Merge branch 'main' into rawdata-example2

julia-pfarr · web-flow · commit fbe869ec6e14 · 2025-11-17T10:56:08.000+01:00
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -27,12 +27,12 @@ jobs:
                 fetch-depth: 0
 
         -   name: Set up Python
-            uses: astral-sh/setup-uv@v6
+            uses: astral-sh/setup-uv@v7
             with:
                 python-version: 3.12
 
         -   name: Set up node
-            uses: actions/setup-node@v5
+            uses: actions/setup-node@v6
             with:
                 node-version: 24
 
diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -27,14 +27,14 @@ jobs:
                 fetch-depth: 0
 
         -   name: Set up Python
-            uses: actions/setup-python@v6
+            uses: astral-sh/setup-uv@v7
             with:
                 python-version: 3.12
 
         -   name: Set up node
-            uses: actions/setup-node@v5
+            uses: actions/setup-node@v6
             with:
-                node-version: 22
+                node-version: 24
 
         -   name: Install dependencies and update content from submodules
             run: make all
diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -34,7 +34,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         -   uses: actions/checkout@v5
-        -   uses: actions/setup-node@v5
+        -   uses: actions/setup-node@v6
             with:
                 node-version: 22
         -   name: Run markdown style checks
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -48,12 +48,12 @@ repos:
         args: [--autofix, --indent, '4', --no-sort, --trailing-commas]
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
+    rev: 25.11.0
     hooks:
     -   id: black
 
 -   repo: https://github.com/pycqa/isort
-    rev: 6.0.1
+    rev: 7.0.0
     hooks:
     -   id: isort
 
diff --git a/data/beps/beps.yml b/data/beps/beps.yml
@@ -398,7 +398,7 @@
     content:
     -   raw
     leads:
-    -   given-names: Eric A.
+    -   given-names: Eric
         family-names: Earl
     -   given-names: Samuel
         family-names: Guay
@@ -407,14 +407,18 @@
     -   given-names: Arshitha
         family-names: Basavaraj
     bids_maintainers:
-    -   given-names: Eric A.
-        family-names: Earl
+    -   given-names: Chris
+        family-names: Markiewicz
+    -   given-names: Ross
+        family-names: Blair
     status:
-    -   PR nearly ready to integrate with modality agnostic files sections.
+    -   BEP entering community review period shortly.
+    -   BIDS specification PR 2123.
+    -   BIDS examples PR 465.
     blocking:
-    -   Finishing bids-examples PR.
+    -   A successful community review.
     google_doc_created: 2021-10
-    pull_request_created:
+    pull_request_created: 2025-05
     pull_request_merged:
 
 -   number: '037'
@@ -626,6 +630,8 @@
 -   number: '045'
     title: Peripheral Physiological Recordings
     display: Physio
+    pull_request: https://github.com/bids-standard/bids-specification/pull/2249
+    html_preview: https://bids-specification--2249.org.readthedocs.build/en/2249/modality-specific-files/physiological-recordings.html
     google_doc: https://docs.google.com/document/d/1oTfjzY5ZnLIYd0kPPWhR81sBmMuy_jC5YYIaqj6OhSA/edit
     leads:
     -   given-names: Mary
@@ -634,15 +640,19 @@
         family-names: Moia
     -   given-names: Sourav
         family-names: Kulkarni
+    bids_maintainers:
+    -   given-names: Seyed Yahya
+        family-names: Shirazi
     status:
+    -   No longer developed in google doc, moved to <https://github.com/physiopy/bids-specification-physio>.
     -   To update standards for physiological data for improved clarity and a broader range of use cases.
     -   Now collecting community comments and feedback. All collaborators are welcome.
-    -   'Original issue: [#1675](https://github.com/bids-standard/bids-specification/issues/1675)'
+    -   'Original issue: [#1675](https://github.com/bids-standard/bids-specification/issues/1675).'
     content:
     -   raw
     blocking:
     google_doc_created: 2024-08-13
-    pull_request_created:
+    pull_request_created: 2025-11-07
     pull_request_merged:
 
 -   number: '046'
diff --git a/data/datasets/examples b/data/datasets/examples
@@ -1 +1 @@
-Subproject commit bd8a95100a66e0b57498fda905da3f048d76f608
+Subproject commit 8f916644b973b44c946b7617e96b04b7be312f89
diff --git a/data/people/maintainers.yml b/data/people/maintainers.yml
@@ -14,6 +14,8 @@
     members:
     -   name: Ross Blair
         git: rwblair
+    -   name: Boris Clénet
+        git: bclenet
     -   name: Eric Earl
         git: ericearl
     -   name: Anthony Galassi
diff --git a/data/tools/apps.yml b/data/tools/apps.yml
@@ -428,6 +428,18 @@ apps:
     -   func
     description:
 
