travis.yml

name: Deps & CI

on: [push, pull_request]

jobs:
  build-linux:
    if: "!contains(github.event.head_commit.message, '[skip ci]')"
    runs-on: ubuntu-latest
    env:
      TEST_DATA_HOME: /home/runner/sdcflows-tests
      FSLDIR: /usr/share/fsl/5.0
      FSLOUTPUTTYPE: NIFTI_GZ
      FSLMULTIFILEQUIT: TRUE
      POSSUMDIR: /usr/share/fsl/5.0
      FSLTCLSH: /usr/bin/tclsh
      FSLWISH: /usr/bin/wish
      AFNI_MODELPATH: /usr/lib/afni/models
      AFNI_IMSAVE_WARNINGS: NO
      AFNI_TTATLAS_DATASET: /usr/share/afni/atlases
      AFNI_PLUGINPATH: /usr/lib/afni/plugins
      ANTSPATH: /usr/lib/ants
    strategy:
      max-parallel: 5
      matrix:
        python-version: [3.7, 3.8, 3.9]

    steps:
    - name: Git settings (pacify DataLad)
      run: |
        git config --global user.name 'NiPreps Bot'
        git config --global user.email 'nipreps@gmail.com'
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/cache@v2
      id: conda
      with:
        path: |
          /usr/share/miniconda/pkgs
          /home/runner/.cache/pip
        key: python-${{ matrix.python-version }}-v2
        restore-keys: |
          python-${{ matrix.python-version }}-
    - name: Install DataLad
      run: |
        $CONDA/bin/conda install -c conda-forge git-annex datalad pip
        $CONDA/bin/pip install datalad-osf
    - uses: actions/checkout@v2
    - name: Install minimal dependencies
      run: |
        $CONDA/bin/pip install -r min-requirements.txt
        $CONDA/bin/pip install .[tests]

    - uses: actions/cache@v2
      with:
        path: ~/.cache/templateflow
        key: tf-cache-v1
        restore-keys: |
          tf-cache-
    - name: Get TemplateFlow's required objects
      run: |
        $CONDA/bin/python tools/cache_templateflow.py

    - uses: actions/cache@v2
      with:
        path: ${{ env.TEST_DATA_HOME }}
        key: data-cache-v1
        restore-keys: |
          data-cache-
    - name: Install test data
      run: |
        export PATH=$CONDA/bin:$PATH
        mkdir -p ${{ env.TEST_DATA_HOME }}
        cd ${{ env.TEST_DATA_HOME }}

        # ds001600
        datalad install -r https://github.com/nipreps-data/ds001600.git
        datalad update -r --merge -d ds001600/
        datalad get -r -d ds001600/ ds001600/sub-1/

        # HCP/sub-101006
        datalad install -r https://github.com/nipreps-data/HCP101006.git
        datalad update -r --merge -d HCP101006/
        datalad get -r -d HCP101006

        # ds001771
        datalad install -r https://github.com/nipreps-data/ds001771.git
        datalad update --merge -d ds001771/
        datalad get -r -d ds001771/ ds001771/sub-36/*

        # ds000054
        datalad install -r https://github.com/nipreps-data/ds000054.git
        datalad update --merge -d ds000054/
        datalad get -r -d ds000054/ ds000054/sub-100185/*
    - uses: actions/cache@v2
      with:
        path: /var/lib/apt
        key: apt-cache-v1
        restore-keys: |
          apt-cache-
    - name: Install NeuroDebian & software packages
      run: |
        bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh);
        sudo apt-get update
        sudo apt-get install -y --no-install-recommends fsl afni
        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

    - name: Install FreeSurfer's mri_robust_template
      env:
        MRI_ROBUST_TEMPLATE: sx2n7/providers/osfstorage/5e825301d0e35400ebb481f2
      run: |
        curl https://files.osf.io/v1/resources/$MRI_ROBUST_TEMPLATE?direct > mri_robust_template
        sudo install mri_robust_template /usr/local/bin
        mkdir -p $HOME/.cache/freesurfer/
        echo "b2VzdGViYW5Ac3RhbmZvcmQuZWR1CjMwNzU2CiAqQ1MzYkJ5VXMxdTVNCiBGU2kvUGJsejJxR1V3Cg==" | base64 -d > $HOME/.cache/freesurfer/license.txt

    - name: Run pytest with coverage
      run: |
        export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
        export PATH=/usr/lib/ants:/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
        $CONDA/bin/pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows

    - name: Submit code coverage
      run: |
        $CONDA/bin/conda install codecov
        $CONDA/bin/python -m codecov --flags travis --file cov.xml -e $GITHUB_RUN_NUMBER