Improve decomposition and geometry reading #432
Workflow file for this run
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| name: Geometry tool | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - '.github/workflows/gmy-*' | |
| - 'geometry-tool/**' | |
| - Code/util/Vector3D.cc | |
| - Code/geometry/SiteDataBare.cc | |
| - Code/lb/lattices/D3Q27.cc | |
| - Code/io/formats/geometry.cc | |
| - Code/io/writers/xdr/XdrFileWriter.cc | |
| - Code/io/writers/xdr/XdrMemWriter.cc | |
| - Code/io/writers/xdr/XdrWriter.cc | |
| - Code/io/writers/Writer.cc | |
| pull_request: | |
| schedule: | |
| # Run every Monday 0700 UTC | |
| - cron: '0 7 * * 1' | |
| jobs: | |
| lint-python: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Run black to check Python formatting | |
| working-directory: geometry-tool | |
| run: pip install black~=22.0 && black --check . | |
| lint-cpp: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Run clang-format | |
| working-directory: geometry-tool/HlbGmyTool/Model/Generation | |
| run: ${{ github.workspace }}/.github/workflows/run-clang-format.py --style file -r . | |
| gmy-tool: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: | |
| - '3.8' | |
| - '3.9' | |
| - '3.10' | |
| - '3.11' | |
| env: | |
| VMTK_VERSION: 1.5.0 | |
| VMTK_DIR: /opt/vmtk | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: APT packages | |
| env: | |
| DEBIAN_FRONTEND: noninteractive | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends \ | |
| libboost-dev \ | |
| libcgal-dev \ | |
| ninja-build \ | |
| libopengl0 libglx0 libxt6 | |
| - name: pip cache | |
| uses: actions/cache@v3 | |
| env: | |
| # Increase this value to reset cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('geometry-tool/pyproject.toml', 'geometry-tool/setup.py') }} | |
| - name: ensure pip is up-to-date | |
| run: pip install --upgrade pip | |
| - name: Get and install VMTK from our builder | |
| run: | | |
| wget -nv -O vmtk.tar.gz https://github.com/hemelb-codes/vmtk-build/releases/download/v${VMTK_VERSION}/all-${VMTK_VERSION}-ubuntu-py${{ matrix.python-version }}.tar.gz | |
| mkdir -p $VMTK_DIR | |
| tar -xzf vmtk.tar.gz -C $VMTK_DIR | |
| echo "PATH=$VMTK_DIR/bin:$PATH" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$VMTK_DIR/lib/python${{ matrix.python-version }}/site-packages:$PYTHONPATH" >> $GITHUB_ENV | |
| echo "CMAKE_PREFIX_PATH=$VMTK_DIR:$CMAKE_PREFIX_PATH" >> $GITHUB_ENV | |
| - name: Check setuptools sees VMTK | |
| run: | | |
| pip list | |
| pip list --format json | jq -e '.[] | select(.name == "vmtk")' | |
| - name: Store VMTK dir on error | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: failed-vmtk-tree | |
| path: ${{ env.VMTK_DIR }} | |
| - name: Build and install the app | |
| working-directory: geometry-tool | |
| run: pip install . | |
| - name: Store build tree on error | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: failed-build-tree | |
| path: geometry-tool/_skbuild | |
| - name: Install test dependencies | |
| working-directory: python-tools | |
| run: pip install pytest 'cython~=0.29' && python setup.py install | |
| - name: Run the tests | |
| working-directory: geometry-tool/tests | |
| run: py.test | |
| - name: Tar failed install | |
| if: failure() | |
| run: tar -czf fail-${{ matrix.python-version }}.tar.gz $pythonLocation | |
| - name: Store failed install | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: failed-python-${{ matrix.python-version }} | |
| path: fail-${{ matrix.python-version }}.tar.gz | |
| - name: Get hemelb-tests repo | |
| uses: ./.github/actions/get-tests-repo | |
| with: | |
| path: hemelb-tests | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| - name: Smoketest the update tool | |
| working-directory: hemelb-tests/diffTest | |
| run: hlb-config2gmy cyl.pro tmp.pr2 | |
| - name: Decompress input mesh | |
| working-directory: hemelb-tests/diffTest | |
| run: gunzip cyl.stl.gz | |
| - name: Run the gmy tool without GUI | |
| working-directory: hemelb-tests/diffTest | |
| run: | | |
| mkdir test | |
| hlb-gmy-cli --xml test/config.xml --geometry test/config.gmy cyl.pr2 | |
| - name: Run the self-consistency checker | |
| working-directory: hemelb-tests/diffTest/test | |
| run: hlb-gmy-selfconsistent config.xml | |
| - name: Count the sites | |
| working-directory: hemelb-tests/diffTest/test | |
| run: "[[ $(hlb-gmy-countsites config.gmy) == 44250 ]]" | |
| - name: Compare XML | |
| working-directory: hemelb-tests/diffTest | |
| run: python compare_xml.py config.xml test/config.xml | |
| - name: Compare GMY | |
| working-directory: hemelb-tests/diffTest | |
| run: python compare_gmy.py config.gmy test/config.gmy |