Merge branch 'master' into enh-project-datasettype

Author: rwblair

.codespellrc

@@ -1,4 +1,4 @@
 [codespell]
-skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*
+skip = .git,env,venv,ds*,asl*,qmr*,genetics*,fnirs*,eeg*,meg*,pet*,ieeg*,motion*,synthetic*,emg*
 builtin = clear,rare
-ignore-words-list = nd,te
+ignore-words-list = nd,te,FLE,Sepulcre

.github/dependabot.yml

@@ -6,3 +6,7 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
+    groups:
+      actions-infrastructure:
+        patterns:
+         - "actions/*"

.github/pull_request_template.md

@@ -0,0 +1,14 @@
+<!-- New examples often relate to in-progress changes to the specification or validator. Link to the relevant PRs, if any. -->
+<!-- Accepted formats: PR number (e.g., 123), GitHub shorthand (e.g., bids-standard/bids-specification#123), or full URL -->
+
+- BIDS Specification PR: NONE
+- BIDS Validator PR: NONE
+- TODOs:
+  - [ ] ...
+
+<!-- PLEASE READ AND DELETE THE TEXT BELOW BEFORE OPENING THE PULL REQUEST -->
+
+See the [CONTRIBUTING](https://github.com/bids-standard/bids-examples/blob/master/CONTRIBUTING.md) guide. Specifically:
+
+- Please keep the title of your Pull Request (PR) short but informative - it will appear in the changelog.
+

.github/workflows/deploy.yml

@@ -16,8 +16,8 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             -   name: Checkout 🛎️
-                uses: actions/checkout@v5
-            -   uses: actions/setup-python@v5
+                uses: actions/checkout@v6
+            -   uses: actions/setup-python@v6
                 with:
                     python-version: "3.11"
             -   name: Install and Build 🔧

.github/workflows/validate_datasets.yml

@@ -2,14 +2,14 @@ name: validate_datasets
 
 on:
   push:
-    branches: ['**']
+    branches: [master, main]
+    tags: ['*']
   pull_request:
-    branches: ['**']
-  create:
-    branches: [master]
-    tags: ['**']
+    types: [opened, synchronize, reopened, edited]
+    branches: [master, main, 'bep*']
   schedule:
     - cron: "0 4 * * 1"
+  workflow_dispatch:
 
 concurrency:
   group: ${{ github.ref }}
@@ -20,25 +20,63 @@ defaults:
     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 }}
+      spec_pr: ${{ steps.find-pr.outputs.spec_pr }}
+      val_pr: ${{ steps.find-pr.outputs.val_pr }}
+    steps:
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0  # Get full history for commit message scanning
+
+    - name: Check for bids-specification PR reference
+      id: find-pr
+      run: |
+        # Check PR description if this is a PR
+        if [ "${{ github.event_name }}" == "pull_request" ]; then
+          cat << 'EOF' > /tmp/pr_body.txt
+        ${{ github.event.pull_request.body }}
+        EOF
+          SPEC_PR=$(grep -oP 'BIDS Specification PR:\s*(https://github\.com/bids-standard/bids-specification/pulls?/|bids-standard/bids-specification#)*\K[0-9]+' /tmp/pr_body.txt | head -1 || true)
+          [ -n "$SPEC_PR" ] && echo "spec_pr=$SPEC_PR" >> $GITHUB_OUTPUT || :
+          VAL_PR=$(grep -oP 'BIDS Validator PR:\s*(https://github\.com/bids-standard/bids-validator/pulls?/|bids-standard/bids-validator#)*\K[0-9]+' /tmp/pr_body.txt | head -1 || true)
+          [ -n "$VAL_PR" ] && echo "val_pr=$VAL_PR" >> $GITHUB_OUTPUT || :
+        fi
+
+    - name: Set matrix
+      id: set-matrix
+      run: |
+        EXTRA_ITEM=''
+        if [ -n "${{ steps.find-pr.outputs.spec_pr }}${{ steps.find-pr.outputs.val_pr }}" ]; then
+          EXTRA_ITEM=', "dev-prs"'
+        fi
+        echo "matrix=[\"stable\", \"main\", \"dev\", \"legacy\"${EXTRA_ITEM}]" >> $GITHUB_OUTPUT
+
   build:
+    needs: prepare-matrix
     strategy:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        bids-validator: [stable, main, dev, legacy]
+        bids-validator: ${{ fromJson(needs.prepare-matrix.outputs.matrix) }}
 
