Build #3354
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |