[pre-commit.ci] pre-commit autoupdate (#1083) #217
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| name: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: "0 5 1,15 * *" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| FORCE_COLOR: "1" | |
| MPLBACKEND: agg | |
| UV_COMPILE_BYTECODE: "1" | |
| COVERAGE_FILE: ${{ github.workspace }}/.coverage | |
| defaults: | |
| run: | |
| # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u). | |
| shell: bash -euo pipefail {0} | |
| jobs: | |
| ensure-data-is-cached: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| enable-cache: false | |
| python-version: "3.13" | |
| - name: Restore data cache | |
| id: data-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes | |
| key: data-${{ hashFiles('**/download_data.py') }} | |
| restore-keys: | | |
| data- | |
| enableCrossOsArchive: true | |
| - name: Download datasets | |
| # Always run to ensure any missing files are downloaded | |
| # (restore-keys may provide partial cache) | |
| run: uvx hatch run data:download | |
| # Get the test environment from hatch as defined in pyproject.toml. | |
| # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are | |
| # run locally and on continuous integration. | |
| # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for more details. | |
| get-environments: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| envs: ${{ steps.get-envs.outputs.envs }} | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| enable-cache: true | |
| cache-dependency-glob: pyproject.toml | |
| - name: Get test environments | |
| id: get-envs | |
| run: | | |
| ENVS_JSON=$(NO_COLOR=1 uvx --quiet hatch env show --json | jq -c 'to_entries | |
| | map( | |
| select(.key | startswith("hatch-test")) | |
| | { | |
| name: .key, | |
| label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end), | |
| python: .value.python | |
| } | |
| )') | |
| echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT | |
| # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above. | |
| test: | |
| needs: [ensure-data-is-cached, get-environments] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| env: ${{ fromJSON(needs.get-environments.outputs.envs) }} | |
| exclude: | |
| - os: macos-latest | |
| env: { name: hatch-test.py3.11-stable } | |
| - os: macos-latest | |
| env: { name: hatch-test.py3.12-stable } | |
| - os: ubuntu-latest | |
| env: { name: hatch-test.py3.13-stable } # skipping because we run this as a coverage job | |
| name: ${{ matrix.env.label }} (${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: ${{ matrix.env.python }} | |
| cache-dependency-glob: pyproject.toml | |
| - name: Ensure figure directory exists | |
| run: mkdir -p "$GITHUB_WORKSPACE/tests/figures" | |
| - name: Restore data cache | |
| id: data-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes | |
| key: data-${{ hashFiles('**/download_data.py') }} | |
| restore-keys: | | |
| data- | |
| enableCrossOsArchive: true | |
| - 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: create hatch environment | |
| run: uvx hatch env create ${{ matrix.env.name }} | |
| - name: run tests using hatch | |
| env: | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: uvx hatch run ${{ matrix.env.name }}:run -v --color=yes -n auto | |
| - name: Archive figures generated during testing | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: visual_test_results_${{ runner.os }}_${{ matrix.env.name }} | |
| path: ${{ github.workspace }}/tests/figures/* | |
| coverage: | |
| name: Coverage (ubuntu-latest, hatch-test.py3.13-stable) | |
| needs: [ensure-data-is-cached] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| filter: blob:none | |
| fetch-depth: 0 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: "3.13" | |
| cache-dependency-glob: pyproject.toml | |
| - name: Ensure figure directory exists | |
| run: mkdir -p "$GITHUB_WORKSPACE/tests/figures" | |
| - name: Restore data cache | |
| id: coverage-data-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: data # IMPORTANT: this will fail if scanpy.settings.datasetdir default changes | |
| key: data-${{ hashFiles('**/download_data.py') }} | |
| restore-keys: | | |
| data- | |
| enableCrossOsArchive: true | |
| - name: System dependencies (Linux) | |
| 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: create hatch environment | |
| run: uvx hatch env create hatch-test.py3.13-stable | |
| - name: run coverage tests | |
| env: | |
| PLATFORM: ubuntu-latest | |
| DISPLAY: :42 | |
| run: | | |
| uvx hatch run hatch-test.py3.13-stable:cov-erase | |
| uvx hatch run hatch-test.py3.13-stable:run-cov -v --color=yes | |
| uvx hatch run hatch-test.py3.13-stable:cov-combine | |
| uvx hatch run hatch-test.py3.13-stable:cov-report | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch | |
| # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why. | |
| check: | |
| name: Tests pass in all hatch environments | |
| if: always() | |
| needs: | |
| - get-environments | |
| - test | |
| - coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} |