CI #239
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| name: CI | |
| on: | |
| merge_group: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 04:44 on Monday, see https://crontab.guru/ | |
| - cron: "44 4 * * 1" | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| - name: Install uv and set the python version | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: "3.12" | |
| - name: Install lint group | |
| run: uv sync --locked --only-group lint | |
| - name: Run prek | |
| run: | | |
| uv run --locked --only-group lint \ | |
| prek -c prek.toml run --all-files --show-diff-on-failure | |
| python_test: | |
| name: Python tests | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [macos-14, ubuntu-latest] | |
| python-version: ["3.12", "3.13"] | |
| exclude: | |
| # Just run macos tests on one Python version | |
| - os: macos-14 | |
| python-version: "3.13" | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Miniconda with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| - name: Install conda test tools | |
| run: conda install bcftools | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Install test dependencies | |
| run: | | |
| uv sync --locked --group test --no-default-groups | |
| - name: Run tests | |
| run: | | |
| uv run pytest | |
| packaging: | |
| name: Packaging | |
| runs-on: ubuntu-24.04 | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install uv and set the python version | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| python-version: "3.12" | |
| - name: Install packaging deps | |
| run: uv sync --locked --group packaging --no-default-groups | |
| - name: Validate pyproject | |
| run: uv run --locked --group packaging --no-default-groups validate-pyproject pyproject.toml -v | |
| - name: Build artefacts | |
| run: uv build | |
| - name: Twine check | |
| run: uv run --locked --group packaging --no-default-groups twine check --strict dist/* | |
| - name: Install into venv | |
| run: | | |
| uv venv cli-test | |
| uv pip install --python=cli-test dist/*.whl | |
| - name: Check vczstore CLI | |
| run: | | |
| ./cli-test/bin/vczstore --help | |
| cd tests | |
| ../cli-test/bin/python -m vczstore --help | |
| test-zarr-version: | |
| name: Test Zarr versions | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| zarr-format: [2, 3] | |
| steps: | |
| - uses: actions/checkout@v4.2.2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: "3.12" | |
| channels: conda-forge,bioconda | |
| - name: Install conda test tools | |
| run: conda install bcftools | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| - name: Install test dependencies | |
| run: | | |
| uv sync --locked --group test --no-default-groups | |
| - name: Run tests | |
| run: | | |
| uv run pytest | |
| env: | |
| BIO2ZARR_DEFAULT_ZARR_FORMAT: ${{ matrix.zarr-format }} |