[ci] Fix typo in new CI job (#3682) #26
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| name: TileDB-SOMA Python CI with varying dependencies | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - 'release-*' | |
| pull_request: | |
| paths-ignore: | |
| - '**.md' | |
| - 'apis/r/**' | |
| - 'docs/**' | |
| - ".github/workflows/python-remote-storage.yml" | |
| workflow_dispatch: | |
| jobs: | |
| ci: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: ensemble1 | |
| os: ubuntu-24.04 | |
| python_version: 3.9 | |
| cc: gcc-13 | |
| cxx: g++-13 | |
| anndata: 0.10.8 | |
| numba: 0.60.0 | |
| numpy: 1.25.0 | |
| pandas: 1.5.3 | |
| pyarrow: 11.0.0 | |
| scanpy: 1.9.8 | |
| scipy: 1.13.1 | |
| - name: ensemble2 | |
| os: ubuntu-24.04 | |
| python_version: 3.9 | |
| cc: gcc-13 | |
| cxx: g++-13 | |
| anndata: 0.10.9 | |
| numba: 0.60.0 | |
| numpy: 1.25.0 | |
| pandas: 1.5.3 | |
| pyarrow: 12.0.1 | |
| scanpy: 1.10.3 | |
| scipy: 1.13.1 | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Show matrix OS | |
| run: echo "matrix.os:" ${{ matrix.os }} | |
| - name: Linux CPU info | |
| if: ${{ matrix.os == 'ubuntu-24.04' }} | |
| run: cat /proc/cpuinfo | |
| - name: MacOS CPU info | |
| if: ${{ matrix.os == 'macOS-latest' }} | |
| run: sysctl -a | grep cpu | |
| - name: Select XCode version | |
| if: startsWith(matrix.os, 'macos') | |
| uses: maxim-lobanov/setup-xcode@v1 | |
| with: | |
| xcode-version: '15.4' | |
| - name: Set up Python ${{ matrix.python_version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python_version }} | |
| cache: pip | |
| cache-dependency-path: ./apis/python/setup.py | |
| - name: Show XCode version | |
| run: clang --version | |
| - name: Check out TileDB-SOMA | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # ensure we get all tags to inform package version determination | |
| - name: Log pip dependencies | |
| run: pip list | |
| - name: Install tiledbsoma | |
| run: pip -v install -e apis/python[all] -C "--build-option=--no-tiledb-deprecated" | |
| env: | |
| CC: ${{ matrix.cc }} | |
| CXX: ${{ matrix.cxx }} | |
| - name: Install dependencies | |
| run: pip install --prefer-binary pytest typeguard | |
| - name: Install variant dependencies | |
| run: | | |
| pip install \ | |
| anndata==${{matrix.anndata}} \ | |
| numba==${{matrix.numba}} \ | |
| numpy==${{matrix.numpy}} \ | |
| pandas==${{matrix.pandas}} \ | |
| pyarrow==${{matrix.pyarrow}} \ | |
| scanpy==${{matrix.scanpy}} \ | |
| scipy==${{matrix.scipy}} | |
| - name: Show package versions | |
| run: python scripts/show-versions.py | |
| - name: Obtain test data | |
| shell: bash | |
| run: | | |
| cd test | |
| rm -rf soco | |
| tar zxf soco.tgz | |
| cd .. | |
| - name: Run pytests for Python | |
| shell: bash | |
| run: python -m pytest apis/python/tests/*.py -v --durations=20 --maxfail=50 |