install necessary packages with apt #3
Workflow file for this run
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| name: Python package | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| cqa: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install packages | |
| run: | | |
| sudo apt install libhts-dev libhts3 libhtscodecs-dev libhtscodecs2 tabix | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --use-deprecated=legacy-resolver -e .[dev] | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Format check with isort | |
| run: | | |
| isort --check src | |
| - name: Format check with black | |
| run: | | |
| black --check src | |
| - name: Security check with bandit | |
| run: | | |
| bandit -ll -r src | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| make develop | |
| - name: Test with pytest | |
| run: | | |
| make test | |
| deploy: | |
| needs: | |
| - cqa | |
| - test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Environment | |
| run: | | |
| echo "::group::Environment info" | |
| echo github.event_name = ${{ github.event_name }} | |
| echo refs = ${{ github.ref }} | |
| echo tags = ${{ startsWith(github.ref, 'refs/tags') }} | |
| echo "::endgroup::" | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine | |
| - name: Build package | |
| run: python -m build | |
| - name: Publish package | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} |