PR for 0.5.0 release

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+    .git,
+    .claude,
+    __pycache__,
+    build,
+    dist,
+    docs/build,
+    *.egg-info,
+    .venv,
+    venv

.github/pull_request_template.md

@@ -0,0 +1,25 @@
+## What and why
+
+<!-- What does this change do, and why is it needed? Link the issue or
+planning/ file it addresses. -->
+
+## How it was verified
+
+<!-- Tests added, commands run, simulations or fits checked. -->
+
+## Checklist
+
+See [CONTRIBUTING.md](https://github.com/harmslab/tfscreen/blob/main/CONTRIBUTING.md) for details on each item.
+
+- [ ] Branch is up to date with `upstream/main`
+- [ ] New and changed code has full unit test coverage, including branches and error paths
+- [ ] Bug fixes include a test that fails without the fix
+- [ ] Slow tests are marked `@pytest.mark.slow`
+- [ ] `pytest tests/tfscreen --runslow` passes locally
+- [ ] `diff-cover coverage.xml --compare-branch=upstream/main` reports 100%
+- [ ] `flake8 . --count --select=E9,F63,F7,F82` reports no errors
+- [ ] Public functions, classes and methods have numpydoc docstrings
+- [ ] New components, CLIs and YAML keys follow the conventions in `CLAUDE.md`
+- [ ] `CLAUDE.md` is updated if the change alters how the code works
+- [ ] `CHANGELOG.md` has an entry under `[Unreleased]` for any user-visible change
+- [ ] No data, checkpoints or other large files are committed

.github/workflows/tests.yml

@@ -12,6 +12,11 @@ on:
         type: boolean
         default: false
 
+# A newer push to the same branch or pull request cancels the older run.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Python ${{ matrix.python-version }} / ${{ matrix.os }}
@@ -20,7 +25,11 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
+        # The coverage job runs this one, plus the slow tests.
+        exclude:
+          - os: ubuntu-latest
+            python-version: "3.12"
 
     steps:
       - uses: actions/checkout@v4
@@ -29,6 +38,7 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
+          cache: pip
 
       - name: Install package and test dependencies
         run: pip install -e ".[test]"
@@ -40,5 +50,47 @@ jobs:
         env:
           NUMBA_DISABLE_JIT: "1"
         run: >
-          pytest tests/tfscreen
+          pytest -n auto tests/tfscreen
           ${{ (github.event_name == 'workflow_dispatch' && inputs.run_slow_tests) && '--runslow' || '' }}
+
+  coverage:
+    name: Coverage
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # diff-cover compares against main, so it needs the full history.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install package and test dependencies
+        run: pip install -e ".[test]"
+
+      # Slow tests are included so code tested only by them counts as covered.
+      # pytest-cov combines the workers' data; settings come from pyproject.toml
+      # (branch coverage, source = tfscreen only, so planning/, tests/ and
+      # docs/ are never measured).
+      - name: Run unit tests under coverage
+        env:
+          NUMBA_DISABLE_JIT: "1"
+        run: pytest -n auto --runslow --cov --cov-report= tests/tfscreen
+
+      - name: Report total coverage
+        run: |
+          coverage xml
+          coverage report --fail-under=90
+
+      # Every line and branch a pull request adds or changes in src/ must be
+      # covered. Files outside coverage.xml are not judged.
+      - name: Check coverage of changed lines
+        if: github.event_name == 'pull_request'
+        run: >
+          diff-cover coverage.xml
+          --compare-branch=origin/${{ github.base_ref }}
+          --fail-under=100

.gitignore

@@ -205,3 +205,45 @@ cython_debug/
 marimo/_static/
 marimo/_lsp/
 __marimo__/
+
+# Local test/lint/coverage output from run_all_tests.sh
+reports/
+docs/badges/
+
+# Lab data for development; never committed (C10)
+planning/dev-data/
+planning/results/
+# Run outputs downloaded into study directories (lab-data fits, multi-GB
+# simulations); the study's scripts and README stay tracked
+planning/studies/recipe/
+planning/studies/full-size-sim/sim_*/
+planning/studies/full-size-sim/pilot_*/
+planning/studies/full-size-sim-*/
+planning/studies/m-bias-factorial/m_bias/
+planning/studies/m-bias-factorial/m_subsets/
+planning/studies/m-bias-factorial/m_subsets_real/
+planning/studies/m-bias-factorial/m_subsets_poisson/
+planning/studies/m-bias-factorial/held_s2/
+planning/studies/m-bias-factorial/held_kanR_*/
+planning/studies/m-bias-factorial/held_all_*/
+planning/studies/m-bias-factorial/held_mix_*/
+planning/studies/m-bias-factorial/kanR_only_*/
+planning/studies/m-bias-factorial/jk_seed*/
+planning/studies/m-bias-factorial/km_draws/
+planning/studies/m-bias-factorial/sim_realistic_seed2/
+planning/studies/m-bias-factorial/sim_realistic_s2/
+planning/studies/m-bias-factorial/real_depth/
+planning/studies/m-bias-factorial/sim_realistic_nocong/
+planning/studies/two-stage-validation/run_*/
+planning/studies/m-bias-factorial/stage2_*/
+
+.DS_Store 
+
+planning/studies/x-vs-binding/out/
+planning/studies/within-tube-m/out/
+planning/studies/within-tube-m/runs/
+planning/studies/relative-m/runs/
+planning/studies/joint-fit-sim/runs/
+planning/studies/joint-fit-sim/out/
+planning/studies/joint-fit-real/runs/
+planning/studies/joint-fit-real/out/