Merge branch 'master' of https://github.com/markmikkelsen/bids-specification

Author: markmikkelsen

.circleci/config.yml

@@ -2,22 +2,14 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.12-node
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
-      - run:
-          name: install dependencies
-          command: |
-            python -m venv env
-            source env/bin/activate
-            python -m pip install --upgrade pip
-            pip install -r requirements.txt
       - run:
           name: generate docs
           command: |
-            source env/bin/activate
-            mkdocs build --clean --strict --verbose
+            uv run mkdocs build --clean --strict --verbose
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
@@ -31,35 +23,28 @@ jobs:
     docker:
       - image: cimg/python:3.12
     steps:
-      # checkout code to default ~/project
       - checkout
       - attach_workspace:
-          # mkdocs build outputs will be in ~/project/site
           at: ~/project
-      - run:
-          name: install linkchecker
-          command: |
-            python -m venv env
-            source env/bin/activate
-            python -m pip install --upgrade pip
-            python -m pip install linkchecker
       - run:
           name: check links
           command: |
-            source env/bin/activate
             git status
             if (! git log -1 --pretty=oneline | grep REL:) ; then
               chmod a+rX -R ~
-              linkchecker -t 1 ~/project/site/
+              uvx linkchecker -t 1 ~/project/site/
               # check external separately by pointing to all *html so no
               # failures for local file:/// -- yoh found no better way,
               linkchecker -t 1 --check-extern \
                 --ignore-url 'file:///.*' \
+                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
+                --ignore-url 'https://doi.org/.*' \
                 --ignore-url 'https://fonts.gstatic.com' \
-                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
                 --ignore-url 'https://github.com/[^/]*' \
-                --ignore-url 'https://doi.org/.*' \
-                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
+                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
+                --ignore-url 'https://www.incf.org' \
+                --ignore-url 'https://dicomlookup.com/dicomtags/.*' \
+                --ignore-url 'https://www.instagram.com/bidsstandard/' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"
@@ -72,20 +57,17 @@ jobs:
       # checkout code to default ~/project
       - checkout
       - run:
-          name: install dependencies
+          name: install uv
           command: |
-            apt-get update && apt install -y python3-pip python3-venv pandoc
-            python3 -m venv .venv
-            source .venv/bin/activate
-            python3 -m pip install --upgrade pip
-            python3 -m pip install -r  ~/project/requirements.txt
-            python3 -m pip install ~/project/tools/schemacode/[render]
+            curl -LsSf https://astral.sh/uv/install.sh | XDG_BIN_HOME=/usr/local/bin sh
       - run:
-          name: install font that works with unicode emojis
-          command: apt-get update && apt-get install -y fonts-symbola
+          name: install dependencies
+          command: |
+            apt-get update && apt install -y fonts-symbola pandoc
       - run:
           name: generate pdf version docs
           command: |
+            uv sync
             source .venv/bin/activate
             cd ~/project/pdf_build_src
             bash build_pdf.sh

.codespellrc

@@ -1,6 +1,7 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
-ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
+skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build,venvs
+ignore-regex = \bHEP\b
+ignore-words-list = acknowledgements,als,bu,fo,te,weill,winn
 builtin = clear,rare,en-GB_to_en-US
 # this overloads default dictionaries and I have not yet figured out
 # how to have multiple https://github.com/codespell-project/codespell/issues/2727

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -17,7 +17,7 @@ body:
           If not, please open an issue in the [bids-2-devel repository](https://github.com/bids-standard/bids-2-devel) instead.
 
         - Is there already a group working on your idea?
-          Check the [BIDS extension proposals](https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification)
+          Check the [BIDS extension proposals](https://bids.neuroimaging.io/extensions/index.html)
 
         - Will your idea potentially require a large effort?
           Read [BEP lead guidelines](https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/).

.github/dependabot.yml

@@ -1,10 +1,21 @@
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
+enable-beta-ecosystems: true
 updates:
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
-      interval: "weekly"
+      interval: "monthly"
+    labels:
+      - "exclude-from-changelog"
+    groups:
+      actions-infrastructure:
+        patterns:
+         - "actions/*"
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "monthly"
     labels:
       - "exclude-from-changelog"

.github/pull_request_template.md

@@ -7,7 +7,7 @@ See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/
 
 - Please ensure your name is credited
   on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
-  To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors)
+  To add your name, please edit our [Recent Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors)
   and add your name with the type of contribution.
   For assistance, please tag @bids-standard/maintainers.
 

.github/workflows/publish_schema.yml

@@ -4,6 +4,7 @@ on:
   push:
     branches:
       - "master"
+      - "maint/*"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -34,13 +35,27 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: 3
+      - run: env
+      - run: git status
+      - name: Determine master/maintenance branch
+        id: branch
+        run: |
+          if [[ "$GITHUB_REF_NAME" = "master" ]]; then
+            echo "branch=jsr-dist" | tee -a $GITHUB_OUTPUT
+            echo "mode=dev" | tee -a $GITHUB_OUTPUT
+          else
+            echo "branch=jsr-maint" | tee -a $GITHUB_OUTPUT
+            echo "mode=maint" | tee -a $GITHUB_OUTPUT
+          fi
       - name: Install bidsschematools
         run: |
           pip install --upgrade tools/schemacode
           git clean -fxd tools/schemacode
-      - name: Checkout jsr-dist
+      - name: Checkout ${{ steps.branch.outputs.branch }}
         run: |
-          git checkout -t origin/jsr-dist
+          git checkout -t origin/$JSR_BRANCH
+        env:
+          JSR_BRANCH: ${{ steps.branch.outputs.branch }}
       - name: Regenerate schema
         run: bst export > schema.json
       - name: Regenerate context types
@@ -54,36 +69,46 @@ jobs:
           bst export-metaschema > /tmp/schema.json
           npx --package=json-schema-to-typescript json2ts --unknownAny /tmp/schema.json > metaschema.ts
       - name: Determine next version
+        id: version
         run: |
           BASE=$( jq -r .schema_version schema.json )
-          if [[ "$BASE" =~ ^[0-9]*.[0-9]*.[0-9]*$ ]]; then
+          if [[ "$BASE" =~ ^[0-9]*\.[0-9]*\.[0-9]*$ ]]; then
             # Release, so unconditionally update version
             VERSION=$BASE
             jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
-          else
+            echo release=true | tee -a $GITHUB_OUTPUT
+          elif [[ "$BASE" =~ ^[0-9]*\.[0-9]*\.[0-9]*\.post[0-9]*$ ]]; then
+            # Post-release, so replace .post with + for JSR semver
+            VERSION=${BASE/.post/+}
+            jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
+            echo release=true | tee -a $GITHUB_OUTPUT
+          elif [[ "$GITHUB_REF_NAME" = "master" ]]; then
             DENOVER=$( jq -r .version jsr.json )
             # Get the reference of the latest commit to touch the schema directory
-            HASH=$( git log -n 1 --pretty=%h $REF -- src/schema )
+            HASH=$( git log -n 1 --pretty=%h $GITHUB_REF -- src/schema )
             if [[ $DENOVER =~ ^"$BASE".[0-9] ]]; then
               PREFIX=${DENOVER%+*}
               let SERIAL=1+${PREFIX#$BASE.}
             else
               SERIAL=1
             fi
             VERSION="$BASE.$SERIAL+$HASH"
+            echo release=true | tee -a $GITHUB_OUTPUT
+          else
+            echo release=false | tee -a $GITHUB_OUTPUT
           fi
           echo VERSION=$VERSION | tee -a $GITHUB_ENV
-        env:
-          REF: ${{ github.ref }}
-      - name: Check for changes, set version and commit
+          echo version=$VERSION | tee -a $GITHUB_OUTPUT
+      - name: Bump version (${{ steps.version.outputs.version }}) if changed
+        if: steps.version.outputs.release == 'true'
         run: |
           if ! git diff -s --exit-code; then
             jq ".version = \"$VERSION\"" jsr.json > tmp.json && mv tmp.json jsr.json
             git add jsr.json schema.json context.ts metaschema.ts
-            git commit -m "Update schema JSR distribution"
+            git commit -m "Update schema JSR distribution ($VERSION)"
             git push
           fi
       - name: Publish to JSR
-        if: success()
+        if: success() && steps.version.outputs.release == 'true'
         run: |
           npx jsr publish