From fdcaaf65201c3657f93c2aeb8bda999a690195f0 Mon Sep 17 00:00:00 2001 From: Marius1311 Date: Thu, 8 Oct 2026 16:13:36 +0200 Subject: [PATCH 1/4] Adopt the analysis-workflow plugin; commit notebook outputs; zarr - Enable the analysis-workflow plugin in .claude/settings.json and depend on its package; FilePaths.ROOT comes from its main_checkout(). - Notebook outputs are committed: drop the nbstripout filter, its install step and CI check. - Examples write AnnData zarr; *.zarr ignored. - data//results/ is a notebook's own outputs; data/ ignored except READMEs. - Task-output rules in .gitignore; REVIEW_GUIDE.md (generic part from the plugin). - AGENTS.md points at the plugin instead of restating conventions. The lock file is regenerated once analysis-workflow v0.1.0 is tagged. Co-Authored-By: Claude Opus 5.5 --- .claude/settings.json | 24 +++++ .gitattributes | 4 - .github/workflows/lint.yaml | 2 - .gitignore | 17 +++- AGENTS.md | 43 ++++----- README.md | 45 ++++++---- REVIEW_GUIDE.md | 90 +++++++++++++++++++ .../ML-2026-01-27_demo_scRNA_workflow.ipynb | 8 +- analysis/XX-2026-01-27_sample_notebook.ipynb | 6 +- data/example_dataset/README.md | 8 +- pixi.toml | 5 +- src/myanalysis/_constants.py | 34 ++----- 12 files changed, 195 insertions(+), 91 deletions(-) create mode 100644 .claude/settings.json delete mode 100644 .gitattributes create mode 100644 REVIEW_GUIDE.md diff --git a/.claude/settings.json b/.claude/settings.json new file mode 100644 index 0000000..71a5088 --- /dev/null +++ b/.claude/settings.json @@ -0,0 +1,24 @@ +{ + "extraKnownMarketplaces": { + "quadbio": { + "source": { + "source": "github", + "repo": "quadbio/claude-plugins" + } + } + }, + "enabledPlugins": { + "analysis-workflow@quadbio": true + }, + "permissions": { + "deny": [ + "Bash(git add -A:*)", + "Bash(git add --all:*)", + "Bash(git reset --hard:*)", + "Bash(git clean -f:*)", + "Bash(git clean -fd:*)", + "Bash(git push --force:*)", + "Bash(git commit --no-verify:*)" + ] + } +} diff --git a/.gitattributes b/.gitattributes deleted file mode 100644 index 8b431fc..0000000 --- a/.gitattributes +++ /dev/null @@ -1,4 +0,0 @@ -# Strip Jupyter notebook outputs on the way into git, while keeping them in your -# working copy. Activate once per clone with `pixi run install-hooks`. -*.ipynb filter=nbstripout -*.ipynb diff=ipynb diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index ad06492..db9a7d5 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -26,5 +26,3 @@ jobs: frozen: true - name: Run pre-commit checks run: pixi run pre-commit run --all-files - - name: Verify notebooks contain no outputs - run: git ls-files -z '*.ipynb' | xargs -0 -r pixi run nbstripout --verify diff --git a/.gitignore b/.gitignore index 54dd2f0..fa3cbba 100644 --- a/.gitignore +++ b/.gitignore @@ -150,8 +150,23 @@ dmypy.json *.gmt *.gmx -# Directories to ignore +*.zarr + +# Data never enters git; only its READMEs and placeholders do. +data/** +!data/**/ +!data/**/README.md +!data/**/.gitkeep + +# Directories to ignore. Unanchored, so they also match inside every analysis task directory +# (analysis//.../_vN/): the untracked half of a task, anchored to the main checkout. figures/ +outputs/ +logs/ + +# A task's results/ (small evidence tables) is tracked even though *.csv / *.txt are ignored above. +!analysis/**/results/**/*.csv +!analysis/**/results/**/*.txt # OS specifics **.DS_Store diff --git a/AGENTS.md b/AGENTS.md index 33d34a9..9ee6071 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -1,39 +1,40 @@ # AGENTS.md β€” working conventions -This file owns the working conventions and is the canonical guidance for any coding agent. -`README.md` is the user-facing overview; anything documented there is referenced from here, -never restated. +This file is the canonical guidance for any coding agent. `README.md` is the user-facing overview; +anything documented there is referenced from here, never