read schema from resources

src/cell_annotation_schema/file_utils.py

@@ -1,13 +1,17 @@
 import os
 import json
+import yaml
 import warnings
 
 from typing import Union
 from urllib.request import urlopen
 from pathlib import Path
+from importlib import resources
 from linkml_runtime.linkml_model import SchemaDefinition
 from linkml_runtime.loaders import yaml_loader
 
+from cell_annotation_schema import schemas
+
 
 def is_web_url(path):
     """
@@ -49,8 +53,15 @@ def read_schema(schema: Union[str, dict]) -> SchemaDefinition:
     """
     try:
         if isinstance(schema, str) and str(schema).lower() in get_cas_schema_names().keys():
-            schema_dir = os.path.join(os.path.dirname(__file__), "../../build")
-            schema = os.path.join(schema_dir, get_cas_schema_names()[str(schema).lower()])
+            schema_name = get_cas_schema_names()[str(schema).lower()]
+            schema_file = resources.files(schemas) / schema_name
+            if os.path.exists(schema_file):
+                # read from resources (schemas) package
+                schema = yaml.safe_load(Path(schema_file).read_text())
+            else:
+                # read from build folder
+                schema_dir = os.path.join(os.path.dirname(__file__), "../../build")
+                schema = os.path.join(schema_dir, schema_name)
         if isinstance(schema, Path):
             schema = str(schema)
         if isinstance(schema, dict):

src/cell_annotation_schema/schemas/README.md

@@ -0,0 +1,4 @@
+Schema files will be copied from the `build` folder and placed into this folder during pypi packaging.
+
+Please see `pypi-publish.yaml` for details.
+