+-   gh: nipreps/petprep
+    status: active
+    dh: nipreps/petprep
+    ds_type:
+    -   raw
+    -   derivative
+    datatype:
+    -   anat
+    -   pet
+    description: PETPrep is a robust and easy-to-use pipeline for preprocessing of diverse PET data. The transparent workflow dispenses of manual intervention,
+        thereby ensuring the reproducibility of the results.
+
 -   gh: nipreps/smriprep
     status: active
     dh: nipreps/smriprep
diff --git a/docs/blog/posts/2024-09-19-steering-group-minutes.md b/docs/blog/posts/2024-09-19-steering-group-minutes.md
@@ -33,10 +33,6 @@ Code of conduct may be ready, but governance will not be ready.
 
 -   this is somewhat reflective of the BIDS community (unfortunately)
 
--   Possible Suggestions:
-    -   ******
-    -   ******
-
 ## Meeting with Chris Holdgraf
 
 ### Context
diff --git a/docs/getting_started/folders_and_files/derivatives.md b/docs/getting_started/folders_and_files/derivatives.md
@@ -16,28 +16,15 @@ As with BIDS datasets, all conformant derivative datasets contain a `dataset_des
 
 New fields include `DatasetType`, which distinguishes `"derivative"` datasets from `"raw"`:
 
--   `GeneratedBy`, a list of processes that generated the data
+-   `GeneratedBy`, identifies the activity (one or more) responsible for the creation of the dataset.
 -   `SourceDatasets`, a list of datasets used to generate the derivative.
 
 ```json
 {
     "Name": "FMRIPREP Outputs",
     "BIDSVersion": "1.4.0",
     "DatasetType": "derivative",
-    "GeneratedBy": [
-        {
-            "Name": "fmriprep",
-            "Version": "1.4.1",
-            "Container": {
-                "Type": "docker",
-                "Tag": "poldracklab/fmriprep:1.4.1"
-            }
-        },
-        {
-            "Name": "Manual",
-            "Description": "Re-added RepetitionTime metadata to bold.json files"
-        }
-    ],
+    "GeneratedBy": "bids::prov#preprocessing-xMpFqB5q",
     "SourceDatasets": [
         {
             "DOI": "10.18112/openneuro.ds000114.v1.0.1",
diff --git a/docs/getting_started/resources/glossary.md b/docs/getting_started/resources/glossary.md
@@ -42,7 +42,9 @@ Brain Imaging Data Structure - a standardized way to organize your neural and as
 The combination of the differential amplifier and the analog-to-digital converter
 that results in the potential different (for EEG and iEEG)
 or magnetic field or gradient (for MEG) to end up on disk.
-This should not be confused with [electrode](#electrode).
+This should not be confused with [electrode](#electrode), although they are often
+used interchangeably since each [electrode](#electrode) is often recorded as an
+individual channel.
 
 #### container
 
@@ -65,7 +67,9 @@ Collection of data that can include many subjects or sessions.
 
 The small metal disk that is in contact with the scalp (EEG)
 or directly touching the brain (iEEG).
-This should not be confused with the EEG or iEGG [channel](#channel).
+This should not be confused with the EEG or iEGG [channel](#channel), although
+they are often used interchangeably since each electrode is often recorded as
+an individual [channel](#channel).
 
 #### extensions
 
diff --git a/docs/getting_started/tutorials/annotation.md b/docs/getting_started/tutorials/annotation.md
@@ -184,7 +184,8 @@ The rules for HED schema vocabularies and HED-compliant tools can be found in th
 The HED standard schema contains basic terms that are common across most human neuroimaging, behavioral, and physiological experiments.
 The HED ecosystem schema libraries extend the standard HED schema with structured vocabularies, including terms unique to specific research fields.
 This allows the expansion of the HED vocabulary in a scalable manner to support specialized data annotations,
-for instance, electrophysiological events ([HED-SCORE](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/score)) or language stimuli ([LISA](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lang)).
+for instance, electrophysiological events ([HED-SCORE](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/score))
+or language stimuli ([LANG](https://github.com/hed-standard/hed-schemas/tree/main/library_schemas/lang)).
 
 Additional details about particular schemas can be found on the [HED schemas](https://hed-schemas.readthedocs.io/en/latest/index.html) documentation page.
 See [HED schema developer’s guide](https://www.hed-resources.org/en/latest/HedSchemaDevelopersGuide.html)
diff --git a/specification b/specification
@@ -1 +1 @@
-Subproject commit 1c539c01ecee4a48785ac803e2af01ecc1273494
+Subproject commit 7c0622846b558fff165288da6c1e0d63bf911997