restated. -## Layout +## Workflow -- **Notebooks**: `analysis/[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` -- **Data**: `data//{raw,processed,resources,results}/`, gitignored -- **Package**: `src//`, installed editable from the checkout +Humans work in notebooks; agents work in scripts, one task per session, git worktree and +`analysis//.../_vN/` directory. The conventions (task lifecycle, output paths, the +`data/` layout, working objects and their write-back) are owned by the +[analysis-workflow](https://github.com/quadbio/analysis-workflow) plugin, enabled in +`.claude/settings.json`: load its skill before writing analysis code, outputs or data. Pull +requests are reviewed against [`REVIEW_GUIDE.md`](REVIEW_GUIDE.md). -## Paths +## This repo -Never hardcode a path into `data/` or `figures/` β€” every path hangs off `FilePaths`: + + +- **Notebooks**: `analysis//[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` +- **Package**: `src//`, installed editable from the main checkout +- **Paths**: every dataset path hangs off `FilePaths` in `src//_constants.py`: ```python from myanalysis import FilePaths -FilePaths.DATA # data/ -FilePaths.FIGURES # figures/ β€” curated output: talk and paper figures -FilePaths.EXAMPLE_DATASET / "processed" / "adata.h5ad" +FilePaths.EXAMPLE_DATASET / "processed" / "adata.zarr" ``` -`FilePaths.ROOT` is resolved from git, so it names the *main* checkout even when called from a -worktree and shared data does not follow your branch. Add a dataset as a constant in -`_constants.py`; each one keeps the `{raw,processed,resources,results}` layout by convention. - ## Environments -Dependencies live in `pixi.toml`, not `pyproject.toml` β€” the latter carries package metadata and -the test config. Run `pixi install` after pulling a change to `pixi.toml`, in the main checkout. +Dependencies live in `pixi.toml`, not `pyproject.toml`, which carries package metadata and the +test config. | Task | Command | | --- | --- | -| Run Python | `pixi run python script.py` | +| Run Python (main checkout) | `pixi run python script.py` | +| Run Python (from a worktree) | `pixi run --manifest-path
/pixi.toml python script.py` | | Run tests | `pixi run test` | -| Add conda package | `pixi add ` | -| Add PyPI package | `pixi add --pypi ` | +| Add a conda / PyPI package (main checkout only) | `pixi add ` / `pixi add --pypi ` | diff --git a/README.md b/README.md index 11785c3..edc49f1 100644 --- a/README.md +++ b/README.md @@ -83,14 +83,13 @@ Then finish by hand: ```bash pixi install # create environment from pixi.toml -pixi run install-hooks # pre-commit hooks + notebook output-stripping filter +pixi run install-hooks # pre-commit hooks pixi run install-kernel # register Jupyter kernel ``` -> `install-hooks` also sets up the [nbstripout](https://github.com/kynan/nbstripout) -> git filter. Notebook outputs are then stripped from commits automatically while -> staying in your working copy. **Run it once in every clone** (including remote -> servers and worktrees), or outputs may slip into git. +> **Notebook outputs are committed.** They are the record of what a notebook actually +> produced, and GitHub renders them. Keep them small: clear a notebook by hand before +> committing if it carries a huge embedded image or an accidental dump. πŸ’‘ **Tip**: Use `pixi shell` to enter the environment interactivelyβ€”then you can run commands directly without the `pixi run` prefix. @@ -126,6 +125,23 @@ git push --- +## πŸ€– Working with coding agents + +Humans work in notebooks; coding agents work in scripts, one task per session, git worktree and +`analysis//.../_vN/` directory. The conventions come from the +[analysis-workflow](https://github.com/quadbio/analysis-workflow) Claude Code plugin, which this +repo enables in `.claude/settings.json`. Install it once per machine: + +```bash +claude plugin marketplace add quadbio/claude-plugins +claude plugin install analysis-workflow@quadbio +``` + +Its package (`analysis_workflow`: task paths, additive write-back to AnnData zarr stores) is +already in `pixi.toml`. Review agents on GitHub read [`REVIEW_GUIDE.md`](REVIEW_GUIDE.md). + +--- + ## β˜• Daily Workflow ```bash @@ -187,12 +203,12 @@ Or edit `pixi.toml` directly and run `pixi install`. πŸ““ Data and notebook conventions - **Notebook naming**: `[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` -- **Data layout** (one folder per dataset): - - `data//raw/` β€” original data files - - `data//processed/` β€” preprocessed data - - `data//resources/` β€” reference data, annotations - - `data//results/` β€” analysis outputs -- **Figures**: `figures/` or `data//results/` +- **Data layout** (one folder per dataset, gitignored): + - `data//raw/` β€” bytes as they arrived; never written by analysis + - `data//resources/` β€” curated inputs that are not data: gene lists, marker tables + - `data//processed/` β€” objects code loads to do new work, as AnnData `.zarr` + - `data//results/` β€” a notebook's own outputs, file names prefixed with the notebook's stem +- **Figures**: `figures//` - **Import paths** via the local package: ```python @@ -212,13 +228,6 @@ This template uses **pre-commit hooks** to automatically check your code before | [Biome](https://biomejs.dev/) | Formats JSON/JSONC files | | [pyproject-fmt](https://github.com/tox-dev/pyproject-fmt) | Formats `pyproject.toml` | -**Notebook outputs** are handled separately by an [nbstripout](https://github.com/kynan/nbstripout) -git *filter* (not a pre-commit hook), set up by `pixi run install-hooks`. The filter -strips outputs from the committed copy while leaving them in your working tree, so -your notebooks stay rendered locally but git history stays clean. CI fails the build -if a notebook with outputs ever lands in the repo (a clone that skipped -`install-hooks`), via `nbstripout --verify`. - Hooks run automatically on `git commit`. To run manually: ```bash diff --git a/REVIEW_GUIDE.md b/REVIEW_GUIDE.md new file mode 100644 index 0000000..bc5f484 --- /dev/null +++ b/REVIEW_GUIDE.md @@ -0,0 +1,90 @@ +# Review Guide + +PR review playbook for **review agents running on GitHub**. Imperative voice. + +**Scope: review only.** Comment and suggest. Do not push commits or apply fixes. + +> Everything above "This repo" comes from the analysis template, which takes it from the analysis-workflow +> plugin; change it there and pull it with `cruft update`. Reviewers cannot load the plugin, which is why this +> copy exists. + +The code has usually already run. That is not a reason to lower the bar: requiring a rerun in better shape is a +normal outcome. Say what to redo, not just what was wrong. + +## Data governance + +Every write to a shared object (a working object under `data/*/processed/`, a SpatialData store, anything other +code loads): + +- **Accumulate by addition.** Adding keys to freshly re-read state is commutative, so concurrent sessions can't + lose each other's work. Removal isn't: that means a new dated copy. +- **Writing back to a shared object needs sign-off on that specific diff.** + +## Priorities + +### 1. Writes that lose data, or silently do nothing + +A write to a working object goes through `commit_adata`, gated behind a dry run. Flag: + +- an in-memory AnnData written back over a working object (`write_zarr`/`write_h5ad` onto its path): it erases + whatever other sessions added since it was read; +- a recomputed key committed under an existing name: `commit_adata` writes only keys not yet on disk, so it is a + no-op and the PR reports a result the object doesn't hold. Use a new key or a new dated copy; +- a replaced SpatialData image, labels, points or shapes element, where a new element name would do. + +### 2. Promotions, which leave no diff + +`data/` is gitignored, so an object written into `data//processed/` appears