remove unused code, nocover some debug arms

nwb_linkml/src/nwb_linkml/adapters/attribute.py

@@ -174,7 +174,7 @@ class AttributeAdapter(Adapter):
         """
         map = self.match()
         res = map.apply(self.cls)
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             res = self._amend_debug(res, map)
         return res
 
@@ -203,7 +203,7 @@ class AttributeAdapter(Adapter):
 
     def _amend_debug(
         self, res: BuildResult, map: Optional[Type[AttributeMap]] = None
-    ) -> BuildResult:
+    ) -> BuildResult:  # pragma: no cover - only used in development
         map_name = "None" if map is None else map.__name__
         for cls in res.classes:
             cls.annotations["attribute_map"] = {"tag": "attribute_map", "value": map_name}

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -92,7 +92,7 @@ class ClassAdapter(Adapter):
         # Get vanilla top-level attributes
         kwargs["attributes"].extend(self.build_attrs(self.cls))
 
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             kwargs["annotations"] = {}
             kwargs["annotations"]["group_adapter"] = {
                 "tag": "group_adapter",
@@ -254,6 +254,6 @@ class ClassAdapter(Adapter):
             inlined=True,
             **QUANTITY_MAP[self.cls.quantity],
         )
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             slot.annotations["group_adapter"] = {"tag": "group_adapter", "value": "self_slot"}
         return slot

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -744,7 +744,7 @@ class DatasetAdapter(ClassAdapter):
         if map is not None:
             res = map.apply(self.cls, res, self._get_full_name())
 
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             res = self._amend_debug(res, map)
         return res
 
@@ -771,7 +771,9 @@ class DatasetAdapter(ClassAdapter):
         else:
             return matches[0]
 
-    def _amend_debug(self, res: BuildResult, map: Optional[Type[DatasetMap]] = None) -> BuildResult:
+    def _amend_debug(
+        self, res: BuildResult, map: Optional[Type[DatasetMap]] = None
+    ) -> BuildResult:  # pragma: no cover - only used in development
         map_name = "None" if map is None else map.__name__
         for cls in res.classes:
             cls.annotations["dataset_map"] = {"tag": "dataset_map", "value": map_name}

nwb_linkml/src/nwb_linkml/adapters/group.py

@@ -70,7 +70,7 @@ class GroupAdapter(ClassAdapter):
 
         annotations = [{"tag": "source_type", "value": "link"}]
 
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             annotations.append({"tag": "group_adapter", "value": "link"})
 
         slots = [
@@ -117,7 +117,7 @@ class GroupAdapter(ClassAdapter):
             inlined_as_list=False,
         )
 
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             slot.annotations["group_adapter"] = {"tag": "group_adapter", "value": "container_group"}
 
         if self.parent is not None:
@@ -162,7 +162,7 @@ class GroupAdapter(ClassAdapter):
             **QUANTITY_MAP[cls.quantity],
         )
 
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             slot.annotations["group_adapter"] = {"tag": "group_adapter", "value": "container_slot"}
 
         return BuildResult(slots=[slot])
@@ -214,7 +214,7 @@ class GroupAdapter(ClassAdapter):
             inlined_as_list=True,
             **QUANTITY_MAP[self.cls.quantity],
         )
-        if self.debug:
+        if self.debug:  # pragma: no cover - only used in development
             slot.annotations["group_adapter"] = {"tag": "group_adapter", "value": "container_slot"}
         return slot
 

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -5,9 +5,7 @@ customized to support NWB models.
 See class and module docstrings for details :)
 """
 
-import pdb
 import re
-import sys
 from dataclasses import dataclass, field
 from pathlib import Path
 from types import ModuleType
@@ -24,7 +22,6 @@ from linkml_runtime.linkml_model.meta import (
     SlotDefinition,
     SlotDefinitionName,
 )
-from linkml_runtime.utils.compile_python import file_text
 from linkml_runtime.utils.formatutils import remove_empty_items
 from linkml_runtime.utils.schemaview import SchemaView
 
