BIDS-2.0

[yarikoptic]

References

• Overarching agenda for 2.0 bids-2-devel#57
• Full list of issues to consider: https://github.com/bids-standard/bids-2-devel/issues
• BIDS 2.0 Project of selected: https://github.com/orgs/bids-standard/projects/10

Plan

• Initial "setup" of needed support tools/tests/changes
  • Closes Develop bids-migration script bids-2-devel#67
  • migrate all examples
  • validate all examples after migration (some are excluded since not passing even in BIDS 1.x using deno validator)
• Establish development procedures
  • See CONTRIBUTING-BIDS2.0.md
  • diff between this branch and with all the "functional patches" applied: bids-2.0...bids-2.0-patched
• Add patch sets to solve specific issues staged for BIDS 2.0 as outlined in https://github.com/orgs/bids-standard/projects/10
  • Major
    • Closes Replace "inheritance" with "summarization" principle bids-2-devel#65
  • Addressing quirks/inconsistencies of 1.x. Full list
    • Closes Homogenize "Subject" Nomenclature bids-2-devel#14
      • ?Introduce deprecation cycle within 2.0 to allow for coexistence of participants.tsv and subjects.tsv .
    • Closes Uniformize .json files for .tsv's first column to be "<entity>_id" bids-2-devel#69
    • Closes Make column names singular bids-2-devel#78, which also generalization over
      • MINOR: Replace "units" with "unit" in channels.tsv bids-2-devel#15
      • WIP: BIDS 2.0: harmonize TSV columns to be singular (ATM "units" and "migrate_plural_columns") #1821
• 1.0 Major Feature Enhancements: changes which are not breaking BIDS datasets compatibility will be suggested independently as PRs against 1.0 (master) while still targeting BIDS 2.0 release.
  • Make it possible to specify folders layout to be other than sub-{label}/[ses-{label}/] bids-2-devel#54 which would help to address
    • Multi-site/center studies bids-2-devel#11
    • WiP: BIDS 2̶.̶0̶1.0: flex BIDS layout (bids-2-devel/issues/54) #1809
  • Allow composition of a BIDS dataset (dataset level) from smaller (subj or subj/ses) level bids-2-devel#59 which would help to address
    • Use-case: AIND schema bids-2-devel#60
  • Populate bids-2 branch/PR against bids-examples with examples depicting new approaches for hierarchy/composition

[codecov]

Codecov Report

Attention: Patch coverage is 80.48780% with 16 lines in your changes are missing coverage. Please review.

Project coverage is 87.50%. Comparing base (f0bc977) to head (59fa77e).

Files	Patch %	Lines
tools/schemacode/bidsschematools/migrations.py	86.36%	9 Missing ⚠️
tools/schemacode/bidsschematools/__main__.py	0.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1775      +/-   ##
==========================================
- Coverage   87.92%   87.50%   -0.43%     
==========================================
  Files          16       17       +1     
  Lines        1375     1456      +81     
==========================================
+ Hits         1209     1274      +65     
- Misses        166      182      +16     

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[yarikoptic]

might want to extend here to any branch with bids-2.0 prefix but without -patched suffix so we support rendering of diffs etc for feature branches against this branch, such as in

• BIDS 2̶.̶0̶1.0: flex BIDS layout (bids-2-devel/issues/54) #1809