance. + Calculate ln(cfu/mL) for each genotype and propagate the variance. + + The calculation is done in log space: ln_cfu = ln(frequency) + + sample_ln_cfu, with ln_cfu_var = var(frequency)/frequency**2 + + sample_ln_cfu_std**2. Linear-space 'cfu' and 'cfu_var' are derived from + these. Parameters ---------- df : pd.DataFrame - Frame with 'frequency', 'sample', 'sample_cfu', and 'sample_cfu_std'. + Frame with 'frequency', 'sample', 'sample_ln_cfu', and + 'sample_ln_cfu_std'. total_counts_per_sample : pd.Series Total adjusted counts per sample (the full oriented-read depth Sigma x + b), indexed by sample. Used as the binomial denominator so @@ -125,37 +161,29 @@ def _calculate_concentrations_and_variance( estimate. """ - # Calculate the cfu/mL for each genotype - df['cfu'] = df['frequency'] * df['sample_cfu'] - - # Convert input standard deviation into variance - sample_cfu_var = (df["sample_cfu_std"])**2 - # Variance in frequency (from binomial uncertainty). Use the same # Sigma x + b denominator as the point estimate rather than re-summing the # (unknown-dropped) adjusted counts, so the binomial N is consistent. total_counts = df['sample'].map(total_counts_per_sample) var_frequency = df['frequency'] * (1 - df['frequency']) / total_counts - # Propagate error from multiplying frequency and cfu + # Relative frequency variance is the variance of ln(frequency) with np.errstate(divide='ignore', invalid='ignore'): - relative_var_freq = np.nan_to_num(var_frequency / (df['frequency']**2)) - relative_var_sample_cfu = np.nan_to_num(sample_cfu_var / (df['sample_cfu']**2)) - - relative_var_sum = relative_var_freq + relative_var_sample_cfu + ln_freq = np.log(df['frequency']) + ln_freq_var = np.nan_to_num(var_frequency / (df['frequency']**2)) - # Calculate the final variance for the genotype cfu - df['cfu_var'] = (df['cfu']**2) * relative_var_sum + # Combine with the sample-level ln_cfu and its variance + df['ln_cfu'] = ln_freq + df['sample_ln_cfu'] + df['ln_cfu_var'] = ln_freq_var + df['sample_ln_cfu_std']**2 - # Calculate log-transformed values and their variance - df['ln_cfu_var'] = relative_var_sum - with np.errstate(divide='ignore'): - df['ln_cfu'] = np.log(df['cfu']) + # Linear-space genotype cfu/mL and its variance + df['cfu'] = df['frequency'] * np.exp(df['sample_ln_cfu']) + df['cfu_var'] = (df['cfu']**2) * df['ln_cfu_var'] - # Handle cases where cfu is 0 or negative - mask_zero_cfu = df['cfu'] <= 0 - df.loc[mask_zero_cfu, 'ln_cfu'] = np.nan - df.loc[mask_zero_cfu, 'ln_cfu_var'] = np.nan + # Handle cases where cfu is 0 (or the sample ln_cfu is not finite) + mask_bad = ~np.isfinite(df['ln_cfu']) + df.loc[mask_bad, 'ln_cfu'] = np.nan + df.loc[mask_bad, 'ln_cfu_var'] = np.nan return df @@ -178,9 +206,14 @@ def counts_to_lncfu( ---------- sample_df : pd.DataFrame DataFrame indexed by a unique 'sample' string. Must contain metadata - for each sample. The required columns are 'library', 'sample_cfu', - and 'sample_cfu_std'. Any additional columns (e.g., 'replicate', - 'time', 'titrant_name') will be preserved in the final output. + for each sample. Requires a 'library' column plus the total + cfu/mL in each sample tube and its uncertainty, given either in log + space ('sample_ln_cfu' with 'sample_ln_cfu_std' or + 'sample_ln_cfu_var') or in linear space ('sample_cfu' with + 'sample_cfu_std' or 'sample_cfu_var'). Log-space columns are used + when present; otherwise they are inferred from the linear-space + ones. Any additional columns (e.g., 'replicate', 'time', + 'titrant_name') will be preserved in the final output. counts_df : pd.DataFrame DataFrame with 'sample', 'genotype', and 'counts' columns. min_genotype_obs : int, optional @@ -201,14 +234,15 @@ def counts_to_lncfu( Raises ------ ValueError - If `sample_df` is not indexed by 'sample'. + If `sample_df` is not indexed by 'sample', or if 'sample_ln_cfu' and + 'sample_ln_cfu_std' cannot be obtained from its columns. """ # Read/clean up dataframes sample_df = read_dataframe(sample_df,index_column="sample") - check_columns(sample_df,required_columns=["library", - "sample_cfu", - "sample_cfu_std"]) + check_columns(sample_df,required_columns=["library"]) + + sample_df = get_sample_ln_cfu(sample_df) # Read counts dataframe counts_df = read_dataframe(counts_df) diff --git a/src/tfscreen/process_raw/scripts/process_counts_cli.py b/src/tfscreen/process_raw/scripts/process_counts_cli.py index 18646491..74b962e6 100644 --- a/src/tfscreen/process_raw/scripts/process_counts_cli.py +++ b/src/tfscreen/process_raw/scripts/process_counts_cli.py @@ -1,7 +1,7 @@ from tfscreen.process_raw import counts_to_lncfu +from tfscreen.process_raw.counts_to_lncfu import get_sample_ln_cfu from tfscreen.process_raw._counts_io import _prep_sample_df, _aggregate_counts from tfscreen.util.cli import generalized_main -from tfscreen.util.dataframe import check_columns from typing import Union @@ -27,9 +27,10 @@ def process_counts( ---------- sample_df : str or pandas.DataFrame Path to (or pre-loaded) sample metadata CSV. Must contain a unique - 'sample' column (used as the index) plus 'sample_cfu' and - 'sample_cfu_std' columns giving the total CFU and its uncertainty for - each sample tube. + 'sample' column (used as the index) plus the total CFU in each + sample tube and its uncertainty, as 'sample_ln_cfu' and + 'sample_ln_cfu_std' (or 'sample_ln_cfu_var'), or as 'sample_cfu' + and 'sample_cfu_std' (or 'sample_cfu_var'). See counts_to_lncfu. counts_csv_path : str Directory containing per-sample count CSV files. Each file must match the glob pattern ``{counts_glob_prefix}*{sample}*.csv``. @@ -58,8 +59,8 @@ def process_counts( counts_glob_prefix, verbose) - # Require the caller to supply sample_cfu and sample_cfu_std directly. - check_columns(sample_df, required_columns=["sample_cfu", "sample_cfu_std"]) + # Check/infer sample_ln_cfu and sample_ln_cfu_std before reading counts. + sample_df = get_sample_ln_cfu(sample_df) # This will be a single dataframe holding all counts for all samples, with # a 'sample' column that can be indexed back to to counts. diff --git a/src/tfscreen/process_raw/scripts/process_presplit_cli.py b/src/tfscreen/process_raw/scripts/process_presplit_cli.py index 338c0292..2beaf981 100644 --- a/src/tfscreen/process_raw/scripts/process_presplit_cli.py +++ b/src/tfscreen/process_raw/scripts/process_presplit_cli.py @@ -1,4 +1,5 @@ from tfscreen.process_raw import counts_to_lncfu +from tfscreen.process_raw.counts_to_lncfu import get_sample_ln_cfu from tfscreen.process_raw._counts_io import _prep_sample_df, _aggregate_counts from tfscreen.util.cli import generalized_main from tfscreen.util.dataframe import check_columns, get_scaled_cfu @@ -30,8 +31,10 @@ def process_presplit( ---------- sample_df : str or pandas.DataFrame Path to (or pre-loaded) sample metadata CSV. Must contain a unique - 'sample' column (used as the index) plus 'replicate', 'condition_pre', - 'sample_cfu', and 'sample_cfu_std' columns. An optional 'library' + 'sample' column (used as the index) plus 'replicate' and + 'condition_pre' columns and the total CFU in each tube with its + uncertainty ('sample_ln_cfu' + 'sample_ln_cfu_std', or 'sample_cfu' + + 'sample_cfu_std'; see counts_to_lncfu). An optional 'library' column groups genotypes for the minimum-observation filter; defaults to 'default' when absent. counts_csv_path : str @@ -63,8 +66,10 @@ def process_presplit( verbose) # Require the caller to supply the presplit-specific metadata columns. - check_columns(sample_df, required_columns=["sample_cfu", "sample_cfu_std", - "replicate", "condition_pre"]) + check_columns(sample_df, required_columns=["replicate", "condition_pre"]) + + # Check/infer sample_ln_cfu and sample_ln_cfu_std before reading counts. + sample_df = get_sample_ln_cfu(sample_df) # counts_to_lncfu requires a 'library' column for grouping; default when absent. if "library" not in sample_df.columns: diff --git a/src/tfscreen/simulate/scripts/build_empirical_cli.py b/src/tfscreen/simulate/scripts/build_empirical_cli.py index 7dafa384..570f543b 100644 --- a/src/tfscreen/simulate/scripts/build_empirical_cli.py +++ b/src/tfscreen/simulate/scripts/build_empirical_cli.py @@ -32,13 +32,13 @@ ) from tfscreen.simulate.empirical.population import fit_population from tfscreen.util.io import read_dataframe -from tfscreen.util.cli import read_lines +from tfscreen.genetics import library_composition_table from tfscreen.util.cli.generalized_main import generalized_main _WT_REF_COLS = ["theta_low", "theta_high", "log_hill_K", "hill_n"] -def _run_configure_and_prefit(growth_file, binding_file, spiked, +def _run_configure_and_prefit(growth_file, binding_file, library_config, base_growth_file, thermo_data, out_prefix, seed): """Configure a linear/hill_geno model and MAP-calibrate k/m. @@ -49,6 +49,10 @@ def _run_configure_and_prefit(growth_file, binding_file, spiked, raise ValueError( "binding data is required to calibrate the growth linkage; pass " "--binding_file, or pass --calibration_file to skip configure+prefit.") + if library_config is None: + raise ValueError( + "--library_config is required to configure the model; pass it, or " + "pass --calibration_file to skip configure+prefit.") from tfscreen.tfmodel.scripts.configure_model_cli import configure_model from tfscreen.tfmodel.scripts.prefit_calibration_cli import ( @@ -62,7 +66,7 @@ def _run_configure_and_prefit(growth_file, binding_file, spiked, binding_df=binding_file, growth_df=growth_file, base_growth_df=base_growth_file, - spiked=spiked, + library_config=library_config, thermo_data=thermo_data, out_prefix=configure_prefix, ) @@ -83,7 +87,7 @@ def build_empirical(growth_file, binding_file=None, out_prefix="tfs_empirical", calibration_file=None, - spiked_file=None, + library_config=None, base_growth_file=None, thermo_data=None, congression_lambda=None, @@ -115,9 +119,11 @@ def build_empirical(growth_file, Skip the configure+prefit step and use this calibration directly — a prefit priors CSV or a wide ``condition_rep,growth_k,growth_m`` CSV. Use this to iterate on the Stage-1/2 knobs without re-running the MAP. - spiked_file : str, optional - Text file of spiked genotype names (one per line) forwarded to - ``configure_model``. + library_config : str, optional + Library YAML describing the screened library (the same file handed to + ``tfs-process-fastq``), forwarded to ``configure_model``. Required + unless ``calibration_file`` is given. Genotypes encoded by a spiked + sequence are congression-free and are left alone by Stage 1.5. base_growth_file : str, optional Direct growth-rate calibration CSV forwarded to ``configure_model``. thermo_data : str, optional @@ -144,7 +150,11 @@ def build_empirical(growth_file, Recommended for large libraries (the fits are embarrassingly parallel). """ growth_df = read_dataframe(growth_file) - spiked = read_lines(spiked_file) if spiked_file else None + spiked = None + if library_config is not None: + composition = library_composition_table(library_config) + spiked = list(composition.loc[composition["in_spiked_origin"], + "genotype"]) icols = [c.strip() for c in str(intercept_cols).split(",") if c.strip()] @@ -155,7 +165,7 @@ def build_empirical(growth_file, # Calibration: reuse a supplied one, or configure+prefit to produce it. if calibration_file is None: calibration_file = _run_configure_and_prefit( - growth_file, binding_file, spiked, base_growth_file, + growth_file, binding_file, library_config, base_growth_file, thermo_data, out_prefix, seed) else: print(f"Using supplied calibration: {calibration_file}", flush=True) @@ -236,6 +246,6 @@ def main(): return generalized_main( build_empirical, manual_arg_types={"binding_file": str, "calibration_file": str, - "spiked_file": str, "base_growth_file": str, + "library_config": str, "base_growth_file": str, "thermo_data": str, "seed": int, "min_obs": int, "congression_lambda": float, "num_workers": int}) diff --git a/src/tfscreen/tfmodel/configuration_io.py b/src/tfscreen/tfmodel/configuration_io.py index f0128db0..e1a4c839 100644 --- a/src/tfscreen/tfmodel/configuration_io.py +++ b/src/tfscreen/tfmodel/configuration_io.py @@ -14,6 +14,8 @@ "components", "priors_file", "guesses_file", + "library_file", + "library", }) def _extract_scalars(obj, prefix=""): @@ -254,7 +256,8 @@ def write_configuration(orchestrator, growth_df_path=None, binding_df_path=None, presplit_df_path=None, - base_growth_df_path=None): + base_growth_df_path=None, + library_meta=None): """ Write model configuration and extracted priors/guesses to files. @@ -273,6 +276,13 @@ def write_configuration(orchestrator, base_growth_df_path : str, optional Path to the base_growth_df CSV (direct growth-rate measurements anchoring the k_ref latent; see model_orchestrator._read_base_growth_df). + library_meta : dict, optional + Provenance for the library composition snapshot named by + ``orchestrator.settings["library_file"]``: the ``source`` library YAML + path and the ``library_mixture`` it declared. Recorded verbatim under + the config's ``library`` key. Nothing downstream reads it -- it is + there because the mixing ratios are declared, never cross-checked + against any other artifact, so the run has to record what it used. """ # Construct priors and guesses dataframes priors_list = [] @@ -302,14 +312,29 @@ def write_configuration(orchestrator, if base_growth_df_path is not None: data_paths["base_growth"] = base_growth_df_path + # The library composition snapshot is a sibling file like the priors and + # guesses CSVs, so it is recorded at the top level (resolved relative to + # the config on read) rather than inside components. When it is present it + # *is* the spiked-genotype definition, so the derived spiked_genotypes list + # is dropped from the written config: one source of truth per file. + settings = dict(orchestrator.settings) + library_file = settings.pop("library_file", None) + if library_file is not None: + settings.pop("spiked_genotypes", None) + config = { "tfscreen_version": __version__, "data": data_paths, - "components": orchestrator.settings, + "components": settings, "priors_file": os.path.basename(priors_path), "guesses_file": os.path.basename(guesses_path) } + if library_file is not None: + config["library_file"] = os.path.basename(library_file) + if library_meta is not None: + config["library"] = library_meta + with open(yaml_path, "w") as f: yaml.dump(config, f, default_flow_style=False, sort_keys=False) @@ -462,12 +487,21 @@ def read_configuration(config_file): # round-tripping the raw path the user originally supplied). settings.pop("presplit_df", None) settings.pop("base_growth_df", None) + # library_file is a sibling file recorded at the top level (like + # priors_file); resolve it relative to the config. A legacy config + # instead carries spiked_genotypes inside components and has no + # library_file at all. + settings.pop("library_file", None) + library_file = config.get("library_file") + if library_file is not None: + library_file = os.path.join(os.path.dirname(config_file), library_file) orchestrator = ModelOrchestrator(growth_df_path, binding_df_path, batch_size=batch_size, presplit_df=presplit_df_path, base_growth_df=base_growth_df_path, + library_file=library_file, **settings) # Update Priors from CSV diff --git a/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py b/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py index a775aff5..1c3fa1c9 100644 --- a/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py +++ b/src/tfscreen/tfmodel/generative/components/theta/thermo/horseshoe.py @@ -35,6 +35,11 @@ _DEFAULT_D0 = 8.0 # Å — residues within ~8 Å Cα-Cα are considered contacts +# Floor on the distance-dependent λ scale. exp(-d/d0) underflows to exactly 0 +# for very distant pairs (d ≳ 100·d0 in float32), and a zero HalfCauchy scale +# is invalid. 1e-12 only binds beyond ~28·d0, where λ is effectively zero anyway. +_MIN_LAM_SCALE = 1e-12 + def sample_pair_ddG(name, struct_names, contact_distances, tau_scale=0.1, slab_scale=2.0, slab_df=4.0, @@ -81,7 +86,7 @@ def sample_pair_ddG(name, struct_names, contact_distances, # Distance-dependent prior scale for local shrinkage: # close contacts (small dist) → scale ≈ 1; distant → scale → 0 - lam_scale = jnp.exp(-dists / d0) # (P, S) + lam_scale = jnp.maximum(jnp.exp(-dists / d0), _MIN_LAM_SCALE) # (P, S) # Sample per-(pair, struct) local scales and offsets. # Plates: struct dim=-2 (outer), pair dim=-1 (inner) → shapes (S, P). diff --git a/src/tfscreen/tfmodel/model_orchestrator.py b/src/tfscreen/tfmodel/model_orchestrator.py index e97d2ed5..50a6e144 100644 --- a/src/tfscreen/tfmodel/model_orchestrator.py +++ b/src/tfscreen/tfmodel/model_orchestrator.py @@ -1,6 +1,7 @@ import tfscreen from tfscreen.util.dataframe import add_group_columns +from tfscreen.genetics import read_library_composition from tfscreen.tfmodel.tensors.tensor_manager import TensorManager from tfscreen.tfmodel.tensors.populate_dataclass import populate_dataclass @@ -802,8 +803,15 @@ class ModelOrchestrator: theta_binding_noise : str, optional Model name for noise on theta in the binding model ('zero' or 'beta'). spiked_genotypes : list or str, optional - Names of genotypes that should be excluded from transformation - correction. + Legacy interface. Names of genotypes that should be excluded from + transformation correction. Every name must appear in the growth data. + Mutually exclusive with ``library_file``. + library_file : str, optional + Path to a library composition table ({out_prefix}_library.csv, written + by ``tfs-configure-model`` from the library YAML). Its + ``in_spiked_origin`` column supplies the spiked genotypes, intersected + with the genotypes present in the growth data. Mutually exclusive with + ``spiked_genotypes``. batch_size : int, optional The batch size for SVI. If None (default), use full batch. @@ -843,6 +851,7 @@ def __init__(self, growth_noise="zero", sample_offset="zero", spiked_genotypes=None, + library_file=None, growth_shares_replicates=False, epistasis=False, thermo_data=None, @@ -874,6 +883,8 @@ def __init__(self, self._growth_noise = growth_noise self._sample_offset = sample_offset self._spiked_genotypes = spiked_genotypes + self._library_file = library_file + self._library_df = None self._growth_shares_replicates = growth_shares_replicates self._epistasis = epistasis self._thermo_data = thermo_data @@ -883,6 +894,17 @@ def __init__(self, self._theta, self._transformation, binding_only=self._binding_only ) + if self._library_file is not None: + if self._spiked_genotypes is not None: + raise ValueError( + "library_file and spiked_genotypes are two ways to say " + "the same thing; pass only one. library_file is the " + "current interface (a library composition table written " + "by tfs-configure-model); spiked_genotypes is the legacy " + "hand-supplied list." + ) + self._library_df = read_library_composition(self._library_file) + if self._dk_geno == "pinned" and self._dk_geno_pins_file is None: raise ValueError( "dk_geno='pinned' requires dk_geno_pins_file (path to a " @@ -966,8 +988,33 @@ def _initialize_data(self): # tells the model which genotypes should be corrected for congression. # Initialize to all True (no masking). mask = np.ones(sizes["num_genotype"],dtype=bool) + + # A library composition table (the current interface) names the spiked + # genotypes itself. The list is machine-derived from the library + # design, so -- unlike the hand-supplied spiked_genotypes below -- a + # spiked genotype that never showed up in the growth data is expected + # (it can be lost to low read depth or min_genotype_obs) and is + # reported rather than raised. + if self._library_df is not None: + genotype_idx = self.growth_tm.tensor_dim_names.index("genotype") + genotype_names = self.growth_tm.tensor_dim_labels[genotype_idx] + + observed = set(genotype_names) + from_library = list(self._library_df.loc[ + self._library_df["in_spiked_origin"], "genotype" + ]) + in_data = [g for g in from_library if g in observed] + absent = [g for g in from_library if g not in observed] + if len(absent) > 0: + print(f"Note: {len(absent)} of {len(from_library)} spiked " + f"genotypes have no growth data and are ignored: " + f"{sorted(absent)}", + flush=True) + + self._spiked_genotypes = in_data + if self._spiked_genotypes is not None: - + # Make sure spiked_genotypes is a list or array if isinstance(self._spiked_genotypes,str): self._spiked_genotypes = [self._spiked_genotypes] @@ -1811,6 +1858,18 @@ def data(self): def priors(self): """The PriorsClass Pytree holding all model priors.""" return self._priors + + @property + def library_df(self): + """ + Library composition table, or None if no library_file was given. + + One row per library genotype (see + ``genetics.library_composition_table``). Holds the design's + ``pool_fraction`` and ``bulk_fraction`` for every genotype, including + genotypes with no growth data. + """ + return self._library_df @property def settings(self): @@ -1834,6 +1893,7 @@ def settings(self): "growth_noise":self._growth_noise, "sample_offset":self._sample_offset, "spiked_genotypes":self._spiked_genotypes, + "library_file":self._library_file, "growth_shares_replicates": self._growth_shares_replicates, "epistasis": self._epistasis, "thermo_data": self._thermo_data, diff --git a/src/tfscreen/tfmodel/scripts/configure_model_cli.py b/src/tfscreen/tfmodel/scripts/configure_model_cli.py index 3bca57b7..5eca4fbe 100644 --- a/src/tfscreen/tfmodel/scripts/configure_model_cli.py +++ b/src/tfscreen/tfmodel/scripts/configure_model_cli.py @@ -6,6 +6,16 @@ write_model_stats, ) from tfscreen.util.cli.generalized_main import generalized_main +from tfscreen.util import read_dataframe, read_yaml +from tfscreen.genetics import ( + RESERVED_GENOTYPES, + library_composition_table, + standardize_genotypes, + write_library_composition, +) + +import numpy as np +import pandas as pd # Maps (condition_growth, theta_rescale) pairs that are fundamentally incompatible # to a human-readable explanation of why. @@ -51,6 +61,66 @@ def check_component_compatibility(condition_growth_model, theta_rescale_model): ) +def check_genotypes_in_library(library_genotypes, data_df, label, + max_report=20): + """ + Fail unless every genotype in a data file is part of the library. + + The library YAML handed to ``tfs-configure-model`` must be the same one + handed to ``tfs-process-fastq``. Nothing cross-checks the two, but a + mismatch in the *genetics* keys (residue numbering, wt sequence, tiles, + spiked sequences) shows up here as genotypes the library does not contain. + A one-off numbering shift, for instance, mismatches essentially every + mutant. + + Parameters + ---------- + library_genotypes : set of str + Standardized genotype names in the library. + data_df : str or pandas.DataFrame + Data file (or frame) with a ``genotype`` column. + label : str + Name of the argument being checked, used in the error message. + max_report : int, optional + Maximum number of offending genotypes to name in the error. + + Raises + ------ + ValueError + If any genotype is absent from the library. Reserved sentinels + (``__unknown__``) are ignored. + """ + + if data_df is None: + return + + df = read_dataframe(data_df) + if "genotype" not in df.columns: + raise ValueError(f"{label} has no 'genotype' column.") + + observed = standardize_genotypes(df["genotype"]) + observed = pd.unique(np.asarray(observed)) + observed = [g for g in observed if g not in RESERVED_GENOTYPES] + + missing = sorted(set(observed) - set(library_genotypes)) + if len(missing) == 0: + return + + shown = missing[:max_report] + suffix = "" if len(missing) <= max_report else f" (and {len(missing) - max_report} more)" + source = data_df if isinstance(data_df, str) else "" + raise ValueError( + f"{len(missing)} of {len(observed)} genotypes in {label} " + f"('{source}') are not in the library described by library_config: " + f"{shown}{suffix}.