Use sgkit.distarray for gwas_linear_regression #241
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| name: Wheels | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - test | |
| tags: | |
| - '*' | |
| release: | |
| types: [published] | |
| jobs: | |
| build: | |
| # This workflow only runs on the origin org | |
| if: github.repository_owner == 'sgkit-dev' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools twine wheel | |
| - name: Build a source distribution and a wheel | |
| run: | | |
| python setup.py sdist bdist_wheel | |
| python -m twine check --strict dist/* | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: dist | |
| unix-test: | |
| # This workflow only runs on the origin org | |
| if: github.repository_owner == 'sgkit-dev' | |
| needs: ['build'] | |
| strategy: | |
| matrix: | |
| # don't use macos-latest as it uses M1 which doesn't work | |
| os: [ubuntu-latest, macos-12] | |
| python-version: ["3.9", "3.10", "3.11"] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| # checkout repo to subdirectory to get access to scripts | |
| - uses: actions/checkout@v2 | |
| with: | |
| path: sgkit-copy | |
| - name: Download artifacts | |
| uses: actions/[email protected] | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install wheel and test | |
| run: | | |
| python -VV | |
| # Install the local wheel | |
| wheel=$(ls artifact/sgkit-*.whl) | |
| pip install ${wheel} ${wheel}[bgen] ${wheel}[plink] ${wheel}[vcf] | |
| python sgkit-copy/.github/scripts/test_sgkit.py | |
| python sgkit-copy/.github/scripts/test_sgkit_bgen.py | |
| python sgkit-copy/.github/scripts/test_sgkit_plink.py | |
| python sgkit-copy/.github/scripts/test_sgkit_vcf.py | |
| # Windows doesn't support vcf | |
| windows-test: | |
| # This workflow only runs on the origin org | |
| if: github.repository_owner == 'sgkit-dev' | |
| runs-on: windows-latest | |
| needs: ['build'] | |
| strategy: | |
| matrix: | |
| python-version: ["3.9"] | |
| steps: | |
| # checkout repo to subdirectory to get access to scripts | |
| - uses: actions/checkout@v2 | |
| with: | |
| path: sgkit-copy | |
| - name: Download artifacts | |
| uses: actions/[email protected] | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install wheel and test | |
| run: | | |
| python -VV | |
| # Install the local wheel | |
| $env:wheel = $(ls artifact/sgkit-*.whl) | |
| pip install $env:wheel "$env:wheel[bgen]" "$env:wheel[plink]" | |
| python sgkit-copy/.github/scripts/test_sgkit.py | |
| python sgkit-copy/.github/scripts/test_sgkit_bgen.py | |
| python sgkit-copy/.github/scripts/test_sgkit_plink.py | |
| pypi-upload: | |
| if: github.repository_owner == 'sgkit-dev' | |
| runs-on: ubuntu-latest | |
| needs: ['unix-test', 'windows-test'] | |
| steps: | |
| - name: Download all | |
| uses: actions/[email protected] | |
| - name: Move to dist | |
| run: | | |
| mkdir dist | |
| cp */*.{whl,gz} dist/. | |
| - name: Publish package to TestPyPI | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| repository_url: https://test.pypi.org/legacy/ | |
| - name: Publish package to PyPI | |
| if: github.event_name == 'release' | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} |