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

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BIDS 2̶.̶0̶1.0: flex BIDS layout (bids-2-devel/issues/54)#1809
yarikoptic wants to merge 1 commit intomasterfrom
bids-2.0-flex-layout

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@yarikoptic yarikoptic commented Apr 27, 2024

Aims to provide a solution to

Name rationale:

Originally I thought to name it BIDSLayout but that one was/is used as a class in pybids. On one hand it is great because corresponds in "principles". But I thought to avoid confusion at least ATM so to make it easier to find issues/code where such a term is used/mentioned. So for now decided to go with BIDSEntitiesLayout but it would be easy to change to anything we want.

TODOs

  • rebase against master. Per conversation with @effigies since change is not breaking existing datasets (if we allow for "optional" session level somehow) we could aim for regular master.
  • seek initial feedback (attn @bids-standard/maintainers @bids-standard/steering et al)
  • formalize "optional" notion of session (for BIDS 2.0 I thought to mandate it being explicit. @effigies pointed out that fmriprep produced both with and without ses- ATM).
  • elaborate on having multiple paths (e.g. "." and `"atlases/" : attn [ENH] BEP038 - Atlases #1714 folks TODO: add a team)
  • provide migration for datasets with sessions: would need to be added explicitly
  • add examples to bids2.0-examples
    • add few examples with alternative layouts (e.g. without session and modality folders, thus getting very close to DANDI BIDS-like setup. Attn @TheChymera who is trying nwb2bids on DANDI dandisets)
    • may be even just migrate them all into some alternative layouts and see validator to still operate correctly...
  • adjust schema
  • adjust bidsschematools to support
  • extend bids-validator to support

@yarikoptic yarikoptic mentioned this pull request Apr 27, 2024
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@yarikoptic yarikoptic added the enhancement New feature or request label Apr 27, 2024
@yarikoptic yarikoptic changed the title BIDS 2.0: flex BIDS layout (bids-2-devel/issues/54) BIDS 2̶.̶0̶1.0: flex BIDS layout (bids-2-devel/issues/54) Jun 22, 2024
Aims to provide a solution to

- bids-standard/bids-2-devel#54

### Name rationale:

Originally I thought to name it BIDSLayout but that one was/is used as
a class in pybids. On one hand it is great because corresponds in "principles".
But I thought to avoid confusion at least ATM so to make it easier to find
issues/code where such a term is used/mentioned.  So for now decided to go
with BIDSEntitiesLayout but it would be easy to change to anything we want.
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