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ruff fix issues for CI #2
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| name: CI | |
| on: | |
| push: | |
| branches: [main, develop] | |
| pull_request: | |
| branches: [main] | |
| release: | |
| types: [published] | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ["3.9", "3.10", "3.11", "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 system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y tabix | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install htslib | |
| - name: Install package | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Run linter | |
| run: | | |
| ruff check src/ | |
| - name: Run tests | |
| run: | | |
| pytest tests/ -v --cov=bsaseq --cov-report=xml | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 | |
| if: matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest' | |
| with: | |
| files: ./coverage.xml | |
| fail_ci_if_error: false | |
| type-check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Run type checker | |
| run: | | |
| mypy src/bsaseq --ignore-missing-imports | |
| continue-on-error: true | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install build tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine | |
| - name: Build package | |
| run: python -m build | |
| - name: Check package | |
| run: twine check dist/* | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: dist | |
| path: dist/ | |
| publish: | |
| needs: [test, build] | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'release' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install build tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine | |
| - name: Build package | |
| run: python -m build | |
| - name: Publish to PyPI | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| run: twine upload dist/* | |
| docker: | |
| runs-on: ubuntu-latest | |
| needs: test | |
| if: github.event_name == 'release' || github.ref == 'refs/heads/main' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| if: github.event_name == 'release' | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Extract metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: username/bsaseq | |
| tags: | | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| type=raw,value=latest,enable=${{ github.event_name == 'release' }} | |
| - name: Build and push | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: ${{ github.event_name == 'release' }} | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max |