Replace nipreps.json with schema-driven config generation#1023
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astewartau wants to merge 7 commits intonipreps:masterfrom
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Replace nipreps.json with schema-driven config generation#1023astewartau wants to merge 7 commits intonipreps:masterfrom
astewartau wants to merge 7 commits intonipreps:masterfrom
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Entity definitions are now generated from the BIDS schema via pybids' generate_extended_config(). NiPreps-specific entities (hash, fmapid, pvc) and the figures datatype are layered on via ConfigExtension. Path patterns are defined inline as they all use NiPreps-specific entities and suffixes. The reports module now receives the generated config dict directly via add_config_paths(). nipreps.json is no longer needed and has been removed.
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Convert 28 monolithic pattern strings to compact rule dicts that specify only datatypes, suffixes, extensions, and entity deviations. Entity ordering and standard derivative entities are inherited from the BIDS schema. Figures patterns remain as literal strings due to their non-standard directory layout.
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…ules Schema splits .json into sidecar patterns, but DerivativesDataSink outputs .nii + .json together as multi-file, requiring a single pattern with all extensions. Document this and other reasons for apparent redundancy.
…a_rules With sidecar_split=False, schema derivative patterns include all extensions in a single pattern, so extra_rules no longer need to duplicate schema-known suffixes for multi-file output. Remove 22 redundant suffixes from 3 rules: - anat: keep only MTw, TSE (removed 16 schema suffixes) - func: keep only boldref, boldmap (removed 4 schema suffixes) - dwi: keep only dwiref, epiref, lowb (removed 2 schema suffixes)
- Extract _SURFACE_SUFFIXES, _SCALAR_SUFFIXES, _CIFTI_EXTENSIONS constants - Merge xfm rules for anat/func/dwi into one multi-datatype rule - Merge fmap fieldmap + mask into one rule - Rename _PET_EXTRA_ENTITIES -> _PET_ENTITIES, _PERF_EXTRA_ENTITIES -> _PERF_ENTITIES - Reorganize rules by category (transforms, surfaces, CIFTI, then per-datatype) 28 rules -> 25 rules, -95 lines net.
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Summary
nipreps.jsonconfig with schema-driven config generation from pybidsrule_groups=["deriv"]) with NiPreps-specifichashentity injectionextra_rulesdicts that declare only datatypes, suffixes, extensions, and entity deviations—entity ordering and standard entities are inherited from the schemadescription→desc,hemisphere→hemi, etc.)Depends on bids-standard/pybids#1215
Test plan