Add example of excluding chromosomes using site masks #315
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| name: Build and test wheels | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - test | |
| tags: | |
| - '*' | |
| release: | |
| types: [published] | |
| jobs: | |
| OSX: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python: [3.9, "3.10", 3.11, 3.12] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install deps | |
| run: | | |
| pip install --upgrade pip build delocate | |
| - name: Build Wheel | |
| run: | | |
| python -m build --wheel | |
| - name: Delocate to bundle dynamic libs | |
| run: | | |
| delocate-wheel -v dist/*.whl | |
| - name: Upload Wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: osx-wheel-${{ matrix.python }} | |
| path: dist | |
| windows: | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| python: [3.9, "3.10", 3.11, 3.12] | |
| wordsize: [64] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| - name: Install deps | |
| env: | |
| PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}" | |
| shell: bash | |
| run: | | |
| set -ex | |
| ${PYTHON} -m pip install --upgrade pip build | |
| - name: Build Wheel | |
| env: | |
| PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}" | |
| shell: bash | |
| run: | | |
| set -ex | |
| ${PYTHON} -m build --wheel | |
| - name: Upload Wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }} | |
| path: dist | |
| manylinux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: true | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Build sdist | |
| shell: bash | |
| run: | | |
| pip install --upgrade pip build | |
| python -m build --sdist | |
| - name: Upload sdist | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sdist | |
| path: dist | |
| - name: Build wheels in docker | |
| shell: bash | |
| run: | | |
| docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh | |
| - name: Upload Wheels | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: linux-wheels | |
| path: dist/wheelhouse | |
| OSX-test: | |
| needs: ['OSX'] | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python: [3.9, "3.10", 3.11, 3.12] | |
| steps: | |
| - name: Download wheels | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: osx-wheel-${{ matrix.python }} | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install wheel and test | |
| run: | | |
| python -VV | |
| # Install the local wheel | |
| pip install --no-index --no-deps --find-links=. tsinfer | |
| pip install tsinfer | |
| python -c "import tsinfer" | |
| windows-test: | |
| needs: ['windows'] | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| python: [3.9, "3.10", 3.11, 3.12] | |
| wordsize: [64] | |
| steps: | |
| - name: Download wheels | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }} | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install wheel and test | |
| run: | | |
| python -VV | |
| #patch-ng required to build lmdb | |
| pip install patch-ng | |
| # Install the local wheel | |
| pip install --no-index --no-deps --find-links=. tsinfer | |
| pip install tsinfer | |
| python -c "import tsinfer" | |
| manylinux-test: | |
| runs-on: ubuntu-latest | |
| needs: ['manylinux'] | |
| strategy: | |
| matrix: | |
| python: [3.9, "3.10", 3.11, 3.12] | |
| steps: | |
| - name: Download wheels | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: linux-wheels | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install wheel and test | |
| run: | | |
| python -VV | |
| # Install the local wheel | |
| pip install --no-index --no-deps --find-links=. tsinfer | |
| pip install tsinfer | |
| python -c "import tsinfer" | |
| PyPI_Upload: | |
| runs-on: ubuntu-latest | |
| environment: release | |
| needs: ['windows-test', 'OSX-test', 'manylinux-test'] | |
| permissions: | |
| id-token: write | |
| steps: | |
| - name: Download all | |
| uses: actions/download-artifact@v3 | |
| - name: Move to dist | |
| run: | | |
| mkdir dist | |
| cp */*.{whl,gz} dist/. | |
| - name: Publish distribution to Test PyPI | |
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| repository_url: https://test.pypi.org/legacy/ | |
| - name: Publish distribution to PRODUCTION PyPI | |
| if: github.event_name == 'release' | |
| uses: pypa/gh-action-pypi-publish@release/v1 |