Local alleles - Add LPL field #219
Workflow file for this run
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: 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"] | |
| 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-14 | |
| python-version: "3.9" | |
| - os: macos-14 | |
| python-version: "3.10" | |
| 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 | |