run.yml

name: run
on:
  push:
    branches: ['**']
    tags: ['**']
    paths-ignore: ['.gitignore', 'LICENSE*', 'LICENCE*', 'README.md', 'SIRF_data_preparation/*']
jobs:
  check:
    runs-on: ubuntu-latest
    container:
      image: ghcr.io/synerbi/sirf:edge
      options: --user root  # https://github.com/actions/checkout/issues/956
    steps:
    - uses: actions/checkout@v4
    - name: Install dependencies
      shell: bash -el {0}
      run: |
        source /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh
        pip install git+https://github.com/TomographicImaging/Hackathon-000-Stochastic-QualityMetrics
        if test -f apt.txt; then
          sudo apt-get update
          xargs -a apt.txt sudo apt-get install -y
        fi
        if test -f environment.yml; then
          sed -i '/^name:.*/d' environment.yml
          conda env update -n base
        fi
        if test -f requirements.txt; then
          pip install -r requirements.txt
        fi
        conda list
    - name: Test imports
      shell: bash -el {0}
      run: |
        source /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh
        dataset=Siemens_mMR_NEMA_IQ
        curl -sfSL -o  ${dataset}.zip https://petric.tomography.stfc.ac.uk/data/${dataset}.zip
        mkdir -p data; cd data; unzip -u ../${dataset}.zip; cd ..
        curl -fsSL https://raw.githubusercontent.com/SyneRBI/PETRIC/main/petric.py > petric.py
        test -f main.py || ln -s main_ISTA.py main.py
        python <<EOF
        import petric
        from main import Submission, submission_callbacks
        from cil.optimisation.algorithms import Algorithm
        assert issubclass(Submission, Algorithm)
        assert isinstance(submission_callbacks, list)
        assert all(callable(callback) for callback in submission_callbacks)
        data = petric.get_data('NeuroLF_Hoffman_Dataset')
        assert data.OSEM_image.max() > 0
        assert data.reference_image.max() > 0
        assert data.FOV_mask.max() > 0
        EOF
  full:
    if: startsWith(github.ref, 'refs/tags')
    runs-on: [self-hosted, docker, cuda]
    steps:
    - uses: actions/checkout@v4
      with: {fetch-depth: 0, submodules: recursive}
    - run: petric