validator.yml

name: Dataset Validator
on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]

jobs:
  Validate:
    runs-on: ubuntu-latest

    steps:

    - name: Checkout
      uses: actions/checkout@v2
      with:
        # make sure to download directly from the PR's repo, whether that is this repo or a fork
        # By default github generates a merge commit for each PR in this repo, but only for the one branch under test
        # but `git-annex` needs access to *two* branches: the current branch and `git-annex`
        # this might be subtly buggy since it is testing the remote version, not the merged version
        #
        # *if* this is not a pull request, this will fall back to its default behaviour.
        repository: ${{github.event.pull_request.head.repo.full_name}}
        ref: ${{ github.event.pull_request.head.ref }}

    - name: Install dos2unix
      run: |
        # the easy way to do this: convert everything to unix and ask git if that changed anything
        sudo apt-get install -y dos2unix

    - name: Check line endings
      run: |
        # the easy way to do this: convert everything to unix and ask git if that changed anything

        find ./ -path ./.git -prune -o -type f -print0 | xargs -0 dos2unix -q
        # this version is safer, but more maintenance:
        #find ./ -path ./.git -prune -o -type f \( ! -name "*.nii" -a ! -name "*.nii.gz" \) -print0 | xargs -0 dos2unix -q

        git diff --stat --exit-code
        if [ "$?" -ne 0 ]; then
          echo "error: Windows line endings found."
          exit 1
        fi

    - name: Lint participants.tsv
      run: .github/workflows/lint-tsv participants.tsv

    #- name: Update software
    #  run: |
    #    # do we want to do this? it's helpful to avoid testing against surprise out-of-date software, but also so slow.
    #    sudo apt-get update &&
    #    sudo DEBIAN_FRONTEND=noninteractive apt-get -y dist-upgrade &&
    #    sudo DEBIAN_FRONTEND=noninteractive apt-get autoremove

    - name: Install git-annex
      run: |
        sudo apt-get install -y git-annex
        git config --global annex.thin true

    - name: Install bids-validator
      run: |
        # install proper NodeJS for bids-validator
        curl -sL https://deb.nodesource.com/setup_current.x | sudo -E bash -
        sudo apt-get install -y nodejs
        sudo npm install -g bids-validator

    - name: Set up Python
      uses: actions/setup-python@v2
      with:
        python-version: 3.7

    - name: Install spine-generic for acquisition parameters check
      run: pip install spinegeneric@git+https://github.com/spine-generic/spine-generic.git@master

    #- name: Increase free space
    #   run: |
    #    # this takes about 2 minutes but saves about 30GB, which is space we might need for git-annex.
    #    # annex.thin saves a lot of space, but if the dataset grows beyond what Github can handle
    #    # try enabling this.
    #    # ref: https://github.com/actions/virtual-environments/issues/2606#issuecomment-772683150
    #    sudo rm -rf /usr/local/lib/android /usr/share/dotnet

    - name: git config
      run: |
        # this is needed by git-annex so that it can write to the local git-annex branch
        # the tracking information about the local copy
        git config --global user.name "gh-actions"
        git config --global user.email "gh-actions"
        # but actually, disable those writes. We don't need them because we're throwing away this copy immediately.
        # this might make the previous two lines unnecessary, but it's safer just to leave them both in
        git config annex.alwayscommit false

    - name: Download dataset
      run: |
        git fetch --depth=1 origin git-annex:git-annex # actions/checkout@v2 does a shallow checkout, so it is missing this important branch
        git annex init
        git annex get -J8

    - name: Checking BIDS compliance
      run: bids-validator --verbose ./
    - name: Checking acquisition parameters
      run: sg_params_checker -path-in ./
    - name: Checking data consistency
      run: sg_check_data_consistency -path-in ./