Merge remote-tracking branch 'origin/master' into bep032

* origin/master: (76 commits)
  [pre-commit.ci] pre-commit autoupdate
  add Julia Pfarr as current BIDS maintainer
  [pre-commit.ci] pre-commit autoupdate
  [pre-commit.ci] pre-commit autoupdate
  fix
  fix
  [MAINT] deal with links redirects
  Temporarily disable dicomlookup urls check
  Fix URL to renamed now "Contributors" wiki
  doc: correct typos
  doc: remove mentioning of `schemacode` install as the third command
  enh: use macro for the physio template
  enh: add metaentities to rules README
  Apply suggestions from code review
  [ENH] Allow plus signs in labels (#1926)
  [pre-commit.ci] pre-commit autoupdate
  [MAINT] update link to new website
  sty: pyupgrade --py39-plus
  chore: Bump schema package to 1.0.4-dev
  chore: Bump schema package to 1.0.3
  ...

Conflicts:
	src/schema/objects/columns.yaml -- added the 3 pipette columns

Author: yarikoptic

.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.
 

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.30.0
+    rev: 0.31.3
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -27,7 +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)
@@ -37,7 +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)
@@ -47,7 +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]
@@ -58,7 +58,7 @@ repos:
         entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742
         files: src/schema/.*/.*\.yaml
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.35.1
+    rev: v1.36.2
     hooks:
       - id: yamllint
         args: [-f=standard, -c=.yamllint.yml]
@@ -69,12 +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

CONTRIBUTING.md

@@ -9,7 +9,7 @@ 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 and GitHub,
-check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+check our [generic contributing guidelines](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html).
 
 If you want to contribute to the BIDS specification,
 make sure you also read the instructions below.
@@ -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:
 

DECISION-MAKING.md

@@ -6,28 +6,27 @@ In October 2019, the BIDS community [voted](https://github.com/bids-standard/bid
 to ratify a governance structure and to elect five members as a *Steering Group*
 to oversee the development and adoption of the standard.
 
-The document outlining our governance structure is hosted on the BIDS website:
-[https://bids.neuroimaging.io/governance.html](https://bids.neuroimaging.io/governance.html)
+The document outlining our governance structure is hosted [on the BIDS website](https://bids.neuroimaging.io/collaboration/governance.html)
 
 In the following, we list the current members of subgroups detailed in the
 BIDS governance.
 
 ### Steering Group
 
 Current and past members of the steering group can be found in the
-[BIDS governance](https://bids.neuroimaging.io/governance.html#bids-steering-group).
+[BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-steering-group).
 
 ### Maintainers Group
 
 Current and past members of the maintainers group can be found in the
-[BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group),
+[BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-maintainers-group),
 and in the
 [Maintainers Guide](Maintainers_Guide.md).
 
 ### BEP Leads Group
 
 Leaders of BIDS Extension Proposals are listed in the
-[table of BEPs](https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification).
+[table of BEPs](https://bids.neuroimaging.io/extensions/beps.html).
 
 ### Contributors Group
 
@@ -42,7 +41,7 @@ according to the instructions listed there.
 
 The following groups are not described in detail.
 Please learn more about these groups from the
-[BIDS governance](https://bids.neuroimaging.io/governance.html).
+[BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html).
 
 - BEP working groups
 - Advisory Group

Maintainers_Guide.md

@@ -11,7 +11,7 @@ which is a recommended reading in conjunction with this guide.
 
 ## Current BIDS Maintainers
 
-See also: [BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+See also: [BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-maintainers-group)
 
 | Name                                                                      | Time commitment | Scope                                 | Joined   |
 | ------------------------------------------------------------------------- | --------------- | ------------------------------------- | -------- |
@@ -25,8 +25,9 @@ See also: [BIDS governance](https://bids.neuroimaging.io/governance.html#bids-ma
 | Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/month        | Interoperability, EEG and multi-modal | Apr 2023 |
 | Nell Hardcastle ([@nellh](https://github.com/nellh))                      | 2h/week         |                                       | Jul 2023 |
 | Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))           | 1h/week         |                                       | Nov 2022 |
+| Julia-Katharina Pfarr ([@julia-pfarr](https://github.com/julia-pfarr))    | 2h/week         |                                       | Mar 2025 |
 
-In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+In addition to the [BIDS Governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-maintainers-group)
 classification of a maintainer, maintainers may declare a limited scope of responsibility.
 Such a scope can range from maintaining a modality supported in the specification to nurturing a
 welcoming BIDS community.
@@ -41,7 +42,7 @@ is rotating among current maintainers.
 