\n" + f"The library config must be the same one used to call the " + f"sequencing reads (tfs-process-fastq). A residue-numbering or " + f"wt-sequence difference between the two will mismatch most or all " + f"genotypes; a handful of mismatches usually means the data include " + f"genotypes the library design does not contain." + ) + + def configure_model(binding_df, growth_df=None, presplit_df=None, @@ -68,7 +138,7 @@ def configure_model(binding_df, theta_growth_noise_model="zero", theta_binding_noise_model="zero", growth_noise_model="zero", - spiked=None, + library_config=None, growth_shares_replicates=False, epistasis=False, thermo_data=None, @@ -79,9 +149,11 @@ def configure_model(binding_df, Build and write the YAML configuration files needed by tfs-fit-model. Constructs a ModelOrchestrator from the supplied data and model-component choices, - then writes three files: {out_prefix}_config.yaml (the main configuration), - {out_prefix}_priors.csv (prior distributions for all parameters), and - {out_prefix}_guesses.csv (initial-value guesses for array parameters). + then writes {out_prefix}_config.yaml (the main configuration), + {out_prefix}_priors.csv (prior distributions for all parameters), + {out_prefix}_guesses.csv (initial-value guesses for array parameters) and, + for a growth model, {out_prefix}_library.csv (the per-genotype library + composition resolved from library_config). When only binding_df is provided (no growth_df), a binding-only model is configured that infers theta directly from observed binding measurements @@ -110,9 +182,9 @@ def configure_model(binding_df, model_orchestrator._read_base_growth_df and generative/model.py's base_growth_obs block. out_prefix : str, optional - Prefix for the three output files ({out_prefix}_config.yaml, - {out_prefix}_priors.csv, {out_prefix}_guesses.csv). - Default 'tfs_configure'. + Prefix for the output files ({out_prefix}_config.yaml, + {out_prefix}_priors.csv, {out_prefix}_guesses.csv and, for a growth + model, {out_prefix}_library.csv). Default 'tfs_configure'. condition_growth_model: str, optional Model to use to describe growth under different conditions (e.g., pheS+4CP). Allowed values are 'linear' (default), 'power', or @@ -170,9 +242,18 @@ def configure_model(binding_df, 'normal_kt' learns a global sigma_k that inflates the observation scale in quadrature with ln_cfu_std, capturing biological variability in growth rates not explained by theta or dk_geno. - spiked : list or str, optional - Names of genotypes that should be excluded from congression - correction. + library_config : str, optional + Path to the library YAML describing the screened library -- the same + file handed to ``tfs-process-fastq``. Required whenever ``growth_df`` + is given (a binding-only model has no congression correction and no + ln_cfu0 latents, so it does not need one). Read keys: + ``reading_frame``, ``first_amplicon_residue``, ``wt_seq``, + ``degen_sites``, ``tiles``, ``tile_combos``, ``spiked_seqs`` and + ``library_mixture``; any other keys (a full simulate config, say) are + ignored. Genotypes encoded by a spiked sequence become the spiked + set, replacing the old hand-supplied ``--spiked`` list. The resolved + per-genotype table is written to {out_prefix}_library.csv and is what + ``tfs-fit-model`` reads. growth_shares_replicates : bool, optional Whether replicates should share the same parameters for the growth and growth transition models. Default is False. @@ -234,6 +315,43 @@ def configure_model(binding_df, f"transformation_lambda=(0.36, 0.05)." ) + # Resolve the library description. The composition table is written + # before the orchestrator is built, because the orchestrator reads the + # snapshot (not the YAML) -- the same file tfs-fit-model will read. + library_file = None + library_meta = None + if binding_only: + if library_config is not None: + raise ValueError( + "library_config was supplied but no growth_df. A " + "binding-only model has no congression correction and no " + "ln_cfu0 latents, so it has no use for the library." + ) + else: + if library_config is None: + raise ValueError( + "library_config is required when growth_df is given. Pass " + "the library YAML that describes the screened library -- the " + "same file used for tfs-process-fastq." + ) + + composition = library_composition_table(library_config) + + for data_df, label in ((growth_df, "growth_df"), + (presplit_df, "presplit_df"), + (base_growth_df, "base_growth_df")): + check_genotypes_in_library(set(composition["genotype"]), + data_df, label) + + library_file = f"{out_prefix}_library.csv" + write_library_composition(composition, library_file) + print(f"Wrote library composition to {library_file}", flush=True) + + library_meta = { + "source": library_config if isinstance(library_config, str) else "", + "library_mixture": read_yaml(library_config)["library_mixture"], + } + # Initialize model to build mappings and get guesses orchestrator = ModelOrchestrator(growth_df, binding_df, @@ -252,7 +370,7 @@ def configure_model(binding_df, theta_growth_noise=theta_growth_noise_model, theta_binding_noise=theta_binding_noise_model, growth_noise=growth_noise_model, - spiked_genotypes=spiked, + library_file=library_file, growth_shares_replicates=growth_shares_replicates, epistasis=epistasis, thermo_data=thermo_data, @@ -269,7 +387,8 @@ def configure_model(binding_df, growth_df_path=growth_path, binding_df_path=binding_df if isinstance(binding_df, str) else "binding.csv", presplit_df_path=presplit_path, - base_growth_df_path=base_growth_path) + base_growth_df_path=base_growth_path, + library_meta=library_meta) # Pre-fit accounting: how many parameters, how many observations, and # which genotypes are individually under-determined. @@ -284,13 +403,12 @@ def main(): "growth_df":str, "presplit_df":str, "base_growth_df":str, - "spiked":list, + "library_config":str, "thermo_data":str, "batch_size":int, "binding_weight":float, "transformation_lambda":float}, - manual_arg_nargs={"spiked":"+", - "transformation_lambda":2}) + manual_arg_nargs={"transformation_lambda":2}) if __name__ == "__main__": main() diff --git a/src/tfscreen/tfmodel/scripts/fit_genotypes_cli.py b/src/tfscreen/tfmodel/scripts/fit_genotypes_cli.py index e94aea6a..81777280 100644 --- a/src/tfscreen/tfmodel/scripts/fit_genotypes_cli.py +++ b/src/tfscreen/tfmodel/scripts/fit_genotypes_cli.py @@ -12,7 +12,7 @@ iterative fixed point (predict theta -> de-attenuate against the population -> refit Hill). It is inherently a population operation: the correction couples all bulk genotypes through their shared background occupancy distribution. -Spiked genotypes (``--spiked_file``) are congression-free and pass through +Spiked genotypes (named by ``--library_config``) are congression-free and pass through untouched. Outputs (under ``--out_prefix``) @@ -35,7 +35,7 @@ fit_phenotypes, fits_to_results_df, predict_theta, ) from tfscreen.util.io import read_dataframe -from tfscreen.util.cli import read_lines +from tfscreen.genetics import library_composition_table from tfscreen.util.cli.generalized_main import generalized_main @@ -43,7 +43,7 @@ def fit_genotypes(growth_file, calibration_file, out_prefix="tfs_mle", congression_lambda=None, - spiked_file=None, + library_config=None, intercept_cols="replicate", dk_geno_prior_sd=1.0, min_obs=None, @@ -65,10 +65,11 @@ def fit_genotypes(growth_file, Zero-truncated Poisson congression rate (the same lambda as the simulator's ``transformation_poisson_lambda``). When given, run the de-attenuation pass; omit for raw MLE fits only. - spiked_file : str, optional - Text file of congression-free (spiked) genotype names, one per line. - These are excluded from the de-attenuation correction and background. - Only relevant with ``--congression_lambda``. + library_config : str, optional + Library YAML describing the screened library (the same file handed to + ``tfs-process-fastq``). Genotypes encoded by a spiked sequence are + congression-free and are excluded from the de-attenuation correction + and its background. Only relevant with ``--congression_lambda``. intercept_cols : str Comma-separated columns whose unique combinations each get a nuisance ``ln_cfu0`` (default ``"replicate"``; empty string -> single intercept). @@ -85,7 +86,11 @@ def fit_genotypes(growth_file, ``--congression_lambda``. """ growth_df = read_dataframe(growth_file) - spiked = read_lines(spiked_file) if spiked_file else None + spiked = None + if library_config is not None: + composition = library_composition_table(library_config) + spiked = list(composition.loc[composition["in_spiked_origin"], + "genotype"]) icols = [c.strip() for c in str(intercept_cols).split(",") if c.strip()] @@ -164,7 +169,7 @@ def fit_genotypes(growth_file, def main(): return generalized_main( fit_genotypes, - manual_arg_types={"spiked_file": str, "congression_lambda": float, + manual_arg_types={"library_config": str, "congression_lambda": float, "min_obs": int, "num_workers": int}) diff --git a/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py b/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py index 0025ce27..046d43e4 100644 --- a/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py +++ b/src/tfscreen/tfmodel/scripts/prefit_calibration_cli.py @@ -345,6 +345,9 @@ def _build_calibration_model(orchestrator_prod, growth_df_cal, binding_df_cal): # through to a "single" calibration model. settings["transformation_lambda"] = None settings["spiked_genotypes"] = None + # library_file would re-derive the spiked list from the library design, so + # it has to be dropped alongside spiked_genotypes. + settings["library_file"] = None # Equal weighting: the calibration MAP must learn the binding→growth # linkage from both data sources together. The production binding_weight # (N_growth_prod / N_binding_prod, often >> 1) would drown the binding diff --git a/src/tfscreen/tfmodel/scripts/setup_grid_cli.py b/src/tfscreen/tfmodel/scripts/setup_grid_cli.py index e607b39a..5778de61 100644 --- a/src/tfscreen/tfmodel/scripts/setup_grid_cli.py +++ b/src/tfscreen/tfmodel/scripts/setup_grid_cli.py @@ -87,6 +87,7 @@ # configure_model arguments that are file paths and need abs→rel rewriting. _PATH_KEYS = frozenset({ "binding_df", "growth_df", "presplit_df", "base_growth_df", "thermo_data", + "library_config", }) # Fixed output prefix used inside every per-combination run. diff --git a/src/tfscreen/util/dataframe/get_scaled_cfu.py b/src/tfscreen/util/dataframe/get_scaled_cfu.py index b5925964..35b3969d 100644 --- a/src/tfscreen/util/dataframe/get_scaled_cfu.py +++ b/src/tfscreen/util/dataframe/get_scaled_cfu.py @@ -11,7 +11,9 @@ ) def get_scaled_cfu( - df: pd.DataFrame, need_columns: Optional[Iterable[str]] = None + df: pd.DataFrame, + need_columns: Optional[Iterable[str]] = None, + prefix: str = "" ) -> pd.DataFrame: """Ensures a DataFrame contains specified CFU-related columns. @@ -28,6 +30,12 @@ def get_scaled_cfu( need_columns : iterable of str, optional A list or set of column names that must be present in the output DataFrame. If None or empty, the original DataFrame is returned. + Names are given without `prefix` (e.g. 