lint

.github/workflows/validation.yml

@@ -35,7 +35,6 @@ jobs:
                 python no-bad-latin.py
             working-directory: tools
 
-
     # Markdown formatting
     remark:
         runs-on: ubuntu-latest
@@ -44,7 +43,5 @@ jobs:
         -   uses: actions/setup-node@v4
             with:
                 node-version: 14
-        -   name: Install dependencies
-            run: npm install `cat npm-requirements.txt`
-        -   name: Run style checks
-            run: npx remark docs/**/*.md --frail --rc-path .remarkrc
+        -   name: Run markdown style checks
+            run: make remark

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

@@ -48,7 +48,7 @@ Regarding discussions on where to host our historical specification pdfs (please
 -   Items to share
 -   1.2.2 release
 -   [BEP018: Genetic information](https://github.com/bids-standard/bids-specification/pull/395)
-  -Do final call before merging into the standard
+    -   Do final call before merging into the standard
 -   Making the standard slide deck
 -   make it longer and presenter can slim down as needed
 -   Making repositories in BIDS standard

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

@@ -40,30 +40,22 @@ The Steering Group gave direction on handling author lists on Zenodo - make it a
 -   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.
 -   Points to consider when designing the infrastructure to support BIDS slides
 
-  -An important feature is that the BIDS slides will be a living and breathing document shared via Google slides.
-  -Google slides gives us the ability to: version control, seamless updating capability, and persistent links.
-  -Discussed preserving and separating the core presentation from the derived versions. Ensuring the references of where they have been used.
-
-  -Event link or other event details
-
-  -Drafting guidelines for how to organize a BIDS event
-  -Pilot at NRM and OHBM (June 2020)
-
-  -Compiling a [list of channels](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0) to share BIDS news. Currently for version releases and community feedback calls on BEPs.
+    -   An important feature is that the BIDS slides will be a living and breathing document shared via Google slides.
+    -   Google slides gives us the ability to: version control, seamless updating capability, and persistent links.
+    -   Discussed preserving and separating the core presentation from the derived versions. Ensuring the references of where they have been used.
+    -   Event link or other event details
+    -   Drafting guidelines for how to organize a BIDS event
+    -   Pilot at NRM and OHBM (June 2020)
+    -   Compiling a [list of channels](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0) to share BIDS news. Currently for version releases and community feedback calls on BEPs.
 
 -   Attending Steering Group members gave approval to move forward with finalizing the [Genetic Information extension](https://github.com/bids-standard/bids-specification/pull/395) and merging into the specification. This will trigger a [v1.3.0 release](https://github.com/bids-standard/bids-specification/pull/435) (according to our [release guidelines](https://github.com/bids-standard/bids-specification/blob/master/Release_Guideline.md)).
-
 -   For future BEPs, they will submit their examples to [BIDS-examples](https://github.com/bids-standard/bids-examples) for review by the Steering Group and confirm the [validator](https://github.com/bids-standard/bids-validator) has been extended properly. The BEP leads can leave it as a draft PR. It was determined that opening the PR from a branch of the [BIDS specification repository](https://github.com/bids-standard/bids-specification) should be done allowing us to render the extension via ReadTheDocs.
-  -Genetic Information was in the BEP lead's fork of BIDS-examples (after the meeting a [PR was opened](https://github.com/bids-standard/bids-examples/pull/178)).
 
--   Regarding the [Zenodo authorship](https://github.com/bids-standard/bids-specification/issues/66) discussion, the Steering Group considered for the list to either be first/last+alphabetical order in the middle or a single authored “[BIDS Contributors Group](https://bids.neuroimaging.io/governance.html#bids-contributors-group)”.
+    -   Genetic Information was in the BEP lead's fork of BIDS-examples (after the meeting a [PR was opened](https://github.com/bids-standard/bids-examples/pull/178)).
 
+-   Regarding the [Zenodo authorship](https://github.com/bids-standard/bids-specification/issues/66) discussion, the Steering Group considered for the list to either be first/last+alphabetical order in the middle or a single authored “[BIDS Contributors Group](https://bids.neuroimaging.io/governance.html#bids-contributors-group)”.
 -   Decision toward “BIDS Contributors Group” similar to how ADNI does it.
-
 -   The Steering Group discussed where to share non-BIDS related information.
-
 -   The consensus was to share on the [bids-discussion](https://groups.google.com/forum/#!forum/bids-discussion) Google group channel.
-
 -   We brainstormed what may be the related initiatives to keep aware of. FF contacted INCF to see if they have information regarding this. Please see the [INCF blog](https://www.incf.org/blogs-list).
-
 -   The Steering Group discussed the format for the BIDS Maintainers monthly update. This will be submitted to Slack and added to the next agenda. This will be implemented starting with the March update and will not be retroactive.

