Merge branch 'bids-standard:master' into master

Author: markmikkelsen

.circleci/config.yml

@@ -47,6 +47,7 @@ jobs:
                 --ignore-url 'https://dicomlookup.com/dicomtags/.*' \
                 --ignore-url 'https://www.instagram.com/bidsstandard/' \
                 --ignore-url 'https://jsoneditoronline.org' \
+                --ignore-url 'https://rrid.site.*' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

.github/dependabot.yml

@@ -13,6 +13,8 @@ updates:
       actions-infrastructure:
         patterns:
          - "actions/*"
+    cooldown:
+      default-days: 14
   - package-ecosystem: "uv"
     directory: "/"
     schedule:
@@ -22,6 +24,8 @@ updates:
     groups:
       build-dependencies:
         patterns: ["*"]
+    cooldown:
+      default-days: 14
   - package-ecosystem: "npm"
     directory: "/"
     schedule:
@@ -31,3 +35,18 @@ updates:
     groups:
       node-utilities:
         patterns: ["*"]
+    cooldown:
+      default-days: 14
+  - package-ecosystem: "npm"
+    target-branch: jsr-maint
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    labels:
+      - "exclude-from-changelog"
+      - "schema-code"
+    groups:
+      node-utilities:
+        patterns: ["*"]
+    cooldown:
+      default-days: 14

.github/workflows/publish_schema.yml

@@ -56,6 +56,17 @@ jobs:
           git checkout -t origin/$JSR_BRANCH
         env:
           JSR_BRANCH: ${{ steps.branch.outputs.branch }}
+      - uses: actions/setup-node@v6
+        with:
+          node-version: 24
+          cache: 'npm'
+      - name: Install npm tools
+        run: npm install
+      - name: Verify installed versions
+        run: |
+          npx quicktype --version
+          npx json2ts --help | head -n2
+          npx jsr --version
       - name: Regenerate schema
         run: bst export > schema.json
       - name: Regenerate context types
@@ -67,7 +78,7 @@ jobs:
         run: |
           # Name the file schema so the type will be named Schema
           bst export-metaschema > /tmp/schema.json
-          npx --package=json-schema-to-typescript json2ts --unknownAny /tmp/schema.json > metaschema.ts
+          npx json2ts --unknownAny /tmp/schema.json > metaschema.ts
       - name: Determine next version
         id: version
         run: |

.github/workflows/schemacode_ci.yml

@@ -33,7 +33,7 @@ jobs:
         with:
           fetch-depth: 0
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
       - name: "Build archive on tag"
         run: |
@@ -65,7 +65,7 @@ jobs:
       - uses: actions/checkout@v5
 
       - name: Set up Python ${{ matrix.python-version }} (uv)
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
           activate-environment: true

.github/workflows/validation.yml

@@ -37,7 +37,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
       - name: Lint yml files in src/schema
         run: uvx yamllint -f standard src/schema/ -c .yamllint.yml
 
@@ -46,7 +46,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
       - run: uvx ruff format --diff
       - run: uvx ruff check
 
@@ -55,7 +55,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
       - name: Check for Latin phrases
         run: uv run tools/no-bad-latin.py
 
@@ -64,7 +64,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v5
-      - uses: astral-sh/setup-uv@v6
+      - uses: astral-sh/setup-uv@v7
       - name: Validate CITATION.cff
         run: uvx cffconvert --validate
       - name: Check for Zenodo compatibility

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.34.0
+    rev: 0.35.0
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -49,7 +49,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
+    rev: v1.19.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

Maintainers_Guide.md

@@ -26,6 +26,7 @@ See also: [BIDS governance](https://bids.neuroimaging.io/collaboration/governanc
 | Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))              | 1h/week         |                                       | Nov 2022 |
 | Julia-Katharina Pfarr ([@julia-pfarr](https://github.com/julia-pfarr))       | 2h/week         |                                       | Mar 2025 |
 | Seyed (Yahya) Shirazi ([@neuromechanist](https://github.com/neuromechanist)) | 2h/week         | ExG, multi-modal, events & annotations | Jul 2025 |
+| Boris Clénet ([@bclenet](https://github.com/bclenet))                        | 2h/week         |                                       | Jul 2025 |
 
 In addition to the [BIDS Governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-maintainers-group)
 classification of a maintainer, maintainers may declare a limited scope of responsibility.

mkdocs.yml

@@ -24,6 +24,7 @@ nav:
           - Near-Infrared Spectroscopy: modality-specific-files/near-infrared-spectroscopy.md
           - Motion: modality-specific-files/motion.md
           - Magnetic Resonance Spectroscopy: modality-specific-files/magnetic-resonance-spectroscopy.md
+          - Electromyography: modality-specific-files/electromyography.md
       - Derivatives:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md
@@ -51,6 +52,9 @@ nav:
       - Website: https://bids.neuroimaging.io/getting_started/
       - Tutorials: https://bids.neuroimaging.io/getting_started/tutorials/
       - GitHub repository: https://github.com/bids-standard/bids-starter-kit
+exclude_docs: |
+  README.md
+  pregh-changes.md
 theme:
   name: material
   favicon: images/favicon.png

package-lock.json

@@ -5,7 +5,7 @@ dependencies = [
   "bidsschematools[render]",
   "mkdocs>=1.1.0",
   "mkdocs-material>=5.4",
-  "pymdown-extensions>=7.0.0",
+  "pymdown-extensions>=9.2.0",
   "mkdocs-branchcustomization-plugin~=0.1.3",
   "mkdocs-macros-plugin",
   "mkdocs-redirects",
@@ -60,3 +60,7 @@ replace = """NEXT_VERSION_HERE
 - '{new_version}'
 - """
 include_bumps = ['pre_label']
+
+[[tool.mypy.overrides]]
+module = ["pymdownx.*"]
+ignore_missing_imports = true