test_cli.yml

# 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@v5
        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