[ENH] Reorganise modality agnostic files section into multiple pages

[bclenet]

BEP028 BIDS-Prov is going to introduce a lot of contents into the Modality agnostic files section of the BIDS specification.

In order to prepare for these changes, this PR splits the contents of the src/modality-agnostic-files.md file into separate files in a src/modality-agnostic-files/ directory:

• src/modality-agnostic-files/dataset-description.md
• src/modality-agnostic-files/data-description.md
• src/modality-agnostic-files/code.md

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 82.10%. Comparing base (1e14c26) to head (fb5a33a).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2106   +/-   ##
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  Coverage   82.10%   82.10%           
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  Files          17       17           
  Lines        1531     1531           
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  Hits         1257     1257           
  Misses        274      274           

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[bclenet]

Hi !
CI seems fails (check_links) fails because of a link that is not related to the PR. Could someone please relaunch the CI pipeline so that this fail disappears ?
Thanks

[cmaumet]

Hi everyone. Is it okay to merge this PR or are there more updates that would be required? As a note, this is only a refactoring of existing info (no new and/or no remove text). Thanks!

[yarikoptic]

I am a little uncertain about using "Data descriptions" here, since "Dataset" includes "Data" as well.
Especially since to a degree summaries like participants.tsv are also "dataset level description": although they already were separated from "Dataset description" section, they were not explicitly sectioned under "Data" section.

here is what is there:

It seems that what is common among all, but phenotype/, those "Data description" files -- they are directly pertinent to data under sub-* folders. phenotype/, sure thing, also but it is under a separate folder. I wonder if we should

• also move out Phenotypic and assessment data into its own file/sub-section.
• rename "Data description" into "Data summary files" since all those sections are "{entity/concept} files" (concept is for scans one) and thus src/modality-agnostic-files/data-summary-files.md
  • this would also better align with a potential bids-2 level enhancement of Replace "inheritance" with "summarization" principle bids-2-devel#65 and Formalize "life-cycle"/movement and placement of metadata bids-2-devel#85 .

[bclenet]

Hi @yarikoptic thanks for the review, I changed the names of the "Data description" section and added a new one for Phenotypic and assessment data, as you suggested.

[yarikoptic]

IMHO looks nice and now more consistent with "Modality specific files" section being expandable too

[effigies]

LGTM, apart from the redirects.

[cmaumet]

Hey @yarikoptic @effigies are we good to merge with your two approvals or should we wait for more input? Sorry just not sure about the process here... Thanks!

[effigies]

I think we can merge. Been over a week since significant changes, just touch-ups since then.

[yarikoptic]

but ideally we are still to add more redirects whenever someone (might be us) brings that mkdocs/mkdocs-redirects#73 over the finish line