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Add DatasetType="project" and rework existing "layout" example into a proper BIDS dataset #1972

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This PR was initially submitted as #1861 but I made a mistake to combine it with a discussion of transformations of existing projects' layouts into such BIDS project dataset. Please refer to that PR for examples but otherwise let's concentrate here on the discussion of this specific proposed change.

  • Rationale 1 (major): BIDS standard already provides reasonable structure to formalize organization of various components of a neuroscientific data project: where to place code, original (source) data, derivative data, README, CHANGES. Many projects (e.g. nipoppy, YODA, etc) propose similar and often might be even "inspired" templates . If we explicitly allow for BIDS standard to prescribe study level organization, IMHO it would help many people and projects decide on how to organize their studies/projects.
  • Rationale 2: IMHO BIDS standard should describe only what standard prescribe and not recommend some potential "non-standardized" layouts. That is why I "reworked" that example into a legitimate BIDS dataset merely by adding dataset_description.json.

TODOs:

This reverts commit a3c12f8 where I have tried
to introduce it in
bids-standard#1741 but it required a
little more of further detailing.
…ttype

* commit 'v1.10.0-35-g5f7004819': (218 commits)
  Include entity-less "scans.json" into an example of inheritance principle (bids-standard#1945)
  fix(checks): Enforce timing mutual exclusions on BOLD/ASL data only (bids-standard#1969)
  refactor contributing (bids-standard#1965)
  [pre-commit.ci] pre-commit autoupdate (bids-standard#1967)
  [SCHEMA] Allow physio files for anat datatype (bids-standard#1961)
  [pre-commit.ci] pre-commit autoupdate
  Add an empty line in hope to get table rendered properly in "Ordering rules" section (bids-standard#1953)
  schema: add check for duplicate READMEs (bids-standard#1952)
  [MAINT] switch bidsschematools to pyproject.toml (bids-standard#1948)
  fix(schema): Disable TaskName check for channels and markers files
  Permit and warn on task/acquisition/run for electrodes and coordsystems
  [FIX] Allow (but discourage) task entity for coordsystem.json
  fix(schema): Limit MRI metadata checks to NIfTIs
  fix: Only check for sorted times in arrays
  py3.13 (bids-standard#1947)
  [pre-commit.ci] pre-commit autoupdate (bids-standard#1946)
  [FIX] Update changelog links to avoid redirects (bids-standard#1944)
  [ENH] Update DWI suffixes to include most common scanner derivatives (bids-standard#1864)
  [pre-commit.ci] pre-commit autoupdate
  [MAINT] Update Release_Protocol.md
  ...
@yarikoptic yarikoptic added the opinions wanted Please read and offer your opinion on this matter label Oct 29, 2024
@yarikoptic yarikoptic requested a review from tsalo October 29, 2024 21:01
@yarikoptic yarikoptic changed the title Enh project datasettype Add DatasetType="project" and rework existing "layout" example into a proper BIDS dataset Oct 30, 2024
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