validator.yml

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

jobs:
  Validate:
    runs-on: ubuntu-latest

    steps:

    - name: Gain disk space by remapping temp disk (`/dev/sdb1`)
      uses: easimon/maximize-build-space@master
      # We use the above action instead of removing unwanted packages because it only takes about 2s;
      # by comparison, removing lots of small file is very time-consuming.
      with:
        # After freeing up space we could have as much as 87GB available, which is overkill.
        # So, we set root == 10GB to save room for installing dependencies (leaving us with ~77GB)
        root-reserve-mb: 10240
        swap-size-mb: 1024

    - name: Checkout
      uses: actions/checkout@v4
      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: Update apt packages
      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 it's helpful to avoid testing against surprise out-of-date software, but also so slow.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
        git config --global annex.retry 2

    - name: Setup NodeJS (for bids-validator)
      uses: actions/setup-node@v4

    - name: Install bids-validator
      run: sudo npm install -g bids-validator

    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.11

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

    - 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@v4 does a shallow checkout, so it is missing this important branch
        git annex init
        git annex get -J8

    - name: Checking BIDS compliance
      if: always()
      run: |
        bids-validator --verbose ./ | tee bids.txt
        printf "\nShort summary:\n\n"
        # FIXME: This should be replaced with bids-validator settings: A) throw error on warning or B) warning ignores
        ! grep "\[WARN\]\|\[ERR\]" bids.txt  # ! -> Reverse error code so "found == error thrown"

    - name: Checking acquisition parameters
      if: always()
      run: |
        sg_params_checker -path-in ./ | tee params.txt
        # FIXME: Checking the output like this should be replaced with SG throwing actual errors
        ! grep "WARNING" params.txt  # ! -> Reverse error code so "found == error thrown"

    - name: Checking data consistency
      if: always()
      run: |
        sg_check_data_consistency -path-in ./ | tee consistency.txt
        # FIXME: Checking the output like this should be replaced with SG throwing actual errors
        ! grep "Warning\|Missing" consistency.txt
        grep "all good" consistency.txt