Build Wheels for Sequenzo #324
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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 }} | |
| CIBW_VERSION: "3.1.4" | |
| jobs: | |
| build: | |
| name: Build ${{ matrix.os }} Py${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| # max-parallel: 6 | |
| matrix: | |
| include: | |
| # Linux 配置 | |
| - os: ubuntu-latest | |
| python-version: '3.9' | |
| python-version-nodot: '39' | |
| - os: ubuntu-latest | |
| python-version: '3.10' | |
| python-version-nodot: '310' | |
| - os: ubuntu-latest | |
| python-version: '3.11' | |
| python-version-nodot: '311' | |
| - os: ubuntu-latest | |
| python-version: '3.12' | |
| python-version-nodot: '312' | |
| - os: ubuntu-latest | |
| python-version: '3.13' | |
| python-version-nodot: '313' | |
| - os: ubuntu-latest | |
| python-version: '3.14' | |
| python-version-nodot: '314' | |
| # Windows 配置 | |
| - os: windows-latest | |
| python-version: '3.9' | |
| python-version-nodot: '39' | |
| - os: windows-latest | |
| python-version: '3.10' | |
| python-version-nodot: '310' | |
| - os: windows-latest | |
| python-version: '3.11' | |
| python-version-nodot: '311' | |
| - os: windows-latest | |
| python-version: '3.12' | |
| python-version-nodot: '312' | |
| - os: windows-latest | |
| python-version: '3.13' | |
| python-version-nodot: '313' | |
| # - os: windows-latest | |
| # python-version: '3.14' | |
| # python-version-nodot: '314' | |
| # macOS x86_64 | |
| - os: macos-15-intel # 使用 Intel Mac 运行器 | |
| python-version: '3.9' | |
| python-version-nodot: '39' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| - os: macos-15-intel | |
| python-version: '3.10' | |
| python-version-nodot: '310' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| - os: macos-15-intel | |
| python-version: '3.11' | |
| python-version-nodot: '311' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| - os: macos-15-intel | |
| python-version: '3.12' | |
| python-version-nodot: '312' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| - os: macos-15-intel | |
| python-version: '3.13' | |
| python-version-nodot: '313' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| - os: macos-15-intel | |
| python-version: '3.14' | |
| python-version-nodot: '314' | |
| macos-arch: 'x86_64' | |
| macos-group: intel | |
| # macOS arm64 | |
| - os: macos-latest # 使用 Apple Silicon Mac 运行器 | |
| python-version: '3.9' | |
| python-version-nodot: '39' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| - os: macos-latest | |
| python-version: '3.10' | |
| python-version-nodot: '310' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| - os: macos-latest | |
| python-version: '3.11' | |
| python-version-nodot: '311' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| - os: macos-latest | |
| python-version: '3.12' | |
| python-version-nodot: '312' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| - os: macos-latest | |
| python-version: '3.13' | |
| python-version-nodot: '313' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| - os: macos-latest | |
| python-version: '3.14' | |
| python-version-nodot: '314' | |
| macos-arch: 'arm64' | |
| macos-group: apple-silicon | |
| env: | |
| PIP_DEFAULT_TIMEOUT: "120" | |
| PIP_RETRIES: "10" | |
| PIP_DISABLE_PIP_VERSION_CHECK: "1" | |
| HOMEBREW_NO_AUTO_UPDATE: "1" | |
| HOMEBREW_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| CIBW_DEPENDENCY_VERSIONS: "pinned" | |
| steps: | |
| - name: Checkout source with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| # cibuildwheel>=3 requires the runner Python to be >=3.11. | |
| # Target wheel tags are still controlled by CIBW_BUILD (cp39/cp310/cp311/cp312). | |
| python-version: "3.11" | |
| - name: Cache pip (Linux) | |
| if: runner.os == 'Linux' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml', 'setup.py', 'setup.cfg', '.github/workflows/python-app.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-pip- | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip (macOS) | |
| if: runner.os == 'macOS' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml', 'setup.py', 'setup.cfg', '.github/workflows/python-app.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-pip- | |
| ${{ runner.os }}-pip- | |
| - name: Cache pip (Windows) | |
| if: runner.os == 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~\AppData\Local\pip\Cache | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-pip-${{ hashFiles('pyproject.toml', 'setup.py', 'setup.cfg', '.github/workflows/python-app.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-pip- | |
| ${{ runner.os }}-pip- | |
| - name: Cache cibuildwheel virtualenv download (Linux) | |
| if: runner.os == 'Linux' | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/.cache/pypa/cibuildwheel/Cache | |
| ~/.cache/cibuildwheel | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-cibw-${{ env.CIBW_VERSION }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-cibw- | |
| ${{ runner.os }}-cibw- | |
| - name: Cache cibuildwheel virtualenv download (macOS) | |
| if: runner.os == 'macOS' | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ~/Library/Caches/pypa/cibuildwheel/Cache | |
| ~/Library/Caches/cibuildwheel | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-cibw-${{ env.CIBW_VERSION }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-cibw- | |
| ${{ runner.os }}-cibw- | |
| - name: Cache cibuildwheel virtualenv download (Windows) | |
| if: runner.os == 'Windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~\AppData\Local\pypa\cibuildwheel\Cache | |
| key: ${{ runner.os }}-py${{ matrix.python-version }}-cibw-${{ env.CIBW_VERSION }} | |
| restore-keys: | | |
| ${{ runner.os }}-py${{ matrix.python-version }}-cibw- | |
| ${{ runner.os }}-cibw- | |
| - name: Warm cibuildwheel virtualenv cache with retry | |
| if: ${{ false }} # Disabled: this warm-up can amplify GitHub rate limits under matrix builds. | |
| continue-on-error: true | |
| run: | | |
| python - <<'PY' | |
| import os | |
| import shutil | |
| import sys | |
| import time | |
| import urllib.request | |
| from pathlib import Path | |
| version = "20.30.0" | |
| url = f"https://raw.githubusercontent.com/pypa/get-virtualenv/{version}/public/virtualenv.pyz" | |
| filename = f"virtualenv-{version}.pyz" | |
| home = Path.home() | |
| candidates = [] | |
| if os.name == "nt": | |
| local_appdata = os.environ.get("LOCALAPPDATA") | |
| if local_appdata: | |
| candidates.append(Path(local_appdata) / "pypa" / "cibuildwheel" / "Cache" / filename) | |
| candidates.append(home / "AppData" / "Local" / "pypa" / "cibuildwheel" / "Cache" / filename) | |
| elif sys.platform == "darwin": | |
| candidates.append(home / "Library" / "Caches" / "pypa" / "cibuildwheel" / "Cache" / filename) | |
| candidates.append(home / "Library" / "Caches" / "cibuildwheel" / filename) | |
| else: | |
| candidates.append(home / ".cache" / "pypa" / "cibuildwheel" / "Cache" / filename) | |
| candidates.append(home / ".cache" / "cibuildwheel" / filename) | |
| existing = next((p for p in candidates if p.exists()), None) | |
| if existing: | |
| print(f"[cache-hit] {existing}") | |
| sys.exit(0) | |
| tmp_file = Path.cwd() / filename | |
| for attempt in range(1, 6): | |
| try: | |
| print(f"[download] attempt {attempt}/5: {url}") | |
| req = urllib.request.Request( | |
| url, | |
| headers={"User-Agent": "sequenzo-ci/1.0 (+github-actions)"} | |
| ) | |
| with urllib.request.urlopen(req, timeout=120) as response: | |
| data = response.read() | |
| tmp_file.write_bytes(data) | |
| print(f"[download] completed, size={len(data)} bytes") | |
| break | |
| except Exception as exc: | |
| if attempt == 5: | |
| print(f"[download] giving up after 5 attempts: {exc}") | |
| sys.exit(0) | |
| sleep_s = attempt * 20 | |
| print(f"[download] failed: {exc}. retry in {sleep_s}s") | |
| time.sleep(sleep_s) | |
| for path in candidates: | |
| path.parent.mkdir(parents=True, exist_ok=True) | |
| shutil.copy2(tmp_file, path) | |
| print(f"[cache-write] {path}") | |
| tmp_file.unlink(missing_ok=True) | |
| PY | |
| shell: bash | |
| - name: Ensure setuptools/wheel for macOS | |
| if: runner.os == 'macOS' | |
| run: python -m pip install --upgrade --retries 10 --timeout 120 pip setuptools wheel "cibuildwheel==${CIBW_VERSION}" | |
| # Build libomp from LLVM source so the bundled dylib's minos matches the | |
| # wheel deployment target (Homebrew libomp 18+ requires macOS 13+, which | |
| # would break the minos guarantee of macosx_10_15 / macosx_11_0 wheels). | |
| # | |
| # Previously this caused "symbol not found in flat namespace | |
| # '___kmpc_dispatch_deinit'" at import time. Root cause: Apple Clang emits | |
| # calls to __kmpc_dispatch_deinit for schedule(dynamic/guided) loops, but the | |
| # LLVM openmp runtime we build from source omits it (removed in LLVM 13). | |
| # -fno-openmp-extensions does NOT suppress this symbol on modern Apple Clang. | |
| # Fix: inject a no-op __kmpc_dispatch_deinit stub into the CI libomp build | |
| # (see build_macos_ci_libomp.sh) so bundled libomp satisfies the reference. | |
| - name: Cache CI libomp (macOS) | |
| if: runner.os == 'macOS' | |
| uses: actions/cache@v4 | |
| with: | |
| path: .local-libomp | |
| key: macos-libomp-${{ matrix.macos-arch }}-${{ matrix.macos-arch == 'x86_64' && '10.15' || '11.0' }}-llvm18.1.8-${{ hashFiles('maintenance_scripts/build_macos_ci_libomp.sh') }} | |
| - name: Install OpenMP (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| set -euo pipefail | |
| if [ "${{ matrix.macos-arch }}" == "x86_64" ]; then | |
| MACOS_DEPLOY_TARGET="10.15" | |
| else | |
| MACOS_DEPLOY_TARGET="11.0" | |
| fi | |
| chmod +x maintenance_scripts/build_macos_ci_libomp.sh | |
| maintenance_scripts/build_macos_ci_libomp.sh \ | |
| "${{ matrix.macos-arch }}" \ | |
| "$MACOS_DEPLOY_TARGET" \ | |
| "$GITHUB_WORKSPACE/.local-libomp" | |
| LIBOMP_PREFIX="$GITHUB_WORKSPACE/.local-libomp" | |
| echo "CI libomp prefix: $LIBOMP_PREFIX" | |
| file "$LIBOMP_PREFIX/lib/libomp.dylib" | |
| otool -l "$LIBOMP_PREFIX/lib/libomp.dylib" | awk '/LC_BUILD_VERSION|LC_VERSION_MIN_MACOSX|minos|version/' | |
| { | |
| echo "CC=clang" | |
| echo "CXX=clang++" | |
| echo "MACOSX_DEPLOYMENT_TARGET=$MACOS_DEPLOY_TARGET" | |
| echo "LDFLAGS=-L$LIBOMP_PREFIX/lib -Wl,-rpath,@loader_path/../.dylibs" | |
| echo "CPPFLAGS=-I$LIBOMP_PREFIX/include" | |
| echo "SEQUENZO_ENABLE_OPENMP=1" | |
| echo "SEQUENZO_LIBOMP_PREFIX=$LIBOMP_PREFIX" | |
| echo "LIBOMP_PATH=$LIBOMP_PREFIX/lib" | |
| } >> "$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 | |
| - name: Set Windows encoding (Windows only) | |
| if: runner.os == 'Windows' | |
| run: | | |
| echo "PYTHONIOENCODING=utf-8" >> $env:GITHUB_ENV | |
| echo "Setting Python encoding to UTF-8 for Windows" | |
| - name: Sanitize PATH for Windows linker resolution | |
| if: runner.os == 'Windows' | |
| shell: pwsh | |
| run: | | |
| $parts = $env:PATH -split ';' | Where-Object { | |
| $_ -and ($_ -notmatch '(?i)\\Git\\usr\\bin\\?$') | |
| } | |
| $cleanPath = $parts -join ';' | |
| "PATH=$cleanPath" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append | |
| $env:PATH = $cleanPath | |
| Write-Host "Resolved cl/link after PATH cleanup:" | |
| where.exe cl | |
| where.exe link | |
| - name: Locate MSVC LLVM OpenMP runtime (Windows) | |
| if: runner.os == 'Windows' | |
| shell: pwsh | |
| run: | | |
| $vswhere = "${env:ProgramFiles(x86)}\Microsoft Visual Studio\Installer\vswhere.exe" | |
| $installPath = & $vswhere -latest -products * -property installationPath | |
| if (-not $installPath) { | |
| throw "vswhere did not return a Visual Studio installation path" | |
| } | |
| $releaseMatches = Get-ChildItem -Path "$installPath\VC\Redist\MSVC\*\x64\Microsoft.VC*.OpenMP.LLVM\libomp140.x86_64.dll" -ErrorAction SilentlyContinue | Sort-Object FullName | |
| $debugMatches = Get-ChildItem -Path "$installPath\VC\Redist\MSVC\*\debug_nonredist\x64\Microsoft.VC*.OpenMP.LLVM\libomp140.x86_64.dll" -ErrorAction SilentlyContinue | Sort-Object FullName | |
| $llvmMatches = @( | |
| Get-ChildItem -Path "$installPath\VC\Tools\Llvm\x64\bin\libomp140.x86_64.dll" -ErrorAction SilentlyContinue | |
| Get-ChildItem -Path "$installPath\VC\Tools\Llvm\x64\bin\libomp140.dll" -ErrorAction SilentlyContinue | |
| ) | Sort-Object FullName | |
| $dll = $null | |
| if ($releaseMatches) { | |
| $dll = $releaseMatches[-1] | |
| } elseif ($debugMatches) { | |
| $dll = $debugMatches[-1] | |
| Write-Host "WARNING: using debug_nonredist OpenMP runtime: $($dll.FullName)" | |
| } elseif ($llvmMatches) { | |
| $dll = $llvmMatches[-1] | |
| } | |
| if (-not $dll) { | |
| throw "libomp140*.dll not found under Visual Studio install: $installPath" | |
| } | |
| Write-Host "Found OpenMP runtime: $($dll.FullName)" | |
| "LIBOMP_DLL_DIR=$($dll.DirectoryName)" | Out-File -FilePath $env:GITHUB_ENV -Encoding utf8 -Append | |
| # Install dependencies with fallback strategy | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade --retries 10 --timeout 120 pip setuptools wheel "cibuildwheel==${CIBW_VERSION}" | |
| # Use oldest-supported-numpy for builds to ensure forward compatibility | |
| pip install --retries 10 --timeout 120 oldest-supported-numpy || pip install --retries 10 --timeout 120 "numpy>=1.21.0" | |
| pip install --retries 10 --timeout 120 --only-binary=all "scipy<1.16" || echo "scipy will be installed in cibuildwheel" | |
| pip install --retries 10 --timeout 120 --prefer-binary Cython pybind11 build twine | |
| shell: bash | |
| - name: Build wheels with cibuildwheel | |
| run: | | |
| set -euo pipefail | |
| for attempt in 1 2 3; do | |
| echo "cibuildwheel attempt ${attempt}/3" | |
| if python -m cibuildwheel --output-dir dist; then | |
| exit 0 | |
| fi | |
| if [ "$attempt" -lt 3 ]; then | |
| sleep_seconds=$((attempt * 30)) | |
| echo "cibuildwheel failed, retrying in ${sleep_seconds}s..." | |
| sleep "$sleep_seconds" | |
| fi | |
| done | |
| echo "cibuildwheel failed after 3 attempts" | |
| exit 1 | |
| shell: bash | |
| env: | |
| CIBW_BUILD: "cp${{ matrix.python-version-nodot }}-*" # 只构建当前 Python 版本的轮子 (e.g., cp39-*, cp310-*) | |
| CIBW_SKIP: "*-musllinux* pp*" # 跳过 musllinux 和 PyPy | |
| # hmmlearn has no Windows py3.14 binary wheel yet (3.14 is still pre-release) | |
| # and its source build fails due to link.exe PATH issues in cibuildwheel's | |
| # isolated test venv. Skip the test phase only; the wheel is still built. | |
| CIBW_TEST_SKIP: "cp314-win_amd64" | |
| CIBW_ARCHS_WINDOWS: "AMD64" | |
| CIBW_ARCHS_LINUX: "x86_64" | |
| CIBW_ARCHS_MACOS: "${{ matrix.macos-arch }}" | |
| # Alternative: Use separate architecture wheels if universal2 causes issues | |
| # CIBW_ARCHS_MACOS: "x86_64 arm64" # Build separate wheels for each architecture | |
| # 或者根据架构设置不同的目标 | |
| # Build libomp from source in CI so bundled dylib matches these targets. | |
| CIBW_TARGET_OSX_x86_64: "10.15" | |
| CIBW_TARGET_OSX_arm64: "11.0" | |
| CIBW_BUILD_VERBOSITY: "3" | |
| # Environment variables | |
| CIBW_ENVIRONMENT_LINUX: SEQUENZO_ENABLE_OPENMP=1 | |
| CIBW_ENVIRONMENT_WINDOWS: SEQUENZO_ENABLE_OPENMP=1 DISTUTILS_USE_SDK=1 | |
| # 显式将 runner 级别的环境变量传入 cibuildwheel 的隔离 venv | |
| # 避免 $LIBOMP_PATH 因隐式继承失败而导致 delocate 找不到 libomp | |
| CIBW_PASS_ENV: "LIBOMP_PATH LIBOMP_DLL_DIR SEQUENZO_LIBOMP_PREFIX SEQUENZO_ENABLE_OPENMP MACOSX_DEPLOYMENT_TARGET GITHUB_WORKSPACE" | |
| # macOS: Set OpenMP environment with proper library paths and rpath for bundling | |
| # REPAIR_LIBRARY_PATH 是 libomp 路径的副本，专用于在 repair 阶段 | |
| # 内部设置 DYLD_LIBRARY_PATH（macOS SIP 会剥离子进程继承的 DYLD_LIBRARY_PATH） | |
| CIBW_ENVIRONMENT_MACOS: > | |
| SEQUENZO_ENABLE_OPENMP=1 | |
| REPAIR_LIBRARY_PATH="$LIBOMP_PATH" | |
| LDFLAGS="-L$LIBOMP_PATH -Wl,-rpath,@loader_path/../.dylibs" | |
| CPPFLAGS="-I$LIBOMP_PATH/../include" | |
| CFLAGS="-fno-openmp-extensions" | |
| CXXFLAGS="-fno-openmp-extensions" | |
| # macOS: ensure libomp is available and properly linked | |
| CIBW_BEFORE_BUILD_MACOS: | | |
| echo "Installing build dependencies for macOS" | |
| python -m pip install --upgrade pip | |
| CURRENT_ARCH=$(uname -m) | |
| echo "Building for architecture: $CURRENT_ARCH" | |
| # 安装 delocate | |
| echo "Installing delocate for wheel repair..." | |
| pip install delocate | |
| # 验证 CI 构建的 libomp（兼容 wheel 最低 macOS 版本） | |
| if [ -n "${SEQUENZO_LIBOMP_PREFIX:-}" ] && [ -f "$SEQUENZO_LIBOMP_PREFIX/lib/libomp.dylib" ]; then | |
| echo "[OK] CI libomp found at: $SEQUENZO_LIBOMP_PREFIX" | |
| file "$SEQUENZO_LIBOMP_PREFIX/lib/libomp.dylib" | |
| elif [ -d "$LIBOMP_PATH" ]; then | |
| echo "[OK] libomp found at: $LIBOMP_PATH" | |
| if [ -f "$LIBOMP_PATH/libomp.dylib" ]; then | |
| echo "libomp.dylib architecture:" | |
| file "$LIBOMP_PATH/libomp.dylib" | |
| fi | |
| else | |
| echo "[WARNING] libomp not found at $LIBOMP_PATH" | |
| fi | |
| # macOS: Use delocate to bundle libomp into the wheel | |
| # 修复关键点： | |
| # 1. 在 repair 命令内部显式设置 DYLD_LIBRARY_PATH | |
| # macOS SIP 会在子进程启动时剥离 DYLD_LIBRARY_PATH， | |
| # 所以必须在 shell 命令内临时设置，delocate 才能找到 libomp.dylib。 | |
| # 2. 添加 --require-archs {delocate_archs} 确保打包的 dylib 架构 | |
| # 与 .so 文件一致（防止 arm64/x86_64 混淆导致用户端 crash）。 | |
| # 3. wheel repair 失败时必须让 CI 失败，不能发布未打包 libomp 的 macOS wheel。 | |
| CIBW_REPAIR_WHEEL_COMMAND_MACOS: | | |
| echo "=== Repairing macOS wheel ===" | |
| echo "Current architecture: $(uname -m)" | |
| echo "Wheel: {wheel}" | |
| echo "REPAIR_LIBRARY_PATH: ${REPAIR_LIBRARY_PATH}" | |
| # 在 repair 命令内部设置 DYLD_LIBRARY_PATH，绕过 macOS SIP 的剥离 | |
| DYLD_LIBRARY_PATH="${REPAIR_LIBRARY_PATH}:${DYLD_LIBRARY_PATH:-}" \ | |
| delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel} || { | |
| echo "[ERROR] delocate failed; refusing to publish an unrepaired macOS wheel." | |
| exit 1 | |
| } | |
| # 验证修复结果：确认 libomp 是否真的打包进去了 | |
| if ls {dest_dir}/*.whl 1> /dev/null 2>&1; then | |
| REPAIRED_WHEEL=$(ls {dest_dir}/*.whl | head -1) | |
| echo "Repaired wheel: $REPAIRED_WHEEL" | |
| echo "=== Bundled dependencies ===" | |
| delocate-listdeps --all "$REPAIRED_WHEEL" 2>&1 || echo "Dependency listing failed" | |
| if delocate-listdeps --all "$REPAIRED_WHEEL" 2>&1 | grep -q "libomp"; then | |
| echo "[OK] libomp successfully bundled into wheel" | |
| else | |
| echo "[ERROR] libomp is not bundled into the macOS wheel." | |
| exit 1 | |
| fi | |
| fi | |
| # Linux: minimal build dependencies (skip R/rpy2 - they're optional) | |
| CIBW_BEFORE_BUILD_LINUX: | | |
| echo "Installing minimal build dependencies for Linux" | |
| python -m pip install --upgrade pip | |
| echo "Skipping R/rpy2 installation - they are optional dependencies" | |
| # 修复 Linux 构建问题 | |
| echo "=== Preparing clean Linux build ===" | |
| python -m pip install --upgrade pip | |
| echo "Ensuring clean build environment..." | |
| # 再次清理，确保没有残留的项目构建文件；不要全仓库扫描依赖/实验目录。 | |
| find ./sequenzo -name "*.so" -type f -delete 2>/dev/null || true | |
| find . -maxdepth 1 -name "*.so" -type f -delete 2>/dev/null || true | |
| find ./sequenzo -path "*/utils/*.c" -type f -print0 | while IFS= read -r -d '' cfile; do | |
| pyxfile="${cfile%.c}.pyx" | |
| if [ -f "$pyxfile" ]; then | |
| rm -f "$cfile" | |
| fi | |
| done | |
| rm -rf build/ dist/ *.egg-info | |
| echo "Clean build environment ready" | |
| # 使用绝对路径验证源文件 | |
| echo "Current working directory: $(pwd)" | |
| echo "Absolute path verification:" | |
| if [ -f "$(pwd)/sequenzo/dissimilarity_measures/src/module.cpp" ]; then | |
| echo "[SUCCESS] module.cpp found at absolute path: $(pwd)/sequenzo/dissimilarity_measures/src/module.cpp" | |
| else | |
| echo "[ERROR] module.cpp NOT FOUND at absolute path: $(pwd)/sequenzo/dissimilarity_measures/src/module.cpp" | |
| echo "Available files in src directory:" | |
| ls -la "$(pwd)/sequenzo/dissimilarity_measures/src/" 2>/dev/null || echo "Cannot list src directory" | |
| fi | |
| # 设置 Linux 修复策略 | |
| CIBW_REPAIR_WHEEL_COMMAND_LINUX: | | |
| echo "=== Attempting wheel repair ===" | |
| echo "Wheel to repair: {wheel}" | |
| # wheel repair 失败时必须让 CI 失败，不能发布未修复 wheel。 | |
| auditwheel repair -w {dest_dir} {wheel} || { | |
| echo "[ERROR] auditwheel repair failed; refusing to publish an unrepaired Linux wheel." | |
| exit 1 | |
| } | |
| # 检查修复结果 | |
| if ls {dest_dir}/*.whl 1> /dev/null 2>&1; then | |
| REPAIRED_WHEEL=$(ls {dest_dir}/*.whl | head -1) | |
| echo "Final wheel: $REPAIRED_WHEEL" | |
| auditwheel show "$REPAIRED_WHEEL" || echo "Cannot show wheel info" | |
| fi | |
| # Windows: setup MSVC environment | |
| CIBW_BEFORE_BUILD_WINDOWS: | | |
| echo "Installing wheel repair dependencies" | |
| python -m pip install --upgrade pip | |
| python -m pip install delvewheel | |
| echo "Setting up MSVC environment" | |
| call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat" | |
| for /f "usebackq tokens=*" %%i in (`"%ProgramFiles(x86)%\Microsoft Visual Studio\Installer\vswhere.exe" -latest -products * -requires Microsoft.VisualStudio.Component.VC.Tools.x86.x64 -find VC\Tools\MSVC\**\bin\Hostx64\x64`) do set "VCTOOLS_BIN=%%i" | |
| if not defined VCTOOLS_BIN ( | |
| echo "ERROR: Unable to locate MSVC linker path via vswhere" | |
| exit /b 1 | |
| ) | |
| set "PATH=%VCTOOLS_BIN%;%PATH%" | |
| where cl | |
| where link | |
| echo "Using minimal build dependencies" | |
| CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: python maintenance_scripts/repair_windows_wheel.py "{dest_dir}" "{wheel}" | |
| # 注意：CIBW_BEFORE_BUILD（通用）在所有平台都提供了平台专用版本时 | |
| # 永远不会执行（平台专用变体会覆盖通用变体），已移除死代码。 | |
| # Test command: use heredoc to keep the entire script in one shell command (fix Linux quoting) | |
| # macOS test: intentionally does NOT set DYLD_LIBRARY_PATH to any system | |
| # libomp. The wheel must be self-contained after delocate repair: the | |
| # bundled .dylibs/libomp.dylib (built from LLVM source in CI) must satisfy | |
| # all OpenMP symbols referenced by the .so files. | |
| # | |
| # Previously this command pre-loaded Homebrew libomp via DYLD_LIBRARY_PATH, | |
| # which masked a "symbol not found in flat namespace '___kmpc_dispatch_deinit'" | |
| # bug: delocate bundles the LLVM-source libomp unless our dispatch_deinit stub | |
| # is present. The pre-load caused CI tests to pass while users hit the error | |
| # locally. Fix: test without any system-libomp fallback so the CI gate is honest. | |
| CIBW_TEST_COMMAND_MACOS: | | |
| echo "=== Testing macOS wheel (bundled libomp only — no DYLD_LIBRARY_PATH fallback) ===" | |
| echo "Architecture: $(uname -m)" | |
| echo "Python version: $(python --version)" | |
| # Verify the wheel is self-contained: .dylibs must exist and contain libomp | |
| python - <<'PY' | |
| import sequenzo, os, glob, sys | |
| pkg_dir = os.path.dirname(sequenzo.__file__) | |
| dylibs_dir = os.path.join(pkg_dir, '.dylibs') | |
| if os.path.exists(dylibs_dir): | |
| libs = glob.glob(os.path.join(dylibs_dir, '*.dylib')) | |
| print(f'[OK] .dylibs found: {[os.path.basename(l) for l in libs]}') | |
| if not any('libomp' in os.path.basename(l) for l in libs): | |
| print('[ERROR] libomp not bundled into wheel .dylibs/') | |
| sys.exit(1) | |
| else: | |
| print('[ERROR] .dylibs directory missing — delocate repair may have failed') | |
| sys.exit(1) | |
| PY | |
| echo "" | |
| echo "=== Testing Sequenzo import ===" | |
| python - <<'PY' | |
| import importlib.util | |
| import sys | |
| import numpy as np | |
| try: | |
| import sequenzo | |
| print('[OK] sequenzo import successful') | |
| except ImportError as e: | |
| print(f'[ERROR] Failed to import sequenzo: {e}') | |
| sys.exit(1) | |
| # clustering_c_code uses OpenMP dynamic schedules — this module previously | |
| # triggered "symbol not found in flat namespace '___kmpc_dispatch_deinit'" | |
| # when bundled libomp lacked the dispatch_deinit compatibility stub. | |
| try: | |
| import sequenzo.clustering.clustering_c_code | |
| print('[OK] clustering_c_code loaded (bundled libomp sufficient)') | |
| except ImportError as e: | |
| print(f'[ERROR] clustering_c_code failed to load: {e}') | |
| if 'kmpc_dispatch_deinit' in str(e): | |
| print('[ERROR] ___kmpc_dispatch_deinit missing from bundled libomp.') | |
| print('[ERROR] Ensure build_macos_ci_libomp.sh injects the dispatch_deinit stub.') | |
| sys.exit(1) | |
| try: | |
| from sequenzo.dissimilarity_measures import c_code | |
| print('[OK] dissimilarity_measures c_code loaded') | |
| for cls in ['OMdistance', 'OMspellDistance', 'DHDdistance', 'LCPdistance', 'dist2matrix']: | |
| if hasattr(c_code, cls): | |
| print(f'[OK] {cls} available') | |
| except ImportError as e: | |
| print(f'[WARNING] dissimilarity_measures c_code failed: {e}') | |
| for module_name in ['get_sm_trate_substitution_cost_matrix', 'seqconc', 'seqdss', 'seqdur', 'seqlength']: | |
| try: | |
| __import__(f'sequenzo.dissimilarity_measures.utils.{module_name}', fromlist=[module_name]) | |
| print(f'[OK] Cython module {module_name} loaded') | |
| except ImportError as e: | |
| print(f'[WARNING] Cython module {module_name} failed: {e}') | |
| print('') | |
| print('=== Testing sequenzo_fastcluster module ===') | |
| try: | |
| from sequenzo.clustering.sequenzo_fastcluster.fastcluster import linkage, linkage_vector | |
| from scipy.spatial.distance import pdist | |
| test_data = np.array([[1, 2], [1, 4], [1, 0], [4, 2], [4, 4], [4, 0]]) | |
| dist_matrix = pdist(test_data) | |
| for method in ['single', 'complete', 'average']: | |
| Z = linkage(dist_matrix, method=method) | |
| assert Z.shape == (len(test_data) - 1, 4) and np.all(np.isfinite(Z)) | |
| print(f'[OK] linkage({method}) works') | |
| # linkage_vector only supports: single, ward, centroid, median | |
| # 'complete' / 'average' are valid for linkage() but NOT linkage_vector() | |
| Z_vec = linkage_vector(test_data, method='ward', metric='euclidean') | |
| assert Z_vec.shape == (len(test_data) - 1, 4) and np.all(np.isfinite(Z_vec)) | |
| print('[OK] linkage_vector works') | |
| except ImportError as e: | |
| print(f'[WARNING] sequenzo_fastcluster not available: {e}') | |
| print('') | |
| print('[INFO] macOS wheel test completed') | |
| PY | |
| # Linux/other platforms test command (original) | |
| CIBW_TEST_COMMAND: | | |
| python - <<'PY' | |
| import importlib.util | |
| import sys | |
| import numpy as np | |
| import sequenzo | |
| print('Sequenzo import successful') | |
| mod = importlib.util.find_spec('sequenzo.clustering.clustering_c_code') | |
| print('Clustering C++ extensions loaded' if mod else 'WARNING: Clustering C++ extensions not found') | |
| try: | |
| from sequenzo.dissimilarity_measures import c_code | |
| print('Dissimilarity measures C++ extensions (c_code) loaded successfully') | |
| # Test specific C++ classes | |
| try: | |
| # Test if classes are available (don't instantiate to avoid errors) | |
| if hasattr(c_code, 'OMdistance'): | |
| print('[OK] OMdistance class available') | |
| if hasattr(c_code, 'OMspellDistance'): | |
| print('[OK] OMspellDistance class available') | |
| if hasattr(c_code, 'DHDdistance'): | |
| print('[OK] DHDdistance class available') | |
| if hasattr(c_code, 'LCPdistance'): | |
| print('[OK] LCPdistance class available') | |
| if hasattr(c_code, 'dist2matrix'): | |
| print('[OK] dist2matrix class available') | |
| except Exception as e: | |
| print(f'WARNING: Some C++ classes may not be available: {e}') | |
| except ImportError as e: | |
| print(f'ERROR: Dissimilarity measures C++ extensions (c_code) failed to load: {e}') | |
| cython_modules = [ | |
| 'get_sm_trate_substitution_cost_matrix', | |
| 'seqconc', | |
| 'seqdss', | |
| 'seqdur', | |
| 'seqlength' | |
| ] | |
| for module_name in cython_modules: | |
| try: | |
| module = __import__(f'sequenzo.dissimilarity_measures.utils.{module_name}', fromlist=[module_name]) | |
| print(f'[OK] Cython module {module_name} loaded successfully') | |
| except ImportError as e: | |
| print(f'ERROR: Cython module {module_name} failed to load: {e}') | |
| try: | |
| from sequenzo.dissimilarity_measures.utils import ( | |
| get_sm_trate_substitution_cost_matrix, seqconc, seqdss, seqdur, seqlength | |
| ) | |
| print('[OK] All utility functions imported successfully') | |
| except ImportError as e: | |
| print(f'ERROR: Utility functions failed to load: {e}') | |
| # Check sequenzo_fastcluster module | |
| print('') | |
| print('=== Testing sequenzo_fastcluster module ===') | |
| try: | |
| from sequenzo.clustering.sequenzo_fastcluster.fastcluster import linkage, linkage_vector, single, complete, average | |
| print('[OK] sequenzo_fastcluster wrapper imported successfully') | |
| # Test linkage function with small dataset | |
| from scipy.spatial.distance import pdist | |
| test_data = np.array([[1, 2], [1, 4], [1, 0], [4, 2], [4, 4], [4, 0]]) | |
| dist_matrix = pdist(test_data) | |
| # Test different linkage methods | |
| for method in ['single', 'complete', 'average']: | |
| try: | |
| Z = linkage(dist_matrix, method=method) | |
| assert Z.shape == (len(test_data) - 1, 4) | |
| assert np.all(np.isfinite(Z)) | |
| print(f'[OK] linkage({method}) works correctly') | |
| except Exception as e: | |
| print(f'[WARNING] linkage({method}) failed: {e}') | |
| # Test linkage_vector | |
| # linkage_vector only supports: single, ward, centroid, median | |
| try: | |
| Z_vec = linkage_vector(test_data, method='ward', metric='euclidean') | |
| assert Z_vec.shape == (len(test_data) - 1, 4) | |
| assert np.all(np.isfinite(Z_vec)) | |
| print('[OK] linkage_vector works correctly') | |
| except Exception as e: | |
| print(f'[WARNING] linkage_vector failed: {e}') | |
| except ImportError as e: | |
| print(f'[WARNING] sequenzo_fastcluster module not available: {e}') | |
| print('[INFO] This module provides optimized hierarchical clustering') | |
| print('[INFO] All tests completed') | |
| PY | |
| # Windows smoke test uses cmd-compatible python -c. | |
| CIBW_TEST_COMMAND_WINDOWS: | | |
| echo "Testing Sequenzo wheel on Windows" | |
| python -c "import numpy as np; from sequenzo import SequenceData, get_distance_matrix, Cluster; import sequenzo.utils.core_distance_operations.core_distance_c_code as core_distance_c_code; from sequenzo.utils.core_distance_operations import weighted_inertia_contrib; contrib = weighted_inertia_contrib(np.array([[0.0, 1.0], [1.0, 0.0]], dtype=np.float64), np.array([0, 1], dtype=np.int32), np.array([1.0, 1.0], dtype=np.float64)); assert contrib.shape == (2,); print('[OK] Windows wheel smoke test passed')" | |
| - name: Show dist content | |
| run: ls -lah dist/ | |
| shell: bash | |
| # Verify macOS wheels can resolve ___kmpc_dispatch_deinit at load time. | |
| # Apple Clang emits calls to __kmpc_dispatch_deinit for schedule(dynamic/guided) | |
| # loops; -fno-openmp-extensions does NOT suppress this on modern Apple Clang. | |
| # nm -u on a linked .so lists the symbol as undefined (U) because it is resolved | |
| # from bundled libomp at dlopen time — that is expected and OK when libomp exports it. | |
| - name: Verify OpenMP dispatch_deinit resolvable in macOS wheels | |
| if: runner.os == 'macOS' | |
| run: | | |
| set -euo pipefail | |
| echo "=== Checking ___kmpc_dispatch_deinit resolution in macOS wheels ===" | |
| FOUND_BAD=0 | |
| for whl in dist/*.whl; do | |
| echo "Inspecting: $whl" | |
| TMPDIR_WHL=$(mktemp -d) | |
| unzip -q "$whl" -d "$TMPDIR_WHL" | |
| LIBOMP="" | |
| while IFS= read -r -d '' dylib; do | |
| case "$(basename "$dylib")" in | |
| libomp*.dylib) LIBOMP="$dylib"; break ;; | |
| esac | |
| done < <(find "$TMPDIR_WHL" -path '*/.dylibs/*.dylib' -print0) | |
| if [ -z "$LIBOMP" ]; then | |
| echo "[ERROR] No bundled libomp.dylib found in $whl" | |
| FOUND_BAD=1 | |
| rm -rf "$TMPDIR_WHL" | |
| continue | |
| fi | |
| if nm -g "$LIBOMP" 2>/dev/null | grep -q '__kmpc_dispatch_deinit'; then | |
| echo "[OK] Bundled libomp exports __kmpc_dispatch_deinit: $LIBOMP" | |
| LIBOMP_HAS_DEINIT=1 | |
| else | |
| echo "[ERROR] Bundled libomp missing __kmpc_dispatch_deinit stub: $LIBOMP" | |
| LIBOMP_HAS_DEINIT=0 | |
| FOUND_BAD=1 | |
| fi | |
| while IFS= read -r -d '' so_file; do | |
| if nm -u "$so_file" 2>/dev/null | grep -q '___kmpc_dispatch_deinit'; then | |
| if [ "$LIBOMP_HAS_DEINIT" -eq 1 ]; then | |
| echo "[OK] $so_file references dispatch_deinit; bundled libomp provides it" | |
| else | |
| echo "[ERROR] $so_file references dispatch_deinit but libomp lacks stub" | |
| FOUND_BAD=1 | |
| fi | |
| else | |
| echo "[OK] $so_file — no dispatch_deinit reference (static OpenMP schedules)" | |
| fi | |
| done < <(find "$TMPDIR_WHL" -name "*.so" -print0) | |
| rm -rf "$TMPDIR_WHL" | |
| done | |
| if [ "$FOUND_BAD" -eq 1 ]; then | |
| echo "[FATAL] macOS wheel OpenMP symbol check failed." | |
| echo " Ensure build_macos_ci_libomp.sh injects the dispatch_deinit stub." | |
| exit 1 | |
| fi | |
| echo "=== All macOS wheels pass OpenMP symbol verification ===" | |
| shell: bash | |
| - name: Check wheels | |
| run: twine check dist/* | |
| # 验证轮子 RECORD 以适应 PyPI 最新要求 | |
| - name: Verify Wheel RECORD Integrity | |
| run: | | |
| echo "=== Verifying wheel RECORD integrity ===" | |
| for wheel in dist/*.whl; do | |
| echo "Checking $wheel" | |
| # 解压并比较 RECORD 与实际文件 | |
| unzip -q $wheel -d temp_wheel | |
| cd temp_wheel | |
| # 提取 RECORD | |
| record_file=$(find . -name RECORD) | |
| if [ -f "$record_file" ]; then | |
| # 检查每个 RECORD 条目是否存在 | |
| awk -F, '{print $1}' $record_file | while read file; do | |
| if [ ! -f "$file" ]; then | |
| echo "[ERROR] Missing file in wheel: $file" | |
| fi | |
| done | |
| # 检查多余文件（可选） | |
| find . -type f | grep -v '.dist-info/' | while read extra; do | |
| if ! grep -q "^${extra#./}," $record_file; then | |
| echo "[WARNING] Extra file not in RECORD: $extra" | |
| fi | |
| done | |
| else | |
| echo "[ERROR] No RECORD file found" | |
| fi | |
| cd .. | |
| rm -rf temp_wheel | |
| done | |
| shell: bash | |
| - name: Set up Python for wheel verification | |
| uses: actions/setup-python@v4 | |
| with: | |
| # cibuildwheel is driven by Python 3.11, but wheel install/import | |
| # checks must run on the target interpreter for this matrix entry. | |
| python-version: ${{ matrix.python-version }} | |
| # allow-prereleases ensures 3.14 (beta) can be installed when it hasn't been officially released yet | |
| allow-prereleases: true | |
| - name: Verify OpenMP Support | |
| run: | | |
| echo "=== Verifying built wheels ===" | |
| python -c " | |
| import subprocess | |
| import sys | |
| import os | |
| # 精确匹配当前 Python 版本的轮子 (e.g., cp39, cp310) | |
| py_tag = 'cp${{ matrix.python-version }}'.replace('.', '') | |
| wheel_files = [f for f in os.listdir('dist') if f.endswith('.whl') and py_tag in f] | |
| if wheel_files: | |
| wheel_file = wheel_files[0] | |
| print(f'Installing wheel: {wheel_file} (Python tag: {py_tag})') | |
| subprocess.run([sys.executable, '-m', 'pip', 'install', '--force-reinstall', f'dist/{wheel_file}'], check=True) | |
| import sequenzo | |
| print('Sequenzo import successful') | |
| try: | |
| import sequenzo.clustering.clustering_c_code as cc | |
| print('C++ extensions loaded successfully') | |
| except ImportError as e: | |
| print(f'WARNING: C++ extensions loading failed: {e}') | |
| else: | |
| print('ERROR: No matching wheel files found') | |
| " || echo "Verification completed with warnings" | |
| shell: bash | |
| - name: Verify built Cython modules | |
| run: | | |
| echo "=== Verifying built cython modules in wheel ===" | |
| # 安装与当前 matrix Python 版本匹配的轮子 | |
| py_tag="cp${{ matrix.python-version-nodot }}" | |
| WHEEL_FILE=$(ls dist/*.whl | grep "$py_tag" | head -1 || true) | |
| if [ -z "$WHEEL_FILE" ]; then | |
| echo "No wheel matches tag $py_tag in dist/" | |