nowhere in the diff; the task +README's `Write-back` section is the only trace. The right subdirectory is not guessable. Check that the PR *says* +where it went and that it was agreed, while moving it is still cheap. + +### 3. The task contract + +Agent work belongs in a task directory `analysis//.../_vN/` with a `README.md` naming real inputs, +outputs and write-back keys. Outputs go through `task_paths(__file__)` to the task's own `results/`, `reports/`, +`figures/`, `outputs/`. Writes to `data//results/` or the central `figures/` are the human lane and are a +finding. + +Every key committed to a shared object carries the task's version suffix **and** appears in that README: an +unrecorded key can't be traced back, an unsuffixed one collides with the next version. + +### 4. Scientific correctness + +The point of the repo. Check that the claim in the PR body follows from what the code computes: the right cells, +the right grouping, a control where one is needed, and a comparison not confounded by condition, time point, +sample or batch. A number that reaches a figure is worth more scrutiny than anything below. + +### 5. Reinvention + +New code needs a reason to exist. Look outward before accepting it: scverse and the Python ecosystem, then the +repo's sibling code packages, then earlier task directories; a near-match found by grep counts. Name the +candidate and what's wrong with it rather than concluding nothing fits. + +The acute case is a helper defined twice in one task or copied between tasks: copies drift, and when they compute +a quantity compared *across* tasks, the result is a wrong conclusion. Copying figure code between versions of one +task is fine. + +### 6. Conciseness + +Prose is reviewed like code. READMEs, docstrings, comments and the PR body: no restating the diff, no filler +preamble, no exhaustive caveats. Padding rots the same way dead code does, and these docs are load-bearing for +the next agent. + +## Do not report + +- Anything the CI linters already gate: formatting, imports, line length. +- Lock files, and anything under `data/`. +- Committed notebook outputs: review changed cells' code, never the output blobs. +- Absolute paths built from `main_checkout()`: task outputs are anchored there deliberately. +- Worktree, temp-dir and cwd-relative `data/`/`figures/` path literals in `analysis/` code: a hook blocks them + before the file is written. + +## Drift older than the diff + +Parts of a repo may predate these rules. When a PR touches such a file, report the drift once at the lowest +severity and don't block; it gets fixed when a task next touches it. Search the open issues before filing one. + +## This repo + + diff --git a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb b/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb index e93671b..f17bd67 100644 --- a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb +++ b/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb @@ -497,11 +497,7 @@ "id": "37", "metadata": {}, "outputs": [], - "source": [ - "output_path = FilePaths.EXAMPLE_DATASET / \"processed\" / \"pbmc3k_processed.h5ad\"\n", - "adata.write(output_path)\n", - "print(f\"Saved to: {output_path}\")" - ] + "source": "output_path = FilePaths.EXAMPLE_DATASET / \"processed\" / \"pbmc3k_processed.zarr\"\nadata.write_zarr(output_path)\nprint(f\"Saved to: {output_path}\")" }, { "cell_type": "markdown", @@ -578,4 +574,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} +} \ No newline at end of file diff --git a/analysis/XX-2026-01-27_sample_notebook.ipynb b/analysis/XX-2026-01-27_sample_notebook.ipynb index 662318e..3524975 100644 --- a/analysis/XX-2026-01-27_sample_notebook.ipynb +++ b/analysis/XX-2026-01-27_sample_notebook.ipynb @@ -127,9 +127,7 @@ { "cell_type": "markdown", "metadata": {}, - "source": [ - "Store data in `data//` with subfolders `raw/`, `processed/`, `resources/`, `results/`. Access