kevinschaper · Sep 4, 2025 · Sep 4, 2025 · Sep 4, 2025 · Sep 4, 2025 · matentzn
diff --git a/Makefile b/Makefile
@@ -126,7 +126,6 @@ gen-examples:
 gen-project: $(PYMODEL)
 	$(RUN) gen-project ${CONFIG_YAML} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 
-
 # non-empty arg triggers owl (workaround https://github.com/linkml/linkml/issues/1453)
 ifneq ($(strip ${GEN_OWL_ARGS}),)
 	mkdir -p ${DEST}/owl || true

diff --git a/poetry.lock b/poetry.lock
diff --git a/project.Makefile b/project.Makefile
@@ -1,15 +1,21 @@
 ## Add your own custom Makefile targets here
 
+.PHONY: generate_biolink_imports
 gen-biolink-imports:  
 	$(RUN) python src/matrix_schema/utils/generate_biolink_imports.py
 
+.PHONY: generate_valid_edge_type_table
 gen-valid-edge-type-table:
 	$(RUN) python src/matrix_schema/utils/generate_valid_edge_type_table.py
 
+.PHONY: gen-pydantic
 gen-pydantic:
 	$(RUN) gen-pydantic --meta None src/matrix_schema/schema/matrix_schema.yaml > src/matrix_schema/datamodel/matrix_schema_pydantic.py
 
-gen-pandera: gen-pydantic
-	@echo "The pandera schema currently needs to be updated manually in src/matrix_schema/datamodel/pandera.py"
+# generate pandera schemas
+.PHONY: gen-pandera
+gen-pandera:
+	python -m matrix_schema.generators.panderagen $(SOURCE_SCHEMA_PATH) -c MatrixNode -c MatrixEdge -c UnionedNode -c UnionedEdge --output $(PYMODEL)/pandera.py
+
 
 gen-project: gen-pydantic gen-pandera gen-biolink-imports gen-valid-edge-type-table
diff --git a/project/excel/matrix_schema.xlsx b/project/excel/matrix_schema.xlsx
diff --git a/project/jsonld/matrix_schema.context.jsonld b/project/jsonld/matrix_schema.context.jsonld
@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2025-08-26T11:42:19",
+      "generation_date": "2025-09-04T16:20:53",
       "source": "matrix_schema.yaml"
    },
    "@context": {

diff --git a/project/jsonld/matrix_schema.jsonld b/project/jsonld/matrix_schema.jsonld
@@ -5609,9 +5609,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "matrix_schema.yaml",
-  "source_file_date": "2025-06-04T10:34:59",
+  "source_file_date": "2025-09-03T12:54:24",
   "source_file_size": 528,
-  "generation_date": "2025-08-26T11:42:19",
+  "generation_date": "2025-09-04T16:20:53",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/matrix_schema.context.jsonld",