     runs-on: ${{ matrix.platform }}
 
     env:
+      SPEC_PR: ${{ needs.prepare-matrix.outputs.spec_pr }}
+      VAL_PR: ${{ needs.prepare-matrix.outputs.val_pr }}
       TZ: Europe/Berlin
       FORCE_COLOR: 1
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
 
     - name: Set up Node.js
       if: matrix.bids-validator == 'legacy'
-      uses: actions/setup-node@v4
+      uses: actions/setup-node@v6
       with:
         node-version: 22
 
@@ -49,7 +87,7 @@ jobs:
 
     - name: Load npm cache
       if: matrix.bids-validator == 'legacy'
-      uses: actions/cache@v4
+      uses: actions/cache@v5
       with:
         path: ~/.npm
         key: npm-${{ runner.os }}-${{ env.MONTH }}
@@ -72,7 +110,7 @@ jobs:
         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'
+      if: ( matrix.bids-validator == 'dev' ) || ( matrix.bids-validator == 'dev-prs' && env.VAL_PR == '' )
       run: |
         git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
         cd ../bids-validator
@@ -83,6 +121,25 @@ jobs:
       run: |
         npm install -g bids-validator
 
+    - name: Install BIDS validator (dev-prs with VAL_PR)
+      if: matrix.bids-validator == 'dev-prs' && env.VAL_PR != ''
+      shell: bash
+      env:
+        GH_TOKEN: ${{ github.token }}
+      run: |
+        # Fetch PR info using gh cli (handles auth automatically)
+        fork_url=$(gh api repos/bids-standard/bids-validator/pulls/${{ env.VAL_PR }} --jq '.head.repo.html_url')
+        branch=$(gh api repos/bids-standard/bids-validator/pulls/${{ env.VAL_PR }} --jq '.head.ref')
+        echo "I: Received fork_url=$fork_url branch=$branch"
+        if [ "$fork_url" = "null" ] || [ -z "$fork_url" ]; then
+          echo "E: Failed to get PR info for VAL_PR=${{ env.VAL_PR }}"
+          exit 1
+        fi
+        # Perform the same installation as in "dev"
+        git clone -b "$branch" "$fork_url" ../bids-validator
+        cd ../bids-validator
+        deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
+
     - name: Display versions and environment information
       run: |
         echo $TZ
@@ -96,7 +153,7 @@ jobs:
       if: "matrix.bids-validator == 'stable'"
       run: |
         echo "Checking for big files ..."
-        found=`find . -not -path "./.git*" -type f -size +500k`
+        found=`find . -not -path "./.git*" -type f -size +1M`
         if [ "$found" == "" ]
         then
             echo "No big files present, great!"
@@ -107,7 +164,7 @@ jobs:
         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
+      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing atlas-*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -119,7 +176,7 @@ jobs:
     - 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
+      run: for DS in atlas-* emg_*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -130,6 +187,13 @@ jobs:
       # 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 dev-prs version
+      if: matrix.bids-validator == 'dev-prs' && env.SPEC_PR != ''
+      # Use the readthedocs PR preview build for the schema
+      run: |
+        echo "Using schema from bids-specification PR #${{ env.SPEC_PR }}"
+        echo BIDS_SCHEMA=https://bids-specification--${{ env.SPEC_PR }}.org.readthedocs.build/en/${{ env.SPEC_PR }}/schema.json >> $GITHUB_ENV
+
     - name: Validate all BIDS datasets using bids-validator
       run: |
         cat ./run_tests.sh

.github/workflows/validation.yml

@@ -16,5 +16,5 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: codespell-project/actions-codespell@master