CI #1760
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| name: Test | |
| on: | |
| schedule: | |
| - cron: 00 00 * * 1 # every Monday at 00:00 | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| workflow_dispatch: | |
| inputs: | |
| reason: | |
| description: Reason for the workflow dispatch. Only "release" is valid. | |
| required: true | |
| default: release | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: ["3.10", "3.11", "3.12"] | |
| os: [ubuntu-latest] | |
| include: | |
| - python: "3.12" | |
| os: macos-latest | |
| pre-release: "allow" | |
| name: "Python 3.12 (pre-release)" | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| UV_PRERELEASE: ${{ matrix.pre-release || 'disallow' }} | |
| steps: | |
| - uses: actions/checkout@v5 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| enable-cache: true | |
| - name: Install dependencies | |
| run: | | |
| ./.scripts/ci/install_dependencies.sh | |
| - name: Install pip dependencies | |
| run: uv tool install tox --with=tox-uv --with=tox-gh-actions | |
| - name: Restore data cache | |
| id: data-cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/squidpy/*.h5ad | |
| key: data-${{ hashFiles('**/download_data.py') }} | |
| - name: Download datasets | |
| if: steps.data-cache.outputs.cache-hit != 'true' | |
| run: | | |
| tox -e download-data | |
| # caching .tox is not encouraged, but since we're private and this shaves off ~1min from the step | |
| # if any problems occur and/or once the package is public, this can be removed | |
| - name: Restore tox cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: .tox | |
| key: tox-${{ runner.os }}-${{ matrix.python }}-${{ hashFiles('**/requirements.txt', '**/tox.ini') }} | |
| - name: Test | |
| timeout-minutes: 60 | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| PYTEST_ADDOPTS: "-n auto" | |
| run: | | |
| tox -vv | |
| # check if this can be deprecated | |
| #- name: List figures for potential debugging | |
| # ls -alh /home/runner/work/squidpy/squidpy/tests/figures | |
| - name: Archive figures generated during testing | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: visual_test_results_${{ matrix.os }}-python${{ matrix.python }} | |
| path: /home/runner/work/squidpy/squidpy/tests/figures/* | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| name: coverage | |
| verbose: true | |
| token: ${{ secrets.CODECOV_TOKEN }} # required | |
| check: | |
| if: always() | |
| needs: [test] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: re-actors/alls-green@release/v1 | |
| with: | |
| jobs: ${{ toJSON(needs) }} |