build-test.yaml

name: Build, test

on:
  push:
    branches: ['main']
  pull_request:

# Allow a subsequently queued workflow run to interrupt previous runs
concurrency:
  group: '${{ github.workflow }}-${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
  cancel-in-progress: true

jobs:
  build:
    if: "!contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ['3.8', '3.9', '3.10', '3.11']
    env:
      ANTSPATH: /opt/ants
      FSLPATH: /opt/fsl
      FSLDIR: /opt/fsl
      FSLOUTPUTTYPE: NIFTI_GZ
      FSLVERSION: 6.0.6.5

    steps:
    - name: Cache Ubuntu dependencies
      uses: actions/cache@v3
      with:
        path: |
          /var/lib/apt
          !/var/lib/apt/lists/partial
          !/var/lib/apt/lists/lock
        key: apt-cache-v1
        restore-keys: |
          apt-cache-v1

    - name: Install Ubuntu dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y --no-install-recommends \
                             bc \
                             bzip2 \
                             ca-certificates \
                             curl \
                             dc \
                             file \
                             libfontconfig1 \
                             libfreetype6 \
                             libgl1-mesa-dev \
                             libgl1-mesa-dri \
                             libglu1-mesa-dev \
                             libgomp1 \
                             libice6 \
                             libxcursor1 \
                             libxft2 \
                             libxinerama1 \
                             libxrandr2 \
                             libxrender1 \
                             libxt6
        sudo apt-get clean

    - name: Cache ANTs install
      uses: actions/cache@v3
      with:
        path: /opt/ants
        key: ants-v1
        restore-keys: |
          ants-v1

    - name: Install ANTs
      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: Cache FSL install
      uses: actions/cache@v3
      with:
        path: $FSLPATH
        key: fsl-v2
        restore-keys: |
          fsl-v2

    # Run with multiple Python versions
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install FSL
      run: |
        if [[ ! -d "${FSLPATH}" ]]; then
          sudo mkdir -p $FSLPATH
          curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -o /tmp/fslinstaller.py -s
          python /tmp/fslinstaller.py -d ${FSLPATH} -V ${FSLVERSION} -o
          sudo rm -rf ${FSLPATH}/data/atlases
          rm /tmp/fslinstaller.py
        fi

    - name: Checkout GitHub repository
      uses: actions/checkout@v3

    - name: Install dependencies for headless display
      run: |
        ${{ github.workspace }}/.github/scripts/setup_headless.sh

    - name: Install Python requirements
      if: steps.cache.outputs.cache-hit != 'true'
      run: |
        python -m pip install --upgrade pip
        pip install -r requirements.txt
        pip install pytest nbval

    - 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

    - name: Run pytest on Jupyter notebooks
      run: |
        export PYTHONPATH=$PYTHONPATH:`realpath ${{ github.workspace }}`
        export PATH=$FSLPATH/bin:$ANTSPATH:$PATH
        pytest --nbval-lax -v code/introduction.ipynb
        pytest --nbval-lax -v code/preprocessing.ipynb
        pytest --nbval-lax -v code/diffusion_tensor_imaging.ipynb
        pytest --nbval-lax -v code/constrained_spherical_deconvolution.ipynb
        pytest --nbval-lax -v code/deterministic_tractography.ipynb
        pytest --nbval-lax -v code/probabilistic_tractography.ipynb