WIP do not extend enumerations past limit for index dtype #426
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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())" |