Generate documentation from docstrings #435
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| # Runs on pull request or release - checks CLI tools are working without raising exception | |
| name: CLI tests | |
| on: | |
| pull_request: | |
| release: | |
| jobs: | |
| test_cli: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest ] | |
| python-version: [ '3.9', '3.10' ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest pytest-cov | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Install hazen | |
| run: | | |
| pip install . | |
| # "if: always option" runs step even if previous fails - useful to ensure all CLI functions tested | |
| - name: test_snr | |
| if: always() | |
| run: | | |
| hazen snr tests/data/snr/Siemens --report | |
| hazen snr tests/data/snr/Siemens --measured_slice_width 5.0012 --report | |
| - name: test_acr_snr | |
| if: always() | |
| run: | | |
| hazen acr_snr tests/data/acr/Siemens --report | |
| hazen acr_snr tests/data/acr/Siemens --subtract tests/data/acr/Siemens2 --report | |
| - name: test acr_uniformity | |
| if: always() | |
| run: | | |
| hazen acr_uniformity tests/data/acr/Siemens --report | |
| - name: test acr_ghosting | |
| if: always() | |
| run: | | |
| hazen acr_ghosting tests/data/acr/Siemens --report | |
| - name: test acr_slice_position | |
| if: always() | |
| run: | | |
| hazen acr_slice_position tests/data/acr/Siemens --report | |
| - name: test acr_slice_thickness | |
| if: always() | |
| run: | | |
| hazen acr_slice_thickness tests/data/acr/Siemens --report | |
| - name: test acr_geometric_accuracy | |
| if: always() | |
| run: | | |
| hazen acr_geometric_accuracy tests/data/acr/Siemens --report | |
| - name: test acr_spatial_resolution | |
| if: always() | |
| run: | | |
| hazen acr_spatial_resolution tests/data/acr/SiemensMTF --report | |
| - name: test slice_position | |
| if: always() | |
| run: | | |
| hazen slice_position tests/data/slicepos/SLICEPOSITION --report | |
| - name: test slice_width | |
| if: always() | |
| run: | | |
| hazen slice_width tests/data/slicewidth/512_matrix --report | |
| hazen slice_width tests/data/slicewidth/SLICEWIDTH --report | |
| - name: test spatial_resolution | |
| if: always() | |
| run: | | |
| hazen spatial_resolution tests/data/resolution/RESOLUTION/ --report | |
| - name: test uniformity | |
| if: always() | |
| run: | | |
| hazen uniformity tests/data/uniformity --report | |
| - name: test ghosting | |
| if: always() | |
| run: | | |
| hazen ghosting tests/data/ghosting/GHOSTING --report | |
| hazen ghosting tests/data/ghosting/PE_COL_PHANTOM_BOTTOM_RIGHT --report | |
| - name: test snr_map | |
| if: always() | |
| run: | | |
| hazen snr_map tests/data/snr/Siemens --report | |
| - name: test relaxometry | |
| if: always() | |
| run: | | |
| hazen relaxometry tests/data/relaxometry/T1/site1_20200218/plate5 --calc T1 --plate_number=5 --report | |
| hazen relaxometry tests/data/relaxometry/T2/site3_ge/plate4/ --calc T2 --plate_number=4 --report | |