Merge branch 'main' into dependabot/submodules/data/datasets/examples-789cc7a

Author: Remi-Gau

.github/workflows/deploy.yml

@@ -1,10 +1,19 @@
 ---
 name: Publish docs via GitHub Pages
+
 on:
     push:
         branches:
         -   main
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+# Force to use color
+env:
+    FORCE_COLOR: true
+
 jobs:
     build:
         name: Deploy docs
@@ -21,6 +30,14 @@ jobs:
             with:
                 python-version: 3.12
 
+        -   name: Set up node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 14
+
+        -   name: Install dependencies and update content from submodules
+            run: make all
+
         -   name: Deploy docs
             uses: mhausenblas/mkdocs-deploy-gh-pages@master
             env:

.github/workflows/linkcheck.yml

@@ -1,9 +1,10 @@
 ---
-name: Validation
+name: Checklinks
 
 on:
     push:
         branches: [main]
+    pull_request:
 
 concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
@@ -18,9 +19,26 @@ jobs:
     link-check:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
+
+        -   name: Checkout
+            uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+
+        -   name: Set up Python
+            uses: actions/setup-python@v5
             with:
-                submodules: true
+                python-version: 3.12
+
+        -   name: Set up node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 14
+
+        -   name: Install dependencies and update content from submodules
+            run: make all
+
         -   uses: gaurav-nelson/github-action-markdown-link-check@v1
             with:
                 use-quiet-mode: yes

CONTRIBUTING.md

@@ -19,9 +19,14 @@ make sure you also read the instructions below.
 ### Requirements
 
 - python >= 3.10
+- node.js >= ???
+- npm >= ???
 
-Even though this is not required, having `make` installed
-will make it easier to easily serve the website locally.
+<!-- TODO find minimal version of node and npm
+For some quality checks and rare operations, you will need node.js and npm. -->
+
+Even though this is not required,
+having `make` installed will make it easier to easily serve the website locally.
 
 ### Install and serve
 
@@ -39,7 +44,18 @@ Install all the dependencies.
 pip install -r requirements.txt
 ```
 
-Generate all the content required for the build.
+Generate all the content required for the build:
+
+-   copies some pages from the specification repo
+
+-   updates the list of contributors
+
+-   generates the page for each BEP based on its metadata
+
+-   updates the list of BIDS examples
+
+-   generates all the 'plotly' interactive plots as html files in the `tmp` folder
+    that will be 'injected' in the website as snippets (with `--8<--`)
 
 ```bash
 make update
@@ -60,8 +76,6 @@ Same as for the install but you will also need to install `tox`.
 ```bash
 pip install tox
 ```
-<!-- TODO find minimal version of node and npm -->
-For some quality checks and rare operations, you will need node.js and npm.
 
