(fix): Accelerate tests: migrate to Github Actions, remove slow param, parallelize #35
Workflow file for this run
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| name: Python application | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - "*.*.x" | |
| pull_request: | |
| branches: | |
| - main | |
| - "*.*.x" | |
| # Cancel the job if new commits are pushed | |
| # https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| pytest: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| include: | |
| - python-version: '3.13' | |
| test-type: coverage | |
| - python-version: '3.11' | |
| test-type: standard | |
| - python-version: '3.13' | |
| dependencies-version: pre-release | |
| test-type: strict-warning | |
| - python-version: '3.11' | |
| dependencies-version: minimum | |
| test-type: coverage | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install UV | |
| uses: hynek/setup-cached-uv@v2 | |
| with: | |
| cache-dependency-path: pyproject.toml | |
| - name: Install dependencies | |
| if: matrix.dependencies-version == null | |
| run: uv pip install --system --compile "anndata[dev,test] @ ." -c ci/constraints.txt | |
| - name: Install minimum dependencies | |
| if: matrix.dependencies-version == 'minimum' | |
| run: | | |
| uv pip install --system --compile tomli packaging | |
| deps=$(python3 ci/scripts/min-deps.py pyproject.toml --extra dev test) | |
| uv pip install --system --compile $deps pytest-cov "anndata @ ." | |
| - name: Install dependencies release candidates | |
| if: matrix.dependencies-version == 'pre-release' | |
| run: uv pip install -v --system --compile --pre "anndata[dev,test] @ ." -c ci/constraints.txt | |
| - name: Display installed versions | |
| run: uv pip list | |
| - name: Run Pytest | |
| if: matrix.test-type == 'standard' | |
| run: pytest -n auto | |
| - name: Run Pytest (coverage) | |
| if: matrix.test-type == 'coverage' | |
| run: pytest --cov --cov-report=xml --cov-context=test | |
| - name: Run Pytest (treat warnings as errors) | |
| if: matrix.test-type == 'strict-warning' | |
| run: pytest --strict-warnings -n auto | |
| - uses: codecov/codecov-action@v4 | |
| if: matrix.test-type == 'coverage' | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| verbose: true | |
| check-build: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.13 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Install build tools and requirements | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine | |
| - name: Display installed versions | |
| run: pip list | |
| - name: Build & Twine check | |
| run: | | |
| python -m build --sdist --wheel . | |
| twine check dist/* | |
| - name: Check runtime version | |
| run: | | |
| pip install dist/*.whl | |
| python -c 'import anndata; print(anndata.__version__)' |