python-so-copying.yml

# Confirm shared object copying when building the Python package
# https://github.com/single-cell-data/TileDB-SOMA/pull/1937

name: Python SO copying

on:
  push:
    paths:
      - '.github/workflows/python-so-copying.yml'
      - 'apis/python/**'
      - 'libtiledbsoma/cmake/**'
  pull_request:
    paths:
      - '.github/workflows/python-so-copying.yml'
      - 'apis/python/**'
      - 'libtiledbsoma/cmake/**'
  workflow_dispatch:

defaults:
  run:
    shell: bash

jobs:
  build:
    runs-on: ubuntu-latest
    name: "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:22.04
    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: ${{ matrix.TILEDB_EXISTS == 'yes' }}
        run: |
          mkdir -p external
          wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.19.1/tiledb-linux-x86_64-2.19.1-29ceb3e7.tar.gz
          tar -C external -xzf tiledb-linux-x86_64-*.tar.gz
          ls external/lib/
          echo "LD_LIBRARY_PATH=$(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 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
        run: |
          python --version
          python -m venv ./venv-soma
          ./venv-soma/bin/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel
          ./venv-soma/bin/python -m 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/python -m 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*
          find . -name '*tile*.so*' # should only show shared objects installed in virtual env
          ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())"