Merge remote-tracking branch 'upstream/master' into bep038

Author: effigies

.circleci/config.yml

@@ -55,11 +55,13 @@ jobs:
               # 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/.*' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

.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/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

.github/workflows/schemacode_ci.yml

@@ -4,10 +4,13 @@ on:
   push:
     branches:
       - "master"
+      - "maint/*"
     tags:
       - "schema-*"
   pull_request:
     branches:
+      - "master"
+      - "maint/*"
       - "*"
 
 concurrency:
@@ -36,7 +39,9 @@ jobs:
         run: pip install --upgrade tools/schemacode[all]
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
       - name: "Build archive on tag"
-        run: pytest tools/schemacode/bidsschematools -k make_archive
+        run: |
+          python -m pytest -k make_archive
+        working-directory: tools/schemacode
         env:
           BIDSSCHEMATOOLS_RELEASE: 1
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
@@ -87,14 +92,15 @@ jobs:
 
       - name: "Run tests"
         run: |
-          python -m pytest -vs --pyargs bidsschematools -m "not validate_schema" \
-              --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules
+          python -m pytest -vs --doctest-modules -m "not validate_schema" \
+              --cov-append --cov-report=xml --cov-report=term --cov=src/bidsschematools
+        working-directory: tools/schemacode
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
         with:
           name: unit_${{ matrix.os }}_${{ matrix.python-version }}
-          path: coverage.xml
+          path: tools/schemacode/coverage.xml
         if: success()
 
   publish:
@@ -143,13 +149,16 @@ jobs:
           python -m pip install -e ./tools/schemacode[all]
 
       - name: Run schema validation tests
-        run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
+        run: |
+          python -m pytest -vs --doctest-modules -m "not validate_schema" \
+              --cov-append --cov-report=xml --cov-report=term --cov=src/bidsschematools
+        working-directory: tools/schemacode
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v4
         with:
           name: schema_validation
-          path: coverage.xml
+          path: tools/schemacode/coverage.xml
         if: success()
 
   upload_to_codecov:
@@ -164,7 +173,7 @@ jobs:
         uses: actions/download-artifact@v4
 
       - name: Upload to CodeCov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
           fail_ci_if_error: true

.pre-commit-config.yaml

@@ -2,21 +2,22 @@
 # See https://pre-commit.com/hooks.html for more hooks
 ci:
   skip: [shellcheck]
-exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
+exclude: 'tools/schemacode/src/bidsschematools/tests/data/broken_dataset_description.json'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+        args: [--unsafe]
       - id: check-json
       - id: check-toml
       - id: check-ast
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.4
+    rev: 0.31.3
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -26,7 +27,7 @@ repos:
       - id: check-readthedocs
         files: readthedocs.yml
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -36,7 +37,7 @@ repos:
         files: tools/schemacode
         args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
   - repo: https://github.com/pyCQA/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
       - id: isort
         files: ^tools/(?!schemacode)
@@ -46,7 +47,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 7.1.1
+    rev: 7.1.2
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/.flake8]
@@ -68,12 +69,12 @@ repos:
       - id: pretty-format-toml
         args: [--autofix, --indent, '4', --no-sort]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.15.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -89,7 +90,7 @@ repos:
           - types-jsonschema
           - jsonschema
           - httpx
-        args: ["tools/schemacode/bidsschematools"]
+        args: ["tools/schemacode/src"]
         pass_filenames: false
   - repo: https://github.com/koalaman/shellcheck-precommit
     rev: v0.10.0

CODE_OF_CONDUCT.md

@@ -8,10 +8,10 @@ We hope that these guidelines are designed to make it as easy as possible to get
 If you have any questions that aren't discussed below, please let us know
 by [opening an issue](https://github.com/bids-standard/bids-specification/issues/new).
 
-If you are not familiar with Git ansd GitHub,
-check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+If you are not familiar with Git and GitHub,
+check our [generic contributing guidelines](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html).
 
-If you want to contribute to the BIDS website,
+If you want to contribute to the BIDS specification,
 make sure you also read the instructions below.
 
 ## Table of contents
@@ -237,13 +237,10 @@ pip install -U pip
 pip install -r requirements.txt
 ```
 
-The first command ensures you are using an up to date version of `pip`,
+The first command ensures you are using an up-to-date version of `pip`,
 and the second command installs all dependencies.
-The third command ensures to install the BIDS schema code as an "editable" install,
-so that if you make changes to the schema files,
-these are automatically reflected in the sourcecode.
 
-Note that if you need to work on the some of the Python code
+Note that if you need to work on some of the Python code
 that is used to render the specification,
 you will probably have to also run: