Wilcoxon refactor #412
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| # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries | |
| # https://github.com/pypa/cibuildwheel/blob/main/examples/github-deploy.yml | |
| name: Build and upload to PyPI | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: [main] | |
| release: | |
| types: [published] | |
| jobs: | |
| build_wheels: | |
| name: Build wheels for ${{ matrix.os }}-cu${{ matrix.cuda_major }} | |
| runs-on: ${{ matrix.runs-on }} | |
| strategy: | |
| matrix: | |
| include: | |
| # CUDA 12 wheels (compiled with 12.2 for runtime 12.2+ compatibility) | |
| - os: linux-intel | |
| cuda_major: "12" | |
| runs-on: ubuntu-latest | |
| cibw_image: "ghcr.io/scverse/rapids_singlecell:manylinux_2_28_x86_64_cuda12.2" | |
| dockerfile: "docker/manylinux_2_28_x86_64_cuda12.2.Dockerfile" | |
| cuda_archs: "75-real;80-real;86-real;89-real;90" | |
| - os: linux-arm | |
| cuda_major: "12" | |
| runs-on: ubuntu-24.04-arm | |
| cibw_image: "ghcr.io/scverse/rapids_singlecell:manylinux_2_28_aarch64_cuda12.2" | |
| dockerfile: "docker/manylinux_2_28_aarch64_cuda12.2.Dockerfile" | |
| cuda_archs: "75-real;80-real;86-real;89-real;90" | |
| # CUDA 13 wheels (native Blackwell support) | |
| - os: linux-intel | |
| cuda_major: "13" | |
| runs-on: ubuntu-latest | |
| cibw_image: "ghcr.io/scverse/rapids_singlecell:manylinux_2_28_x86_64_cuda13.0" | |
| dockerfile: "docker/manylinux_2_28_x86_64_cuda13.0.Dockerfile" | |
| cuda_archs: "75-real;80-real;86-real;89-real;90-real;100-real;120" | |
| - os: linux-arm | |
| cuda_major: "13" | |
| runs-on: ubuntu-24.04-arm | |
| cibw_image: "ghcr.io/scverse/rapids_singlecell:manylinux_2_28_aarch64_cuda13.0" | |
| dockerfile: "docker/manylinux_2_28_aarch64_cuda13.0.Dockerfile" | |
| cuda_archs: "75-real;80-real;86-real;89-real;90-real;100-real;120" | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get version from setuptools-scm | |
| id: version | |
| run: | | |
| pip install setuptools-scm | |
| VERSION=$(python -m setuptools_scm) | |
| echo "version=$VERSION" >> $GITHUB_OUTPUT | |
| echo "Detected version: $VERSION" | |
| - name: Set package name, extras, and CUDA archs for CUDA ${{ matrix.cuda_major }} | |
| run: | | |
| python3 - ${{ matrix.cuda_major }} "${{ matrix.cuda_archs }}" <<'SCRIPT' | |
| import sys, pathlib | |
| cuda = sys.argv[1] | |
| cuda_archs = sys.argv[2] | |
| other = "13" if cuda == "12" else "12" | |
| path = pathlib.Path("pyproject.toml") | |
| text = path.read_text() | |
| def remove_toml_array(text, key): | |
| lines = text.splitlines(keepends=True) | |
| out = [] | |
| i = 0 | |
| while i < len(lines): | |
| if lines[i].startswith(f"{key} = ["): | |
| depth = lines[i].count("[") - lines[i].count("]") | |
| i += 1 | |
| while i < len(lines) and depth > 0: | |
| depth += lines[i].count("[") - lines[i].count("]") | |
| i += 1 | |
| continue | |
| out.append(lines[i]) | |
| i += 1 | |
| return "".join(out) | |
| # Rename package | |
| text = text.replace( | |
| 'name = "rapids-singlecell"', | |
| f'name = "rapids-singlecell-cu{cuda}"', | |
| ) | |
| # Rename matching extra to "rapids", remove the other | |
| text = text.replace(f'rapids-cu{cuda} = [', 'rapids = [') | |
| text = remove_toml_array(text, f"rapids-cu{other}") | |
| # librmm is needed at build time because CMake links the CUDA | |
| # extension against librmm. Add the matching wheel to the isolated | |
| # PEP 517 build requirements after selecting the CUDA package variant. | |
| for dep in ( | |
| f' "librmm-cu{other}>=25.10",\n', | |
| f' "rmm-cu{other}>=25.10",\n', | |
| ): | |
| text = text.replace(dep, "") | |
| rmm_build_req = f' "librmm-cu{cuda}>=25.10",\n' | |
| build_system_text = text.split("[project]", 1)[0] | |
| if f'"librmm-cu{cuda}>=25.10"' not in build_system_text: | |
| text = text.replace( | |
| ']\nbuild-backend = "scikit_build_core.build"', | |
| f'{rmm_build_req}]\nbuild-backend = "scikit_build_core.build"', | |
| 1, | |
| ) | |
| # Set CUDA architectures (replace "native" with CI target archs) | |
| text = text.replace( | |
| 'CMAKE_CUDA_ARCHITECTURES = "native"', | |
| f'CMAKE_CUDA_ARCHITECTURES = "{cuda_archs}"', | |
| ) | |
| path.write_text(text) | |
| # Verify | |
| for line in path.read_text().splitlines(): | |
| if "name" in line or "rapids" in line.lower() or "CUDA_ARCH" in line: | |
| print(line) | |
| SCRIPT | |
| - name: Sanity check pyproject.toml | |
| run: | | |
| python3 -c "import tomllib; tomllib.load(open('pyproject.toml', 'rb'))" | |
| grep -E "name|rapids|CUDA_ARCH" pyproject.toml | |
| - name: Build CUDA manylinux image | |
| run: | | |
| docker build -t "${{ matrix.cibw_image }}" -f "${{ matrix.dockerfile }}" docker | |
| - name: Build wheels | |
| uses: pypa/cibuildwheel@v3.1.4 | |
| env: | |
| SETUPTOOLS_SCM_PRETEND_VERSION: ${{ steps.version.outputs.version }} | |
| CIBW_BUILD: 'cp312-*' | |
| CIBW_SKIP: '*-musllinux*' | |
| CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.os == 'linux-intel' && matrix.cibw_image || '' }} | |
| CIBW_MANYLINUX_AARCH64_IMAGE: ${{ matrix.os == 'linux-arm' && matrix.cibw_image || '' }} | |
| CIBW_ENVIRONMENT_PASS_LINUX: SETUPTOOLS_SCM_PRETEND_VERSION | |
| CIBW_ENVIRONMENT: > | |
| CUDA_PATH=/usr/local/cuda | |
| LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH | |
| PATH=/usr/local/cuda/bin:$PATH | |
| CIBW_BEFORE_BUILD: > | |
| rm -f build/.librmm_dir && | |
| mkdir -p build && | |
| python -m pip install -U pip | |
| scikit-build-core cmake ninja nanobind | |
| librmm-cu${{ matrix.cuda_major }} && | |
| RMM_ROOT=$(python -c "import librmm; print(librmm.__path__[0])") && | |
| LOG_ROOT=$(python -c "import rapids_logger; print(rapids_logger.__path__[0])") && | |
| echo "[rsc-build] librmm=$RMM_ROOT" && | |
| echo "[rsc-build] rapids_logger=$LOG_ROOT" && | |
| ln -sf "$RMM_ROOT/lib64/librmm.so" /usr/local/lib/librmm.so && | |
| ln -sf "$LOG_ROOT/lib64/librapids_logger.so" /usr/local/lib/librapids_logger.so && | |
| ldconfig && | |
| python -c "import librmm; print(librmm.__path__[0])" > build/.librmm_dir && | |
| echo "[rsc-build] marker=$(cat build/.librmm_dir)" | |
| CIBW_TEST_SKIP: "*" | |
| CIBW_TEST_COMMAND: "" | |
| CIBW_REPAIR_WHEEL_COMMAND: "auditwheel repair --exclude libcublas.so.${{ matrix.cuda_major }} --exclude libcublasLt.so.${{ matrix.cuda_major }} --exclude libcudart.so.${{ matrix.cuda_major }} --exclude librmm.so --exclude librapids_logger.so -w {dest_dir} {wheel}" | |
| CIBW_BUILD_VERBOSITY: "1" | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: cibw-wheels-${{ matrix.os }}-cu${{ matrix.cuda_major }}-${{ strategy.job-index }} | |
| path: ./wheelhouse/*.whl | |
| build_sdist: | |
| name: Build source distribution | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v5 | |
| - name: Build sdist | |
| run: pipx run build --sdist | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: cibw-sdist | |
| path: dist/*.tar.gz | |
| upload_wheels: | |
| needs: [build_wheels] | |
| runs-on: ubuntu-latest | |
| environment: publish-cu${{ matrix.cuda_major }} | |
| permissions: | |
| id-token: write | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| strategy: | |
| matrix: | |
| cuda_major: ["12", "13"] | |
| steps: | |
| - uses: actions/download-artifact@v5 | |
| with: | |
| pattern: cibw-wheels-*-cu${{ matrix.cuda_major }}-* | |
| path: dist | |
| merge-multiple: true | |
| - uses: pypa/gh-action-pypi-publish@release/v1 | |
| upload_sdist: | |
| needs: [build_sdist] | |
| runs-on: ubuntu-latest | |
| environment: publish | |
| permissions: | |
| id-token: write | |
| if: github.event_name == 'release' && github.event.action == 'published' | |
| steps: | |
| - uses: actions/download-artifact@v5 | |
| with: | |
| name: cibw-sdist | |
| path: dist | |
| - uses: pypa/gh-action-pypi-publish@release/v1 |