'ln_cfu', not + 'sample_ln_cfu'). + prefix : str, optional + Prefix shared by every CFU column this call reads and writes. For + example, ``prefix="sample_"`` infers 'sample_ln_cfu' from + 'sample_cfu' and ignores any unprefixed 'cfu' columns. Default ''. Returns ------- @@ -73,6 +81,24 @@ def get_scaled_cfu( invalid_cols = need_columns - VALID_COLS if invalid_cols: raise ValueError(f"Invalid column(s) requested: {', '.join(invalid_cols)}") + + # With a prefix, strip it, run the unprefixed calculation on just the + # prefixed columns, then add the new columns back under the prefix. + if prefix: + to_base = {f"{prefix}{c}": c for c in VALID_COLS if f"{prefix}{c}" in df.columns} + base_df = df[list(to_base)].rename(columns=to_base) + try: + base_df = get_scaled_cfu(base_df, need_columns=need_columns) + except ValueError: + missing = sorted(f"{prefix}{c}" for c in need_columns - set(base_df.columns)) + raise ValueError( + f"Could not calculate the following columns: {missing}. " + "Insufficient source data in the DataFrame." + ) + new_cols = [c for c in base_df.columns if c not in to_base.values()] + if not new_cols: + return df + return df.join(base_df[new_cols].add_prefix(prefix)) if need_columns.issubset(df.columns): return df diff --git a/tests/smoke-tests/conftest.py b/tests/smoke-tests/conftest.py index 13cb5f60..87d3513d 100644 --- a/tests/smoke-tests/conftest.py +++ b/tests/smoke-tests/conftest.py @@ -17,6 +17,12 @@ def binding_smoke_csv(smoke_test_dir): """Return the path to the binding smoke test data.""" return os.path.join(smoke_test_dir, "test_data", "binding-smoke.csv") +@pytest.fixture(scope="session") +def library_smoke_yaml(smoke_test_dir): + """Library description covering every genotype in the smoke data.""" + return os.path.join(smoke_test_dir, "test_data", "library-smoke.yaml") + + @pytest.fixture(scope="session") def struct_smoke_h5_path(tmp_path_factory, growth_smoke_csv): """ diff --git a/tests/smoke-tests/test_configure_run_smoke.py b/tests/smoke-tests/test_configure_run_smoke.py index 3bc85d99..9cc2d76e 100644 --- a/tests/smoke-tests/test_configure_run_smoke.py +++ b/tests/smoke-tests/test_configure_run_smoke.py @@ -18,7 +18,7 @@ def test_configure_run_binding_only_smoke(tmpdir): """ # Minimal binding dataset: two genotypes, two titrant concentrations binding_df = pd.DataFrame({ - "genotype": ["wt", "wt", "A123B", "A123B"], + "genotype": ["wt", "wt", "M42I", "M42I"], "titrant_name": ["T1", "T1", "T1", "T1"], "titrant_conc": [0.1, 1.0, 0.1, 1.0], "theta_obs": [0.8, 0.3, 0.7, 0.2], @@ -63,7 +63,7 @@ def test_configure_run_binding_only_smoke(tmpdir): @pytest.mark.slow -def test_configure_run_pipeline_smoke(tmpdir): +def test_configure_run_pipeline_smoke(tmpdir, library_smoke_yaml): """ Smoke test for the full configuration -> running pipeline. """ @@ -73,7 +73,7 @@ def test_configure_run_pipeline_smoke(tmpdir): "replicate": ["R1", "R1"], "condition_pre": ["C1-", "C1-"], "condition_sel": ["C2+", "C2+"], - "genotype": ["A123B", "C456D"], + "genotype": ["M42I", "L45P"], "t": [0, 10], "t_sel": [0, 10], "t_pre": [12, 12], @@ -86,7 +86,7 @@ def test_configure_run_pipeline_smoke(tmpdir): growth_df.to_csv(growth_path, index=False) binding_df = pd.DataFrame({ - "genotype": ["A123B", "C456D"], + "genotype": ["M42I", "L45P"], "titrant_name": ["T1", "T1"], "titrant_conc": [0.1, 0.1], "theta_obs": [0.5, 0.6], @@ -100,6 +100,7 @@ def test_configure_run_pipeline_smoke(tmpdir): # Run configuration configure_model(binding_path, growth_df=growth_path, + library_config=library_smoke_yaml, out_prefix=out_prefix) config_file = f"{out_prefix}_config.yaml" @@ -143,7 +144,7 @@ def test_configure_run_pipeline_smoke(tmpdir): @pytest.mark.slow -def test_configure_run_binding_weight_smoke(tmpdir): +def test_configure_run_binding_weight_smoke(tmpdir, library_smoke_yaml): """ Smoke test for the binding_weight feature end-to-end. @@ -159,7 +160,7 @@ def test_configure_run_binding_weight_smoke(tmpdir): "replicate": ["R1"] * 20, "condition_pre": ["C1-"] * 20, "condition_sel": ["C2+"] * 20, - "genotype": ["A123B"] * 10 + ["C456D"] * 10, + "genotype": ["M42I"] * 10 + ["L45P"] * 10, "t_sel": [10.0] * 20, "t_pre": [12.0] * 20, "ln_cfu": [1.0] * 20, @@ -168,7 +169,7 @@ def test_configure_run_binding_weight_smoke(tmpdir): "titrant_conc": [0.1] * 20, }) binding_df = pd.DataFrame({ - "genotype": ["A123B", "A123B", "C456D", "C456D"], + "genotype": ["M42I", "M42I", "L45P", "L45P"], "titrant_name": ["T1", "T1", "T1", "T1"], "titrant_conc": [0.1, 1.0, 0.1, 1.0], "theta_obs": [0.5, 0.3, 0.6, 0.4], @@ -183,6 +184,7 @@ def test_configure_run_binding_weight_smoke(tmpdir): out_explicit = os.path.join(tmpdir, "tfs_explicit") configure_model(binding_path, growth_df=growth_path, + library_config=library_smoke_yaml, out_prefix=out_explicit, binding_weight=99.0) @@ -196,6 +198,7 @@ def test_configure_run_binding_weight_smoke(tmpdir): out_auto = os.path.join(tmpdir, "tfs_auto") configure_model(binding_path, growth_df=growth_path, + library_config=library_smoke_yaml, out_prefix=out_auto) with open(f"{out_auto}_config.yaml") as f: diff --git a/tests/smoke-tests/test_data/library-smoke.yaml b/tests/smoke-tests/test_data/library-smoke.yaml new file mode 100644 index 00000000..ab509154 --- /dev/null +++ b/tests/smoke-tests/test_data/library-smoke.yaml @@ -0,0 +1,20 @@ +# Library description for the smoke-test data (tests/smoke-tests/test_data). +# +# The same file plays two roles: it is what tfs-process-fastq would use to call +# reads, and what tfs-configure-model uses to resolve the library composition. +# Sites 42/45 (tile 1) and 64/68/74/79/81/84 (tile 2) are NNT, which covers +# every genotype in growth-smoke.csv. wt and M42I are spiked. +reading_frame: 0 +first_amplicon_residue: 27 +wt_seq: gccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatg +degen_sites: .............................................nnt......nnt......................................................nnt.........nnt...............nnt............nnt...nnt......nnt.......................................... +tiles: .............................................111111111111......................................................222222222222222222222222222222222222222222222222222222222222222.......................................... +tile_combos: ["single-1", "single-2", "double-1-2"] +spiked_seqs: +- ........................................................................................................................................................................................................................ +- .............................................ata........................................................................................................................................................................ +library_mixture: + single-1: 100 + single-2: 100 + double-1-2: 1_000 + spiked: 1 diff --git a/tests/smoke-tests/test_prefit_calibration_smoke.py b/tests/smoke-tests/test_prefit_calibration_smoke.py index 67f25471..67948529 100644 --- a/tests/smoke-tests/test_prefit_calibration_smoke.py +++ b/tests/smoke-tests/test_prefit_calibration_smoke.py @@ -23,7 +23,7 @@ def _write_inputs(tmpdir): """Two genotypes x three conditions x two titrant concs x two timepoints.""" - genotypes = ["wt", "A123B"] + genotypes = ["wt", "M42I"] conc = [0.1, 1.0] # condition_pre is a control ('-'); two distinct selection ('+') conditions # give three distinct condition_reps: C1-, C2+, C3+. @@ -43,7 +43,7 @@ def _write_inputs(tmpdir): "t_sel": t_sel, "t_pre": 12.0, # mild genotype/condition-dependent slope so the MAP has signal - "ln_cfu": 1.0 + 0.05 * t_sel + (0.2 if g == "A123B" else 0.0), + "ln_cfu": 1.0 + 0.05 * t_sel + (0.2 if g == "M42I" else 0.0), "ln_cfu_std": 0.1, "titrant_name": "T1", "titrant_conc": c, @@ -51,7 +51,7 @@ def _write_inputs(tmpdir): growth_df = pd.DataFrame(rows) binding_df = pd.DataFrame({ - "genotype": ["wt", "wt", "A123B", "A123B"], + "genotype": ["wt", "wt", "M42I", "M42I"], "titrant_name": ["T1"] * 4, "titrant_conc": [0.1, 1.0, 0.1, 1.0], "theta_obs": [0.8, 0.3, 0.7, 0.2], @@ -71,12 +71,14 @@ def _write_inputs(tmpdir): ("power", "k_loc"), ("saturation", "min_loc"), ]) -def test_prefit_writes_per_condition_baseline_prior(tmpdir, cg_model, baseline_loc): +def test_prefit_writes_per_condition_baseline_prior(tmpdir, library_smoke_yaml, + cg_model, baseline_loc): growth_path, binding_path = _write_inputs(tmpdir) out_prefix = os.path.join(tmpdir, f"tfs_{cg_model}") configure_model(binding_path, growth_df=growth_path, + library_config=library_smoke_yaml, condition_growth_model=cg_model, theta_model="categorical_geno", out_prefix=out_prefix) @@ -115,7 +117,8 @@ def test_prefit_writes_per_condition_baseline_prior(tmpdir, cg_model, baseline_l @pytest.mark.slow -def test_configure_prefit_fit_full_loop_with_per_condition_priors(tmpdir): +def test_configure_prefit_fit_full_loop_with_per_condition_priors(tmpdir, + library_smoke_yaml): """The full configure -> prefit -> fit loop runs once the priors CSV holds per-condition (array) baseline priors — i.e. the SVI actually consumes them without a tracing/shape error.""" @@ -124,6 +127,7 @@ def test_configure_prefit_fit_full_loop_with_per_condition_priors(tmpdir): configure_model(binding_path, growth_df=growth_path, + library_config=library_smoke_yaml, condition_growth_model="linear", theta_model="categorical_geno", out_prefix=out_prefix) diff --git a/tests/tfscreen/genetics/test_library_composition_table.py b/tests/tfscreen/genetics/test_library_composition_table.py new file mode 100644 index 00000000..8fd9f4dc --- /dev/null +++ b/tests/tfscreen/genetics/test_library_composition_table.py @@ -0,0 +1,133 @@ +""" +Tests for library_composition_table / read/write_library_composition. + +The fixture library is deliberately tiny but has the property that motivated +this interface: wt and one single mutant are encoded by BOTH a spiked sequence +and the bulk sub-library, so they are neither purely spiked nor purely bulk. +""" + +import numpy as np +import pandas as pd +import pytest + +from tfscreen.genetics import ( + library_composition_table, + read_library_composition, + write_library_composition, +) +from tfscreen.genetics.library_design import LIBRARY_COMPOSITION_COLUMNS + + +@pytest.fixture +def library_config(): + # Codons: atg gca aaa ccg gaa tgc. Site 2 (gca, Ala) is tile 1 and site 5 + # (gaa, Glu) is tile 2, both NNT. NNT encodes Ala (gct) but not Glu, so wt + # is reachable in tile 1 only. Spikes: wt and A2L. + return { + "reading_frame": 0, + "first_amplicon_residue": 1, + "wt_seq": "atggcaaaaccggaatgc", + "degen_sites": "...nnt......nnt...", + "tiles": "...111......222...", + "tile_combos": ["single-1", "single-2", "double-1-2"], + "spiked_seqs": ["..................", # wt + "...ctt............"], # A2L + "library_mixture": {"single-1": 10, + "single-2": 10, + "double-1-2": 100, + "spiked": 1}, + } + + +class TestLibraryCompositionTable: + + def test_columns_and_uniqueness(self, library_config): + table = library_composition_table(library_config) + assert list(table.columns) == LIBRARY_COMPOSITION_COLUMNS + assert not table["genotype"].duplicated().any() + assert table["pool_fraction"].sum() == pytest.approx(1.0) + + def test_wt_is_flagged(self, library_config): + table = library_composition_table(library_config).set_index("genotype") + assert table.loc["wt", "is_wt"] + assert not table["is_wt"].drop("wt").any() + + def test_spiked_genotypes_are_also_in_the_bulk(self, library_config): + """The case --spiked cannot express: spiked *and* bulk.""" + table = library_composition_table(library_config).set_index("genotype") + + for genotype in ("wt", "A2L"): + assert table.loc[genotype, "in_spiked_origin"] + # Encoded by a spiked sequence and by the bulk single-1 library, + # so most of its cells are congression-affected bulk cells. + assert 0 < table.loc[genotype, "bulk_fraction"] < 1 + assert "spiked" in table.loc[genotype, "origins"] + assert "single-1" in table.loc[genotype, "origins"] + + def test_bulk_only_genotype(self, library_config): + table = library_composition_table(library_config).set_index("genotype") + assert not table.loc["A2C", "in_spiked_origin"] + assert table.loc["A2C", "bulk_fraction"] == 1.0 + + def test_spiked_share_scales_with_mixture(self, library_config): + """More spike in the pool -> less of wt's mass is bulk.""" + low = library_composition_table(library_config).set_index("genotype") + + library_config["library_mixture"]["spiked"] = 100 + high = library_composition_table(library_config).set_index("genotype") + + assert (high.loc["wt", "bulk_fraction"] + < low.loc["wt", "bulk_fraction"]) + + def test_no_spiked_seqs(self, library_config): + library_config.pop("spiked_seqs") + library_config["library_mixture"].pop("spiked") + table = library_composition_table(library_config) + assert not table["in_spiked_origin"].any() + assert (table["bulk_fraction"] == 1.0).all() + + def test_missing_library_mixture_raises(self, library_config): + library_config.pop("library_mixture") + with pytest.raises(ValueError, match="library_mixture"): + library_composition_table(library_config) + + def test_mixture_key_mismatch_raises(self, library_config): + library_config["library_mixture"].pop("spiked") + with pytest.raises(ValueError, match="library_mixture"): + library_composition_table(library_config) + + +class TestReadWriteRoundTrip: + + def test_round_trip(self, library_config, tmp_path): + table = library_composition_table(library_config) + path = str(tmp_path / "tfs_configure_library.csv") + write_library_composition(table, path) + + back = read_library_composition(path) + assert list(back.columns) == LIBRARY_COMPOSITION_COLUMNS + assert back["is_wt"].dtype == bool + assert back["in_spiked_origin"].dtype == bool + pd.testing.assert_frame_equal(back, table, check_dtype=False) + + def test_missing_file(self, tmp_path): + with pytest.raises(FileNotFoundError): + read_library_composition(str(tmp_path / "nope.csv")) + + def test_missing_column(self, tmp_path): + path = str(tmp_path / "bad.csv") + pd.DataFrame({"genotype": ["wt"]}).to_csv(path, index=False) + with pytest.raises(ValueError, match="missing columns"): + read_library_composition(path) + + def test_duplicate_genotype(self, library_config, tmp_path): + table = library_composition_table(library_config) + path = str(tmp_path / "dup.csv") + pd.concat([table, table.head(1)]).to_csv(path, index=False) + with pytest.raises(ValueError, match="duplicate genotypes"): + read_library_composition(path) + + def test_write_requires_columns(self, tmp_path): + with pytest.raises(ValueError, match="missing columns"): + write_library_composition(pd.DataFrame({"genotype": ["wt"]}), + str(tmp_path / "x.csv")) diff --git a/tests/tfscreen/genetics/test_library_design.py b/tests/tfscreen/genetics/test_library_design.py new file mode 100644 index 00000000..edcc723e --- /dev/null +++ b/tests/tfscreen/genetics/test_library_design.py @@ -0,0 +1,294 @@ +import doctest + +import numpy as np +import pandas as pd +import pytest + +import tfscreen.genetics.library_design as library_design +from tfscreen.genetics import ( + estimate_library_mixture, + expected_library_composition, + scale_library_design, +) + + +def _library(rows): + """rows: (origin, genotype, degeneracy) -> build_library_df-like frame.""" + df = pd.DataFrame(rows, columns=["library_origin", "genotype", "degeneracy"]) + df["weight"] = df["degeneracy"] / df.groupby("library_origin")["degeneracy"].transform("sum") + return df + + +@pytest.fixture +def reference_library(): + # single-1: 10 sequences (wt x2, M42I x1, others), double: 100 sequences, + # spiked: wt + M42I + H74A/K84L (not encoded by the bulk). + return _library([ + ("single-1", "wt", 2), + ("single-1", "M42I", 1), + ("single-1", "M42V", 7), + ("double-1-2", "wt", 4), + ("double-1-2", "M42I", 6), + ("double-1-2", "M42V/H74A", 90), + ("spiked", "wt", 1), + ("spiked", "M42I", 1), + ("spiked", "H74A/K84L", 1), + ]) + + +def test_doctests(): + assert doctest.testmod(library_design).failed == 0 + + +class TestExpectedLibraryComposition: + + def test_bulk_fraction_by_hand(self, reference_library): + mixture = {"single-1": 10, "double-1-2": 100, "spiked": 3} + out = expected_library_composition(reference_library, mixture).set_index("genotype") + + # masses: single-1 = 10*deg/10 = deg; double = 100*deg/100 = deg; + # spiked = 3 * 1/3 = 1 per spiked genotype + wt_bulk, wt_spike = 2 + 4, 1 + m42i_bulk, m42i_spike = 1 + 6, 1 + assert out.loc["wt", "bulk_fraction"] == pytest.approx(wt_bulk / (wt_bulk + wt_spike)) + assert out.loc["M42I", "bulk_fraction"] == pytest.approx(m42i_bulk / (m42i_bulk + m42i_spike)) + assert out.loc["H74A/K84L", "bulk_fraction"] == 0.0 + assert out.loc["M42V", "bulk_fraction"] == 1.0 + assert out.loc["M42V/H74A", "bulk_fraction"] == 1.0 + + total = 10 + 100 + 3 + assert out.loc["wt", "pool_fraction"] == pytest.approx((wt_bulk + wt_spike) / total) + assert out["pool_fraction"].sum() == pytest.approx(1.0) + + def test_only_ratios_matter(self, reference_library): + a = expected_library_composition(reference_library, + {"single-1": 1, "double-1-2": 2, "spiked": 3}) + b = expected_library_composition(reference_library, + {"single-1": 10, "double-1-2": 20, "spiked": 30}) + pd.testing.assert_frame_equal(a, b) + + def test_zero_spike_mixture_gives_pure_bulk(self, reference_library): + out = expected_library_composition( + reference_library, {"single-1": 1, "double-1-2": 1, "spiked": 0} + ).set_index("genotype") + assert out.loc["wt", "bulk_fraction"] == 1.0 + # A genotype with no mass at all has an undefined bulk fraction. + assert np.isnan(out.loc["H74A/K84L", "bulk_fraction"]) + assert out.loc["H74A/K84L", "pool_fraction"] == 0.0 + + def test_unnormalized_weights_are_normalized(self, reference_library): + mixture = {"single-1": 10, "double-1-2": 100, "spiked": 3} + scaled = reference_library.assign(weight=reference_library["weight"] * 7.0) + pd.testing.assert_frame_equal( + expected_library_composition(reference_library, mixture), + expected_library_composition(scaled, mixture), + ) + + def test_custom_spiked_origin(self, reference_library): + df = reference_library.replace({"library_origin": {"spiked": "controls"}}) + out = expected_library_composition( + df, {"single-1": 10, "double-1-2": 100, "controls": 3}, + spiked_origin="controls", + ).set_index("genotype") + assert out.loc["H74A/K84L", "bulk_fraction"] == 0.0 + + def test_mixture_keys_must_match(self, reference_library): + with pytest.raises(ValueError, match="Missing"): + expected_library_composition(reference_library, {"single-1": 1, "spiked": 1}) + with pytest.raises(ValueError, match="Not in the library"): + expected_library_composition( + reference_library, + {"single-1": 1, "double-1-2": 1, "spiked": 1, "single-2": 1}, + ) + + def test_bad_mixture_values(self, reference_library): + with pytest.raises(ValueError, match="non-negative"): + expected_library_composition( + reference_library, {"single-1": -1, "double-1-2": 1, "spiked": 1}) + with pytest.raises(ValueError, match="non-negative"): + expected_library_composition( + reference_library, {"single-1": 0, "double-1-2": 0, "spiked": 0}) + + def test_missing_column(self, reference_library): + with pytest.raises(ValueError, match="weight"): + expected_library_composition(reference_library.drop(columns="weight"), + {"single-1": 1, "double-1-2": 1, "spiked": 1}) + + +class TestScaleLibraryDesign: + + @pytest.fixture + def target_library(self): + # Same degeneracy patterns for the spikes, fewer bulk sequences. + return _library([ + ("single-1", "wt", 1), + ("single-1", "M42I", 1), + ("single-1", "M42V", 3), + ("double-1-2", "wt", 2), + ("double-1-2", "M42I", 3), + ("double-1-2", "M42V/H74A", 5), + ("spiked", "wt", 1), + ("spiked", "M42I", 1), + ("spiked", "H74A/K84L", 1), + ]) + + def test_per_sequence_quantities_preserved(self, reference_library, target_library): + mixture = {"single-1": 100, "double-1-2": 1000, "spiked": 1} + sizes = {"single-1": 100_000, "double-1-2": 300_000, "spiked": 1_000} + out = scale_library_design(reference_library, target_library, mixture, sizes, + cfu0=6.5e7, total_num_reads=1_000_000_000) + + ref_seqs = {"single-1": 10, "double-1-2": 100, "spiked": 3} + tgt_seqs = {"single-1": 5, "double-1-2": 10, "spiked": 3} + + ref_total = sum(mixture.values()) + tgt_total = sum(out["library_mixture"].values()) + ref_spike_seq = mixture["spiked"] / ref_seqs["spiked"] + tgt_spike_seq = out["library_mixture"]["spiked"] / tgt_seqs["spiked"] + for k in mixture: + # abundance of one sequence relative to one spiked sequence + assert (out["library_mixture"][k] / tgt_seqs[k] / tgt_spike_seq + == pytest.approx(mixture[k] / ref_seqs[k] / ref_spike_seq)) + # cells per sequence + assert (out["cfu0"] * out["library_mixture"][k] / tgt_total / tgt_seqs[k] + == pytest.approx(6.5e7 * mixture[k] / ref_total / ref_seqs[k])) + # transformants per sequence (to rounding) + assert (out["transform_sizes"][k] / tgt_seqs[k] + == pytest.approx(sizes[k] / ref_seqs[k], rel=1e-3)) + + # Unchanged sequence count keeps the reference value. + assert out["library_mixture"]["spiked"] == 1.0 + assert out["transform_sizes"]["spiked"] == 1_000 + assert isinstance(out["transform_sizes"]["double-1-2"], int) + assert isinstance(out["total_num_reads"], int) + + def test_bulk_fraction_carries_over_with_matching_degeneracy(self, reference_library): + # Target library: each bulk origin has half the reference's sequences, + # but wt and M42I keep the same number of encoding sequences. Scaling + # preserves mass per sequence, so their bulk fractions carry over. + target = _library([ + ("single-1", "wt", 2), + ("single-1", "M42I", 1), + ("single-1", "M42V", 2), # 5 sequences (ref 10) + ("double-1-2", "wt", 4), + ("double-1-2", "M42I", 6), + ("double-1-2", "M42V/H74A", 40), # 50 sequences (ref 100) + ("spiked", "wt", 1), + ("spiked", "M42I", 1), + ("spiked", "H74A/K84L", 1), + ]) + mixture = {"single-1": 100, "double-1-2": 1000, "spiked": 1} + sizes = {"single-1": 1, "double-1-2": 1, "spiked": 1} + scaled = scale_library_design(reference_library, target, mixture, sizes) + + ref = expected_library_composition(reference_library, mixture).set_index("genotype") + tgt = expected_library_composition(target, scaled["library_mixture"]).set_index("genotype") + + for g in ("wt", "M42I", "H74A/K84L"): + assert tgt.loc[g, "bulk_fraction"] == pytest.approx(ref.loc[g, "bulk_fraction"]) + + # Copying the reference mixture unscaled would not preserve them. + naive = expected_library_composition(target, mixture).set_index("genotype") + assert naive.loc["M42I", "bulk_fraction"] != pytest.approx(ref.loc["M42I", "bulk_fraction"]) + + def test_optional_totals(self, reference_library, target_library): + out = scale_library_design(reference_library, target_library, + {"single-1": 1, "double-1-2": 1, "spiked": 1}, + {"single-1": 1, "double-1-2": 1, "spiked": 1}) + assert out["cfu0"] is None + assert out["total_num_reads"] is None + # Tiny scaled transform sizes are floored at one transformant. + assert min(out["transform_sizes"].values()) >= 1 + + def test_origins_must_match(self, reference_library, target_library): + bad = target_library[target_library["library_origin"] != "double-1-2"] + with pytest.raises(ValueError, match="same origins"): + scale_library_design(reference_library, bad, + {"single-1": 1, "double-1-2": 1, "spiked": 1}, + {"single-1": 1, "double-1-2": 1, "spiked": 1}) + with pytest.raises(ValueError, match="transform_sizes"): + scale_library_design(reference_library, target_library, + {"single-1": 1, "double-1-2": 1, "spiked": 1}, + {"single-1": 1, "spiked": 1}) + + def test_needs_degeneracy(self, reference_library, target_library): + with pytest.raises(ValueError, match="degeneracy"): + scale_library_design(reference_library.drop(columns="degeneracy"), + target_library, + {"single-1": 1, "double-1-2": 1, "spiked": 1}, + {"single-1": 1, "double-1-2": 1, "spiked": 1}) + + +class TestEstimateLibraryMixture: + + @pytest.fixture + def library(self): + # Two tiles: singles in each, cross-tile doubles, and spikes. + return _library([ + ("single-1", "wt", 2), ("single-1", "A1V", 3), ("single-1", "A1G", 5), + ("single-2", "wt", 1), ("single-2", "B2V", 4), ("single-2", "B2G", 5), + ("double-1-2", "wt", 2), ("double-1-2", "A1V", 3), ("double-1-2", "B2V", 4), + ("double-1-2", "A1V/B2V", 6), ("double-1-2", "A1G/B2G", 5), + ("spiked", "wt", 1), ("spiked", "A1V", 1), ("spiked", "C3D", 1), + ]) + + def _expected_abundance(self, library, mixture, total=1e6): + comp = expected_library_composition(library, mixture) + return pd.Series(comp["pool_fraction"].to_numpy() * total, + index=comp["genotype"].to_numpy()) + + def test_recovers_mixture_from_expected_abundance(self, library): + truth = {"single-1": 400, "single-2": 550, "double-1-2": 1000, "spiked": 20} + observed = self._expected_abundance(library, truth) + mixture, groups, unexplained = estimate_library_mixture(library, observed) + total = sum(truth.values()) + for k, v in truth.items(): + assert mixture[k] == pytest.approx(v / total, rel=1e-6) + assert unexplained == 0.0 + assert groups["fitted_share"].to_numpy() == pytest.approx( + groups["observed_share"].to_numpy()) + + def test_wt_excess_is_ignored_by_default(self, library): + truth = {"single-1": 1, "single-2": 1, "double-1-2": 2, "spiked": 0.5} + observed = self._expected_abundance(library, truth) + observed["wt"] *= 50.0 + mixture, _, _ = estimate_library_mixture(library, observed) + total = sum(truth.values()) + for k, v in truth.items(): + assert mixture[k] == pytest.approx(v / total, rel=1e-6) + # Including wt distorts the estimate. + biased, _, _ = estimate_library_mixture(library, observed, exclude_genotypes=()) + assert biased["single-1"] != pytest.approx(truth["single-1"] / total, rel=1e-3) + + def test_undesigned_genotypes_reported_not_fit(self, library): + truth = {"single-1": 1, "single-2": 1, "double-1-2": 2, "spiked": 0.5} + observed = self._expected_abundance(library, truth) + design_total = observed.sum() + observed["A1V/A1G"] = design_total / 9.0 # 10% of the new total + mixture, _, unexplained = estimate_library_mixture(library, observed) + assert unexplained == pytest.approx(0.1) + assert