Recompute INFO fields on sample selection #130
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - uses: pre-commit/[email protected] | |
| python_test: | |
| name: Python tests | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| # Use macos-13 because pip binary packages for ARM aren't | |
| # available for many dependencies | |
| os: [macos-13, macos-14, ubuntu-latest] | |
| python-version: ["3.9", "3.10", "3.11"] | |
| exclude: | |
| # Just run macos tests on one Python version | |
| - os: macos-13 | |
| python-version: "3.10" | |
| - os: macos-13 | |
| python-version: "3.11" | |
| - os: macos-14 | |
| python-version: "3.9" | |
| - os: macos-14 | |
| python-version: "3.10" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - 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 dependencies | |
| run: | | |
| conda install bcftools | |
| python -m pip install --upgrade pip | |
| python -m pip install '.[dev]' | |
| # Build the extension module in-place so pytest can find it | |
| python3 setup.py build_ext --inplace | |
| - name: Run tests | |
| run: | | |
| pytest | |
| c_python_test: | |
| name: CPython interface tests | |
| 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 system dependencies | |
| run: | | |
| sudo apt install -y gcovr | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install numpy pytest pytest_cov | |
| - name: Build module with coverage | |
| run: | | |
| # Build the extension module in-place so pytest can find it | |
| CFLAGS="--coverage" python3 setup.py build_ext --inplace | |
| - name: Run tests | |
| run: | | |
| pytest -vs tests/test_cpython_interface.py | |
| - name: Show coverage | |
| run: | | |
| gcovr --filter vcztools | |
| c_test: | |
| name: C tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| sudo apt install -y ninja-build libcunit1-dev valgrind meson gcovr | |
| - name: Build | |
| working-directory: ./lib | |
| run: | | |
| meson setup -Db_coverage=true build | |
| - name: Tests | |
| working-directory: ./lib | |
| run: | | |
| ninja -C build test | |
| - name: Show coverage | |
| working-directory: ./lib | |
| run: | | |
| ninja -C build coverage-text | |
| cat build/meson-logs/coverage.txt | |
| - name: Valgrind | |
| working-directory: ./lib | |
| run: | | |
| valgrind --leak-check=full --error-exitcode=1 ./build/tests | |
| packaging: | |
| name: Packaging | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install build twine validate-pyproject[all] | |
| - name: Check and install package | |
| run: | | |
| validate-pyproject pyproject.toml | |
| python -m build | |
| python -m twine check --strict dist/* | |
| python -m pip install dist/*.whl | |
| - name: Check vcztools CLI | |
| run: | | |
| vcztools --help | |
| # Make sure we don't have ``vcztools`` in the CWD | |
| cd tests | |
| python -m vcztools --help | |