[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -11,13 +11,13 @@ repos:
       - id: check-case-conflict
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: ["--config=.codespellrc"]
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 24.10.0
     hooks:
     - id: black
       name: black

_data/advisory.yml

@@ -44,7 +44,7 @@
 #   leads:
     - name: Cyril Pernet
       git: CPernet
-      other_beps: ["BEP018"]      
+      other_beps: ["BEP018"]
     - name: Stefan Appelhoff
       git: sappelhoff
     - name: Robert Oostenveld

_data/converters.yml

@@ -126,8 +126,8 @@
         - MRI # not sure
       expected_input:
       language:
-      comment: 
-        Convert OpenfMRI dataset to BIDS. (Possibly deprecated due to openfmri.org moving 
+      comment:
+        Convert OpenfMRI dataset to BIDS. (Possibly deprecated due to openfmri.org moving
         to <a href="https://openneuro.org/" target="_blank">openneuro.org</a>).
 
     - name: ReproIn
@@ -366,15 +366,14 @@
         - Python
       documentation: https://github.com/mercure-imaging/mercure-dcm2bids
       comment: |
-        A containerized app that can be used to perform BIDS conversion of 
-        DICOM studies sent directly to mercure from a scanner or PACS. mercure 
-        is an open-source DICOM orchestration platform that can integrate 
-        containerized apps into clinical workflows. It has a graphical user 
-        interface making it easy to setup and manage BIDS configurations for 
+        A containerized app that can be used to perform BIDS conversion of
+        DICOM studies sent directly to mercure from a scanner or PACS. mercure
+        is an open-source DICOM orchestration platform that can integrate
+        containerized apps into clinical workflows. It has a graphical user
+        interface making it easy to setup and manage BIDS configurations for
         multiple protocols. The Dcm2Bids tool is used for conversion.
       distribution:
         - name: dockerhub
-          url: https://hub.docker.com/r/mercureimaging/mercure-dcm2bids 
+          url: https://hub.docker.com/r/mercureimaging/mercure-dcm2bids
       GUI: true
       license: GPL-3.0
-

_includes/steering_group_election_section.html

@@ -8,12 +8,12 @@ <h2>BIDS steering group election</h2>
 
     <h2><b>BIDS steering group election</b></h2>
     <p>
-    This year's election has started. 
-    
+    This year's election has started.
+
     If you are <a href="https://bids-specification.readthedocs.io/en/latest/appendices/contributors.html">a BIDS contributor</a>,
-    
+
     please check your BIDS email for an <a href="https://opavote.com" target="_blank">opavote voting link</a> to cast your vote.
-    
+
     The polls will open on <b>Monday, October 21st</b> and close on <b>Friday, November 1st</b>
     </p>
     <!--
@@ -28,7 +28,7 @@ <h3>
       <b>Friday September 23rd at 11:59pm<br>
       (<a href="https://time.is/Anywhere_on_Earth" target="_blank">Anywhere on Earth</a>)</b>.
     </h3>
-  
+
 
     <p>
       This year, we are seeking candidates who will replace

_pages/acknowledgments.md

@@ -6,19 +6,19 @@
 This work has been done by the community of [individual contributors](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html). Their work was
 supported by the
 
-Support source | Description of the contributions 
+Support source | Description of the contributions
 ----- | -----
 [International Neuroinformatics Coordinating Facility](https://www.incf.org/){:target="_blank"} | [Neuroimaging Data Sharing Task Force](https://web.archive.org/web/20170813183704/http://wiki.incf.org/mediawiki/index.php/Neuroimaging_Task_Force){:target="_blank"} collated initial group of people to push pilot BIDS development and promotion
 Laura and John Arnold Foundation |
 [NIMH R24MH114705](https://reporter.nih.gov/project-details/9411944) | BIDS common derivatives BEP
-[NSF OAC-1760950](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1760950) | 
+[NSF OAC-1760950](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1760950) |
 [NIMH 1R24MH117295](https://reporter.nih.gov/project-details/9795271) | DANDI archive contributed development of Microscopy BEP
 [NIMH 2P41EB019936](https://reporter.nih.gov/project-details/10334133) | ReproNim project contributed various enhancements and fixes
 [NIMH MH117179](https://reporter.nih.gov/project-details/10145071) | OpenNeuro archive contributed various enhancements and fixes
-[NIMH 1ZIAMH002977-01](https://reporter.nih.gov/project-details/10489085) |  OpenNeuroPET project contributed various enhancements and fixes 
+[NIMH 1ZIAMH002977-01](https://reporter.nih.gov/project-details/10489085) |  OpenNeuroPET project contributed various enhancements and fixes
 [NIMH 5R01MH126699-02](https://reporter.nih.gov/project-details/10460628) | [Brain Connectivity Project](https://pestillilab.github.io/bids-connectivity/)
 [NIMH MH109682](https://reporter.nih.gov/project-details/9982125) | NeuroScout
-Novo Nordisk Foundation NNF20OC0063277 | 
+Novo Nordisk Foundation NNF20OC0063277 |
 [NIMH 1RF1MH126700-01A1](https://reporter.nih.gov/project-details/10480619) | Hierarchical Event Descriptors (HED)
 [NIBIB 1R01EB020740](https://reporter.nih.gov/project-details/9053094) | Nipype
 [The Neuro-Irv and Helga Cooper Foundation](https://www.mcgill.ca/neuro/open-science/open-science-awards-and-prizes/neuro-irv-and-helga-cooper-foundation-open-science-prizes) | 2023 International Open Science Prize

_posts/2024-01-11-Steering-Group-minutes.md

@@ -158,7 +158,7 @@ Github project is established with many ideas but there aren\'t many
         there are at least 20 different file formats for
         electrophysiology data
 
--   
+-
 
 **Open Science Prize!**
 
@@ -174,12 +174,12 @@ Github project is established with many ideas but there aren\'t many
 -   \$55k CAD will be split with U Washington and Cyril (sub-contract
     with xx Institution) so funds will be in both US and Europe
 
--   
+-
 
 ```{=html}
 <!-- -->
 ```
--   
+-
 
 **BIDS Steering Committee Theme for the year: Improve adoption**
 
@@ -211,12 +211,12 @@ Github project is established with many ideas but there aren\'t many
 
         -   Had questions, but could not find answers
 
-        -   
+        -
 
     -   [[Yaroslav Halchenko]{.underline}](mailto:[email protected])
         will create a pull request on github:
         [[https://github.com/bids-standard/bids-starter-kit/pull/376]{.underline}](https://github.com/bids-standard/bids-starter-kit/pull/376)
 
-    -   
+    -
 
-    -   
+    -

tools/bep_gantt_html_create.py

@@ -2,6 +2,7 @@
 
 Also include a timeline of the main BIDS events.
 """
+
 from __future__ import annotations
 
 from datetime import datetime

tools/bep_gantt_mermaid_insert.py

@@ -1,4 +1,5 @@
 """Creates a Gantt chart for the completed BEPs"""
+
 from __future__ import annotations
 
 from pathlib import Path

tools/convert_to_md.py

@@ -10,6 +10,7 @@
     - using the html version of the tables instead of the markdown version
       because the pandoc version of the markdown tables is not very good
 """
+
 import datetime
 from pathlib import Path