mixture["double-1-2"] == pytest.approx(2 / 4.5, rel=1e-6) + + def test_absent_genotypes_count_as_zero_and_dataframe_input(self, library): + truth = {"single-1": 1, "single-2": 1, "double-1-2": 2, "spiked": 0.0} + observed = self._expected_abundance(library, truth) + observed = observed[observed > 0] # spike-only genotype missing + df = observed.rename("abundance").rename_axis("genotype").reset_index() + mixture, _, _ = estimate_library_mixture(library, df) + assert mixture["spiked"] == pytest.approx(0.0, abs=1e-12) + assert mixture["double-1-2"] == pytest.approx(0.5, rel=1e-6) + + def test_validation(self, library): + good = pd.Series({"A1V": 1.0, "B2V": 1.0}) + with pytest.raises(ValueError, match="weight"): + estimate_library_mixture(library.drop(columns="weight"), good) + with pytest.raises(ValueError, match="abundance"): + estimate_library_mixture(library, pd.DataFrame({"genotype": ["A1V"]})) + with pytest.raises(ValueError, match="non-negative"): + estimate_library_mixture(library, pd.Series({"A1V": -1.0})) + with pytest.raises(ValueError, match="duplicate"): + estimate_library_mixture(library, pd.Series([1.0, 2.0], index=["A1V", "A1V"])) + with pytest.raises(ValueError, match="sum to zero"): + estimate_library_mixture(library, pd.Series({"A1V": 0.0})) + with pytest.raises(ValueError, match="No observed abundance"): + estimate_library_mixture(library, pd.Series({"wt": 5.0})) diff --git a/tests/tfscreen/process_raw/test_counts_to_lncfu.py b/tests/tfscreen/process_raw/test_counts_to_lncfu.py index 623fd058..b11a5ab2 100644 --- a/tests/tfscreen/process_raw/test_counts_to_lncfu.py +++ b/tests/tfscreen/process_raw/test_counts_to_lncfu.py @@ -10,6 +10,7 @@ _impute_missing_genotypes, _calculate_frequencies, _calculate_concentrations_and_variance, + get_sample_ln_cfu, counts_to_lncfu ) @@ -151,8 +152,8 @@ def test_calculate_concentrations_and_variance(): df = pd.DataFrame({ 'sample': ['s1'], 'frequency': [0.9], - 'sample_cfu': [1e8], # Original sample-level data - 'sample_cfu_std': [1e7], # Original sample-level data + 'sample_ln_cfu': [np.log(1e8)], # Original sample-level data + 'sample_ln_cfu_std': [0.1], # = 1e7/1e8 'adjusted_counts': [91] }) # The Sigma x + b denominator is now supplied explicitly (the sample had a @@ -180,10 +181,14 @@ def test_calculate_concentrations_and_variance(): assert np.isclose(result['cfu'].iloc[0], expected_genotype_cfu) assert np.isclose(result['cfu_var'].iloc[0], expected_genotype_var) - # FIX: Check that the RENAMED columns contain the ORIGINAL sample data - assert 'ln_cfu' in result.columns - assert 'ln_cfu_var' in result.columns - assert np.isclose(result['sample_cfu'].iloc[0], sample_cfu) + # Log-space values: ln_cfu = ln(freq) + sample_ln_cfu, and ln_cfu_var is + # the summed relative variance + assert np.isclose(result['ln_cfu'].iloc[0], np.log(freq * sample_cfu)) + assert np.isclose(result['ln_cfu_var'].iloc[0], + rel_var_freq + rel_var_sample_cfu) + + # Sample-level data is preserved + assert np.isclose(result['sample_ln_cfu'].iloc[0], np.log(sample_cfu)) def test_calculate_concentrations_zero_cfu(): @@ -194,8 +199,8 @@ def test_calculate_concentrations_zero_cfu(): df = pd.DataFrame({ 'sample': ['s1'], 'frequency': [0.0], - 'sample_cfu': [1e8], - 'sample_cfu_std': [1e7], + 'sample_ln_cfu': [np.log(1e8)], + 'sample_ln_cfu_std': [0.1], 'adjusted_counts': [100] }) total_counts_per_sample = pd.Series({'s1': 100}) @@ -318,3 +323,81 @@ def test_counts_to_lncfu_all_filtered(sample_df, counts_df, mocker): # Set min_obs so high that all genotypes are removed result = counts_to_lncfu(sample_df, counts_df, min_genotype_obs=1000) assert result.empty + + +# ---- Tests for sample ln_cfu inference ---- + +def test_get_sample_ln_cfu_from_linear(): + """sample_ln_cfu/_std are inferred from sample_cfu/_std.""" + df = pd.DataFrame({'sample_cfu': [1e8, 2e7], + 'sample_cfu_std': [1e7, 4e6]}, + index=pd.Index(['s1', 's2'], name='sample')) + result = get_sample_ln_cfu(df) + np.testing.assert_allclose(result['sample_ln_cfu'], np.log([1e8, 2e7])) + np.testing.assert_allclose(result['sample_ln_cfu_std'], [0.1, 0.2]) + # Original columns kept + assert 'sample_cfu' in result.columns + + +def test_get_sample_ln_cfu_from_ln_var(): + """sample_ln_cfu_std is inferred from sample_ln_cfu_var.""" + df = pd.DataFrame({'sample_ln_cfu': [18.0], + 'sample_ln_cfu_var': [0.04]}, + index=pd.Index(['s1'], name='sample')) + result = get_sample_ln_cfu(df) + np.testing.assert_allclose(result['sample_ln_cfu_std'], [0.2]) + + +def test_get_sample_ln_cfu_log_space_wins(): + """When log-space columns exist, linear-space columns are not used.""" + df = pd.DataFrame({'sample_ln_cfu': [18.0], + 'sample_ln_cfu_std': [0.3], + 'sample_cfu': [1e8], + 'sample_cfu_std': [1e7]}, + index=pd.Index(['s1'], name='sample')) + result = get_sample_ln_cfu(df) + assert result['sample_ln_cfu'].iloc[0] == 18.0 + assert result['sample_ln_cfu_std'].iloc[0] == 0.3 + + +def test_get_sample_ln_cfu_ignores_unprefixed_columns(): + """Unprefixed cfu columns must not be used to infer sample columns.""" + df = pd.DataFrame({'sample_cfu': [1e8], + 'cfu_std': [1e7]}, + index=pd.Index(['s1'], name='sample')) + with pytest.raises(ValueError, match="sample_ln_cfu_std"): + get_sample_ln_cfu(df) + + +@pytest.mark.parametrize("cols", [ + {}, + {'sample_cfu': [1e8]}, + {'sample_cfu_std': [1e7]}, + {'sample_ln_cfu': [18.0]}, +]) +def test_get_sample_ln_cfu_insufficient(cols): + df = pd.DataFrame({'library': ['libA'], **cols}, + index=pd.Index(['s1'], name='sample')) + with pytest.raises(ValueError, match="sample_df must give"): + get_sample_ln_cfu(df) + + +def test_counts_to_lncfu_log_and_linear_inputs_agree(sample_df, counts_df, mocker): + """Supplying sample_ln_cfu/_std gives the same result as sample_cfu/_std.""" + mocker.patch('tfscreen.process_raw.counts_to_lncfu.read_dataframe', + side_effect=lambda df, **kwargs: df.copy()) + mocker.patch( + 'tfscreen.process_raw.counts_to_lncfu.set_categorical_genotype', + side_effect=lambda df, standardize, sort: df.sort_values("genotype") + ) + + lin = counts_to_lncfu(sample_df, counts_df) + + ln_sample_df = sample_df.drop(columns=['sample_cfu', 'sample_cfu_std']) + ln_sample_df['sample_ln_cfu'] = np.log(sample_df['sample_cfu']) + ln_sample_df['sample_ln_cfu_std'] = (sample_df['sample_cfu_std'] / + sample_df['sample_cfu']) + log = counts_to_lncfu(ln_sample_df, counts_df) + + for col in ['ln_cfu', 'ln_cfu_var', 'cfu', 'cfu_var']: + np.testing.assert_allclose(log[col], lin[col]) diff --git a/tests/tfscreen/process_raw/test_process_counts_cli.py b/tests/tfscreen/process_raw/test_process_counts_cli.py index cda97b65..b7810643 100644 --- a/tests/tfscreen/process_raw/test_process_counts_cli.py +++ b/tests/tfscreen/process_raw/test_process_counts_cli.py @@ -49,10 +49,17 @@ def test_process_counts_orchestration( ) mock_prep.assert_called_once_with(fx_sample_df, "/counts/path", "test_prefix", False) - mock_agg.assert_called_once_with(df_prepped) - mock_lncfu.assert_called_once_with( - df_prepped, df_aggregated, min_genotype_obs=20, pseudocount=2 - ) + # sample_ln_cfu/_std are inferred before counts are aggregated + mock_agg.assert_called_once() + handed_off = mock_agg.call_args.args[0] + assert {"sample_ln_cfu", "sample_ln_cfu_std"} <= set(handed_off.columns) + pd.testing.assert_frame_equal(handed_off[df_prepped.columns], df_prepped) + + mock_lncfu.assert_called_once() + args, kwargs = mock_lncfu.call_args + assert args[0] is handed_off + assert args[1] is df_aggregated + assert kwargs == {"min_genotype_obs": 20, "pseudocount": 2} mock_to_csv.assert_called_once_with("/out/final.csv", index=False) @@ -67,7 +74,7 @@ def test_process_counts_missing_cfu_columns(tmp_path): prepped["obs_file"] = "dummy.csv" with patch('tfscreen.process_raw.scripts.process_counts_cli._prep_sample_df', return_value=prepped): - with pytest.raises(ValueError, match="Not all required columns seen"): + with pytest.raises(ValueError, match="sample_ln_cfu_std"): process_counts( sample_df=bad_df, counts_csv_path=str(tmp_path), diff --git a/tests/tfscreen/process_raw/test_process_presplit_cli.py b/tests/tfscreen/process_raw/test_process_presplit_cli.py index 2c0b9f4c..6746e362 100644 --- a/tests/tfscreen/process_raw/test_process_presplit_cli.py +++ b/tests/tfscreen/process_raw/test_process_presplit_cli.py @@ -189,7 +189,7 @@ def test_process_presplit_missing_cfu_column(tmp_path, fx_sample_df): with patch('tfscreen.process_raw.scripts.process_presplit_cli._prep_sample_df', return_value=prepped): - with pytest.raises(ValueError, match="Not all required columns seen"): + with pytest.raises(ValueError, match="sample_ln_cfu_std"): process_presplit( sample_df=bad_df, counts_csv_path=str(tmp_path), diff --git a/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py b/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py index bb8b57bd..a04e0dcd 100644 --- a/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py +++ b/tests/tfscreen/simulate/empirical/test_build_empirical_cli.py @@ -2,6 +2,7 @@ import numpy as np import pandas as pd +import yaml import pytest from tfscreen.simulate.empirical.fit_phenotypes import _hill_theta @@ -134,12 +135,25 @@ def fake_configure(**kwargs): prefit = mocker.patch( "tfscreen.tfmodel.scripts.prefit_calibration_cli.run_prefit_calibration") - spiked_file = tmp_path / "spiked.txt" - spiked_file.write_text("wt\nA1V\n") + # Library with residues 1-2 degenerate; wt and A1V are the spikes. + library_config = tmp_path / "library.yaml" + with open(library_config, "w") as f: + yaml.dump({ + "reading_frame": 0, + "first_amplicon_residue": 1, + "wt_seq": "gccgcaaaaccggaatgc", + "degen_sites": "nntnnt............", + "tiles": "111222............", + "tile_combos": ["single-1", "single-2", "double-1-2"], + "spiked_seqs": ["..................", # wt + "gtt..............."], # A1V + "library_mixture": {"single-1": 10, "single-2": 10, + "double-1-2": 100, "spiked": 1}, + }, f) build_empirical( str(growth_csv), binding_file=str(binding_csv), out_prefix=out_prefix, - spiked_file=str(spiked_file), seed=5) + library_config=str(library_config), seed=5) # configure_model wired with the experimental inputs and fixed prefix. conf.assert_called_once() @@ -147,7 +161,7 @@ def fake_configure(**kwargs): assert ckw["binding_df"] == str(binding_csv) assert ckw["growth_df"] == str(growth_csv) assert ckw["out_prefix"] == f"{out_prefix}_configure" - assert ckw["spiked"] == ["wt", "A1V"] + assert ckw["library_config"] == str(library_config) # prefit called on the produced config with the seed. prefit.assert_called_once() diff --git a/tests/tfscreen/tfmodel/analysis/test_prediction.py b/tests/tfscreen/tfmodel/analysis/test_prediction.py index 5458267b..40f2a725 100644 --- a/tests/tfscreen/tfmodel/analysis/test_prediction.py +++ b/tests/tfscreen/tfmodel/analysis/test_prediction.py @@ -15,6 +15,17 @@ predict, ) + +def _feasible_draw(site): + """ + One-draw fake posterior value for a traced sample site: zeros for + real-support sites, a valid in-support value (e.g. ones) for constrained + ones. Plain zeros put positive-support sites (noise sigmas, scales) on + the boundary, which numpyro >= 0.20 rejects as an invalid scale. + """ + value = site["fn"].support.feasible_like(site["value"]) + return np.asarray(value)[None, ...] + @pytest.fixture def dummy_orchestrator(): """Create a dummy ModelOrchestrator instance for testing.""" @@ -489,7 +500,7 @@ def __call__(self, rng_key, **kwargs): priors=dummy_orchestrator.priors, ) fake_posteriors = { - name: np.zeros((1,) + site["value"].shape) + name: _feasible_draw(site) for name, site in model_tr.items() if site["type"] == "sample" and not site.get("is_observed", False) } @@ -599,7 +610,7 @@ def _fake_posteriors_with_theta_growth_pred(self, orchestrator): priors=orchestrator.priors, ) fake_posteriors = { - name: np.zeros((1,) + site["value"].shape) + name: _feasible_draw(site) for name, site in model_tr.items() if site["type"] == "sample" and not site.get("is_observed", False) } @@ -672,7 +683,7 @@ def test_no_population_reference_when_transformation_does_not_need_one( data=single_orchestrator.data, priors=single_orchestrator.priors, ) fake_posteriors = { - name: np.zeros((1,) + site["value"].shape) + name: _feasible_draw(site) for