Merge branch 'bids-standard:master' into master

Author: ericearl

.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/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: 0.34.1
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

mkdocs.yml

@@ -52,6 +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

pyproject.toml

@@ -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

src/appendices/hed.md

@@ -14,7 +14,7 @@ Individual terms are comma-separated and may be grouped using parentheses to ind
 association.
 See the [HED Schema Browser](https://www.hedtags.org/display_hed.html)
 to view the HED schema and the
-[HED resources](https://www.hed-resources.org/en/latest/) site for additional information.
+[HED resources](https://www.hedtags.org/hed-resources/) site for additional information.
 
 Starting with HED version 8.0.0, HED allows users to annotate using individual
 terms or partial paths in the HED vocabulary (for example, `Red` or `Visual-presentation`)

src/common-principles.md

@@ -591,7 +591,7 @@ Example:
 ```
 
 Each level can be described with a string as in the example above,
-or with an object containing the fields [`Description`](./glossary.md#description-metadata)
+or with an object containing the fields [`Description`](./glossary.md#description-sense-1-metadata)
 and [`TermURL`](./glossary.md#termurl-metadata)
 like in the example below.
 

src/derivatives/imaging.md

@@ -548,9 +548,9 @@ standard BIDS labels:
 
 ```tsv
 index	name	abbreviation
-137	pars	opercularis	IFGop
-138	pars	triangularis	IFGtr
-139	pars	orbitalis	IFGor
+137	pars opercularis	IFGop
+138	pars triangularis	IFGtr
+139	pars orbitalis	IFGor
 ```
 
 <!-- Link Definitions -->

src/metaschema.json

@@ -71,6 +71,9 @@
             "additionalProperties": false
           }
         },
+        "templates": {
+          "type": "object"
+        },
         "versions": {
           "type": "array",
           "items": {