Move eliminate_empty function into utils (#429)

src/ontogpt/io/json_wrapper.py

@@ -5,25 +5,10 @@
 import json
 from typing import Any, Optional, TextIO
 
-import pydantic
-
-logger = logging.getLogger(__name__)
+from ontogpt.io.utils import eliminate_empty
 
 
-def eliminate_empty(obj: Any, preserve=False) -> Any:
-    """Eliminate empty lists and dicts from an object."""
-    if isinstance(obj, list):
-        return [eliminate_empty(x, preserve) for x in obj if x or preserve]
-    elif isinstance(obj, dict):
-        return {k: eliminate_empty(v, preserve) for k, v in obj.items() if v or preserve}
-    elif isinstance(obj, pydantic.BaseModel):
-        return eliminate_empty(obj.model_dump(), preserve)
-    elif isinstance(obj, tuple):
-        return [eliminate_empty(x, preserve) for x in obj]
-    elif isinstance(obj, str):
-        return str(obj)
-    else:
-        return obj
+logger = logging.getLogger(__name__)
 
 
 def dump_minimal_json(obj: Any, minimize=True, file: Optional[TextIO] = None) -> str:

src/ontogpt/io/utils.py

@@ -0,0 +1,21 @@
+"""IO Utilities."""
+
+from typing import Any
+
+import pydantic
+
+
+def eliminate_empty(obj: Any, preserve=False) -> Any:
+    """Eliminate empty lists and dicts from an object."""
+    if isinstance(obj, list):
+        return [eliminate_empty(x, preserve) for x in obj if x or preserve]
+    elif isinstance(obj, dict):
+        return {k: eliminate_empty(v, preserve) for k, v in obj.items() if v or preserve}
+    elif isinstance(obj, pydantic.BaseModel):
+        return eliminate_empty(obj.model_dump(), preserve)
+    elif isinstance(obj, tuple):
+        return [eliminate_empty(x, preserve) for x in obj]
+    elif isinstance(obj, str):
+        return str(obj)
+    else:
+        return obj

src/ontogpt/io/yaml_wrapper.py

@@ -4,26 +4,11 @@
 import logging
 from typing import Any, Optional, TextIO
 
-import pydantic
 from ruamel.yaml import YAML, RoundTripRepresenter
 
-logger = logging.getLogger(__name__)
-
+from ontogpt.io.utils import eliminate_empty
 
-def eliminate_empty(obj: Any, preserve=False) -> Any:
-    """Eliminate empty lists and dicts from an object."""
-    if isinstance(obj, list):
-        return [eliminate_empty(x, preserve) for x in obj if x or preserve]
-    elif isinstance(obj, dict):
-        return {k: eliminate_empty(v, preserve) for k, v in obj.items() if v or preserve}
-    elif isinstance(obj, pydantic.BaseModel):
-        return eliminate_empty(obj.model_dump(), preserve)
-    elif isinstance(obj, tuple):
-        return [eliminate_empty(x, preserve) for x in obj]
-    elif isinstance(obj, str):
-        return str(obj)
-    else:
-        return obj
+logger = logging.getLogger(__name__)
 
 
 def repr_str(dumper: RoundTripRepresenter, data: str):