name, site in model_tr.items() if site["type"] == "sample" and not site.get("is_observed", False) } @@ -743,7 +754,7 @@ def _fake_posteriors(self, orchestrator, condition_growth_k_values): data=orchestrator.data, priors=orchestrator.priors, ) fake_posteriors = { - name: np.zeros((1,) + site["value"].shape) + name: _feasible_draw(site) for name, site in model_tr.items() if site["type"] == "sample" and not site.get("is_observed", False) } diff --git a/tests/tfscreen/tfmodel/generative/test_loglikelihood.py b/tests/tfscreen/tfmodel/generative/test_loglikelihood.py index 82b0598c..2683ffb4 100644 --- a/tests/tfscreen/tfmodel/generative/test_loglikelihood.py +++ b/tests/tfscreen/tfmodel/generative/test_loglikelihood.py @@ -279,11 +279,17 @@ def test_normal_at_loc(self): expected = -0.5 * math.log(2 * math.pi) - math.log(0.05) npt.assert_allclose(lp, expected, rtol=1e-5) - def test_half_normal_at_zero(self): - """HalfNormal(scale).log_prob(0) = log(2) - log(scale) - 0.5*log(2*pi).""" - lp = float(dist.HalfNormal(1.0).log_prob(jnp.array(0.0))) + def test_half_normal_known_value(self): + """HalfNormal(s).log_prob(x) = log(2) - log(s) - 0.5*log(2*pi) - x²/(2s²). + + Evaluated at x > 0: numpyro >= 0.20 treats the support as open, so + log_prob(0) is -inf rather than the x→0 limit. + """ + x, s = 0.3, 1.5 + lp = float(dist.HalfNormal(s).log_prob(jnp.array(x))) import math - expected = math.log(2) - math.log(1.0) - 0.5 * math.log(2 * math.pi) + expected = (math.log(2) - math.log(s) - 0.5 * math.log(2 * math.pi) + - x**2 / (2 * s**2)) npt.assert_allclose(lp, expected, rtol=1e-5) def test_gamma_known_value(self): diff --git a/tests/tfscreen/tfmodel/genotype_fit/test_fit_genotypes_cli.py b/tests/tfscreen/tfmodel/genotype_fit/test_fit_genotypes_cli.py index c7b964ba..5c4dd064 100644 --- a/tests/tfscreen/tfmodel/genotype_fit/test_fit_genotypes_cli.py +++ b/tests/tfscreen/tfmodel/genotype_fit/test_fit_genotypes_cli.py @@ -54,6 +54,28 @@ def paths(tmp_path): return str(growth), str(calib), tmp_path +@pytest.fixture +def library_config(tmp_path): + """Library YAML covering wt/A1V/A2V, with wt as the only spiked genotype.""" + import yaml + + config = { + "reading_frame": 0, + "first_amplicon_residue": 1, + "wt_seq": "gccgcaaaaccggaatgc", + "degen_sites": "nntnnt............", + "tiles": "111222............", + "tile_combos": ["single-1", "single-2", "double-1-2"], + "spiked_seqs": [".................."], # wt only + "library_mixture": {"single-1": 10, "single-2": 10, + "double-1-2": 100, "spiked": 1}, + } + path = tmp_path / "library.yaml" + with open(path, "w") as f: + yaml.dump(config, f) + return str(path) + + def test_raw_only_writes_params_and_theta(paths): growth, calib, tmp_path = paths prefix = str(tmp_path / "run") @@ -78,14 +100,12 @@ def test_raw_only_writes_params_and_theta(paths): assert res.loc[geno, "theta_low"] == pytest.approx(p["theta_low"], abs=2e-3) -def test_congression_writes_deattenuated_and_history(paths): +def test_congression_writes_deattenuated_and_history(paths, library_config): growth, calib, tmp_path = paths - spiked = tmp_path / "spiked.txt" - spiked.write_text("wt\n") prefix = str(tmp_path / "run") fit_genotypes(growth, calib, out_prefix=prefix, dk_geno_prior_sd=0.0, - congression_lambda=1.0, spiked_file=str(spiked), + congression_lambda=1.0, library_config=library_config, save_theta_history=True) deatt = pd.read_csv(f"{prefix}_params_deattenuated.csv") @@ -109,14 +129,12 @@ def test_congression_writes_deattenuated_and_history(paths): assert history["iter"].max() >= 1 -def test_congression_without_history_skips_history_file(paths): +def test_congression_without_history_skips_history_file(paths, library_config): growth, calib, tmp_path = paths - spiked = tmp_path / "spiked.txt" - spiked.write_text("wt\n") prefix = str(tmp_path / "run") fit_genotypes(growth, calib, out_prefix=prefix, dk_geno_prior_sd=0.0, - congression_lambda=1.0, spiked_file=str(spiked)) + congression_lambda=1.0, library_config=library_config) assert (tmp_path / "run_params_deattenuated.csv").exists() assert not (tmp_path / "run_theta_history.csv").exists() diff --git a/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py b/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py index c5a735b7..b72a573e 100644 --- a/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py +++ b/tests/tfscreen/tfmodel/scripts/test_configure_and_run.py @@ -50,9 +50,37 @@ def mock_orchestrator(mocker): "ln_cfu0": pd.DataFrame({"replicate": ["R1"], "condition_pre": ["CP1"], "genotype": ["G1"], "map_ln_cfu0": [0]}) } mock_orchestrator_inst.growth_tm = mock_tm - + return mock_orchestrator_class, mock_orchestrator_inst + +@pytest.fixture(autouse=True) +def mock_library(mocker): + """ + Stub out library resolution for the wiring tests in this module. + + These tests hand configure_model paths to files that do not exist and mock + ModelOrchestrator, so they cannot build (or check against) a real library. + The real library path -- composition table, snapshot, content check -- is + covered end to end in tests/tfscreen/tfmodel/test_library_file.py. + """ + composition = pd.DataFrame({"genotype": ["wt"], + "is_wt": [True], + "in_spiked_origin": [False], + "pool_fraction": [1.0], + "bulk_fraction": [1.0], + "origins": ["single-1"]}) + mocker.patch( + "tfscreen.tfmodel.scripts.configure_model_cli.library_composition_table", + return_value=composition) + mocker.patch( + "tfscreen.tfmodel.scripts.configure_model_cli.write_library_composition") + mocker.patch( + "tfscreen.tfmodel.scripts.configure_model_cli.check_genotypes_in_library") + mocker.patch( + "tfscreen.tfmodel.scripts.configure_model_cli.read_yaml", + return_value={"library_mixture": {"single-1": 1}}) + def test_configure_growth_analysis_coverage(mock_orchestrator, tmpdir): _, mock_orchestrator_inst = mock_orchestrator out_prefix = os.path.join(tmpdir, "test") @@ -81,7 +109,7 @@ def test_configure_growth_analysis_coverage(mock_orchestrator, tmpdir): "unknown_3d": np.zeros((2, 2, 2)) # 3D } - configure_model("b.csv", growth_df="g.csv", out_prefix=out_prefix, + configure_model("b.csv", growth_df="g.csv", library_config="lib.yaml", out_prefix=out_prefix, skip_model_stats=True) assert os.path.exists(f"{out_prefix}_config.yaml") @@ -105,6 +133,7 @@ def test_configure_model_passes_base_growth_df_to_orchestrator_and_config(mock_o out_prefix = os.path.join(tmpdir, "test") configure_model("b.csv", growth_df="g.csv", base_growth_df="bg.csv", + library_config="lib.yaml", out_prefix=out_prefix, skip_model_stats=True) assert mock_orchestrator_class.call_args.kwargs["base_growth_df"] == "bg.csv" @@ -120,7 +149,7 @@ def test_configure_model_requires_transformation_lambda_for_empirical(mock_orche out_prefix = os.path.join(tmpdir, "test") with pytest.raises(ValueError, match="transformation_lambda"): configure_model( - "b.csv", growth_df="g.csv", + "b.csv", growth_df="g.csv", library_config="lib.yaml", transformation_model="empirical", out_prefix=out_prefix, ) @@ -129,7 +158,7 @@ def test_configure_model_requires_transformation_lambda_for_empirical(mock_orche def test_configure_model_allows_single_without_transformation_lambda(mock_orchestrator, tmpdir): """transformation_model='single' (the default) never requires transformation_lambda.""" out_prefix = os.path.join(tmpdir, "test") - configure_model("b.csv", growth_df="g.csv", out_prefix=out_prefix, + configure_model("b.csv", growth_df="g.csv", library_config="lib.yaml", out_prefix=out_prefix, skip_model_stats=True) assert os.path.exists(f"{out_prefix}_config.yaml") @@ -139,7 +168,7 @@ def test_configure_model_forwards_transformation_lambda_to_orchestrator(mock_orc out_prefix = os.path.join(tmpdir, "test") configure_model( - "b.csv", growth_df="g.csv", + "b.csv", growth_df="g.csv", library_config="lib.yaml", transformation_model="empirical", transformation_lambda=(0.3572, 0.13), out_prefix=out_prefix, @@ -155,7 +184,7 @@ def test_configure_model_omits_base_growth_when_not_given(mock_orchestrator, tmp mock_orchestrator_class, mock_orchestrator_inst = mock_orchestrator out_prefix = os.path.join(tmpdir, "test") - configure_model("b.csv", growth_df="g.csv", out_prefix=out_prefix, + configure_model("b.csv", growth_df="g.csv", library_config="lib.yaml", out_prefix=out_prefix, skip_model_stats=True) assert mock_orchestrator_class.call_args.kwargs["base_growth_df"] is None diff --git a/tests/tfscreen/tfmodel/scripts/test_setup_grid_cli.py b/tests/tfscreen/tfmodel/scripts/test_setup_grid_cli.py index eb573e8d..cd37358f 100644 --- a/tests/tfscreen/tfmodel/scripts/test_setup_grid_cli.py +++ b/tests/tfscreen/tfmodel/scripts/test_setup_grid_cli.py @@ -241,10 +241,12 @@ def test_resolve_cm_paths_resolves_all_df_args(tmp_path): "growth_df": "g.csv", "presplit_df": "p.csv", "base_growth_df": "bg.csv", + "library_config": "library.yaml", "theta_model": "hill_mut", # not a path: untouched } out = _resolve_cm_paths(cm_vars, base) - for key in ("binding_df", "growth_df", "presplit_df", "base_growth_df"): + for key in ("binding_df", "growth_df", "presplit_df", "base_growth_df", + "library_config"): assert out[key] == os.path.normpath(os.path.join(base, cm_vars[key])) assert os.path.isabs(out[key]) assert out["theta_model"] == "hill_mut" diff --git a/tests/tfscreen/tfmodel/test_base_growth.py b/tests/tfscreen/tfmodel/test_base_growth.py index 724cc4ff..383d4e6d 100644 --- a/tests/tfscreen/tfmodel/test_base_growth.py +++ b/tests/tfscreen/tfmodel/test_base_growth.py @@ -52,6 +52,26 @@ def minimal_growth_df(): return pd.DataFrame(rows) +@pytest.fixture +def minimal_library_config(tmp_path): + """Library YAML containing wt, A1V and A2V (residues 1-2, both NNT).""" + import yaml as _yaml + + config = { + "reading_frame": 0, + "first_amplicon_residue": 1, + "wt_seq": "gccgcaaaaccggaatgc", + "degen_sites": "nntnnt............", + "tiles": "111222............", + "tile_combos": ["single-1", "single-2", "double-1-2"], + "library_mixture": {"single-1": 10, "single-2": 10, "double-1-2": 100}, + } + path = os.path.join(tmp_path, "library.yaml") + with open(path, "w") as f: + _yaml.dump(config, f) + return path + + @pytest.fixture def minimal_binding_df(): return pd.DataFrame({ @@ -163,7 +183,8 @@ def test_jax_model_guide_base_growth_k_ref_site_present(minimal_growth_df, def test_base_growth_obs_masks_genotypes_without_measurement(minimal_growth_df, minimal_binding_df, - minimal_base_growth_df): + minimal_base_growth_df, + minimal_library_config): """A2V has no base_growth measurement, so its base_growth_obs log_prob contribution must be exactly zero (fully masked out).""" orchestrator = ModelOrchestrator(minimal_growth_df, minimal_binding_df, @@ -193,7 +214,8 @@ def test_base_growth_obs_masks_genotypes_without_measurement(minimal_growth_df, def test_configure_model_to_read_configuration_round_trip(tmp_path, minimal_growth_df, minimal_binding_df, - minimal_base_growth_df): + minimal_base_growth_df, + minimal_library_config): """base_growth_df must survive the real tfs-configure-model -> YAML -> tfs-fit-model (read_configuration) round trip, ending up as a proper BaseGrowthData on the orchestrator rebuilt from the config file.""" @@ -207,6 +229,7 @@ def test_configure_model_to_read_configuration_round_trip(tmp_path, out_prefix = os.path.join(tmp_path, "tfs_configure") configure_model(binding_path, growth_df=growth_path, base_growth_df=base_growth_path, + library_config=minimal_library_config, out_prefix=out_prefix, theta_growth_noise_model="zero") diff --git a/tests/tfscreen/tfmodel/test_library_file.py b/tests/tfscreen/tfmodel/test_library_file.py new file mode 100644 index 00000000..b973ef36 --- /dev/null +++ b/tests/tfscreen/tfmodel/test_library_file.py @@ -0,0 +1,301 @@ +""" +Tests for the library-composition interface to ModelOrchestrator and +configure_model, which replaced the hand-supplied --spiked list. + +The gate on the whole change is TestEquivalence: a library file whose spiked +origin is {G} must produce exactly the masks the old spiked_genotypes=[G] +produced. +""" + +import os + +import numpy as np +import pandas as pd +import pytest +import yaml + +from tfscreen.genetics import library_composition_table, write_library_composition +from tfscreen.tfmodel.model_orchestrator import ModelOrchestrator +from tfscreen.tfmodel.configuration_io import write_configuration, read_configuration +from tfscreen.tfmodel.scripts.configure_model_cli import ( + configure_model, + check_genotypes_in_library, +) + + +GENOTYPES = ["wt", "A2L", "A2C"] + + +@pytest.fixture +def library_config_dict(): + """Tiny library: wt and A2L are spiked AND in the bulk; A2C is bulk only.""" + return { + "reading_frame": 0, + "first_amplicon_residue": 1, + "wt_seq": "atggcaaaaccggaatgc", + "degen_sites": "...nnt......nnt...", + "tiles": "...111......222...", + "tile_combos": ["single-1", "single-2", "double-1-2"], + "spiked_seqs": ["..................", # wt + "...ctt............"], # A2L + "library_mixture": {"single-1": 10, + "single-2": 10, + "double-1-2": 100, + "spiked": 1}, + } + + +@pytest.fixture +def library_config_file(library_config_dict, tmp_path): + path = tmp_path / "library.yaml" + with open(path, "w") as f: + yaml.dump(library_config_dict, f) + return str(path) + + +@pytest.fixture +def library_file(library_config_dict, tmp_path): + path = str(tmp_path / "tfs_library.csv") + write_library_composition(library_composition_table(library_config_dict), + path) + return path + + +def _growth_df(genotypes=GENOTYPES): + rows = [] + for g in genotypes: + for t in (0.0, 10.0): + rows.append({"library": "lib", + "replicate": 1, + "time": t, + "genotype": g, + "ln_cfu": 1.0, + "ln_cfu_std": 0.1, + "condition_pre": "pre-cond", + "condition_sel": "sel+cond", + "t_pre": 1.0, + "t_sel": 10.0, + "titrant_name": "iptg", + "titrant_conc": 0.0}) + return pd.DataFrame(rows) + + +def _binding_df(genotypes=GENOTYPES): + return pd.DataFrame([{"genotype": g, + "titrant_name": "iptg", + "titrant_conc": 0.0, + "theta_obs": 0.5, + "theta_std": 0.05} + for g in genotypes]) + + +def _masks(orchestrator): + idx = orchestrator.growth_tm.tensor_dim_names.index("genotype") + labels = list(orchestrator.growth_tm.tensor_dim_labels[idx]) + return (labels, + np.array(orchestrator.data.growth.congression_mask), + np.array(orchestrator.data.growth.ln_cfu0_spiked_mask)) + + +class TestEquivalence: + """library_file must reproduce the legacy spiked_genotypes behavior.""" + + def test_masks_match_legacy_spiked_list(self, library_file): + growth_df, binding_df = _growth_df(), _binding_df() + + legacy = ModelOrchestrator(growth_df, binding_df, + spiked_genotypes=["wt", "A2L"]) + from_library = ModelOrchestrator(growth_df, binding_df, + library_file=library_file) + + legacy_labels, legacy_cong, legacy_spiked = _masks(legacy) + lib_labels, lib_cong, lib_spiked = _masks(from_library) + + assert legacy_labels == lib_labels + np.testing.assert_array_equal(legacy_cong, lib_cong) + np.testing.assert_array_equal(legacy_spiked, lib_spiked) + + def test_spiked_genotypes_are_derived(self, library_file): + orchestrator = ModelOrchestrator(_growth_df(), _binding_df(), + library_file=library_file) + assert sorted(orchestrator.settings["spiked_genotypes"]) == ["A2L", "wt"] + assert orchestrator.settings["library_file"] == library_file + + def test_library_df_exposed(self, library_file): + orchestrator = ModelOrchestrator(_growth_df(), _binding_df(), + library_file=library_file) + table = orchestrator.library_df + # The whole library, not just the genotypes with growth data. + assert len(table) > len(GENOTYPES) + assert set(["pool_fraction", "bulk_fraction"]).issubset(table.columns) + + def test_no_library_file_leaves_everything_congressed(self): + orchestrator = ModelOrchestrator(_growth_df(), _binding_df()) + _, congression, spiked = _masks(orchestrator) + assert congression.all() + assert not spiked.any() + + +class TestSpikedGenotypesAbsentFromData: + """A library-derived spiked genotype with no growth data is not fatal.""" + + def test_absent_spike_is_reported_not_raised(self, library_file, capsys): + growth_df = _growth_df(["wt", "A2C"]) # A2L never observed + orchestrator = ModelOrchestrator(growth_df, _binding_df(["wt", "A2C"]), + library_file=library_file) + + assert orchestrator.settings["spiked_genotypes"] == ["wt"] + assert "A2L" in capsys.readouterr().out + + labels, congression, spiked = _masks(orchestrator) + assert not congression[labels.index("wt")] + assert congression[labels.index("A2C")] + + def test_legacy_list_still_raises(self): + with pytest.raises(ValueError, match="not found in the growth"): + ModelOrchestrator(_growth_df(["wt", "A2C"]), + _binding_df(["wt", "A2C"]), + spiked_genotypes=["A2L"]) + + +class TestMutualExclusion: + + def test_both_raises(self, library_file): + with pytest.raises(ValueError, match="only one"): + ModelOrchestrator(_growth_df(), _binding_df(), + spiked_genotypes=["wt"], + library_file=library_file) + + +class TestContentCheck: + + def test_passes_for_library_genotypes(self, library_config_dict): + table = library_composition_table(library_config_dict) + check_genotypes_in_library(set(table["genotype"]), _growth_df(), + "growth_df") + + def test_unknown_sentinel_ignored(self, library_config_dict): + table = library_composition_table(library_config_dict) + growth_df = _growth_df(["wt", "__unknown__"]) + check_genotypes_in_library(set(table["genotype"]), growth_df, + "growth_df") + + def test_undesigned_genotype_fails(self, library_config_dict): + table = library_composition_table(library_config_dict) + growth_df = _growth_df(["wt", "Q3W"]) + with pytest.raises(ValueError, match="Q3W"): + check_genotypes_in_library(set(table["genotype"]), growth_df, + "growth_df") + + def test_numbering_shift_fails(self, library_config_dict): + """The presplit failure mode: residue numbering off by one.""" + table = library_composition_table(library_config_dict) + # Same mutations, every residue number one lower. + growth_df = _growth_df(["A1L", "A1C"]) + with pytest.raises(ValueError, match="not in the library"): + check_genotypes_in_library(set(table["genotype"]), growth_df, + "growth_df") + + +class TestConfigureModel: + + def _configure(self, tmp_path, library_config_file, **kwargs): + growth_path = str(tmp_path / "growth.csv") + binding_path = str(tmp_path / "binding.csv") + _growth_df().to_csv(growth_path, index=False) + _binding_df().to_csv(binding_path, index=False) + + out_prefix = str(tmp_path / "tfs_configure") + configure_model(binding_df=binding_path, + growth_df=growth_path, + library_config=library_config_file, + out_prefix=out_prefix, + skip_model_stats=True, + **kwargs) + return out_prefix + + def test_writes_snapshot_and_records_it(self, tmp_path, library_config_file): + out_prefix = self._configure(tmp_path, library_config_file) + + library_path = f"{out_prefix}_library.csv" + assert os.path.exists(library_path) + + with open(f"{out_prefix}_config.yaml") as f: + config = yaml.safe_load(f) + + assert config["library_file"] == os.path.basename(library_path) + assert config["library"]["source"] == library_config_file + assert config["library"]["library_mixture"]["spiked"] == 1 + # One source of truth: the derived list is not also written out. + assert "spiked_genotypes" not in config["components"] + + def test_round_trip_reproduces_masks(self, tmp_path, library_config_file): + out_prefix = self._configure(tmp_path, library_config_file) + orchestrator, _ = read_configuration(f"{out_prefix}_config.yaml") + assert sorted(orchestrator.settings["spiked_genotypes"]) == ["A2L", "wt"] + _, congression, spiked = _masks(orchestrator) + assert spiked.any() + assert not congression.all() + + def test_requires_library_config_with_growth(self, tmp_path): + growth_path = str(tmp_path / "growth.csv") + binding_path = str(tmp_path / "binding.csv") + _growth_df().to_csv(growth_path, index=False) + _binding_df().to_csv(binding_path, index=False) + + with pytest.raises(ValueError, match="library_config is required"): + configure_model(binding_df=binding_path, + growth_df=growth_path, + out_prefix=str(tmp_path / "tfs_configure"), + skip_model_stats=True) + + def test_binding_only_rejects_library_config(self, tmp_path, + library_config_file): + binding_path = str(tmp_path / "binding.csv") + _binding_df().to_csv(binding_path, index=False) + + with pytest.raises(ValueError, match="binding-only"): + configure_model(binding_df=binding_path, + library_config=library_config_file, + out_prefix=str(tmp_path / "tfs_configure"), + skip_model_stats=True) + + def test_undesigned_genotype_fails_configure(self, tmp_path, + library_config_file): + growth_path = str(tmp_path / "growth.csv") + binding_path = str(tmp_path / "binding.csv") + _growth_df(["wt", "Q3W"]).to_csv(growth_path, index=False) + _binding_df(["wt", "Q3W"]).to_csv(binding_path, index=False) + + with pytest.raises(ValueError, match="growth_df"): + configure_model(binding_df=binding_path, + growth_df=growth_path, + library_config=library_config_file, + out_prefix=str(tmp_path / "tfs_configure"), + skip_model_stats=True) + + +class TestLegacyConfig: + + def test_config_with_spiked_genotypes_still_loads(self, tmp_path): + """Configs written before this change must keep working.""" + growth_path = str(tmp_path / "growth.csv") + binding_path = str(tmp_path / "binding.csv") + _growth_df().to_csv(growth_path, index=False) + _binding_df().to_csv(binding_path, index=False) + + orchestrator = ModelOrchestrator(growth_path, binding_path, + spiked_genotypes=["wt", "A2L"]) + out_prefix = str(tmp_path / "legacy") + write_configuration(orchestrator=orchestrator, + out_prefix=out_prefix, + growth_df_path=growth_path, + binding_df_path=binding_path) + + with open(f"{out_prefix}_config.yaml") as f: + config = yaml.safe_load(f) + assert config["components"]["spiked_genotypes"] == ["wt", "A2L"] + assert "library_file" not in config + + reloaded, _ = read_configuration(f"{out_prefix}_config.yaml") + assert reloaded.settings["spiked_genotypes"] == ["wt", "A2L"] diff --git a/tests/tfscreen/tfmodel/test_model_orchestrator.py b/tests/tfscreen/tfmodel/test_model_orchestrator.py index f32b4506..5b992b1d 100644 --- a/tests/tfscreen/tfmodel/test_model_orchestrator.py +++ b/tests/tfscreen/tfmodel/test_model_orchestrator.py @@ -926,6 +926,7 @@ def test_model_class_properties(initialized_model_class): model._growth_noise = "grn" model._sample_offset = "so" model._spiked_genotypes = ["s"] + model._library_file = None model._binding_only = False model._growth_shares_replicates = False model._epistasis = True diff --git a/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py b/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py index 1910a4b7..02c5cbe3 100644 --- a/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py +++ b/tests/tfscreen/util/dataframe/test_get_scaled_cfu.py @@ -143,4 +143,30 @@ def test_already_present_columns_returns_original_df(): # --- FIX is here: Assert 'is' not 'is not' --- assert result_df is df - pd.testing.assert_frame_equal(result_df, df) \ No newline at end of file + pd.testing.assert_frame_equal(result_df, df) + +def test_prefix_infers_prefixed_columns(): + """With a prefix, only prefixed columns are read and written.""" + df = pd.DataFrame({'sample_cfu': [100.0], 'sample_cfu_std': [10.0], + 'cfu': [5.0], 'other': [1]}) + result = get_scaled_cfu(df, need_columns=['ln_cfu', 'ln_cfu_std'], + prefix='sample_') + assert np.isclose(result['sample_ln_cfu'].iloc[0], np.log(100)) + assert np.isclose(result['sample_ln_cfu_std'].iloc[0], 0.1) + # Unprefixed columns untouched and no unprefixed columns added + assert 'ln_cfu' not in result.columns + assert result['cfu'].iloc[0] == 5.0 + assert result['other'].iloc[0] == 1 + + +def test_prefix_present_returns_original_df(): + df = pd.DataFrame({'sample_ln_cfu': [1.0], 'sample_ln_cfu_std': [0.1]}) + result = get_scaled_cfu(df, need_columns=['ln_cfu', 'ln_cfu_std'], + prefix='sample_') + assert result is df + + +def test_prefix_insufficient_names_prefixed_columns(): + df = pd.DataFrame({'sample_cfu': [100.0], 'cfu_std': [10.0]}) + with pytest.raises(ValueError, match="sample_ln_cfu_std"): + get_scaled_cfu(df, need_columns=['ln_cfu_std'], prefix='sample_') diff --git a/wipe.sh b/wipe.sh index 394d53ea..9bd5548e 100644 --- a/wipe.sh +++ b/wipe.sh @@ -1,4 +1,5 @@ rm -rf ~/miniconda3/lib/python3.13/site-packages/tfscreen* rm -rf ~/miniconda3/bin/tfs-* rm -rf build/ +rm -f ~/miniconda3/lib/python3.13/site-packages/__editable__.tfscreen-*.pth for x in `find . -iname "__pycache__"`; do rm -rf $x; done