paths via `FilePaths`:" - ] + "source": "Store data in `data//` with subfolders `raw/` (as it arrived), `resources/` (curated inputs), `processed/` (objects code loads, as AnnData `.zarr`) and `results/` (this notebook's own outputs, prefixed with its file name). Access paths via `FilePaths`:" }, { "cell_type": "code", @@ -195,4 +193,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/data/example_dataset/README.md b/data/example_dataset/README.md index 8bc566d..63f7b4c 100644 --- a/data/example_dataset/README.md +++ b/data/example_dataset/README.md @@ -1,6 +1,6 @@ # Dataset structure -- `raw`: Raw state of the data we received. -- `processed`: Processed / intermediate data. -- `resources`: Reference data, gene sets, annotations. -- `results`: Any results we compute for this dataset. +- `raw`: bytes as they arrived (instrument output, downloads). Never written by analysis. +- `resources`: curated inputs that are not data: gene lists, marker tables, panel descriptions. +- `processed`: objects code loads to do new work, as AnnData `.zarr` stores. +- `results`: a notebook's own outputs, file names prefixed with the notebook's stem. diff --git a/pixi.toml b/pixi.toml index 6aa9e8e..c72eeba 100644 --- a/pixi.toml +++ b/pixi.toml @@ -11,7 +11,7 @@ lab = "jupyter lab" test = "pytest" rename = { cmd = "python scripts/rename_package.py", description = "Rename the placeholder package/project (run once on a fresh clone; see scripts/rename_package.py)" } install-kernel = "python -m ipykernel install --user --name=analysis-template --display-name='Analysis Template (Pixi)'" -install-hooks = { cmd = "pre-commit install --install-hooks && nbstripout --install && git config diff.ipynb.textconv 'nbstripout -t'", description = "Install pre-commit hooks + the nbstripout notebook-output filter (run once per clone)" } +install-hooks = { cmd = "pre-commit install --install-hooks", description = "Install pre-commit hooks (run once per clone)" } [dependencies] python = "3.12.*" @@ -54,12 +54,13 @@ seaborn = "*" # Utilities pre-commit = "*" -nbstripout = "*" pytest = "*" session-info2 = "*" # Local editable package for path helpers myanalysis = { path = ".", editable = true } +# Task paths and additive write-back for agent-run tasks (README: "Working with coding agents") +analysis-workflow = { git = "https://github.com/quadbio/analysis-workflow", tag = "v0.1.0" } igraph = ">=1.0.0, <2" celltypist = ">=1.7.1, <2" diff --git a/src/myanalysis/_constants.py b/src/myanalysis/_constants.py index 7eebb98..1b9ff3b 100644 --- a/src/myanalysis/_constants.py +++ b/src/myanalysis/_constants.py @@ -1,39 +1,15 @@ """Project-wide paths for notebooks and scripts.""" -from __future__ import annotations +from analysis_workflow import main_checkout -import subprocess -from functools import lru_cache -from pathlib import Path +class FilePaths: + """Project-wide paths. Add a dataset as a constant here; never hardcode one. -@lru_cache(maxsize=1) -def _repo_root() -> Path: - """The repository root, from git so a worktree still names the main checkout. - - Falls back to walking up for ``pixi.toml``/``.git`` outside a repository. + ``ROOT`` is the *main* checkout even from a git worktree, so shared data does not follow your branch. """ - try: - git_dir = subprocess.run( - ["git", "rev-parse", "--path-format=absolute", "--git-common-dir"], - cwd=Path(__file__).resolve().parent, - capture_output=True, - text=True, - check=True, - ).stdout.strip() - return Path(git_dir).parent - except (subprocess.CalledProcessError, OSError): - here = Path(__file__).resolve() - for parent in (here, *here.parents): - if (parent / "pixi.toml").exists() or (parent / ".git").exists(): - return parent - return here.parents[2] - - -class FilePaths: - """Project-wide paths. Add a dataset as a constant here; never hardcode one.""" - ROOT = _repo_root() + ROOT = main_checkout(__file__) DATA = ROOT / "data" FIGURES = ROOT / "figures" From 1103a32f691b3eb2d8ae7df43e8dccfcc4fc8b97 Mon Sep 17 00:00:00 2001 From: Marius1311 Date: Thu, 8 Oct 2026 17:13:04 +0200 Subject: [PATCH 2/4] Lock analysis-workflow v0.1.0 Co-Authored-By: Claude Opus 5.5 --- pixi.lock | 3918 ++++++++++++++++++++++++++++------------------------- 1 file changed, 2082 insertions(+), 1836 deletions(-) diff --git a/pixi.lock b/pixi.lock index 048c3ad..4918c67 100644 --- a/pixi.lock +++ b/pixi.lock @@ -101,202 +101,212 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/ucx-1.20.0-hf72d326_1.