Build Wheels for Sequenzo #129
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| # GitHub Actions workflow for Sequenzo package | |
| name: Build Wheels for Sequenzo | |
| on: | |
| push: | |
| tags: | |
| - "v*" | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| build: | |
| name: Build ${{ matrix.os }} Py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, windows-latest] | |
| python-version: ['3.9', '3.10', '3.11'] | |
| steps: | |
| - name: Checkout source with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| # Add OpenMP support | |
| - name: Install OpenMP (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install libomp | |
| echo "CC=clang" >> $GITHUB_ENV | |
| echo "CXX=clang++" >> $GITHUB_ENV | |
| echo "LDFLAGS=-L$(brew --prefix libomp)/lib" >> $GITHUB_ENV | |
| echo "CPPFLAGS=-I$(brew --prefix libomp)/include" >> $GITHUB_ENV | |
| echo "SEQUENZO_ENABLE_OPENMP=1" >> $GITHUB_ENV | |
| - name: Install OpenMP (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libomp-dev | |
| echo "SEQUENZO_ENABLE_OPENMP=1" >> $GITHUB_ENV | |
| - name: Setup MSVC with OpenMP (Windows) | |
| if: runner.os == 'Windows' | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| with: | |
| arch: x64 | |
| - name: Enable OpenMP (Windows) | |
| if: runner.os == 'Windows' | |
| run: | | |
| echo "SEQUENZO_ENABLE_OPENMP=1" >> $env:GITHUB_ENV | |
| # 强制使用预编译包，避免源码编译问题 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --only-binary=all --prefer-binary "numpy<2.0" "scipy<1.14" | |
| pip install --prefer-binary Cython pybind11 build "cibuildwheel==2.23.3" twine | |
| # 针对 fastcluster，尝试安装预编译版本 | |
| pip install --only-binary=fastcluster fastcluster || pip install fastcluster | |
| - name: Build Cython wheels on macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| python setup.py build_ext --inplace | |
| python -m build | |
| - name: Clean previous build outputs | |
| if: runner.os != 'macOS' | |
| run: | | |
| rm -rf build/ dist/ *.egg-info | |
| find . -name "*.so" -delete | |
| shell: bash | |
| - name: Build wheels with cibuildwheel | |
| if: runner.os != 'macOS' | |
| run: python -m cibuildwheel --output-dir dist | |
| env: | |
| CIBW_SKIP: "*-musllinux*" # 跳过 musllinux | |
| CIBW_ARCHS_WINDOWS: "AMD64" | |
| CIBW_ARCHS_LINUX: "x86_64" | |
| CIBW_BUILD_VERBOSITY: "3" | |
| # 环境变量配置 | |
| CIBW_ENVIRONMENT_LINUX: > | |
| SEQUENZO_ENABLE_OPENMP=1 | |
| PIP_PREFER_BINARY=1 | |
| CIBW_ENVIRONMENT_WINDOWS: > | |
| SEQUENZO_ENABLE_OPENMP=1 | |
| PIP_PREFER_BINARY=1 | |
| # Linux: 安装更完整的依赖 | |
| CIBW_BEFORE_BUILD_LINUX: > | |
| yum install -y libgomp-devel openblas-devel lapack-devel || | |
| apt-get update && apt-get install -y libomp-dev libopenblas-dev liblapack-dev || | |
| echo "Dependency installation attempted" | |
| # 使用预编译包安装依赖 | |
| CIBW_BEFORE_BUILD: > | |
| pip install --upgrade pip && | |
| pip install --only-binary=all "numpy<2.0" "scipy<1.14" && | |
| pip install --prefer-binary fastcluster || echo "fastcluster installation attempted" | |
| # 测试命令 | |
| CIBW_TEST_COMMAND: > | |
| python -c "import sequenzo; print('Sequenzo import successful'); | |
| import importlib; | |
| mod = importlib.util.find_spec('sequenzo.clustering.clustering_c_code'); | |
| print('C++ extensions loaded' if mod else 'WARNING: C++ extensions not found')" | |
| - name: Show dist content | |
| run: ls -lah dist/ | |
| shell: bash | |
| - name: Check wheels | |
| run: twine check dist/* | |
| - name: Verify OpenMP Support | |
| run: | | |
| echo "=== 验证构建的wheel中的OpenMP支持 ===" | |
| python -c " | |
| import subprocess | |
| import sys | |
| import os | |
| wheel_files = [f for f in os.listdir('dist') if f.endswith('.whl') and 'cp${{ matrix.python-version }}' in f.replace('.', '')] | |
| if wheel_files: | |
| wheel_file = wheel_files[0] | |
| print(f'Installing wheel: {wheel_file}') | |
| subprocess.run([sys.executable, '-m', 'pip', 'install', '--force-reinstall', f'dist/{wheel_file}'], check=True) | |
| import sequenzo | |
| print('Sequenzo导入成功') | |
| try: | |
| import sequenzo.clustering.clustering_c_code as cc | |
| print('C++扩展加载成功') | |
| except ImportError as e: | |
| print(f'ERROR C++扩展加载失败: {e}') | |
| else: | |
| print('ERROR 未找到对应的wheel文件') | |
| " | |
| shell: bash | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: dist/ |