Merge branch 'bids-standard:master' into master

Author: markmikkelsen

.circleci/config.yml

@@ -32,10 +32,10 @@ jobs:
             git status
             if (! git log -1 --pretty=oneline | grep REL:) ; then
               chmod a+rX -R ~
-              uvx linkchecker -t 1 ~/project/site/
+              uvx linkchecker -t 1 --no-warnings ~/project/site/
               # check external separately by pointing to all *html so no
               # failures for local file:/// -- yoh found no better way,
-              uvx linkchecker -t 1 --check-extern \
+              uvx linkchecker -t 1 --no-warnings --check-extern \
                 --ignore-url 'file:///.*' \
                 --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
                 --ignore-url "https://bids-specification.readthedocs.io/en/v${CIRCLE_BRANCH#rel/}/" \
@@ -48,6 +48,7 @@ jobs:
                 --ignore-url 'https://www.instagram.com/bidsstandard/' \
                 --ignore-url 'https://jsoneditoronline.org' \
                 --ignore-url 'https://rrid.site.*' \
+                --ignore-url 'https://jsr.io/.*' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

.github/workflows/publish_schema.yml

@@ -28,7 +28,7 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
           filter: "blob:none"
@@ -61,7 +61,7 @@ jobs:
           node-version: 24
           cache: 'npm'
       - name: Install npm tools
-        run: npm install
+        run: npm install --no-save
       - name: Verify installed versions
         run: |
           npx quicktype --version

.github/workflows/schemacode_ci.yml

@@ -29,7 +29,7 @@ jobs:
       attestations: write
       id-token: write
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
       - name: Install the latest version of uv
@@ -62,7 +62,7 @@ jobs:
             python-version: 3.13
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }} (uv)
         uses: astral-sh/setup-uv@v7
@@ -74,7 +74,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
 
       - name: "Fetch packages"
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v7
         with:
           name: Packages
           path: dist
@@ -95,7 +95,7 @@ jobs:
         working-directory: tools/schemacode
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: unit_${{ matrix.os }}_${{ matrix.python-version }}
           path: tools/schemacode/coverage.xml
@@ -112,7 +112,7 @@ jobs:
 
     steps:
       - name: Download packages built by build-and-inspect-python-package
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v7
         with:
           name: Packages
           path: dist
@@ -131,7 +131,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate schema
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
 
       - name: Set Up Python environment
         uses: actions/setup-python@v6
@@ -150,7 +150,7 @@ jobs:
         working-directory: tools/schemacode
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: schema_validation
           path: tools/schemacode/coverage.xml
@@ -162,10 +162,10 @@ jobs:
     needs: [test, validate_schema]
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Download artifacts
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v7
 
       - name: Upload to CodeCov
         uses: codecov/codecov-action@v5

.github/workflows/shellcheck.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
       - name: Install dependencies
         run: |
           sudo apt update && sudo apt install -y shellcheck

.github/workflows/validation.yml

@@ -16,15 +16,15 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: codespell-project/actions-codespell@master
 
   # Markdown formatting
   remark:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
-      - uses: actions/setup-node@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-node@v6
         with:
           node-version: 22
       - name: Install dependencies
@@ -36,7 +36,7 @@ jobs:
   yamllint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v7
       - name: Lint yml files in src/schema
         run: uvx yamllint -f standard src/schema/ -c .yamllint.yml
@@ -45,7 +45,7 @@ jobs:
   python-style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v7
       - run: uvx ruff format --diff
       - run: uvx ruff check
@@ -54,7 +54,7 @@ jobs:
   latin-phrases:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v7
       - name: Check for Latin phrases
         run: uv run tools/no-bad-latin.py
@@ -63,7 +63,7 @@ jobs:
   validate_cff:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v7
       - name: Validate CITATION.cff
         run: uvx cffconvert --validate

.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: 0.35.0
+    rev: 0.36.0
     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: v1.19.0
+    rev: v1.19.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

CONTRIBUTING.md

@@ -268,11 +268,12 @@ such as when you build the documentation locally.
 ### 4. Ready to build!
 
 Using the terminal (command line) please enter `uv run mkdocs serve`.
+Alternatively, if you would like to use `make`, run `make serve`, which will run `uv sync` and then `mkdocs`.
 This will allow you to see a local version of the specification.
 The local address will be `http://127.0.0.1:8000`.
 You may enter that into your browser and this will bring up the specification!
 
-(If you are not using `uv`, activate your environment and then run `mkdocs serve`.)
+(If you are not using `uv` or `make`, activate your environment and then run `mkdocs serve`.)
 
 ## Fixing Markdown style errors
 

Makefile

@@ -1,5 +1,15 @@
 .PHONY:  tools/contributors.tsv
+
+.PHONY: all serve install update_contributors formatschema
+
 all:
+	@echo "Nothing is done by default. Consider following targets:"
+	@echo "  install -- prep environment"
+	@echo "  serve   -- prep environment and build and serve docs"
+	@echo "  formatschema -- format and commit(!) schema"
+
+serve: .venv
+	uv run mkdocs serve
 
 install: .venv node_modules
 

mkdocs.yml

@@ -29,6 +29,7 @@ nav:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md
           - Imaging data types: derivatives/imaging.md
+          - Templates and atlases: derivatives/atlas.md
       - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
       - Glossary: glossary.md
       - BIDS Extension Proposals: extensions.md