| ls -la dist/ | |
| exit 1 | |
| fi | |
| echo "Installing wheel: $WHEEL_FILE" | |
| # On Windows, git-bash may re-introduce C:/Program Files/Git/usr/bin into | |
| # PATH, causing Git's link.exe to shadow MSVC's when pip builds packages | |
| # from source (e.g. hmmlearn on Python 3.14 where no binary wheel exists). | |
| if [[ "$RUNNER_OS" == "Windows" ]]; then | |
| PATH=$(echo ":$PATH:" | tr ':' '\n' | grep -iv '/git/usr/bin' | grep -iv '\\Git\\usr\\bin' | grep . | tr '\n' ':' | sed 's/^://;s/:$//') | |
| export PATH | |
| fi | |
| # Try a full install first; if it fails (e.g. hmmlearn source build on | |
| # pre-release Python where no binary wheel exists), fall back to --no-deps | |
| # and install hmmlearn separately with --prefer-binary. | |
| if ! python -m pip install --force-reinstall "$WHEEL_FILE"; then | |
| echo "Full install failed; retrying with --no-deps + prefer-binary hmmlearn..." | |
| python -m pip install --force-reinstall --no-deps "$WHEEL_FILE" | |
| python -m pip install "hmmlearn>=0.2.0" --prefer-binary --retries 5 --timeout 120 \ | |
| || echo "INFO: hmmlearn binary wheel not yet available for this Python version (pre-release); skipping" | |
| fi | |
| # 检查安装的模块 - 使用 ASCII 字符 | |
| echo "=== Checking installed modules ===" | |
| python -c " | |
| import os | |
| import sys | |
| # Remove '' (cwd) from sys.path so Python finds the installed wheel in | |
| # site-packages rather than the source tree, which may contain stale | |
| # cpython-311 .so files built by the pre-cibuildwheel 'Build Cython | |
| # extensions' step and would cause ABI-mismatch segfaults on py3.12+. | |
| sys.path = [p for p in sys.path if p] | |
| import importlib.util | |
| # 设置标准输出编码为 UTF-8 以避免 Windows 编码问题 | |
| if sys.platform == 'win32': | |
| import io | |
| sys.stdout = io.TextIOWrapper(sys.stdout.buffer, encoding='utf-8', errors='replace') | |
| def check_module(module_name): | |
| try: | |
| spec = importlib.util.find_spec(module_name) | |
| if spec: | |
| print(f'[OK] {module_name}: {spec.origin}') | |
| return True | |
| else: | |
| print(f'[FAIL] {module_name}: NOT FOUND') | |
| return False | |
| except Exception as e: | |
| print(f'[FAIL] {module_name}: ERROR - {e}') | |
| return False | |
| # 检查主包 | |
| check_module('sequenzo') | |
| check_module('sequenzo.dissimilarity_measures') | |
| check_module('sequenzo.dissimilarity_measures.utils') | |
| # 检查 Cython 模块 | |
| cython_modules = [ | |
| 'sequenzo.dissimilarity_measures.utils.get_sm_trate_substitution_cost_matrix', | |
| 'sequenzo.dissimilarity_measures.utils.seqconc', | |
| 'sequenzo.dissimilarity_measures.utils.seqdss', | |
| 'sequenzo.dissimilarity_measures.utils.seqdur', | |
| 'sequenzo.dissimilarity_measures.utils.seqlength' | |
| ] | |
| print('\\\\n=== Checking Cython modules ===') | |
| for module in cython_modules: | |
| check_module(module) | |
| # 检查包内容 | |
| print('\\\\n=== Package contents ===') | |
| try: | |
| import sequenzo | |
| pkg_path = os.path.dirname(sequenzo.__file__) | |
| print(f'Package path: {pkg_path}') | |
| # 列出所有文件 | |
| for root, dirs, files in os.walk(pkg_path): | |
| for file in files: | |
| if file.endswith(('.so', '.pyd', '.dylib')): | |
| print(f'Shared lib: {os.path.join(root, file)}') | |
| except Exception as e: | |
| print(f'Error examining package: {e}') | |
| " | |
| shell: bash | |
| - name: Run Integration Tests (Quickstart Workflow) | |
| run: | | |
| echo "=== Running integration tests based on quickstart tutorial ===" | |
| # 详细的调试信息 | |
| echo "Current Python: $(which python)" | |
| echo "Python version: $(python --version)" | |
| echo "Platform: $(python -c 'import platform; print(platform.platform())')" | |
| echo "Architecture: $(python -c 'import platform; print(platform.machine())')" | |
| # 更智能的轮子选择逻辑 | |
| python -c " | |
| import subprocess | |
| import sys | |
| import os | |
| import platform | |
| # 获取当前平台信息 | |
| current_platform = platform.system().lower() | |
| current_machine = platform.machine().lower() | |
| python_version = f'cp{sys.version_info.major}{sys.version_info.minor}' | |
| print(f'Current platform: {current_platform}') | |
| print(f'Current machine: {current_machine}') | |
| print(f'Python version tag: {python_version}') | |
| # 查找匹配的轮子文件 | |
| wheel_files = [f for f in os.listdir('dist') if f.endswith('.whl')] | |
| print(f'Available wheel files: {wheel_files}') | |
| # 优先选择与当前平台匹配的轮子 | |
| matching_wheels = [] | |
| for wheel_file in wheel_files: | |
| # 检查平台标签 | |
| platform_ok = False | |
| arch_ok = False | |
| if current_platform == 'darwin': | |
| # macOS 平台检查 | |
| if 'macosx' in wheel_file: | |
| platform_ok = True | |
| # 检查架构 | |
| if current_machine == 'arm64' and 'arm64' in wheel_file: | |
| arch_ok = True | |
| elif current_machine == 'x86_64' and 'x86_64' in wheel_file: | |
| arch_ok = True | |
| elif current_platform == 'linux': | |
| if 'linux' in wheel_file: | |
| platform_ok = True | |
| arch_ok = True # Linux 通常兼容性更好 | |
| elif current_platform == 'windows': | |
| if 'win' in wheel_file: | |
| platform_ok = True | |
| arch_ok = True | |
| if platform_ok and arch_ok and python_version in wheel_file: | |
| matching_wheels.append(wheel_file) | |
| print(f'Matching wheels: {matching_wheels}') | |
| if matching_wheels: | |
| # 选择最匹配的轮子 | |
| wheel_file = matching_wheels[0] | |
| print(f'Selected wheel for testing: {wheel_file}') | |
| # 卸载可能存在的旧版本 | |
| subprocess.run([sys.executable, '-m', 'pip', 'uninstall', '-y', 'sequenzo'], | |
| capture_output=True) | |
| # 安装新轮子 | |
| result = subprocess.run([ | |
| sys.executable, '-m', 'pip', 'install', '--force-reinstall', | |
| f'dist/{wheel_file}' | |
| ], capture_output=True, text=True) | |
| if result.returncode == 0: | |
| print('Wheel installed successfully') | |
| print('Installation output:', result.stdout) | |
| else: | |
| print(f'Wheel installation failed: {result.stderr}') | |
| # 尝试使用 --ignore-requires-python | |
