pre-commit run on 1.0.0-snapshot.2025-02 gks-core branch

examples/mappable-concept-gene.yaml

@@ -2,20 +2,20 @@ conceptType: Gene
 name: BRCA2
 primaryCoding:
   code: HGNC:1101
-  system: https://www.genenames.org/    
+  system: https://www.genenames.org/
   iris:
   - https://identifiers.org/hgnc:1101
-  - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/1101   
+  - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/1101
 mappings:
-- coding: 
+- coding:
     code: ENSG00000139618
     system: https://www.ensembl.org/
     iris:
       - https://identifiers.org/ensembl:ENSG00000139618
       - https://www.ensembl.org/id/ENSG00000139618
 
   relation: closeMatch
-- coding: 
+- coding:
     code: "675"
     system: https://www.ncbi.nlm.nih.gov/gene/
     iris:
@@ -26,4 +26,4 @@ extensions:
 - name: "AlsoKnownAs"
   value: "FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2"
 - name: "description"
-  value: "BRCA2 DNA repair associated"
+  value: "BRCA2 DNA repair associated"

schema/Makefile

@@ -2,4 +2,4 @@ all:
 	(cd gks-core; make all)
 
 clean:
-	(cd gks-core; make clean)
+	(cd gks-core; make clean)

schema/gks-core/gks-core-source.yaml

@@ -209,7 +209,7 @@ $defs:
       - code
 
   # primitive data types section for convenience and consistency -- code, iriReference, date, datetime
-  code:    
+  code:
     type: string
     maturity: trial use
     description: >-
@@ -242,4 +242,4 @@ $defs:
     description: >-
       A string is valid against this format if it represents a date-time in the following format:
       YYYY:MM::DDThh:mm:ss.sTZD.
-    format: date-time
+    format: date-time

schema/gks-core/prune.mk

@@ -8,4 +8,4 @@ FILTER_DEFS = $(FILTER_CLASSES:%=def/%.rst)
 .DEFAULT: prune
 
 prune: $(filter-out ${FILTER_JSONS} ${FILTER_DEFS},$(wildcard def/* json/*))
-	$(if $^,rm $^)
+	$(if $^,rm $^)

tests/config.py

@@ -6,7 +6,7 @@
 import re
 
 root_path = Path(__file__).parent.parent
-schema_path = root_path / "schema" 
+schema_path = root_path / "schema"
 test_path = root_path / "tests"
 examples_path = root_path / "examples"
 gks_core_source = schema_path / "gks-core" / "gks-core-source.yaml"
@@ -40,4 +40,4 @@ def retrieve_rel_ref(ga4gh_ref: str):
     ])
 
 for cls in js_def:
-    validator[cls] = Draft202012Validator(js_def[cls], registry=js_registry)
+    validator[cls] = Draft202012Validator(js_def[cls], registry=js_registry)