build-test.yaml

name: Build, test

on:
  push:
    branches: main
  pull_request

jobs:
  build:
    if: "!contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.7, 3.8, 3.9]
    env:
      ANTSPATH: /opt/ants
      FSLPATH: /opt/fsl

    steps:
    - name: Checkout GitHub repository
      uses: actions/checkout@v2

    # Run with multiple Python versions
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}

    # Install Python requirements
    - name: Install requirements
      uses: actions/cache@v2
      id: cache
      with:
        path: ${{ env.pythonLocation }}
        key: ${{ env.pythonLocation }}-${{ hashFiles('requirements.txt') }}
        restore-keys: |
            ${{ env.pythonLocation }}-
      if: steps.cache.outputs.cache-hit != 'true'
      run: |
        python -m pip install --upgrade pip
        pip install -r requirements.txt
        pip install pytest nbval

    - name: Install ANTs
      uses: actions/cache@v2
      with:
        path: /opt/ants
        key: ants-v1
        restore-keys: |
          ants-v1
        run: |
            if [[ ! -d "${ANTSPATH}" ]]; then
              sudo mkdir -p $ANTSPATH
              curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | sudo tar -xzC $ANTSPATH --strip-components 1
            fi

    - name: Install FSL
      uses: actions/cache@v2
      with:
        path: /opt/fsl
        key: fsl-v1
        restore-keys: |
          fsl-v1
        run: |
            if [[ ! -d "${FSLPATH}" ]]; then
              wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py || echo "Failed to download FSL installer"
              python fslinstaller.py -d $FSLPATH -p -q || echo "Failed to install FSL"
              rm -rf /opt/fsl/*/data/atlases
            fi

    # Download the necessary data
    - name: Download data
      run: |
        pushd `pwd`
        cd ${{ github.workspace }}/data
        osf -p cmq8a fetch ds000221_subject/ds000221_sub-010006.zip
        unzip ds000221_sub-010006.zip
        rm ds000221_sub-010006.zip
        popd

    # Run the actual tests of all the Python Notebooks.
    - name: Test Notebooks
      run: |
        export PYTHONPATH=$PYTHONPATH:`realpath ${{ github.workspace }}`
        pytest --nbval-lax -v code/introduction/introduction.ipynb
        pytest --nbval-lax -v code/introduction/solutions/introduction_solutions.ipynb
        pytest --nbval-lax -v code/diffusion_tensor_imaging/diffusion_tensor_imaging.ipynb
        pytest --nbval-lax -v code/diffusion_tensor_imaging/solutions/diffusion_tensor_imaging_solutions.ipynb
        pytest --nbval-lax -v code/constrained_spherical_deconvolution/constrained_spherical_deconvolution.ipynb
        pytest --nbval-lax -v code/constrained_spherical_deconvolution/solutions/constrained_spherical_deconvolution_solutions.ipynb
        pytest --nbval-lax -v code/deterministic_tractography/deterministic_tractography.ipynb
        pytest --nbval-lax -v code/deterministic_tractography/solutions/deterministic_tractography_solutions.ipynb
        pytest --nbval-lax -v code/probabilistic_tractography/probabilistic_tractography.ipynb