[ENH] Use BIDS schema to "drive" pybids #818

[astewartau]

This is my first PR as a BIDS maintainer. Appreciate any feedback! This attempts to address #818.

Summary

• Implement schema-driven BIDSLayout configuration loading
• Enables version-specific schema loading via bidsschematools
• Existing JSON-based config is unchanged

Implementation

• Added Config._from_schema() method that loads schema via bidsschematools.schema.load_schema()
• Support remote schema loading from versioned URLs (e.g., https://bids-specification.readthedocs.io/en/v1.9.0/schema.json)
• Extract entity names from schema file rules across raw/deriv/common sections using rules.regexify_filename_rules()
• Generate Entity objects with regex patterns derived from schema format definitions (bids_schema.objects.formats)
• Combine BIDS entity prefixes with schema format patterns (e.g., sub- + [0-9a-zA-Z]+ for subjects)
• Special entities (suffix, extension, datatype) still require some special handling logic

Usage

# Load from current schema
config = Config.load('bids-schema')

# Load specific BIDS version
config = Config.load({'schema_version': '1.9.0'})

[codecov]

Codecov Report

❌ Patch coverage is 90.97345% with 51 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.48%. Comparing base (504a861) to head (476d32f).
⚠️ Report is 14 commits behind head on main.

Files with missing lines	Patch %	Lines
...ids/layout/tests/test_schema_pattern_validation.py	77.55%	10 Missing and 12 partials ⚠️
...rc/bids/layout/tests/test_schema_vs_json_config.py	88.19%	8 Missing and 11 partials ⚠️
src/bids/layout/layout.py	93.93%	0 Missing and 4 partials ⚠️
src/bids/layout/tests/test_schema_config.py	94.52%	1 Missing and 3 partials ⚠️
src/bids/layout/models.py	97.93%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1163      +/-   ##
==========================================
+ Coverage   89.34%   89.48%   +0.13%     
==========================================
  Files          66       70       +4     
  Lines        7276     7828     +552     
  Branches      854      951      +97     
==========================================
+ Hits         6501     7005     +504     
- Misses        567      584      +17     
- Partials      208      239      +31     

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[bendhouseart]

Awesome, will start with trying the notebook!

[bendhouseart]

Sold!

Legacy initialization: 1.531 seconds
Schema initialization: 1.282 seconds

Difference: 0.249 seconds
Schema is faster by 16.3%

Get the CI passing and will approve, although I think folks will want to increase coverage, so maybe that too?

[astewartau]

Hi @bendhouseart, I've improved code coverage, and CI looks to be passing. :)

[bendhouseart]

lgtm 👍