fix multiallelic sample-filtering bug #4
Workflow file for this run
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| name: Test pgenlib | |
| on: | |
| push: | |
| paths: | |
| - 2.0/Python/** | |
| - .github/workflows/ci.yaml | |
| jobs: | |
| wheel: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-13, macos-latest] | |
| python-version: [7, 8, 9, 10, 11, 12] | |
| exclude: | |
| - python-version: 7 | |
| os: macos-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.${{ matrix.python-version }} | |
| - name: Install prerequisites | |
| run: | | |
| pip install -U pip | |
| pip install pytest | |
| - name: Build and install | |
| working-directory: ./2.0/Python | |
| run: | | |
| mkdir -p dist | |
| pip wheel --wheel-dir dist --no-deps . | |
| pip install dist/*.whl | |
| - name: Run tests | |
| working-directory: ./2.0/Python | |
| run: | | |
| pytest tests/ | |
| - name: Test against oldest supported numpy version | |
| working-directory: ./2.0/Python | |
| if: matrix.python-version <= 8 && matrix.os != 'macos-latest' | |
| run: | | |
| pip install --force-reinstall --no-cache-dir 'numpy==1.19.0' | |
| pytest tests/ | |
| - name: Test against newest numpy version | |
| working-directory: ./2.0/Python | |
| run: | | |
| pip install -U numpy | |
| pytest tests/ | |
| sdist: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: [8, 12] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python 3.${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.${{ matrix.python-version }} | |
| - name: Install prerequisites | |
| run: | | |
| pip install -U pip | |
| pip install build pytest | |
| - name: Build and install | |
| working-directory: ./2.0/Python | |
| run: | | |
| python -m build . --sdist | |
| pip install --no-cache-dir --no-binary=pgenlib dist/pgenlib-*.tar.gz | |
| - name: Run tests | |
| working-directory: ./2.0/Python | |
| run: | | |
| pytest tests/ |