Merge branch 'master' into schema/rules/ephys

.github/workflows/changelog_generator.yml

@@ -101,10 +101,11 @@ jobs:
 
     commit_generated_changelog:
         permissions:
-            # Give the default GITHUB_TOKEN write permission to commit and push the
-            # added or changed files to the repository.
             contents: write
+            pull-requests: write
         needs: lint_generated_changelog
+        # Run only if the head commit message contains "[build changelog]""
+        if: contains(github.event.head_commit.message, '[build changelog]')
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
@@ -113,18 +114,21 @@ jobs:
           with:
             name: changelog_post_lint
             path: ~/changelog_build
-        - name: Changelog deployment
+        - name: add changelog to git
           run: |
-            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
-              merge_message=$(git log -1 | grep Merge | grep "pull")
-              PR_number=$(echo $merge_message | cut -d ' ' -f 4)
-              git config credential.helper 'cache --timeout=120'
-              git config user.email "[email protected]"
-              git config user.name "bids-maintenance"
-              git add ${{ github.workspace }}/src/CHANGES.md
-              git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
-              git push https://${{ secrets.GITHUB_TOKEN }}@github.com/bids-standard/bids-specification.git master
-            else
-              echo "Did not detect a "Merge commit" to master, or detected a Release ... doing nothing."
-            fi
+            mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
+            git config credential.helper 'cache --timeout=120'
+            git config user.email "[email protected]"
+            git config user.name "bids-maintenance"
+            git add ${{ github.workspace }}/src/CHANGES.md
+            git commit -m "[DOC] Auto-generated changelog entry"
+        - name: Create Pull Request
+          uses: peter-evans/create-pull-request@v6
+          with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+            branch: changelog_generator_update
+            delete-branch: true
+            title: '[DOC] Auto-generated changelog entry'
+            labels: |
+              exclude-from-changelog
+            draft: false

requirements.txt

@@ -1,4 +1,4 @@
-mkdocs>=1.1
+mkdocs>=1.1.0
 mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3

src/appendices/coordinate-systems.md

@@ -108,11 +108,12 @@ Restricted keywords for the `<CoordSysType>CoordinateSystem` field in the
 `coordinatesystem.json` file for MEG datasets:
 
 -   `CTF`: ALS orientation and the origin between the ears
--   `ElektaNeuromag`: RAS orientation and the origin between the ears
+-   `NeuromagElektaMEGIN`: RAS orientation and the origin between the ears
 -   `4DBti`: ALS orientation and the origin between the ears
 -   `KitYokogawa`: ALS orientation and the origin between the ears
 -   `ChietiItab`: RAS orientation and the origin between the ears
 -   Any keyword from the list of [Standard template identifiers](#standard-template-identifiers): RAS orientation and the origin at the center of the gradient coil for template NifTI images
+-   The use of `ElektaNeuromag` is [DEPRECATED][deprecated]. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
 
 In the case that MEG was recorded simultaneously with EEG,
 the restricted keywords for
@@ -146,7 +147,7 @@ the restricted keywords for
 can also be applied to EEG:
 
 -   `CTF`
--   `ElektaNeuromag`
+-   `NeuromagElektaMEGIN`
 -   `4DBti`
 -   `KitYokogawa`
 -   `ChietiItab`

src/schema/objects/enums.yaml

@@ -20,7 +20,8 @@ _MEGCoordSys:
   type: string
   enum:
     - $ref: objects.enums.CTF.value
-    - $ref: objects.enums.ElektaNeuromag.value
+    - $ref: objects.enums.ElektaNeuromag.value # deprecated
+    - $ref: objects.enums.NeuromagElektaMEGIN.value
     - $ref: objects.enums.4DBti.value
     - $ref: objects.enums.KitYokogawa.value
     - $ref: objects.enums.ChietiItab.value
@@ -305,6 +306,13 @@ CTF:
 ElektaNeuromag:
   value: ElektaNeuromag
   display_name: Elekta Neuromag
+  description: |
+    RAS orientation and the origin between the ears.
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
+    Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
+NeuromagElektaMEGIN:
+  value: NeuromagElektaMEGIN
+  display_name: Neuromag Elekta MEGIN
   description: |
     RAS orientation and the origin between the ears.
 4DBti:

src/schema/rules/sidecars/meg.yaml

@@ -20,8 +20,11 @@ MEGHardware:
       level: recommended
       description_addendum: |
         For MEG scanners, this must be one of:
-        `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
+        `"CTF"`, `"Neuromag/Elekta/MEGIN"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
         `"ITAB"`, `"KRISS"`, `"Other"`.
+        The use of `"Elekta/Neuromag"` is
+        [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
+        Dataset curators SHOULD use `"Neuromag/Elekta/MEGIN"` instead.
         See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for
         preferred names.
     ManufacturersModelName: