Functions to QC histopathology images #1839
Workflow file for this run
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| name: CI | |
| on: | |
| schedule: | |
| - cron: 00 00 * * 1 # every Monday at 00:00 | |
| push: | |
| branches: | |
| - main | |
| - "[0-9]+.[0-9]+.x" | |
| pull_request: | |
| env: | |
| PYTEST_ADDOPTS: "-v --color=yes -n auto" | |
| FORCE_COLOR: "1" | |
| MPLBACKEND: agg | |
| # It's impossible to ignore SyntaxWarnings for a single module, | |
| # so because leidenalg 0.10.0 has them, we pre-compile things: https://github.com/vtraag/leidenalg/issues/173 | |
| UV_COMPILE_BYTECODE: "1" | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: hatch-test.py3.11-stable | |
| os: ubuntu-latest | |
| python: "3.11" | |
| - name: hatch-test.py3.12-stable | |
| os: ubuntu-latest | |
| python: "3.12" | |
| - name: hatch-test.py3.13-stable | |
| os: ubuntu-latest | |
| python: "3.13" | |
| test-type: "coverage" | |
| - name: hatch-test.py3.13-pre | |
| os: macos-latest | |
| python: "3.13" | |
| env: # environment variable for use in codecov's env_vars tagging | |
| ENV_NAME: ${{ matrix.name }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| filter: blob:none | |
| - uses: astral-sh/setup-uv@v6 | |
| with: | |
| enable-cache: true | |
| python-version: ${{ matrix.python }} | |
| cache-dependency-glob: pyproject.toml | |
| - name: Ensure figure directory exists | |
| run: mkdir -p "$GITHUB_WORKSPACE/tests/figures" | |
| - name: Restore data cache | |
| id: data-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/squidpy/*.h5ad | |
| key: data-${{ hashFiles('**/download_data.py') }} | |
| - name: Download datasets | |
| if: steps.data-cache.outputs.cache-hit != 'true' | |
| run: | | |
| uvx hatch run ${{ matrix.name }}:download | |
| - name: System dependencies (Linux) | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install automake -y | |
| # PyQt5 related | |
| sudo apt install libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 -y | |
| sudo Xvfb :42 -screen 0 1920x1080x24 -ac +extension GLX </dev/null & | |
| - name: System dependencies (macOS) | |
| if: matrix.os == 'macos-latest' | |
| run: brew install automake | |
| - name: Install dependencies | |
| run: uvx hatch -v env create ${{ matrix.name }} | |
| - name: Run tests | |
| if: matrix.test-type == null | |
| run: uvx hatch run ${{ matrix.name }}:run | |
| - name: Run tests (coverage) | |
| if: matrix.test-type == 'coverage' | |
| run: | | |
| uvx hatch run ${{ matrix.name }}:run-cov | |
| uvx hatch run ${{ matrix.name }}:coverage combine | |
| uvx hatch run ${{ matrix.name }}:coverage xml | |
| - name: Archive figures generated during testing | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: visual_test_results_${{ runner.os }}_py${{ matrix.name }} | |
| path: ${{ github.workspace }}/tests/figures/* | |
| - name: Upload coverage data | |
| if: matrix.test-type == 'coverage' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| env_vars: ENV_NAME | |
| fail_ci_if_error: true | |
| check: | |
| if: always() | |
| needs: | |
| - test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} |