build-test.yaml

name: Build, test

on:
  push:
    branch: 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
      FSLDIR: /opt/fsl
      FSLOUTPUTTYPE: NIFTI_GZ

    steps:
    - name: Cache Ubuntu dependencies
      uses: actions/cache@v2
      with:
        path: /var/lib/apt
        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

    - name: Cache ANTs install
      uses: actions/cache@v2
      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@v2
      with:
        path: /opt/fsl
        key: fsl-v2
        restore-keys: |
          fsl-v2

    - name: Install FSL
      run: |
        if [[ ! -d "${FSLPATH}" ]]; then
          sudo mkdir -p $FSLPATH
          curl -sSL "https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.2-centos6_64.tar.gz" | sudo tar -xzC $FSLPATH --strip-components 1
          sudo bash ${FSLPATH}/etc/fslconf/fslpython_install.sh -f $FSLPATH
          sudo rm -rf ${FSLPATH}/data/atlases
        fi

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

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

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

    - 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 nbmake

    - 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 ${{ github.workspace }}`
        export PATH=/opt/fsl/bin:/opt/ants:$PATH
        pytest --nbmake -v code/introduction.ipynb
        pytest --nbmake --nbmake-timeout=5400 -v code/preprocessing.ipynb
        pytest --nbmake -v code/diffusion_tensor_imaging.ipynb
        pytest --nbmake -v code/constrained_spherical_deconvolution.ipynb
        pytest --nbmake -v code/deterministic_tractography.ipynb
        pytest --nbmake -n=2 -v code/probabilistic_tractography.ipynb