update to snakemake>=9 and introduce CI #3
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| name: CI | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| env: | |
| UV_VERSION: "0.8.5" | |
| jobs: | |
| quality-checks: | |
| name: Quality Checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| version: ${{ env.UV_VERSION }} | |
| enable-cache: true | |
| - name: Set up Python | |
| run: uv python install 3.11 | |
| - name: Install project dependencies | |
| run: uv sync --all-groups | |
| - name: Check formatting | |
| run: uv run tox -e format-check | |
| - name: Linting | |
| run: uv run tox -e lints | |
| test: | |
| name: Test (Python ${{ matrix.python-version }}) | |
| needs: [quality-checks] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.14"] | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v6 | |
| with: | |
| version: ${{ env.UV_VERSION }} | |
| enable-cache: true | |
| - name: Set up Python ${{ matrix.python-version }} | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install project dependencies | |
| run: uv sync --all-groups | |
| - name: Run tests | |
| run: uv run tox -e py${{ matrix.python-version }} |