| print('Trying with --ignore-requires-python flag...') | |
| subprocess.run([ | |
| sys.executable, '-m', 'pip', 'install', '--force-reinstall', | |
| '--ignore-requires-python', f'dist/{wheel_file}' | |
| ], check=True) | |
| else: | |
| print('ERROR: No matching wheel files found') | |
| sys.exit(1) | |
| " | |
| # 检查安装状态 | |
| echo "=== Checking installation ===" | |
| python -c " | |
| import sys | |
| import subprocess | |
| # 检查已安装的包 | |
| result = subprocess.run([sys.executable, '-m', 'pip', 'list'], | |
| capture_output=True, text=True) | |
| print('Installed packages:') | |
| print(result.stdout) | |
| # 检查 sequenzo 是否在列表中 | |
| if 'sequenzo' in result.stdout: | |
| print('✓ sequenzo found in pip list') | |
| else: | |
| print('✗ sequenzo NOT found in pip list') | |
| " | |
| # 详细的导入测试 | |
| echo "=== Testing sequenzo import ===" | |
| python -c " | |
| import sys | |
| import os | |
| print('Python path:') | |
| for p in sys.path: | |
| print(f' {p}') | |
| # 尝试找到 sequenzo 包 | |
| try: | |
| import importlib.util | |
| spec = importlib.util.find_spec('sequenzo') | |
| if spec: | |
| print(f'✓ Found sequenzo at: {spec.origin}') | |
| else: | |
| print('✗ sequenzo module not found in Python path') | |
| except Exception as e: | |
| print(f'Error finding sequenzo: {e}') | |
| # 尝试导入 | |
| try: | |
| import sequenzo | |
| print('✓ Successfully imported sequenzo') | |
| print(f'Sequenzo version: {getattr(sequenzo, \"__version__\", \"unknown\")}') | |
| print(f'Sequenzo location: {sequenzo.__file__}') | |
| except ImportError as e: | |
| print(f'✗ Failed to import sequenzo: {e}') | |
| # 打印详细的错误信息 | |
| import traceback | |
| traceback.print_exc() | |
| except Exception as e: | |
| print(f'✗ Error during import: {e}') | |
| import traceback | |
| traceback.print_exc() | |
| " | |
| # 如果导入成功，运行集成测试 | |
| echo "=== Running integration tests ===" | |
| if python -c "import sequenzo" 2>/dev/null; then | |
| echo "Sequenzo imported successfully, running integration tests..." | |
| # 安装 pytest 如果尚未安装 | |
| pip install pytest || echo "pytest installation failed, but continuing..." | |
| # 检查测试文件是否存在 | |
| if [ -f "tests/test_quickstart_integration.py" ]; then | |
| pytest tests/test_quickstart_integration.py -v -s || echo "Integration tests completed with warnings" | |
| else | |
| echo "Test file not found" | |
| fi | |
| else | |
| echo "ERROR: Cannot import sequenzo, skipping integration tests" | |
| # 退出并显示错误 | |
| exit 1 | |
| fi | |
| shell: bash | |
| - name: Set up Miniconda for Windows wheel smoke | |
| if: runner.os == 'Windows' | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: sequenzo-wheel-smoke | |
| auto-update-conda: true | |
| - name: Windows Conda wheel smoke test | |
| if: runner.os == 'Windows' | |
| shell: bash -el {0} | |
| run: | | |
| echo "=== Windows Conda wheel smoke test ===" | |
| conda info | |
| python -m pip install --upgrade pip | |
| echo "Installing $WHEEL into Conda environment" | |
| python - <<'PY' | |
| import glob | |
| import os | |
| import zipfile | |
| py_tag = "cp${{ matrix.python-version-nodot }}" | |
| wheels = sorted(glob.glob(f"dist/*{py_tag}*win_amd64.whl")) | |
| if not wheels: | |
| raise SystemExit(f"No Windows wheel found for {py_tag}") | |
| wheel = os.path.abspath(wheels[-1]) | |
| with zipfile.ZipFile(wheel) as zf: | |
| native = [ | |
| name | |
| for name in zf.namelist() | |
| if "core_distance_c_code" in name.replace("\\", "/") | |
| and name.lower().endswith((".pyd", ".so")) | |
| ] | |
| if not native: | |
| raise SystemExit( | |
| f"Wheel missing core_distance_c_code binary: {wheel}" | |
| ) | |
| print(f"[OK] wheel contains core_distance_c_code: {native[0]}") | |
| with open(os.path.join(os.environ["RUNNER_TEMP"], "sequenzo-wheel-smoke.env"), "w", encoding="utf-8") as fh: | |
| fh.write(f"WHEEL={wheel}\n") | |
| PY | |
| python -m pip install --force-reinstall "$(grep '^WHEEL=' "$RUNNER_TEMP/sequenzo-wheel-smoke.env" | cut -d= -f2-)" | |
| mkdir -p "$RUNNER_TEMP/sequenzo-wheel-smoke" | |
| cd "$RUNNER_TEMP/sequenzo-wheel-smoke" | |
| python - <<'PY' | |
| import importlib.util | |
| import os | |
| import sys | |
| workspace = os.path.abspath(os.environ.get("GITHUB_WORKSPACE", "")) | |
| sys.path = [ | |
| p | |
| for p in sys.path | |
| if p | |
| and (not workspace or os.path.abspath(p) != workspace) | |
| ] | |
| import numpy as np | |
| print("CONDA_PREFIX=" + os.environ.get("CONDA_PREFIX", "")) | |
| print("CWD=" + os.getcwd()) | |
| from sequenzo import SequenceData, get_distance_matrix, Cluster | |
| import sequenzo.utils.core_distance_operations.core_distance_c_code as core_distance_c_code | |
| from sequenzo.utils.core_distance_operations import weighted_inertia_contrib | |
| spec = importlib.util.find_spec( | |
| "sequenzo.utils.core_distance_operations.core_distance_c_code" | |
| ) | |
| if spec is None or not spec.origin: | |
| raise SystemExit( | |
| "core_distance_c_code not found after wheel install; " | |
| f"sys.path={sys.path!r}" | |
| ) | |
| print(f"[OK] core_distance_c_code loaded from: {spec.origin}") | |
| contrib = weighted_inertia_contrib( | |
| np.array([[0.0, 1.0], [1.0, 0.0]], dtype=np.float64), | |
| np.array([0, 1], dtype=np.int32), | |
| np.array([1.0, 1.0], dtype=np.float64), | |
| ) | |
| assert contrib.shape == (2,) | |
| print("[OK] Windows Conda wheel smoke test passed") | |
| PY | |
| - name: Upload wheels | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: wheels-${{ matrix.os }}-${{ matrix.python-version }} | |
| path: dist/ | |
| # 在所有 build matrix job 完成后，把所有分散的 wheels-* artifact 合并为一个 | |
| # all-wheels artifact，用户只需下载这一个 zip，pip 会自动挑选兼容的 wheel。 | |
| merge-wheels: | |
| name: Merge all wheels into one artifact | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Merge wheel artifacts | |
| uses: actions/upload-artifact/merge@v4 | |
| with: | |
| name: all-wheels | |
| pattern: wheels-* | |
| delete-merged: false |