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h280c20c_3.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda - - pypi: https://files.pythonhosted.org/packages/18/a6/907a406bb7d359e6a63f99c313846d9eec4f7e6f7437809e03aa00fa3074/absl_py-2.4.0-py3-none-any.whl - 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nvidia-nvfatbin==13.0.85.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'all') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'all') + - nvidia-nvjitlink>=13.0.88,<14 ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'all') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'all') + - nvidia-nvjpeg==13.0.1.86.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'all') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'all') + - nvidia-nvml-dev==13.0.87.* ; (platform_machine == 'AMD64' and sys_platform == 'win32' and extra == 'all') or (platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'all') or (platform_machine == 'x86_64' and sys_platform == 'linux' and extra == 'all') + - 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pypi: https://pypi.nvidia.com/cudf-cu12/cudf_cu12-26.2.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl name: cudf-cu12 version: 26.2.1 @@ -2649,15 +2706,15 @@ packages: - dask-cuda==26.2.* ; extra == 'test-dask' - dask-ml>=2024 ; extra == 'test-dask' requires_python: '>=3.10' -- pypi: https://files.pythonhosted.org/packages/f6/6e/dc03c1ddc940f33b3d32803898e2fdae5c9538a2127a25f499494c84b183/cupy_cuda12x-14.1.1-cp312-cp312-manylinux2014_x86_64.whl +- pypi: https://files.pythonhosted.org/packages/7c/5b/65124de2dbaf2e85109f611a41947e39acd6dd938751c04b4c4d7bf6fc82/cupy_cuda12x-14.2.0-cp312-cp312-manylinux2014_x86_64.whl name: cupy-cuda12x - version: 14.1.1 - sha256: a1138f20080489a46209291498cd12f792226d0a57d50c64a586c162a875a069 + version: 14.2.0 + sha256: f82141761f2c81905d49387464ae29438887956d99063381c93a1d5d1b7d32e8 requires_dist: - numpy>=2.0,<2.6 - cuda-pathfinder==1.*,>=1.3.4 - - scipy>=1.14,<1.17 ; extra == 'all' - - cython>=3 ; extra == 'all' + - scipy>=1.14,<1.18 ; extra == 'all' + - cython>=3,!=3.2.6 ; extra == 'all' - optuna>=2.0 ; extra == 'all' - packaging ; extra == 'test' - pytest>=7.2 ; extra == 'test' @@ -2724,6 +2781,37 @@ packages: - pytest-xdist ; extra == 'test' - pre-commit ; extra == 'test' requires_python: '>=3.10' +- pypi: https://files.pythonhosted.org/packages/f8/3a/4fc99e788bcfa1b3b3f21abf57da45898d807d007e7f6fd1c7300904eb70/dask-2026.8.0-py3-none-any.whl + name: dask + version: 2026.8.0 + sha256: ccc0c83a189b0398602435189771d28dad7b5773b6089bb8dce14ae732dd782c + requires_dist: + - click>=8.1 + - cloudpickle>=3.0.0 + - fsspec>=2021.9.0 + - packaging>=20.0 + - partd>=1.4.0 + - pyyaml>=5.4.1 + - toolz>=0.12.0 + - importlib-metadata>=4.13.0 ; python_full_version < '3.12' + - numpy>=1.24 ; extra == 'array' + - dask[array] ; extra == 'dataframe' + - pandas>=2.0 ; extra == 'dataframe' + - pyarrow>=16.0 ; extra == 'dataframe' + - distributed>=2026.8.0,<2026.8.1 ; extra == 'distributed' + - bokeh>=3.1.0 ; extra == 'diagnostics' + - jinja2>=2.10.3 ; extra == 'diagnostics' + - dask[array,dataframe,diagnostics,distributed] ; extra == 'complete' + - lz4>=4.3.2 ; extra == 'complete' + - pandas[test] ; extra == 'test' + - pytest ; extra == 'test' + - pytest-cov ; extra == 'test' + - pytest-mock ; extra == 