 ## Update all files
 
@@ -75,3 +89,12 @@ make update
 tox
 make remark
 ```
+
+## Updating the `requirements.txt`
+
+Update the appropriate line `requirements.in` and run:
+
+```bash
+python -m pip install pip-tools
+pip-compile --strip-extras requirements.in
+```

docs/blog/posts/2020-03-12-steering-group-minutes.md

@@ -27,7 +27,7 @@ The plan is that there should be multiple people committed to the repository (ot
 [CODEOWNERS file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners#about-code-owners)
 at the top level), there should be a code of conduct in the repository that is consistent with that of the BIDS specification, and (as a consequence of the code of conduct) the repository should welcome contributions from others.
 
-We want to host another [Community Forum](https://bids.neuroimaging.io/2020/01/02/announcement-community-forum-events.html) (but not too frequent) and potentially a starter kit/demo in the Open Science Room at [OHBM](https://www.humanbrainmapping.org).
+We want to host another [Community Forum](https://bids.neuroimaging.io/blog/2020/01/02/Announcing%20Community%20Forum%20Events.html) (but not too frequent) and potentially a starter kit/demo in the Open Science Room at [OHBM](https://www.humanbrainmapping.org).
 
 Regarding discussions on where to host our historical specification pdfs (please refer to issue [#407](https://github.com/bids-standard/bids-specification/pull/407)), we consider [Zenodo](https://zenodo.org/) to be a suitable location to store our specification pdfs.
 

docs/blog/posts/2020-03-23-steering-group-minutes.md

@@ -49,9 +49,9 @@ The Steering Group gave direction on handling author lists on Zenodo - make it a
 
 ## Minutes
 
--   Reviewed [previous meeting action items](https://bids.neuroimaging.io/2020/03/12/Steering-Group-executive-summary,-action-items,-and-minutes.html#action-items)
+-   Reviewed [previous meeting action items](https://bids.neuroimaging.io/blog/2020/03/12/Steering%20Group%20minutes.html#action-items)
 
--   A [survey](https://docs.google.com/forms/d/e/1FAIpQLSfGjTA-U_1LECRsbuBQ9X7kdi34aEdxTMoWCwwkEgou-qpb4A/viewform) with an accompanying [blog post](https://bids.neuroimaging.io/2020/03/20/engage-with-the-bids-ecosystem.html) was drafted to evaluate how the community would like to engage with each other, what barriers may exist that makes engaging more challenging, and ways that we can engage colleagues that do not know about BIDS.
+-   A [survey](https://docs.google.com/forms/d/e/1FAIpQLSfGjTA-U_1LECRsbuBQ9X7kdi34aEdxTMoWCwwkEgou-qpb4A/viewform) with an accompanying [blog post](https://bids.neuroimaging.io/blog/2020/03/20/engage%20with%20the%20bids%20ecosystem.html) was drafted to evaluate how the community would like to engage with each other, what barriers may exist that makes engaging more challenging, and ways that we can engage colleagues that do not know about BIDS.
 
 -   Points to consider when designing the infrastructure to support BIDS slides
 

docs/blog/posts/2020-06-18-steering-group-minutes.md

@@ -12,14 +12,14 @@ categories:
 
 We discussed and decided on utilizing the [BrainHack Mattermost platform][brainhack_mattermost] for our instant messaging solution. This fits nicely into where our community has been informally organized.
 
-We went over our BIDS presentations occurring in the [Open Science Room](https://ohbm.github.io/osr2020/schedule/) at [OHBM](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3885). We are sharing on the website [all the BIDS presentations and posters](https://bids.neuroimaging.io/2020/06/19/BIDS-OHBM-OSR-2020.html) happening at OHBM. There are many BIDS-aware tools being developed, but an emphasis should be put on generating the associated documentation.
+We went over our BIDS presentations occurring in the [Open Science Room](https://ohbm.github.io/osr2020/schedule/) at [OHBM](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageID=3885). We are sharing on the website [all the BIDS presentations and posters](https://bids.neuroimaging.io/blog/2020/06/19/BIDS%20at%20OHBM%202020.html) happening at OHBM. There are many BIDS-aware tools being developed, but an emphasis should be put on generating the associated documentation.
 
 ## Action Items
 
-| Action items                                                                                                                                                                  |
-| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [Website post announcing our intention of joining the BrainHack Mattermost](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html) |
-| [Website post listing the BIDS sessions and posters at OHBM](https://bids.neuroimaging.io/2020/06/19/BIDS-OHBM-OSR-2020.html)                                                 |
+| Action items                                                                                                                                                                                     |
+| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| [Website post announcing our intention of joining the BrainHack Mattermost](https://bids.neuroimaging.io/blog/2020/06/24/Join%20the%20BIDS%20community%20on%20the%20BrainHack%20Mattermost.html) |
+| [Website post listing the BIDS sessions and posters at OHBM](https://bids.neuroimaging.io/blog/2020/06/19/BIDS%20at%20OHBM%202020.html)                                                          |
 
 ## Minutes
 

docs/blog/posts/announcement-community-forum-events.md

@@ -6,7 +6,7 @@ author: Kirstie Whitaker
 
 ## Join the first BIDS Community Forum events in January 2020
 
-The [BIDS Steering Group](https://bids.neuroimaging.io/2019/12/31/meet-the-bids-steering-group.html) are excited to announce two **Community Forums**!
+The [BIDS Steering Group](https://bids.neuroimaging.io/blog/2019/12/31/meet%20the%20bids%20steering%20group.html) are excited to announce two **Community Forums**!
 
 <!-- more -->
 

docs/blog/posts/bids-news-september-2024.md

@@ -53,10 +53,10 @@ BIDS continues to be featured in different venues. Our very own maintainer extra
 
 The BEPs carry on to help us all update the standard with new and previously unestablished data types and improvements. If there's a BEP here that affects you, consider getting involved by commenting on open Google Docs or GitHub pull requests or contacting the leads listed in the BEP. Here’s some of our newest BEPs.
 
--   [BEP041](https://bids.neuroimaging.io/bep041): Statistical Model (Taylor Salo)
--   [BEP042](https://bids.neuroimaging.io/bep042): Electromyography (Seyed Yahya Shirazi)
--   [BEP043](https://bids.neuroimaging.io/bep043): Term mapping (Chris Markiewicz & Eric Earl)
--   [BEP044](https://bids.neuroimaging.io/bep044): Stimuli (Seyed Yahya Shirazi)
+-   [BEP041]("https://bids.neuroimaging.io/extensions/beps/bep_041.html"): Statistical Model (Taylor Salo)
+-   [BEP042]("https://bids.neuroimaging.io/extensions/beps/bep_042.html"): Electromyography (Seyed Yahya Shirazi)
+-   [BEP043]("https://bids.neuroimaging.io/extensions/beps/bep_043.html"): Term mapping (Chris Markiewicz & Eric Earl)
+-   [BEP044]("https://bids.neuroimaging.io/extensions/beps/bep_044.html"): Stimuli (Seyed Yahya Shirazi)
 
 Other BEPs are listed on [the BIDS website](https://bids.neuroimaging.io/extensions/beps.html).
 

docs/blog/posts/steering-group-election-2021.md

@@ -11,7 +11,7 @@ The nomination period will close on Friday, October 1st at 11:59pm (Pacific time
 
 <!-- more -->
 
-This new member will be taking the place of our outgoing member, [Kirstie Whitaker](https://bids.neuroimaging.io/2019/12/31/meet-the-bids-steering-group.html#kirstie-whitaker-).
+This new member will be taking the place of our outgoing member, [Kirstie Whitaker](https://bids.neuroimaging.io/blog/2019/12/31/Meet%20the%20BIDS%20Steering%20Group.html#kirstie-whitaker).
 While submitting your nomination, we please ask to prepare a brief description of what you would add to the Steering Group if elected and include it within [this form](https://forms.gle/JDryfJRLP2AiHVPg9).
 We are looking to maintain and enhance our range of diverse perspectives and experiences currently present on the Steering Group.
 To learn more about the Steering Group, please take a few minutes and watch a [recent video discussing this](https://www.youtube.com/watch?v=-c4PUhTwmz4).

docs/blog/posts/v1.9.0-release.md

@@ -16,7 +16,7 @@ BIDS-Motion makes motion data interoperable across different laboratories and wi
 
 We would like to thank contributors to this BEP, led by Sein Jeung and Julius Welzel with significant contributions from Helena Cockx and others.
 
-Check out the [preprint associated with this BEP](https://osf.io/preprints/psyarxiv/w6z79/).
+Check out the [preprint associated with this BEP](https://osf.io/preprints/psyarxiv/w6z79_v1/).
 
 Example datasets for motion data can be found on our [BIDS example repository][bids_examples_gh]: