Merge pull request #2189 from bids-standard/rel/1.10.1

REL: v1.10.1

Author: effigies

.all-contributorsrc

@@ -423,6 +423,16 @@
             "name": "Benjamin Beasley",
             "profile": "https://github.com/musicinmybrain"
         },
+        {
+            "contributions": [
+                "doc",
+                "code",
+                "test"
+            ],
+            "login": "bendichter",
+            "name": "Benjamin Dichter",
+            "profile": "https://bendichter.com/"
+        },
         {
             "avatar_url": [
                 "https://avatars.githubusercontent.com/u/844306?v=4"

.circleci/config.yml

@@ -38,6 +38,7 @@ jobs:
               uvx linkchecker -t 1 --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/}/" \
                 --ignore-url 'https://doi.org/.*' \
                 --ignore-url 'https://fonts.gstatic.com' \
                 --ignore-url 'https://github.com/[^/]*' \

CITATION.cff

@@ -8,7 +8,7 @@ abstract: >-
   The Brain Imaging Data Structure (BIDS) is a simple and intuitive way to
   organize and describe data.
 
-version: 1.10.1-dev
+version: 1.10.1
 
 license: CC-BY-4.0
 

Makefile

@@ -6,7 +6,7 @@ validate_citation_cff: CITATION.cff
 update_contributors:
 	uv run tools/add_contributors.py
 	uv run tools/print_contributors.py
-	npx all-contributors generate
+	npx all-contributors-cli generate
 
 runprettier:
 	prettier --write "src/schema/**/*.yaml"

README.md

@@ -44,7 +44,20 @@ git checkout -b rel/1.2.0 upstream/master
 
 #### 2.1 Update the version
 
-Update the version in CITATION.cff.
+Update the specification and schema versions using [bump-my-version][]
+
+
+```Shell
+uvx bump-my-version bump pre_label
+(cd tools/schemacode; uvx bump-my-version bump pre_label)
+```
+
+This will update the version in:
+
+* `CITATION.cff`
+* `mkdocs.yml`
+* `src/schema/*_VERSION`
+* `src/schema/meta/versions.yaml`
 
 Change the "Unreleased" heading in
 [src/CHANGES.md](https://github.com/bids-standard/bids-specification/blob/master/src/CHANGES.md)
@@ -59,20 +72,6 @@ the link.
 
 The date can be changed or added later, so accurate prediction is not necessary.
 
-Remove the `-dev` from the version in
-[mkdocs.yml](https://github.com/bids-standard/bids-specification/blob/master/mkdocs.yml)
-configuration, so the title will be correct for the released specification.
-If the version preceding the `-dev` is not the target version, update the version as well.
-In the figure below, we update `1.2.0-dev` to `1.2.0`.
-![dev-to-stable](release_images/site_name_release_1.2dev-1.2.png "dev-to-stable")
-
-Additionally, implement the same change in the version name perform above in the `src/schema/BIDS_VERSION` file.
-
-Note:
-this will make our continuous integration ([CircleCI](https://circleci.com/)) fail.
-This fails because the URL of the new ReadTheDocs rendering has not been generated at this time.
-It will be generated once the GitHub release has been completed.
-
 #### 2.2 Update the contributors list
 
 We want to ensure that all contributors are duly credited.
@@ -99,14 +98,7 @@ make update_contributors
 - make sure to review the changes and not commit them blindly
 - commit the changes
 
-#### 2.3 Update the previous version URLs
-
-In `src/CHANGES.md`,
-please change the previous version links from GitHub to ReadTheDocs.
-In the figure below, we update 1.2.2.
-![github-to-rtd](release_images/GitHub_to_RTD_spec_rendering.png "github-to-rtd")
-
-#### 2.4 Update the Changelog
+#### 2.3 Update the Changelog
 
 Review `src/CHANGES.md` to ensure that the document produces a changelog that is useful to a
 reader of the specification.
@@ -116,10 +108,6 @@ You can also make use of the `exclude-from-changelog` label.
 Adding this label to PRs in the GitHub web interface will prevent the changelog generator from
 considering this item for inclusion in the changelog.
 
-#### 2.5 Update the schema
-
-Add the new version to `src/schema/meta/versions.yaml`.
-
 ### 3. Commit changes and push to upstream
 
 By pushing `rel/` branches to the main repository, the chances of continuous integration
@@ -284,3 +272,5 @@ If the release relates to the merge of a BEP, add the BEP leads to the BIDS advi
 
 Please share news of the release on the [identified platforms](https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels).
 Please use our previous release posts as a guide.
+
+[bump-my-version]: https://callowayproject.github.io/bump-my-version/

Release_Protocol.md

@@ -1,4 +1,4 @@
-site_name: Brain Imaging Data Structure 1.10.1-dev
+site_name: Brain Imaging Data Structure 1.10.1
 site_url: https://bids-specification.readthedocs.io/en/stable/
 repo_url: https://github.com/bids-standard/bids-specification
 nav:

mkdocs.yml

@@ -26,3 +26,34 @@ doc = [
   "universal_pathlib",
   "fsspec[http]",
 ]
+
+[tool.bumpversion]
+current_version = "1.10.1"
+parse = """(?x)
+    (?P<major>[0-9]+)
+    \\.(?P<minor>[0-9]+)
+    \\.(?P<patch>[0-9]+)
+    (?:-(?P<pre_label>dev))?
+"""
+serialize = ["{major}.{minor}.{patch}-{pre_label}", "{major}.{minor}.{patch}"]
+commit = true
+message = "chore: Bump BIDS version to {new_version}"
+
+[tool.bumpversion.parts.pre_label]
+values = ["dev", "final"]
+optional_value = "final"
+
+[[tool.bumpversion.files]]
+filename = "CITATION.cff"
+[[tool.bumpversion.files]]
+filename = "mkdocs.yml"
+[[tool.bumpversion.files]]
+filename = "src/schema/BIDS_VERSION"
+[[tool.bumpversion.files]]
+filename = "src/schema/meta/versions.yaml"
+search = """NEXT_VERSION_HERE
+- """
+replace = """NEXT_VERSION_HERE
+- '{new_version}'
+- """
+include_bumps = ['pre_label']