'test' + - pytest-rerunfailures ; extra == 'test' + - pytest-timeout ; extra == 'test' + - pytest-xdist ; extra == 'test' + - pre-commit ; extra == 'test' + requires_python: '>=3.10' - pypi: https://pypi.nvidia.com/dask-cuda/dask_cuda-26.2.0-py3-none-manylinux_2_28_aarch64.manylinux_2_28_x86_64.whl name: dask-cuda version: 26.2.0 @@ -2820,34 +2908,23 @@ packages: - toolz - xarray requires_python: '>=3.10' -- pypi: https://files.pythonhosted.org/packages/95/51/67e7cf11a53e40694f720457d5b3a1cdaaa3d5a9a633e482f225456b93ff/debugpy-1.8.21-py2.py3-none-any.whl +- pypi: https://files.pythonhosted.org/packages/56/3d/c7dc9f35bc9e22cdb53679f844bee40fd5cff871862f60595869a433400d/debugpy-1.8.22-py2.py3-none-any.whl name: debugpy - version: 1.8.21 - sha256: b1e37d333663c8851516a47364ef473da127f9caebe4417e6df6f5825a7e9a92 - 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name: zstandard - version: 0.25.0 - sha256: 5a56ba0db2d244117ed744dfa8f6f5b366e14148e00de44723413b2f3938a902 - requires_dist: - - cffi~=1.17 ; python_full_version < '3.14' and platform_python_implementation != 'PyPy' and extra == 'cffi' - - cffi>=2.0.0b0 ; python_full_version >= '3.14' and platform_python_implementation != 'PyPy' and extra == 'cffi' - requires_python: '>=3.9' -- pypi: https://files.pythonhosted.org/packages/aa/1c/d920d64b22f8dd028a8b90e2d756e431a5d86194caa78e3819c7bf53b4b3/zstandard-0.25.0-cp312-cp312-macosx_11_0_arm64.whl - name: zstandard - version: 0.25.0 - sha256: 913cbd31a400febff93b564a23e17c3ed2d56c064006f54efec210d586171c00 - requires_dist: - - cffi~=1.17 ; python_full_version < '3.14' and platform_python_implementation != 'PyPy' and extra == 'cffi' - - cffi>=2.0.0b0 ; python_full_version >= '3.14' and platform_python_implementation != 'PyPy' and extra == 'cffi' - requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7 md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829 From 6d3d2207027c5876e0d6259390e3f2b8bdfae43d Mon Sep 17 00:00:00 2001 From: Marius1311 Date: Thu, 8 Oct 2026 17:34:14 +0200 Subject: [PATCH 3/4] Restore the notebooks' trailing newlines Co-Authored-By: Claude Opus 5.5 --- analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb | 2 +- analysis/XX-2026-01-27_sample_notebook.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb b/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb index f17bd67..9d57fa1 100644 --- a/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb +++ b/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb @@ -574,4 +574,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/analysis/XX-2026-01-27_sample_notebook.ipynb b/analysis/XX-2026-01-27_sample_notebook.ipynb index 3524975..16f4c07 100644 --- a/analysis/XX-2026-01-27_sample_notebook.ipynb +++ b/analysis/XX-2026-01-27_sample_notebook.ipynb @@ -193,4 +193,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} \ No newline at end of file +} From a8ce86b1e12d6cba6ca7c1f59d6db73507b5cd7a Mon Sep 17 00:00:00 2001 From: Marius1311 Date: Fri, 9 Oct 2026 14:57:11 +0200 Subject: [PATCH 4/4] Cut the repeated workflow text from README and AGENTS.md The README keeps only the plugin install step and points at AGENTS.md; AGENTS.md names what the plugin owns without restating it, and drops the worktree commands the skill and its hook already own. The data layout now lives once for humans, in the README; the dataset README and the sample notebook point there. Co-Authored-By: Claude Opus 5.5 --- AGENTS.md | 16 ++++++---------- README.md | 10 +++------- analysis/XX-2026-01-27_sample_notebook.ipynb | 2 +- data/example_dataset/README.md | 6 ++---- 4 files changed, 12 insertions(+), 22 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index 9ee6071..17c1d5e 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -5,19 +5,16 @@ anything documented there is referenced from here, never restated. ## Workflow -Humans work in notebooks; agents work in scripts, one task per session, git