docs/blog/posts/2020-03-30-steering-group-minutes.md

@@ -40,10 +40,10 @@ We invited the [ASL BEP](https://bids.neuroimaging.io/bep005) leads to the next
 
 -   Less than 1page, high level, 1 sentence for an issue (as needed)
 -   Update covers action of the last month: achievements, struggles, next month outlook, and blocking items.
-  -The blocking items may be most important for Steering Group to be aware of.
-  -Link to the issues on GitHub
+    -   The blocking items may be most important for Steering Group to be aware of.
+    -   Link to the issues on GitHub
 -   This update will provide strong historical perspective
-  -Keep in mind the purpose of the update: The Steering Group wants to capture the work performed to maintain BIDS and what are the hard parts/blockers of the project.
+    -   Keep in mind the purpose of the update: The Steering Group wants to capture the work performed to maintain BIDS and what are the hard parts/blockers of the project.
 
 -   Addressing issues related to lowering the barriers to contribute to BIDS.
 

docs/blog/posts/2020-05-07-steering-group-minutes.md

@@ -32,16 +32,16 @@ This was a joint meeting between the Steering Group and Maintainers Group to go
 
 -   [Zenodo author lists](https://github.com/bids-standard/bids-specification/issues/66)
 -   Recognizing diverse contributions
-  -Author: sustained substantial contributions, regularly answering questions
-  -Contributor is more flexible
+    -   Author: sustained substantial contributions, regularly answering questions
+    -   Contributor is more flexible
 -   Alphabetical order and the author list can only be added to not removed
 -   Proposal to add an author’s and contributor’s page to the appendix of the specification
 
 -   Add more details of the specific contribution to BIDS
-  -Can be up to a paragraph narrative
+    -   Can be up to a paragraph narrative
 -   The goal is to list and give more credit to contributors
 -   This can also be hosted on GitHub
-  -Perhaps GitHub Wiki
+    -   Perhaps GitHub Wiki
 
 -   Accepted BEPs
 
@@ -57,7 +57,7 @@ This was a joint meeting between the Steering Group and Maintainers Group to go
 
 -   [Enhancing our definition of a Maintainer](https://github.com/bids-standard/bids-specification/pull/467)
 -   Adding a specialty or domain expert responsibility to the role
-  -Workshopping the semantics
-  -Gives more clarity and specificity to the responsibilities of the role
+    -   Workshopping the semantics
+    -   Gives more clarity and specificity to the responsibilities of the role
 -   The goal is to nurture more diverse contributions and build in more resilience and sustainability into the organization
 -   This will be managed by the Maintainers Group

docs/blog/posts/2020-05-28-steering-group-minutes.md

@@ -29,11 +29,11 @@ Briefly, we discussed our plan to host a town hall at [OHBM](https://www.humanbr
 -   Timeline approved
 -   Very helpful having the RTD rendering
 -   Review perspective taken by RO
-  -Could I make it?
-  -Could I explain it to someone else?
+    -   Could I make it?
+    -   Could I explain it to someone else?
 -   GitHub can look very complicated
 -   Barrier to contributing?
-  -Generate guide for how to comment on a PR
+    -   Generate guide for how to comment on a PR
 -   Proposals for future BEPs submissions
 -   The final proposal is clean of comments
 -   Clear direction for review and what to look at

docs/blog/posts/2020-07-09-steering-group-minutes.md

@@ -22,7 +22,7 @@ We were joined by Franco Pestilli to discuss his potential BIDS grant. We went o
 
 -   Discussed Franco Pestilli's grant
 -   Provided insights and suggestions for enhancements
-  -Thinking about the scope and framing of the proposal
+    -   Thinking about the scope and framing of the proposal
 -   Evaluated similar community initiatives
 -   We can establish a process for future BIDS grant writers
 -   Letting the BIDS team know of their intention

docs/blog/posts/2020-08-20-steering-group-minutes.md

@@ -27,7 +27,7 @@ We were joined by [Dave Keator](https://faculty.sites.uci.edu/davidkeator/people
 -   Extracting terms from the BIDS-Specification and created jsonld representation
 -   Use case: A BEP can consult this list to ensure no terms are being reused
 -   Potentially working with our BIDS-schema
-  -Related to the [yaml conversion of our entity table](https://github.com/bids-standard/bids-specification/pull/475)
+    -   Related to the [yaml conversion of our entity table](https://github.com/bids-standard/bids-specification/pull/475)
 -   Determining approaches for integrating this into our processes
 -   Developing tool to work with: adding existing/new terminology, add dataset annotations
 -   Potentially adding new terms through a GUI application

