ENH: add ability to test examples PR against PR in bids-specification #1415
Workflow file for this run
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| name: validate_datasets | |
| on: | |
| push: | |
| branches: ['**'] | |
| pull_request: | |
| types: [opened, synchronize, reopened, edited] | |
| branches: ['**'] | |
| create: | |
| branches: [master] | |
| tags: ['**'] | |
| schedule: | |
| - cron: "0 4 * * 1" | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| # Prepare the matrix dynamically based on whether a bids-specification PR is referenced | |
| prepare-matrix: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-matrix.outputs.matrix }} | |
| bids_pr: ${{ steps.find-pr.outputs.pr_number }} | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| fetch-depth: 0 # Get full history for commit message scanning | |
| - name: Check for bids-specification PR reference | |
| id: find-pr | |
| run: | | |
| # Check PR description if this is a PR | |
| if [ "${{ github.event_name }}" == "pull_request" ]; then | |
| cat << 'EOF' > /tmp/pr_body.txt | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| PR_NUM=$(grep -oP 'bids-specification-pr:\s*(https://github\.com/bids-standard/bids-specification/pulls?/)*\K[0-9]+' /tmp/pr_body.txt | head -1 || true) | |
| [ -n "$PR_NUM" ] && echo "pr_number=$PR_NUM" >> $GITHUB_OUTPUT || : | |
| fi | |
| - name: Set matrix | |
| id: set-matrix | |
| run: | | |
| EXTRA_ITEM='' | |
| if [ -n "${{ steps.find-pr.outputs.pr_number }}" ]; then | |
| EXTRA_ITEM=', "bids-pr"' | |
| fi | |
| echo "matrix=[\"stable\", \"main\", \"dev\", \"legacy\"${EXTRA_ITEM}]" >> $GITHUB_OUTPUT | |
| build: | |
| needs: prepare-matrix | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [ubuntu-latest, macos-latest, windows-latest] | |
| bids-validator: ${{ fromJson(needs.prepare-matrix.outputs.matrix) }} | |
| runs-on: ${{ matrix.platform }} | |
| env: | |
| BIDS_PR: ${{ needs.prepare-matrix.outputs.bids_pr }} | |
| TZ: Europe/Berlin | |
| FORCE_COLOR: 1 | |
| steps: | |
| - uses: actions/checkout@v5 | |
| - name: Set up Node.js | |
| if: matrix.bids-validator == 'legacy' | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22 | |
| - name: Set cache name | |
| if: matrix.bids-validator == 'legacy' | |
| run: | |
| echo "MONTH=$( date +%Y%m )" >> $GITHUB_ENV | |
| - name: Load npm cache | |
| if: matrix.bids-validator == 'legacy' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.npm | |
| key: npm-${{ runner.os }}-${{ env.MONTH }} | |
| - uses: denoland/setup-deno@v2 | |
| if: matrix.bids-validator != 'legacy' | |
| with: | |
| deno-version: v2.x | |
| - name: Install BIDS validator (stable) | |
| if: matrix.bids-validator == 'stable' | |
| run: | | |
| deno install -Agf -n bids-validator jsr:@bids/validator | |
| - name: Install BIDS validator (main) | |
| if: matrix.bids-validator == 'main' || matrix.bids-validator == 'bids-pr' | |
| run: | | |
| # If unmerged validator PRs are needed for testing, you can use | |
| # https://github.com/<FORK>/bids-validator/raw/<BRANCH>/bids-validator/src/bids-validator.ts | |
| deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js | |
| - name: Install BIDS validator (dev) | |
| if: matrix.bids-validator == 'dev' | |
| run: | | |
| git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator | |
| cd ../bids-validator | |
| deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts | |
| - name: Install BIDS validator (legacy) | |
| if: "matrix.bids-validator == 'legacy'" | |
| run: | | |
| npm install -g bids-validator | |
| - name: Display versions and environment information | |
| run: | | |
| echo $TZ | |
| date | |
| which deno && echo "deno\n----" && deno --version || true | |
| echo "node\n----"; node --version | |
| echo "npm\n----"; npm --version | |
| echo "bids-validator"; bids-validator --version | |
| - name: Check that no large files are present | |
| if: "matrix.bids-validator == 'stable'" | |
| run: | | |
| echo "Checking for big files ..." | |
| found=`find . -not -path "./.git*" -type f -size +500k` | |
| if [ "$found" == "" ] | |
| then | |
| echo "No big files present, great!" | |
| else | |
| echo "Found big files:" | |
| echo "$found" | |
| exit 1; | |
| fi | |
| - name: Skip legacy validation for post-legacy datasets | |
| run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done | |
| if: matrix.bids-validator == 'legacy' | |
| - name: Skip stable validation for datasets with unreleased validator features | |
| # Replace ${EMPTY} with dataset patterns, when this is needed | |
| # Reset to "for DS in ${EMPTY}; ..." after a validator release | |
| run: for DS in ${EMPTY}; do touch $DS/.SKIP_VALIDATION; done | |
| if: matrix.bids-validator == 'stable' | |
| - name: Skip main validation for datasets with unreleased spec features | |
| # Replace ${EMPTY} with dataset patterns, when this is needed | |
| # Reset to "for DS in ${EMPTY}; ..." after a spec release | |
| run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done | |
| if: matrix.bids-validator != 'dev' | |
| - name: Set BIDS_SCHEMA variable for dev version | |
| if: matrix.bids-validator == 'dev' | |
| # When proposing new features, schema changes may be necessary. | |
| # Update this URL to the schema.json from PRs to the spec, when needed. | |
| # If this variable is unset, dev will generally track the latest development | |
| # release of https://jsr.io/@bids/schema | |
| run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV | |
| - name: Set BIDS_SCHEMA variable for bids-pr version | |
| if: matrix.bids-validator == 'bids-pr' | |
| # Use the readthedocs PR preview build for the schema | |
| run: | | |
| echo "Using schema from bids-specification PR #${{ env.BIDS_PR }}" | |
| echo BIDS_SCHEMA=https://bids-specification--${{ env.BIDS_PR }}.org.readthedocs.build/en/${{ env.BIDS_PR }}/schema.json >> $GITHUB_ENV | |
| - name: Validate all BIDS datasets using bids-validator | |
| run: | | |
| cat ./run_tests.sh | |
| ./run_tests.sh |