python-ci-packaging.yml

# This CI confirms the Python package continues to install properly in the many
# different required contexts

name: TileDB-SOMA Python CI (Packaging)

on:
  push:
    paths:
      - '.github/workflows/python-ci-packaging.yml'
      - 'apis/python/MANIFEST.in'
      - 'apis/python/pyproject.toml'
      - 'apis/python/setup.py'
      - 'apis/python/version.py'
      - 'apis/python/src/tiledbsoma/__init__.py'
      - 'libtiledbsoma/cmake/inputs/Config.cmake.in'
      - 'libtiledbsoma/cmake/inputs/tiledbsoma.pc.in'
      - 'libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake'
      - 'libtiledbsoma/cmake/Modules/TileDBCommon.cmake'
      - 'libtiledbsoma/cmake/Superbuild.cmake'
      - 'libtiledbsoma/CMakeLists.txt'
  pull_request:
    paths:
      - '.github/workflows/python-ci-packaging.yml'
      - 'apis/python/MANIFEST.in'
      - 'apis/python/pyproject.toml'
      - 'apis/python/setup.py'
      - 'apis/python/version.py'
      - 'apis/python/src/tiledbsoma/__init__.py'
      - 'libtiledbsoma/cmake/inputs/Config.cmake.in'
      - 'libtiledbsoma/cmake/inputs/tiledbsoma.pc.in'
      - 'libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake'
      - 'libtiledbsoma/cmake/Modules/TileDBCommon.cmake'
      - 'libtiledbsoma/cmake/Superbuild.cmake'
      - 'libtiledbsoma/CMakeLists.txt'
  workflow_dispatch:

jobs:

  # Confirm shared object copying when building the Python package
  # https://github.com/single-cell-data/TileDB-SOMA/pull/1937
  docker:
    runs-on: ubuntu-24.04
    name: "SO copying (docker) TILEDB_EXISTS: ${{ matrix.TILEDB_EXISTS }} TILEDBSOMA_EXISTS: ${{ matrix.TILEDBSOMA_EXISTS }}"
    strategy:
      fail-fast: false
      matrix:
        TILEDB_EXISTS: ["no", "yes"]
        TILEDBSOMA_EXISTS: ["no", "yes"]
        exclude:
          - TILEDB_EXISTS: "no"
            TILEDBSOMA_EXISTS: "yes"
    container:
      image: ubuntu:latest
    defaults:
      run:
        shell: bash
    steps:
      - name: Docker image info
        run: |
          uname -a
          cat /etc/lsb-release
      - name: Setup
        run: |
          apt-get update
          apt-get install --yes cmake git python-is-python3 python3 python3-pip python3-venv unzip wget
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0  # for setuptools-scm
      - name: Configure Git
        run: |
          # This is a permissions quirk due to running Git as root inside of a Docker container
          git config --global --add safe.directory $(pwd)
          git branch
      - name: Install pre-built libtiledb
        if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
        run: |
          mkdir -p external
          # Please do not edit manually -- let scripts/update-tiledb-version.py update this
          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-linux-x86_64-2.27.0-2862c30.tar.gz
          tar -C external -xzf tiledb-linux-x86_64-*.tar.gz
          ls external/lib/
          echo "LD_LIBRARY_PATH=$(pwd)/external/lib" >> $GITHUB_ENV
          echo "PKG_CONFIG_PATH=$(pwd)/external/lib/pkgconfig" >> $GITHUB_ENV
          echo "TILEDB_PATH=$(pwd)/external" >> $GITHUB_ENV
      - name: Build and install libtiledbsoma
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'yes' }}
        run: |
          cmake -S libtiledbsoma -B build-libtiledbsoma \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_PREFIX_PATH=$(pwd)/external/ \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/external/ \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D DOWNLOAD_TILEDB_PREBUILT=OFF \
            -D TILEDB_REMOVE_DEPRECATIONS=ON \
            -D TILEDBSOMA_ENABLE_WERROR=ON \
            -D FORCE_BUILD_TILEDB=OFF
          cmake --build build-libtiledbsoma -j $(nproc) --verbose
          cmake --build build-libtiledbsoma --target install-libtiledbsoma
          ls external/lib/
          echo "TILEDBSOMA_PATH=$(pwd)/external" >> $GITHUB_ENV
      - name: Setup Python
        run: |
          python --version
          python -m venv ./venv-soma
          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
          ./venv-soma/bin/pip list
      - name: Build wheel
        run: |
          echo env vars: $LD_LIBRARY_PATH $PKG_CONFIG_PATH $TILEDB_PATH $TILEDBSOMA_PATH
          cd apis/python
          ../../venv-soma/bin/python setup.py bdist_wheel
      - name: Inspect wheel
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep '\.so'
      - name: Confirm libtiledb.so is copied
        if: ${{ matrix.TILEDB_EXISTS == 'no' }}
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledb.so
      - name: Confirm libtiledb.so is **not** copied when using external shared object
        if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
        run: |
          if unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledb.so
          then
            echo "libtiledb.so was copied into the wheel when it was built against an external shared object"
            exit 1
          fi
      - name: Confirm libtiledbsoma.so is copied
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'no' }}
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledbsoma.so
      - name: Confirm libtiledbsoma.so is **not** copied when using external shared object
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'yes' }}
        run: |
          if unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledbsoma.so
          then
            echo "libtiledbsoma.so was copied into the wheel when it was built against an external shared object"
            exit 1
          fi
      - name: Install wheel
        run: ./venv-soma/bin/pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
      - name: Check linking and RPATH
        run: |
          ldd ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
          readelf -d ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so  | grep R*PATH
      - name: Runtime test
        run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
      - name: Confirm linking to installed shared objects
        run: |
          rm -fr build/ build-libtiledbsoma/ dist/ apis/python/build apis/python/src/tiledbsoma/*tile*.so*
          # should only show shared objects installed in virtual env or in ./external/
          find . -name '*tile*.so*'
          ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"

