bids-specification/.github/workflows/validate_bids-examples.yml at b43da8f572c657e1807d6896c81ccece3b287082 · bids-standard/bids-specification · GitHub

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---
name: validate_datasets

on:
  push:
    branches: ["master"]
  pull_request:
    branches: ["**"]

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

jobs:
  build:
    strategy:
      fail-fast: false
      matrix:
        platform: [ubuntu-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

      # 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
        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 \"\$@\"" >| /tmp/bids-validator
          chmod a+x /tmp/bids-validator
          sudo mv /tmp/bids-validator /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:
          # 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: |
          for dataset in */dataset_description.json; do
            dataset_dir=$(dirname "$dataset")
            echo "Migrating $dataset_dir..."
            bst migrate all "$dataset_dir" \
              --skip fix_inheritance_overloading \
              --skip fix_tsv_entity_prefix || \
              echo "Migration failed for $dataset_dir"
          done
        shell: bash
        working-directory: bids-examples

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

      - 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