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| Original file line number | Diff line number | Diff line change |
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| # 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())" |
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