  # Confirm shared object copying when building the Python package
  # https://github.com/single-cell-data/TileDB-SOMA/pull/1937
  # Same as job above, but running on macOS instead of in a Docker container
  macos:
    runs-on: macos-latest
    name: "SO copying (macos) TILEDB_EXISTS: ${{ matrix.TILEDB_EXISTS }} TILEDBSOMA_EXISTS: ${{ matrix.TILEDBSOMA_EXISTS }}"
    strategy:
      fail-fast: false
      matrix:
        TILEDB_EXISTS: ["no", "yes"]
        TILEDBSOMA_EXISTS: ["no", "yes"]
        exclude:
          - TILEDB_EXISTS: "no"
            TILEDBSOMA_EXISTS: "yes"
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0  # for setuptools-scm
      - name: Check if System Integrity Protection (SIP) is enabled
        run: csrutil status
      - name: Select XCode version
        uses: maxim-lobanov/setup-xcode@v1
        with:
          xcode-version: '15.4'
      - name: Install pre-built libtiledb
        if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
        run: |
          mkdir -p external
          # Please do not edit manually -- let scripts/update-tiledb-version.py update this
          if [ `uname -m` == "arm64" ]; then
            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-macos-arm64-2.27.0-2862c30.tar.gz
            tar -C external -xzf tiledb-macos-arm64-*.tar.gz
          else
            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-macos-x86_64-2.27.0-2862c30.tar.gz
            tar -C external -xzf tiledb-macos-x86_64-*.tar.gz
          fi
          ls external/lib/
          echo "DYLD_LIBRARY_PATH=$(pwd)/external/lib" >> $GITHUB_ENV
          echo "PKG_CONFIG_PATH=$(pwd)/external/lib/pkgconfig" >> $GITHUB_ENV
          echo "TILEDB_PATH=$(pwd)/external" >> $GITHUB_ENV
      - name: Build and install libtiledbsoma
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'yes' }}
        run: |
          cmake -S libtiledbsoma -B build-libtiledbsoma \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_PREFIX_PATH=$(pwd)/external/ \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/external/ \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D DOWNLOAD_TILEDB_PREBUILT=OFF \
            -D TILEDB_REMOVE_DEPRECATIONS=ON \
            -D FORCE_BUILD_TILEDB=OFF
          cmake --build build-libtiledbsoma -j $(nproc)
          cmake --build build-libtiledbsoma --target install-libtiledbsoma
          ls external/lib/
          echo "TILEDBSOMA_PATH=$(pwd)/external" >> $GITHUB_ENV
      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Setup Python virtual env
        run: |
          python --version
          python -m venv ./venv-soma
          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
          ./venv-soma/bin/pip list
      - name: Build wheel
        run: |
          echo env vars: $DYLD_LIBRARY_PATH $PKG_CONFIG_PATH $TILEDB_PATH $TILEDBSOMA_PATH
          cd apis/python
          ../../venv-soma/bin/python setup.py bdist_wheel
      - name: Inspect wheel
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep -e '\.dylib' -e '\.so'
      - name: Confirm libtiledb.dylib is copied
        if: ${{ matrix.TILEDB_EXISTS == 'no' }}
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledb.dylib
      - name: Confirm libtiledb.dylib is **not** copied when using external shared object
        if: ${{ matrix.TILEDB_EXISTS == 'yes' }}
        run: |
          if unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledb.dylib
          then
            echo "libtiledb.dylib was copied into the wheel when it was built against an external shared object"
            exit 1
          fi
      - name: Confirm libtiledbsoma.dylib is copied
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'no' }}
        run: unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledbsoma.dylib
      - name: Confirm libtiledbsoma.dylib is **not** copied when using external shared object
        if: ${{ matrix.TILEDBSOMA_EXISTS == 'yes' }}
        run: |
          if unzip -l apis/python/dist/tiledbsoma-*.whl | grep -q libtiledbsoma.dylib
          then
            echo "libtiledbsoma.dylib was copied into the wheel when it was built against an external shared object"
            exit 1
          fi
      - name: Install wheel
        run: ./venv-soma/bin/pip install --prefer-binary apis/python/dist/tiledbsoma-*.whl
      - name: Check linking and RPATH
        run: otool -L ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
      - name: Runtime test
        run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"
      - name: Confirm linking to installed shared objects
        run: |
          rm -fr build/ build-libtiledbsoma/ dist/ apis/python/build apis/python/src/tiledbsoma/*tile*.dylib*
          # should only show shared objects installed in virtual env or in ./external/
          find . -name '*tile*.so*'
          find . -name '*tile*.dylib*'
          ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"

  # Tests that the --libtiledbsoma flag to setup.py continues working
  setuptools:
    runs-on: ${{ matrix.os }}
    name: "setuptools (${{ matrix.os }})"
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-24.04", "macos-latest"]
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0  # for setuptools-scm
      - name: Install pre-built libtiledb
        run: |
          mkdir -p external
          if [ `uname -s` == "Darwin" ]; then
            if [ `uname -m` == "arm64" ]; then
                # Please do not edit manually -- let scripts/update-tiledb-version.py update this
                wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-macos-arm64-2.27.0-2862c30.tar.gz
            else
                # Please do not edit manually -- let scripts/update-tiledb-version.py update this
                wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-macos-x86_64-2.27.0-2862c30.tar.gz
            fi
          else
            # Please do not edit manually -- let scripts/update-tiledb-version.py update this
            wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.27.0/tiledb-linux-x86_64-2.27.0-2862c30.tar.gz
          fi
          tar -C external -xzf tiledb-*.tar.gz
          ls external/lib/
      - name: Build and install libtiledbsoma
        run: |
          cmake -S libtiledbsoma -B build-libtiledbsoma \
            -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_PREFIX_PATH=$(pwd)/external/ \
            -D CMAKE_INSTALL_PREFIX:PATH=$(pwd)/external/ \
            -D OVERRIDE_INSTALL_PREFIX=OFF \
            -D DOWNLOAD_TILEDB_PREBUILT=OFF \
            -D TILEDB_REMOVE_DEPRECATIONS=ON \
            -D FORCE_BUILD_TILEDB=OFF
          cmake --build build-libtiledbsoma -j 2
          cmake --build build-libtiledbsoma --target install-libtiledbsoma
          ls external/lib/
      # Delete all cmake executables from the runner. This will ensure that
      # tiledbsoma-py has to use the cli flags to find the external
      # libtiledbsoma.so and not build it from source by shelling out to cmake
      - name: Delete cmake
        run: |
          echo before
          which -a cmake
          which -a cmake | xargs sudo rm -f
          echo after
          which -a cmake || echo cmake removed
      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Setup Python virtual env
        run: |
          python --version
          python -m venv ./venv-soma
          ./venv-soma/bin/pip install --prefer-binary pybind11-global typeguard sparse wheel 'setuptools>=70.1'
          ./venv-soma/bin/pip list
      - name: Install TileDB-SOMA-Py with setuptools and --libtiledbsoma
        run: |
          cd apis/python
          ../../venv-soma/bin/python setup.py install \
            --single-version-externally-managed \
            --record record.txt \
            --tiledb=$GITHUB_WORKSPACE/external/ \
            --libtiledbsoma=$GITHUB_WORKSPACE/external/
      - name: Check linking and RPATH (Linux)
        if: runner.os == 'Linux'
        run: |
          ldd ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
          readelf -d ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so  | grep R*PATH
      - name: Check linking and RPATH (macOS)
        if: runner.os == 'macOS'
        run: |
          otool -L ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
          otool -l ./venv-soma/lib/python*/site-packages/tiledbsoma/pytiledbsoma.*.so
      - name: Install runtime dependencies
        run: |
          grep -v '^\[' apis/python/src/tiledbsoma.egg-info/requires.txt > runtime-reqs.txt
          ./venv-soma/bin/pip install --prefer-binary -r runtime-reqs.txt
      - name: Runtime test
        run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"

  # Build a wheel from a source tarball (confirms all required files are
  # distributed in the sdist). This is in preparation for the official building of
  # the PyPI wheels in python-packaging.yml.
  # https://github.com/single-cell-data/TileDB-SOMA/pull/2506
  #
  #
  #  Differences to python-packaging.yml:
  #
  #  * Uses transparent python commands instead of the opaque action
  #    `pypa/cibuildwheel`, and therefore easier to debug
  #  * Only builds two wheels total (python 3.11 on Ubuntu and macOS), so it is
  #    much faster. It's not creating the wheels for distribution, but instead just
  #    providing a quick check that all the required files are distributed in the
  #    source tarball
  #  * Runs whenever an installation-related file is modified instead of only
  #    after a release
  #
  # In summary, the goal is to identify any potential problems with building
  # the PyPI wheels when a PR is submitted, and not at release time.
  sdist:
    runs-on: ${{ matrix.os }}
    name: "Wheel from sdist (${{ matrix.os }})"
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-24.04", "macos-latest"]
    steps:
      - uses: actions/checkout@v4
        with:
          path: TileDB-SOMA
          fetch-depth: 0  # for setuptools-scm
      - name: Setup Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Install dependencies
        run: pip install --prefer-binary pybind11 'setuptools>=70.1' wheel
      - name: Build source tarball (sdist)
        run: |
          cd TileDB-SOMA/apis/python
          python setup.py sdist
      - name: Extract source tarball
        run: |
          tar --list -f TileDB-SOMA/apis/python/dist/tiledbsoma-*.tar.gz
          tar -xzf TileDB-SOMA/apis/python/dist/tiledbsoma-*.tar.gz
      - name: Build wheel
        run: |
          cd tiledbsoma-*/
          python setup.py bdist_wheel
      - name: Install wheel
        run: |
          pip install --prefer-binary tiledbsoma-*/dist/tiledbsoma-*.whl
          python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"