Remove check on PL values when computing local alleles #252
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: pre-commit/[email protected] | |
| test: | |
| name: Test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # Use macos-13 because pip binary packages for ARM aren't | |
| # available for many dependencies | |
| os: [macos-13, macos-14, ubuntu-latest] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| exclude: | |
| # Just run macos tests on one Python version | |
| - os: macos-13 | |
| python-version: "3.10" | |
| - os: macos-13 | |
| python-version: "3.11" | |
| - os: macos-13 | |
| python-version: "3.12" | |
| - os: macos-14 | |
| python-version: "3.9" | |
| - os: macos-14 | |
| python-version: "3.10" | |
| - os: macos-14 | |
| python-version: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install '.[dev]' | |
| - name: Run basic vcf2zarr example | |
| run: | | |
| python -m bio2zarr vcf2zarr convert tests/data/vcf/sample.vcf.gz sample.vcz -f | |
| - name: Run two-pass vcf2zarr example | |
| run: | | |
| python -m bio2zarr vcf2zarr explode tests/data/vcf/sample.vcf.gz sample.icf -f | |
| python -m bio2zarr vcf2zarr encode sample.icf sample.vcz -f | |
| - name: Run distributed explode example | |
| run: | | |
| python -m bio2zarr vcf2zarr dexplode-init tests/data/vcf/sample.vcf.gz sample.icf -fn 3 | |
| python -m bio2zarr vcf2zarr dexplode-partition sample.icf 0 | |
| python -m bio2zarr vcf2zarr dexplode-partition sample.icf 1 | |
| python -m bio2zarr vcf2zarr dexplode-partition sample.icf 2 | |
| python -m bio2zarr vcf2zarr dexplode-finalise sample.icf | |
| - name: Run distributed encode example | |
| run: | | |
| python -m bio2zarr vcf2zarr dencode-init sample.icf sample.vcz -fn 3 --variants-chunk-size=3 | |
| python -m bio2zarr vcf2zarr dencode-partition sample.vcz 0 | |
| python -m bio2zarr vcf2zarr dencode-partition sample.vcz 1 | |
| python -m bio2zarr vcf2zarr dencode-partition sample.vcz 2 | |
| python -m bio2zarr vcf2zarr dencode-finalise sample.vcz | |
| - name: Run tests | |
| run: | | |
| pytest --cov=bio2zarr | |
| - name: Upload coverage to Coveralls | |
| uses: coverallsapp/[email protected] | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # The first coveralls upload will succeed and others seem to fail now. | |
| # This is a quick workaround for doing a proper "parallel" setup: | |
| # https://github.com/coverallsapp/github-action | |
| fail-on-error: false | |
| packaging: | |
| name: Packaging | |
| runs-on: ubuntu-latest | |
| 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 | |
| python -m pip install build twine validate-pyproject[all] | |
| - name: Check and install package | |
| run: | | |
| validate-pyproject pyproject.toml | |
| python -m build | |
| python -m twine check --strict dist/* | |
| python -m pip install dist/*.whl | |
| - name: Check vcf2zarr CLI | |
| run: | | |
| vcf2zarr --help | |
| python -m bio2zarr vcf2zarr --help | |
| - name: Check vcfpartition CLI | |
| run: | | |
| vcfpartition --help | |
| python -m bio2zarr vcfpartition --help | |