docs/blog/posts/2020-11-12-steering-group-minutes.md

@@ -33,19 +33,19 @@ The majority of this meeting we were joined by Melissa Kline of the [Psych-DS](h
 -   Initiative was borne out of the ManyBabies project
 -   During SIPS began the standardization of behavioral data using BIDS as the model
 -   Psych-DS goal is to nudge people toward using a standard
-  -Well structured tsv’s are recommended
+    -   Well structured tsv’s are recommended
 -   Challenge has been thinking through how the file structure can look. Behavioral studies are more heterogeneous than imaging studies - very little consensus among the community
 -   This will make implementing an inheritance principle more difficult
 -   Seeking agreement on metadata terms
 -   Have a schema to validate against
 -   Data practices can be a framework to move forward
 -   Convert common raw data formats (for example Qualtrics) to the standard Psych-DS format
-  -1st step is writing converters to get to Psych-DS
+    -   1st step is writing converters to get to Psych-DS
 -   If a dataset is Psych-DS compliant we can make certain assumptions about the data
 -   Push to have recommended and required keywords
 -   While keeping Psych-DS flexible for the many different use cases
 -   Do not have many keywords - this is not the purpose of Psych-DS
-  -Prefer to point to existing ontologies
+    -   Prefer to point to existing ontologies
 -   Want to give some sort of BIDS + Psych-DS compatible recommendations
 -   Looking for a volunteer to write validator
 -   Psych-DS group is pushing toward v1.0.0
@@ -55,7 +55,7 @@ The majority of this meeting we were joined by Melissa Kline of the [Psych-DS](h
 -   Privacy is a high concern
 -   Psych-DS may share metadata
 -   Could separate the metadata from the data
-  -There is a use for metadata stores pointing to DUA’s for the data
+    -   There is a use for metadata stores pointing to DUA’s for the data
 -   Community is unsure of what they can and cannot share
 -   Appetite for specific instructions to do Open Science
 -   Psych-DS may not be BIDS compliant, but does not block capability

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

@@ -26,11 +26,11 @@ This was a joint meeting between the Steering and Maintainers Group. We began th
 -   Crediting:
 -   Maintainership counts as "substantial contributions to the conception of the work" (one of [ICMJE](http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html) criteria).
 -   Look at [https://credit.niso.org/](https://credit.niso.org/) for authorship roles
-  -Roles that are applicable: data curation and software
-  -Resources potentially too
+    -   Roles that are applicable: data curation and software
+    -   Resources potentially too
 -   Include recommended (but not required) text for including Steering/Maintainers as coauthors and description of roles. Requiring credit goes against open values of standard.
-  -Split Steering group and Maintainer group descriptions/recommendations given different levels of engagement.
-  -Generally will be Steering Group + Maintainers or just Maintainers.
+    -   Split Steering group and Maintainer group descriptions/recommendations given different levels of engagement.
+    -   Generally will be Steering Group + Maintainers or just Maintainers.
 -   Add columns to Maintainers table with start date and end date, and self-selection on whether to include on papers if authors think the ex-Maintainer contributed.
 -   Authorship credit could be equal among our groups. BEP leads can make the decision.
 -   Preference may be a BIDS Maintainers consortia author -[Credit taxonomy](https://credit.niso.org/) could address and report specific contributions

docs/blog/posts/2021-01-14-steering-group-minutes.md

@@ -25,12 +25,12 @@ This meeting was primarily spent discussing our approach for crediting the Steer
 -   PET community review can be extended
 -   Crediting Steering and Maintainer groups
 -   Separate Steering and Maintainer group entities
-  -Forward thinking and very inclusive -[Credit taxonomy](https://credit.niso.org/)
-  -Articulating why they are authors
-  -Individual or groups
-  -Argument against consortium level authorship
-  -Consortium will be dynamic
-  -Value in having the names listed rather than a consortium listed
+    -   Forward thinking and very inclusive -[Credit taxonomy](https://credit.niso.org/)
+    -   Articulating why they are authors
+    -   Individual or groups
+    -   Argument against consortium level authorship
+    -   Consortium will be dynamic
+    -   Value in having the names listed rather than a consortium listed
 -   If individual doesn’t feel comfortable can be moved to acknowledgments
    -   Following the [vancouver guidelines](http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html)
    -   Data collection, analysis, preprocess, manuscript prep
@@ -41,12 +41,12 @@ This meeting was primarily spent discussing our approach for crediting the Steer
    -   No time period dependent based decision
 -   Recognizing those that present and promote the standard
 -   Responsibility of the BEP lead to track major contributions
-  -Invite all and prune respondents
+    -   Invite all and prune respondents
 -   Add credit taxonomy to BEP lead guidelines
 -   Contributors could fill out a google form
-  -Focus on credit taxonomy rather than emoji
-  -Have mapping of credit taxonomy to emoji representation
-  -Credit taxonomy shared via GitHub rather than Google docs
+    -   Focus on credit taxonomy rather than emoji
+    -   Have mapping of credit taxonomy to emoji representation
+    -   Credit taxonomy shared via GitHub rather than Google docs
 -   Add the ultimate consent form to website
-  -Promote it
-  -Maybe with a news article
+    -   Promote it
+    -   Maybe with a news article

