Stage requirements.txt into its own file. #536
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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/setup.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-so-copying.yml' | |
| - 'apis/python/setup.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: | |
| docker: | |
| runs-on: ubuntu-latest | |
| name: "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:22.04 | |
| 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: ${{ matrix.TILEDB_EXISTS == 'yes' }} | |
| run: | | |
| mkdir -p external | |
| # Please do not edit manually -- let scripts/update-tiledb-version.py update this | |
| wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.22.0/tiledb-linux-x86_64-2.22.0-52e981e.tar.gz | |
| tar -C external -xzf tiledb-linux-x86_64-*.tar.gz | |
| ls external/lib/ | |
| echo "LD_LIBRARY_PATH=$(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* | |
| # 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())" | |
| macos: | |
| runs-on: macos-13 | |
| name: "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: Install pre-built libtiledb | |
| if: ${{ matrix.TILEDB_EXISTS == 'yes' }} | |
| run: | | |
| mkdir -p external | |
| # Please do not edit manually -- let scripts/update-tiledb-version.py update this | |
| wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.22.0/tiledb-macos-x86_64-2.22.0-52e981e.tar.gz | |
| tar -C external -xzf tiledb-macos-x86_64-*.tar.gz | |
| ls external/lib/ | |
| echo "DYLD_LIBRARY_PATH=$(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 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/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools | |
| ./venv-soma/bin/python -m 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/python -m 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: ${{ matrix.os }} | |
| name: "${{ matrix.os }} setuptools" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-22.04", "macos-12"] | |
| 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 | |
| # Please do not edit manually -- let scripts/update-tiledb-version.py update this | |
| wget --quiet https://github.com/TileDB-Inc/TileDB/releases/download/2.22.0/tiledb-macos-x86_64-2.22.0-52e981e.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/2.22.0/tiledb-linux-x86_64-2.22.0-52e981e.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 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/python -m pip install --prefer-binary pybind11-global typeguard sparse wheel setuptools | |
| ./venv-soma/bin/python -m 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 >/tmp/filtered-requirements.txt | |
| ./venv-soma/bin/pip install --prefer-binary -r filtered-requirements.txt | |
| - name: Runtime test | |
| run: ./venv-soma/bin/python -c "import tiledbsoma; print(tiledbsoma.pytiledbsoma.version())" |