 ## Past BIDS Maintainers
 
-See also: [BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+See also: [BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html#bids-maintainers-group)
 
 | Name                                                                           | Duration            |
 | ------------------------------------------------------------------------------ | ------------------- |
@@ -131,5 +132,5 @@ https://docs.google.com/document/d/1yQdYOw7WMpkcFgT4tNalOjKuH34nhmRqg4luI4V9uhE/
 
 ## Notes
 
-As detailed in the [BIDS governance](https://bids.neuroimaging.io/governance.html),
+As detailed in the [BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html),
 this guide is subject to change and to amendment by the BIDS Steering Group.

README.md

@@ -1,8 +1,10 @@
 [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml)
 [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification)
+[![Bluesky Follow](https://img.shields.io/badge/bluesky-Follow_bidsstandard-blue?logo=bluesky)](https://bsky.app/profile/bidsstandard.bsky.social)
+![YouTube Channel Subscribers](https://img.shields.io/youtube/channel/subscribers/UCxZUcYfd_nvIVWAbzRB1tlw)
 [![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
 [![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10175845.svg)](https://doi.org/10.5281/zenodo.10175845)
 
 <img src="./BIDS_logo/BIDS_logo_white_transparent_background_crop.png#gh-dark-mode-only" alt="bids-logo" width="600"/>
 <img src="./BIDS_logo/BIDS_logo_black_transparent_background_crop.png#gh-light-mode-only" alt="bids-logo" width="600"/>
@@ -18,7 +20,8 @@ In this repository, we develop the
 To organize your data in BIDS, all you need is neuro data, a computer, and the
 [BIDS specification](https://bids-specification.readthedocs.io/en/stable/).
 
-BIDS currently supports the following data modalities with more to come in the future:
+BIDS currently supports the following data modalities with
+[more to come in the future](https://bids.neuroimaging.io/extensions/index.html):
 
 - MRI
 - MEG
@@ -71,9 +74,9 @@ adhere to our [code of conduct](https://github.com/bids-standard/bids-specificat
     for reporting problems or making suggestions
   - The [NeuroStars Discourse forum](https://neurostars.org/tags/bids), for asking usage questions
   - The [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging
-    (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html))
+    (see also this [news item](https://bids.neuroimaging.io/blog/2020/06/24/Join%20the%20BIDS%20community%20on%20the%20BrainHack%20Mattermost.html))
   - The [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions and announcements surrounding BIDS
-  - The [BIDS website "news"](https://bids.neuroimaging.io/news.html), similar to the Google group, for broader discussions and announcements
+  - The [BIDS website "blog"](https://bids.neuroimaging.io/blog/index.html), similar to the Google group, for broader discussions and announcements
 
 ## Social media channels
 

macros_doc.md

@@ -162,7 +162,7 @@ To do this get this output, your macro call would look like this:
 ```
 
 When you have complex files and directory structure, we suggest you use this
-[Jupyter notebook](tools/filetree_example.ipynb) for sandboxing your example
+[Jupyter notebook](https://github.com/bids-standard/bids-specification/blob/master/tools/filetree_example.ipynb) for sandboxing your example
 before you insert the macro call into the markdown document.
 
 ### Generating tables
@@ -172,11 +172,11 @@ the PET page.
 
 The HTML version of the this section is here:
 
-https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/09-positron-emission-tomography.html#reconstruction
+https://bids-specification.readthedocs.io/en/stable/modality-specific-files/positron-emission-tomography.html#reconstruction
 
 In the markdown document, it is here:
 
-https://github.com/bids-standard/bids-specification/blob/master/src/04-modality-specific-files/09-positron-emission-tomography.md#reconstruction
+https://github.com/bids-standard/bids-specification/blob/master/src/modality-specific-files/positron-emission-tomography.md#reconstruction
 
 GitHub's way of directly rendering markdown documents makes it a bit harder to
 read, so if you opened the markdown document in your code editor it would look