docs/blog/posts/2021-02-04-steering-group-minutes.md

@@ -31,16 +31,16 @@ The Steering Group was joined by [BEP20: Eye Tracking](https://bids.neuroimaging
 -   BEP status
 -   Most people are receptive to the BEP
 -   There was a preprint released that is related to the BEP effort
-  -BEP leads reached out and received good feedback from the authors
-  -The preprint was a bit more high-level, but is compatible with the BEP
-  -Preprint focused on how to report Eye Tracking in a paper rather than how to organize and share the data
+    -   BEP leads reached out and received good feedback from the authors
+    -   The preprint was a bit more high-level, but is compatible with the BEP
+    -   Preprint focused on how to report Eye Tracking in a paper rather than how to organize and share the data
 -   The community is sharing data
 -   BEP does have a constrained scope with a clear goal
 -   Core aspect: position of the area and recording that along with the stimuli map
 -   BIDS is an interoperable standard
 -   Community focused to wrap BEP into BIDS
 -   Some colleagues have had trouble getting over the Brain Imaging part of BIDS
-  -Could be an impediment to adoption
+    -   Could be an impediment to adoption
 -   BIDS is a practical implementation, would rather be in BIDS
 -   Eye Tracking with EEG, MEG, and/or MRI is becoming more common
 -   We can use the existing infrastructure to continue unlocking multimodal studies

docs/blog/posts/2021-03-18-steering-group-minutes.md

@@ -30,6 +30,7 @@ N/A
 -   Process to promote and deprecate tools
 -   Classes: converters, Apps, libraries (more bids-adjacent)
 -   Sorting a little differently
-  -Maybe by modality
+    -   Maybe by modality
+
 -   BIDS previous slideshows from the community
 -   [slideshare search](https://www.slideshare.net/search/slideshow?searchfrom=header&q=bids+neuroimaging&ud=any&ft=all&lang=**&sort=)

docs/blog/posts/2021-04-08-steering-group-minutes.md

@@ -20,7 +20,7 @@ N/A
 
 -   Lessons learned from incorporating multiple BEPs at the same time
 -   Enhance the expectation management to BEP leads
-  -Potentially update BEP template
+    -   Potentially update BEP template
 -   Nudge BEP leads toward modular PRs
 -   BIDS website: evaluate needs and does it convey the needs of a user
 -   Focus on colleagues not part of the BIDS community

docs/blog/posts/2021-04-29-steering-group-minutes.md

@@ -36,11 +36,11 @@ The Steering Group began the meeting by discussing a new potential BEP and meeti
 -   Monthly basis
 -   BIDS website
 -   Contribution ability for the platform affects decision?
-  -Should be on GitHub because we are a community project
+    -   Should be on GitHub because we are a community project
 -   Documents are in markdown
 -   Maintain a staging and production to enable the capability of previewing prior to release
 -   Tease apart rendering from layout
-  -Focus on layout then on content
-  -Layout and information design directly influence user journey
+    -   Focus on layout then on content
+    -   Layout and information design directly influence user journey
 -   The problem is how the information is conveyed
 -   Include guidelines for how contributions are done on the website

docs/blog/posts/2023-06-15-steering-group-minutes.md

@@ -191,15 +191,15 @@ Imaging Neuroscience Response from Steve Smith
 
 -   Getting started for:
 
-  -Users
+    -   Users
 
-  -tools developers,
+    -   tools developers,
 
-  -reviewers,
+    -   reviewers,
 
-  -funding agencies
+    -   funding agencies
 
-  -Institute directors
+    -   Institute directors
 
 -   Should this be in the form of a
   [Checklist](https://www.nmind.org/standards-checklist/)

docs/blog/posts/2024-01-11-steering-group-minutes.md

@@ -191,13 +191,13 @@ Github project is established with many ideas but there aren\'t many
 
 -   Create a pull request for this survey:
 
-  -Are they aware of BIDS?
+    -   Are they aware of BIDS?
 
-  -Was it hard to convert data?
+    -   Was it hard to convert data?
 
-  -Do you use data that do not yet fit within BIDS?
+    -   Do you use data that do not yet fit within BIDS?
 
-  -Had questions, but could not find answers
+    -   Had questions, but could not find answers
 
 -