New features related to the revision of the accompanying manuscript #63
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| name: Run tox | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| tests_basic: | |
| name: Basic tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install tox-gh-actions | |
| - name: Lint | |
| if: ${{matrix.python-version == '3.10'}} | |
| run: | | |
| tox -e lint | |
| - name: Run tests for all Pythons | |
| run: | | |
| tox -e unit | |
| - name: Run coverage | |
| if: ${{matrix.python-version == '3.10'}} | |
| run: | | |
| tox -e coverage | |
| - name: Upload to codecov | |
| if: ${{matrix.python-version == '3.10'}} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: false | |
| files: ./coverage.xml | |
| flags: pytest | |
| name: "connectome-manipulator-py310" | |
| tests_functional: | |
| name: Functional tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/checkout@v4 | |
| with: | |
| repository: BlueBrain/parquet-converters | |
| path: parquet-converters | |
| submodules: true | |
| - name: Set up Apache Arrow repositories | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y ca-certificates lsb-release wget | |
| wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb | |
| sudo apt-get install -y ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb | |
| sudo apt-get update | |
| - name: Install build dependencies | |
| run: | | |
| sudo apt-get install -y cmake g++ libhdf5-openmpi-dev librange-v3-dev ninja-build nlohmann-json3-dev | |
| sudo apt-get install -y libarrow-dev libparquet-dev | |
| - name: Install test dependencies | |
| run: | | |
| sudo apt-get install -y hdf5-tools | |
| - name: Configure and build | |
| run: | | |
| cd parquet-converters | |
| cmake -B build -S . -GNinja \ | |
| -DCMAKE_INSTALL_PREFIX=$PWD/install \ | |
| -DCMAKE_CXX_COMPILER=$(which mpicxx) | |
| cmake --build build | |
| ctest --test-dir build --output-on-failure | |
| cmake --install build | |
| echo "parquet2hdf5 --version: $(./install/bin/parquet2hdf5 --version)" | |
| echo "$PWD/install/bin" >> $GITHUB_PATH | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| pip install tox-gh-actions | |
| - name: Run tox | |
| run: | | |
| tox -e functional | |
| tox -e integration |