chore: Migrate to pyproject.toml #263
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| cancel-previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| strategy: | |
| matrix: | |
| python-version: | |
| - 3.10 | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v3 | |
| with: | |
| # Install a specific version of uv and enable caching. | |
| version: "0.5.16" | |
| enable-cache: true | |
| - name: Set up Python | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --all-extras --dev | |
| - name: Run linting tools | |
| run: | | |
| make lint | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/[email protected] | |
| with: | |
| message: 'Please format your code with [black](https://black.readthedocs.io): `make black`.' | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| testing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - '3.10' | |
| # - "3.11" # no compatible pysam yet | |
| # - "3.12" # no compatible pysam yet | |
| needs: linting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v3 | |
| with: | |
| # Install a specific version of uv and enable caching. | |
| version: "0.5.16" | |
| enable-cache: true | |
| - name: Set up Python | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --all-extras --dev | |
| - name: Setup conda. | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda,nodefaults | |
| - name: Install hashdeep for testing purposes | |
| run: conda install hashdeep | |
| - name: Run tests | |
| run: uv run pytest | |
| - uses: codecov/codecov-action@v3 |