[MAINT] run remark as frail (#530)

* run remark as frail

* improve config and fix

* Update docs/datasets/index.md

Author: Remi-Gau

.remarkignore

@@ -0,0 +1,5 @@
+docs/collaboration/bids_github/
+docs/datasets/index.md
+docs/getting_started/folders_and_files/files.md
+docs/standards/bids_stats_model/src
+docs/standards/bids_stats_model/variable-transform

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

@@ -16,25 +16,32 @@ The BIDS Maintainers, Steering Group, working groups, and other contributors hav
 
 The BIDS specification has released a new minor version\! The highlights are:
 
-* Integrating BEP022 for Magnetic Resonance Spectroscopy
-* Publishing the BIDS schema to [JavaScript Registry](https://jsr.io/@bids/schema)
-* For the full list of changes, you can read [the changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html#v1100-2024-09-06)
+-   Integrating BEP022 for Magnetic Resonance Spectroscopy
+-   Publishing the BIDS schema to [JavaScript Registry](https://jsr.io/@bids/schema)
+-   For the full list of changes, you can read [the changelog](https://bids-specification.readthedocs.io/en/stable/CHANGES.html#v1100-2024-09-06)
 
 ## Schema-based BIDS validator deployed on validator site
 
 A culmination of years of hard work, the schema-based validator makes maintenance of the validator and inclusion of new rules more sustainable (and very reusable).
 
-The “schema” is a machine readable set of definitions and rules for BIDS. The new validator now makes use of this schema by reading the different rules from it and checking if a dataset complies with them. With this new BIDS validator, it will be easier to start validating new data types, but also to start validating derivatives, an issue that has blocked some BIDS extensions for years. You can try it out now on the [BIDS validator website](https://bids-standard.github.io/bids-validator) and it will soon replace the “legacy” validator.
+The “schema” is a machine readable set of definitions and rules for BIDS.
+The new validator now makes use of this schema by reading the different rules from it and checking if a dataset complies with them.
+With this new BIDS validator, it will be easier to start validating new data types, but also to start validating derivatives, an issue that has blocked some BIDS extensions for years.
+You can try it out now on the [BIDS validator website](https://bids-standard.github.io/bids-validator) and it will soon replace the “legacy” validator.
 
 ## BIDS website is currently in transition
 
-With the support of INCF, Google Season of Docs, BIDS maintainer mentors, and a technical writer, BIDS has been able to improve its online presence. Instead of a large collection of websites, we now have one central site and only a few separate specification/standards sites. You can preview it at [its temporary site](https://bids-website.readthedocs.io/) now. Expect it to replace the current BIDS website around the end of this year.
+With the support of INCF, Google Season of Docs, BIDS maintainer mentors, and a technical writer, BIDS has been able to improve its online presence.
+Instead of a large collection of websites, we now have one central site and only a few separate specification/standards sites.
+You can preview it at [its temporary site](https://bids-website.readthedocs.io/) now.
+Expect it to replace the current BIDS website around the end of this year.
 
 You can also provide feedback now with our [BIDS website survey](https://cryptpad.fr/form/#/2/form/view/f3b2wVPL5VK1HhvBNwtW3-4LXeEpJ9xMY+uOaoahyqQ/), open until October 1st, 2024\.
 
 ## BIDS election on the horizon
 
-Per BIDS governance, the steering group members have a term of 3 years. This year, Ariel Rokem's term ends. Keep an eye out for the upcoming election which BIDS contributors can vote upon. And on behalf of the community, thank you so much Ariel for your service\!
+Per BIDS governance, the steering group members have a term of 3 years.
+This year, Ariel Rokem's term ends. Keep an eye out for the upcoming election which BIDS contributors can vote upon. And on behalf of the community, thank you so much Ariel for your service\!
 
 You can find more [about BIDS governance](https://bids-website.readthedocs.io/en/latest/collaboration/governance.html) here.
 
@@ -46,10 +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/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)
 
 Other BEPs are listed on [the BIDS website](https://bids-website.readthedocs.io/en/latest/extensions/beps.html).
 

docs/blog/posts/town-hall-2024-debrief.md

@@ -55,9 +55,12 @@ The slides can be found on our [Open-science Framework project](https://osf.io/5
     -   potential BEP: "Peripheral" physiological signals <!-- TODO  add link -->
 
     -   BIDS Connectivity Project Updates
+
         -   7 BEPS
+
         -   **lessons learned**: there is no procedure for addressing and resolving BEP feedback,
             establishing a timeline would help to continue progress
+
         -   **Suggestions**: clarify roles and responsibilities of BEP leads, define timelines for BEP tasks
 
 -   BIDS 2.0 (*Yaroslav Halchenko*)

docs/collaboration/index.md

@@ -1,6 +1,12 @@
 # Help make BIDS better!
 
-BIDS is informed, supported, and guided by its users. BIDS standards are intended to change and evolve as methods, resources, and the needs of the BIDS community changes. We encourage all researchers to contribute to the ongoing development of BIDS standards, be it through discussion on websites, the creation of new BIDS tools, or contributing to extending the BIDS specification through proposals. Below is a list of common resources where users can get involved in making the BIDS standard better!
+BIDS is informed, supported, and guided by its users.
+BIDS standards are intended to change and evolve as methods, resources,
+and the needs of the BIDS community changes.
+We encourage all researchers to contribute to the ongoing development of BIDS standards,
+be it through discussion on websites, the creation of new BIDS tools,
+or contributing to extending the BIDS specification through proposals.
+Below is a list of common resources where users can get involved in making the BIDS standard better!
 
 <u>Neurostars Website</u>
 

docs/extensions/general-guidelines.md

@@ -44,66 +44,68 @@ Development on Google Docs is preferred as this is a low barrier to entry
 for colleagues who do not use GitHub and/or Markdown,
 allowing more people to get involved.
 
-1. Explore [the specification][the bids specification repository]
+1.  Explore [the specification][the bids specification repository]
     and [the BEP lists](./beps.md)
     to find existing or ongoing efforts
     that may support what you are trying to add into the BIDS Specification.
     Someone may have already done work for you.
 
-1. Read the [BIDS governance document](../collaboration/governance.md).
+1.  Read the [BIDS governance document](../collaboration/governance.md).
 
-1. Familiarize yourself with the BIDS community by browsing current issues,
+1.  Familiarize yourself with the BIDS community by browsing current issues,
     discussions, and proposed changes on
     [the bids specification repository].
     Search for issues relating to your feature or BEP idea
     before creating a new issue.
 
-1. Open an initial “issue” on
+1.  Open an initial “issue” on
     [the bids specification repository] issues page
     to gauge interest in your potential BEP, and to collect
     feedback by more community members and
     [BIDS maintainers](https://github.com/bids-standard/bids-specification/blob/master/DECISION-MAKING.md#maintainers-group).
     **This is an important step before proceeding in order to make sure that
     more consensus arises and more contributors are aware what is happening**.
 
-1. Communicate with the BIDS maintainers to make your BEP official.
+1.  Communicate with the BIDS maintainers to make your BEP official.
     This entails registering the BEP with a number on the BIDS website.
     To obtain a number for your BEP, follow the previous steps
     and then [open a new issue](https://github.com/bids-standard/bids-website/issues)
     or [submit a pull request](https://github.com/bids-standard/bids-website/pulls) to the
     [website GitHub repository](https://github.com/bids-standard/bids-website/),
     cross-linking to any other already existing issues.
 
-1. Create a draft of your extension by discussing among colleagues. The
+1.  Create a draft of your extension by discussing among colleagues. The
     [BIDS Extension Proposal template](https://docs.google.com/document/d/1W7--Mf3gCCb1mVfhsoRJCAKFhmf2umG1PFkyZ1jEgMw/edit#)
     provides some boilerplate and formatting conventions.
 
-1. List on the draft the contributor(s) leading the effort.
+1.  List on the draft the contributor(s) leading the effort.
 
-1. Share the draft (remember to
+1.  Share the draft (remember to
     [share a link that allows anyone to comment](https://support.google.com/docs/answer/2494822?co=GENIE.Platform%3DDesktop&hl=en))
     with the
     [bids-discussion mailing list](https://groups.google.com/forum/#!forum/bids-discussion)
     and ask for comments.
 
-1. Incorporate the feedback and strive for consensus.
+1.  Incorporate the feedback and strive for consensus.
 
-1. Help to merge the extension into the main specification (this will require
-    converting the proposal to Markdown and submitting a Pull Request at
-    [the bids specification repository])
+1.  Help to merge the extension into the main specification
+    (this will require converting the proposal to Markdown
+    and submitting a Pull Request at [the bids specification repository])
 
-1. Create example datasets. Complete source data (for example DICOM, EDF, Excel) and its
-    corresponding target BIDS datasets, _must be_ supplied along with instructions on how
-    to transform data from source to target. When possible, data from multiple vendors
+1.  Create example datasets. Complete source data (for example DICOM, EDF, Excel) and its
+    corresponding target BIDS datasets,
+    _must be_ supplied along with instructions on how to transform data from source to target.
+    When possible, data from multiple vendors
     such as Siemens, Philips, or General Electric (in the case of MR) should be included.
     These datasets are vital for the development of resources that will, ultimately, increase the adoption of
-    the BEP following its integration into the BIDS Specification; see [this discussion](https://github.com/bids-standard/bids-specification/issues/1350).
+    the BEP following its integration into the BIDS Specification;
+    see [this discussion](https://github.com/bids-standard/bids-specification/issues/1350).
     BIDS maintainers **are available to assist** in the collection, organization, or at
     any step in the preparation of these datasets.
 
-1. If necessary, contribute a pull request to the
-      [BIDS Validator repository](https://github.com/bids-standard/bids-validator)
-      as well to incorporate the extension.
+1.  If necessary, contribute a pull request
+    to the [BIDS Validator repository](https://github.com/bids-standard/bids-validator)
+    as well to incorporate the extension.
 
 ![bep_process](../assets/img/bep_process.png)
 

makefile

@@ -58,22 +58,6 @@ lint: remark
 
 remark: package.json
 	npx remark \
-		./docs/*.md \
-		./docs/blog \
-		./docs/collaboration \
-		./docs/contact \
-		./docs/datasets \
-		./docs/extensions/*md \
-		./docs/faq/ \
-		./docs/getting_started/*.md \
-		./docs/getting_started/bids_apps/**/*.md \
-		./docs/getting_started/folders_and_files/**/*.md \
-		./docs/getting_started/resources/**/*.md \
-		./docs/getting_started/tutorials/**/*.md \
-		./docs/impact \
-		./docs/standards/bids_app_specification \
-		./docs/standards/bids_specification \
-		./docs/standards/schema \
-		./docs/standards/index.md \
-		./docs/tools \
+		./docs \
+		--frail \
 		--rc-path .remarkrc