validate_bids-examples.yml

name: validate_datasets

on:
  push:
    branches: ['master']
  pull_request:
    branches: ['**']
#  create:
#    branches: [master]
#    tags: ['**']
#  schedule:
#    - cron: "0 4 * * 1"

concurrency:
  group: ${{ github.ref }}
  cancel-in-progress: true

jobs:
  build:
    strategy:
      fail-fast: false
      matrix:
        platform: [ubuntu-latest] # , macos-latest, windows-latest]
        bids-validator: [master-deno]
        python-version: ["3.11"]

    runs-on: ${{ matrix.platform }}

    env:
      TZ: Europe/Berlin
      FORCE_COLOR: 1

    steps:
    - uses: actions/checkout@v4

    - name: "Apply patches for BIDS-2.0"
      run: |
        set -o pipefail
        tools/bids-2.0/apply_all 2>&1 | tee /tmp/patch.log

    - name: "Show differences after patching"
      run: |
        git add .
        git diff --cached

    - name: "Commit and push patched version online for possible introspection"
      # Run only on a non-merge commit for the PR
      if: >
        github.repository == 'bids-standard/bids-specification' &&
        github.event.pull_request.head.ref == 'bids-2.0' &&
        github.event.pull_request.merge_commit_sha != github.sha
      run: |
        set -x
        commit=$(git rev-parse HEAD)
        branch=${GITHUB_HEAD_REF}-patched
        git checkout -b "$branch"
        {
          echo -e "Applied patches for ${GITHUB_HEAD_REF} to ${commit}\n";
          cat /tmp/patch.log;
        } | git commit -F -
        git push -f origin "$branch"

    # Setup Python with bst
    - uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: "Install build dependencies"
      run: pip install --upgrade build twine
    - name: "Build source distribution and wheel"
      run: python -m build tools/schemacode
    - name: "Check distribution metadata"
      run: twine check tools/schemacode/dist/*
    - name: "Install bst tools from the build"
      run: pip install $( ls tools/schemacode/dist/*.whl )[all]
    - name: "Produce dump of the schema as schema.json"
      run: bst -v export --output src/schema.json

    - uses: denoland/setup-deno@v1.1.2
      if: "matrix.bids-validator == 'master-deno'"
      with:
        deno-version: v1.x

    - name: Install BIDS validator (master deno build)
      if: "matrix.bids-validator == 'master-deno'"
      run: |
        pushd ..
        # Let's use specific commit for now
        # TODO: progress it once in a while
        commit=a7b291b882a8c6184219ccb84faae255ba96203a
        git clone --depth 1 https://github.com/bids-standard/bids-validator
        cd bids-validator
        git fetch --depth 1 origin $commit;
        echo -e '#!/bin/sh\n'"$PWD/bids-validator/bids-validator-deno \"\$@\"" >| /usr/local/bin/bids-validator
        chmod a+x /usr/local/bin/bids-validator
        which -a bids-validator
        bids-validator --help
        popd

    - name: Display versions and environment information
      run: |
        echo $TZ
        date
        echo -n "npm: "; npm --version
        echo -n "node: "; node --version
        echo -n "bids-validator: "; bids-validator --version
        echo -n "python: "; python --version

    # Checkout bids-examples
    - uses: actions/checkout@v4
      with:
        # repository: bids-standard/bids-examples
        # For now use the forked repository with support for deno validator
        # from https://github.com/bids-standard/bids-examples/pull/435
        repository: yarikoptic/bids-examples
        ref: deno-validator
        path: bids-examples

    - name: Mark known not yet to be deno-legit BIDS datasets
      run: touch {ds000117,ds000246,ds000247,ds000248,eeg_ds003645s_hed_demo,ieeg_motorMiller2007,ieeg_visual}/.SKIP_VALIDATION
      shell: bash
      working-directory: bids-examples

    - name: Validate using bids-validator without migration
      run: ./run_tests.sh
      working-directory: bids-examples

    - name: Migrate all BIDS datasets
      run: /bin/ls */dataset_description.json | sed -e 's,/.*,,g' | xargs bst migrate-datasets
      shell: bash
      working-directory: bids-examples

    - name: Show migrated datasets diff
      run: git diff HEAD
      working-directory: bids-examples

    # TODO: commit as a merge from current state of bids-examples
    # and prior bids-2.0 branch there, but overloading with new updated
    # state and recording commit hash of bids-specification used.

    - name: Validate all BIDS datasets using bids-validator after migration
      run: VALIDATOR_ARGS="--schema file://$PWD/../src/schema.json" bash ./run_tests.sh
      working-directory: bids-examples