worktree and -`analysis//.../_vN/` directory. The conventions (task lifecycle, output paths, the -`data/` layout, working objects and their write-back) are owned by the -[analysis-workflow](https://github.com/quadbio/analysis-workflow) plugin, enabled in -`.claude/settings.json`: load its skill before writing analysis code, outputs or data. Pull -requests are reviewed against [`REVIEW_GUIDE.md`](REVIEW_GUIDE.md). +The human and agent lanes, task lifecycle, output paths, `data/` layout, working objects and their +write-back are owned by the [analysis-workflow](https://github.com/quadbio/analysis-workflow) +plugin, enabled in `.claude/settings.json`: load its skill before writing analysis code, outputs or +data. Pull requests are reviewed against [`REVIEW_GUIDE.md`](REVIEW_GUIDE.md). ## This repo -- **Notebooks**: `analysis//[INITIALS]-[YYYY]-[MM]-[DD]_description.ipynb` - **Package**: `src//`, installed editable from the main checkout - **Paths**: every dataset path hangs off `FilePaths` in `src//_constants.py`: @@ -34,7 +31,6 @@ test config. | Task | Command | | --- | --- | -| Run Python (main checkout) | `pixi run python script.py` | -| Run Python (from a worktree) | `pixi run --manifest-path
/pixi.toml python script.py` | +| Run Python | `pixi run python script.py` | | Run tests | `pixi run test` | -| Add a conda / PyPI package (main checkout only) | `pixi add ` / `pixi add --pypi ` | +| Add a conda / PyPI package | `pixi add ` / `pixi add --pypi ` | diff --git a/README.md b/README.md index edc49f1..dc650eb 100644 --- a/README.md +++ b/README.md @@ -127,19 +127,15 @@ git push ## πŸ€– Working with coding agents -Humans work in notebooks; coding agents work in scripts, one task per session, git worktree and -`analysis//.../_vN/` directory. The conventions come from the -[analysis-workflow](https://github.com/quadbio/analysis-workflow) Claude Code plugin, which this -repo enables in `.claude/settings.json`. Install it once per machine: +Agents follow [`AGENTS.md`](AGENTS.md) and the +[analysis-workflow](https://github.com/quadbio/analysis-workflow) Claude Code plugin (a skill plus +guard hooks) that this repo enables. Install the plugin once per machine: ```bash claude plugin marketplace add quadbio/claude-plugins claude plugin install analysis-workflow@quadbio ``` -Its package (`analysis_workflow`: task paths, additive write-back to AnnData zarr stores) is -already in `pixi.toml`. Review agents on GitHub read [`REVIEW_GUIDE.md`](REVIEW_GUIDE.md). - --- ## β˜• Daily Workflow diff --git a/analysis/XX-2026-01-27_sample_notebook.ipynb b/analysis/XX-2026-01-27_sample_notebook.ipynb index 16f4c07..ff4165c 100644 --- a/analysis/XX-2026-01-27_sample_notebook.ipynb +++ b/analysis/XX-2026-01-27_sample_notebook.ipynb @@ -127,7 +127,7 @@ { "cell_type": "markdown", "metadata": {}, - "source": "Store data in `data//` with subfolders `raw/` (as it arrived), `resources/` (curated inputs), `processed/` (objects code loads, as AnnData `.zarr`) and `results/` (this notebook's own outputs, prefixed with its file name). Access paths via `FilePaths`:" + "source": "Store data in `data//` (layout in the README) and access paths via `FilePaths`:" }, { "cell_type": "code", diff --git a/data/example_dataset/README.md b/data/example_dataset/README.md index 63f7b4c..73a1fa8 100644 --- a/data/example_dataset/README.md +++ b/data/example_dataset/README.md @@ -1,6 +1,4 @@ # Dataset structure -- `raw`: bytes as they arrived (instrument output, downloads). Never written by analysis. -- `resources`: curated inputs that are not data: gene lists, marker tables, panel descriptions. -- `processed`: objects code loads to do new work, as AnnData `.zarr` stores. -- `results`: a notebook's own outputs, file names prefixed with the notebook's stem. +`raw/`, `resources/`, `processed/` and `results/`, as described under *Data and notebook +conventions* in the top-level `README.md`.