pyproject.toml

@@ -1,5 +1,45 @@
 # Changelog
 
+## [v1.10.1](https://bids-specification.readthedocs.io/en/v1.10.1/) (2025-09-03)
+
+-   \[ENH] Expand fieldmaps section to include B1 maps, including qMRI maps [#2183](https://github.com/bids-standard/bids-specification/pull/2183) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Clarify that task label is not required to derive from TaskName [#2179](https://github.com/bids-standard/bids-specification/pull/2179) ([effigies](https://github.com/effigies))
+-   \[ENH] Remove explicitly worded requirement of events file association with the task [#1440](https://github.com/bids-standard/bids-specification/pull/1440) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Clarify that recording entity may be used to distinguish recording instruments [#2090](https://github.com/bids-standard/bids-specification/pull/2090) ([drammock](https://github.com/drammock))
+-   \[ENH] Specify that dir-<label> should correspond to PhaseEncodingDirection [#2097](https://github.com/bids-standard/bids-specification/pull/2097) ([effigies](https://github.com/effigies))
+-   \[ENH] Allow direction entity in MESE files [#2100](https://github.com/bids-standard/bids-specification/pull/2100) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Add "study" DatasetType to organize a collection of source and derivative datasets [#1972](https://github.com/bids-standard/bids-specification/pull/1972) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Deprecate 89+ string for default age column, increase expressiveness of column definitions in sidecar files [#2162](https://github.com/bids-standard/bids-specification/pull/2162) ([effigies](https://github.com/effigies))
+-   \[ENH] Update extension citations in Introduction [#2168](https://github.com/bids-standard/bids-specification/pull/2168) ([markmikkelsen](https://github.com/markmikkelsen))
+-   \[ENH] Add "Keywords" to `dataset_description.json` [#2158](https://github.com/bids-standard/bids-specification/pull/2158) ([markmikkelsen](https://github.com/markmikkelsen))
+-   \[ENH] Update AcquisitionDuration definition to match DICOM, define FrameAcquisitionDuration for sparse sequences [#1974](https://github.com/bids-standard/bids-specification/pull/1974) ([effigies](https://github.com/effigies))
+-   \[ENH] Inheritance Principle: Advise against value overloading. Plan to deprecate support for overloading for BIDS 2.0 [#1834](https://github.com/bids-standard/bids-specification/pull/1834) ([Lestropie](https://github.com/Lestropie))
+-   \[ENH] Allow `mod-*` entity to relate physio data to MRI data in `anat/` [#1991](https://github.com/bids-standard/bids-specification/pull/1991) ([tstoeter](https://github.com/tstoeter))
+-   \[ENH] Accept UTC offsets in datetimes [#2001](https://github.com/bids-standard/bids-specification/pull/2001) ([effigies](https://github.com/effigies))
+-   \[ENH] Clarify that electrodes.tsv are REQUIRED for iEEG data [#1896](https://github.com/bids-standard/bids-specification/pull/1896) ([effigies](https://github.com/effigies))
+-   \[ENH] Allow additional columns if defined for various TSV files [#2054](https://github.com/bids-standard/bids-specification/pull/2054) ([effigies](https://github.com/effigies))
+-   \[ENH] Reorganise modality agnostic files section into multiple pages [#2106](https://github.com/bids-standard/bids-specification/pull/2106) ([bclenet](https://github.com/bclenet))
+-   \[ENH] Define "phenotype" as a data type not nested inside subjects [#2050](https://github.com/bids-standard/bids-specification/pull/2050) ([effigies](https://github.com/effigies))
+-   \[ENH] Formalize presence of optional docs/ folder [#2104](https://github.com/bids-standard/bids-specification/pull/2104) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Clarify definition of space entity [#2105](https://github.com/bids-standard/bids-specification/pull/2105) ([effigies](https://github.com/effigies))
+-   \[ENH] Formalize presence of optional logs/ folder [#1962](https://github.com/bids-standard/bids-specification/pull/1962) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Add `matches` and `source_entity` to glossary and file templates [#1781](https://github.com/bids-standard/bids-specification/pull/1781) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Allow plus signs in labels [#1926](https://github.com/bids-standard/bids-specification/pull/1926) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Allow participants.tsv to contain a superset of subject directories and subjects listed in phenotype files [#2044](https://github.com/bids-standard/bids-specification/pull/2044) ([ericearl](https://github.com/ericearl))
+-   \[ENH] Allow LICENSE files to have .txt, .md, or .rst extensions [#2036](https://github.com/bids-standard/bids-specification/pull/2036) ([monique2208](https://github.com/monique2208))
+-   \[ENH] Render code blocks with language "tsv" as tables [#1794](https://github.com/bids-standard/bids-specification/pull/1794) ([effigies](https://github.com/effigies))
+-   \[ENH] Do explicitly "allow" for having dotfiles and explicitly ignore them [#1992](https://github.com/bids-standard/bids-specification/pull/1992) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Add interpretation of "n/a" onsets in events.tsv files [#1966](https://github.com/bids-standard/bids-specification/pull/1966) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Update DWI suffixes to include most common scanner derivatives [#1864](https://github.com/bids-standard/bids-specification/pull/1864) ([Lestropie](https://github.com/Lestropie))
+-   \[FIX] Update ResonantFrequency and SpectrometerFrequency to support both string/number and arrays [#2172](https://github.com/bids-standard/bids-specification/pull/2172) ([markmikkelsen](https://github.com/markmikkelsen))
+-   \[FIX] Rescope or downgrade excess RECOMMENDED fields [#2116](https://github.com/bids-standard/bids-specification/pull/2116) ([effigies](https://github.com/effigies))
+-   \[FIX] Remove incorrect DICOM correspondence of PartialFourier [#2128](https://github.com/bids-standard/bids-specification/pull/2128) ([effigies](https://github.com/effigies))
+-   \[FIX] Re-align the text and the schema for filenames in derivatives [#1567](https://github.com/bids-standard/bids-specification/pull/1567) ([mguaypaq](https://github.com/mguaypaq))
+-   \[FIX] Show example defaced derivative in a pipeline subdirectory [#2065](https://github.com/bids-standard/bids-specification/pull/2065) ([robertoostenveld](https://github.com/robertoostenveld))
+-   \[FIX] Remove reference to dicm2nii and point to page with more converters [#2119](https://github.com/bids-standard/bids-specification/pull/2119) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] Fix typos in specification about iEEG photo [#2091](https://github.com/bids-standard/bids-specification/pull/2091) ([qian-chu](https://github.com/qian-chu))
+-   \[FIX] Allow (but discourage) task, acquisition and run entities for coordsystem.json and electrodes.tsv [#1888](https://github.com/bids-standard/bids-specification/pull/1888) ([effigies](https://github.com/effigies))
+
 ## [v1.10.0](https://bids-specification.readthedocs.io/en/v1.10.0/) (2024-09-06)
 
 -   \[ENH] Add noRF and n/a ASL volume types [1884](https://github.com/bids-standard/bids-specification/pull/1884) ([tsalo](https://github.com/tsalo))

src/CHANGES.md

@@ -1 +1 @@
-1.10.1-dev
+1.10.1