Build #3341
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| name: Build | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| # Run at the end of every day | |
| - cron: "0 0 * * *" | |
| jobs: | |
| build: | |
| # Scheduled runs only on the origin org | |
| if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule') | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt -r requirements-dev.txt | |
| - name: Run pre-commit | |
| uses: pre-commit/[email protected] | |
| - name: Test with pytest (numba jit disabled) | |
| env: | |
| NUMBA_DISABLE_JIT: 1 | |
| run: | | |
| # avoid guvectorized functions #1194 | |
| pytest -v sgkit/tests/test_pedigree.py | |
| - name: Test with pytest and coverage | |
| run: | | |
| pytest -v --cov=sgkit --cov-report=term-missing | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| test-zarr-version: | |
| name: Test Zarr Python v3 | |
| # Scheduled runs only on the origin org | |
| if: (github.event_name == 'schedule' && github.repository_owner == 'sgkit-dev') || (github.event_name != 'schedule') | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| zarr: ["==3.0.0b1"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt -r requirements-dev.txt | |
| - name: Install zarr${{ matrix.zarr }} | |
| run: | | |
| python -m pip install --pre 'zarr${{ matrix.zarr }}' | |
| python -m pip uninstall -y bio2zarr # TODO: remove when bio2zarr supports Zarr Python 3 | |
| - name: Run tests | |
| run: | | |
| pytest |