publish.yml

# 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()

          # 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 =')
          # Remove the other CUDA extra line entirely
          lines = text.splitlines(keepends=True)
          text = "".join(l for l in lines if f'rapids-cu{other}' not in l)

          # 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: |
          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_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:$PATH
          CIBW_BEFORE_BUILD: >
            python -m pip install -U pip
            scikit-build-core cmake ninja nanobind
          CIBW_TEST_SKIP: "*"
          CIBW_TEST_COMMAND: ""
          CIBW_REPAIR_WHEEL_COMMAND: "auditwheel repair --exclude libcublas.so.${{ matrix.cuda_major }} --exclude libcublasLt.so.${{ matrix.cuda_major }} --exclude libcudart.so.${{ matrix.cuda_major }} -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