@@ -214,15 +211,17 @@ class AfterGenerateSlot:
                 # merge injects/imports from the numpydantic array without using the merge method
                 if slot.injected_classes is None:
                     slot.injected_classes = NumpydanticArray.INJECTS.copy()
-                else:
+                else:  # pragma: no cover - for completeness, shouldn't happen
                     slot.injected_classes.extend(NumpydanticArray.INJECTS.copy())
-                if isinstance(slot.imports, list):
+                if isinstance(
+                    slot.imports, list
+                ):  # pragma: no cover - for completeness, shouldn't happen
                     slot.imports = (
                         Imports(imports=slot.imports) + NumpydanticArray.IMPORTS.model_copy()
                     )
                 elif isinstance(slot.imports, Imports):
                     slot.imports += NumpydanticArray.IMPORTS.model_copy()
-                else:
+                else:  # pragma: no cover - for completeness, shouldn't happen
                     slot.imports = NumpydanticArray.IMPORTS.model_copy()
 
         return slot
@@ -239,13 +238,15 @@ class AfterGenerateSlot:
             named_injects = [ModelTypeString, _get_name, NamedString]
             if slot.injected_classes is None:
                 slot.injected_classes = named_injects
-            else:
+            else:  # pragma: no cover - for completeness, shouldn't happen
                 slot.injected_classes.extend([ModelTypeString, _get_name, NamedString])
-            if isinstance(slot.imports, list):
+            if isinstance(
+                slot.imports, list
+            ):  # pragma: no cover - for completeness, shouldn't happen
                 slot.imports = Imports(imports=slot.imports) + NamedImports
             elif isinstance(slot.imports, Imports):
                 slot.imports += NamedImports
-            else:
+            else:  # pragma: no cover - for completeness, shouldn't happen
                 slot.imports = NamedImports
         return slot
 
@@ -268,16 +269,20 @@ class AfterGenerateClass:
         if cls.cls.name == "DynamicTable":
             cls.cls.bases = ["DynamicTableMixin", "ConfiguredBaseModel"]
 
-            if cls.injected_classes is None:
+            if (
+                cls.injected_classes is None
+            ):  # pragma: no cover - for completeness, shouldn't happen
                 cls.injected_classes = DYNAMIC_TABLE_INJECTS.copy()
             else:
                 cls.injected_classes.extend(DYNAMIC_TABLE_INJECTS.copy())
 
             if isinstance(cls.imports, Imports):
                 cls.imports += DYNAMIC_TABLE_IMPORTS
-            elif isinstance(cls.imports, list):
+            elif isinstance(
+                cls.imports, list
+            ):  # pragma: no cover - for completeness, shouldn't happen
                 cls.imports = Imports(imports=cls.imports) + DYNAMIC_TABLE_IMPORTS
-            else:
+            else:  # pragma: no cover - for completeness, shouldn't happen
                 cls.imports = DYNAMIC_TABLE_IMPORTS.model_copy()
         elif cls.cls.name == "VectorData":
             cls.cls.bases = ["VectorDataMixin", "ConfiguredBaseModel"]
@@ -298,16 +303,20 @@ class AfterGenerateClass:
         elif cls.cls.name == "TimeSeriesReferenceVectorData":
             # in core.nwb.base, so need to inject and import again
             cls.cls.bases = ["TimeSeriesReferenceVectorDataMixin", "VectorData"]
-            if cls.injected_classes is None:
+            if (
+                cls.injected_classes is None
+            ):  # pragma: no cover - for completeness, shouldn't happen
                 cls.injected_classes = TSRVD_INJECTS.copy()
             else:
                 cls.injected_classes.extend(TSRVD_INJECTS.copy())
 
             if isinstance(cls.imports, Imports):
                 cls.imports += TSRVD_IMPORTS
-            elif isinstance(cls.imports, list):
+            elif isinstance(
+                cls.imports, list
+            ):  # pragma: no cover - for completeness, shouldn't happen
                 cls.imports = Imports(imports=cls.imports) + TSRVD_IMPORTS
-            else:
+            else:  # pragma: no cover - for completeness, shouldn't happen
                 cls.imports = TSRVD_IMPORTS.model_copy()
 
         return cls
@@ -362,28 +371,6 @@ class AfterGenerateClass:
         return cls
 
 
-def compile_python(
-    text_or_fn: str, package_path: Path = None, module_name: str = "test"
-) -> ModuleType:
-    """
-    Compile the text or file and return the resulting module
-    @param text_or_fn: Python text or file name that references python file
-    @param package_path: Root package path.  If omitted and we've got a python file,
-    the package is the containing
-    directory
-    @return: Compiled module
-    """
-    python_txt = file_text(text_or_fn)
-    if package_path is None and python_txt != text_or_fn:
-        package_path = Path(text_or_fn)
-    spec = compile(python_txt, "<string>", "exec")
-    module = ModuleType(module_name)
-
-    exec(spec, module.__dict__)
-    sys.modules[module_name] = module
-    return module
-
-
 def wrap_preserving_optional(annotation: str, wrap: str) -> str:
     """
     Add a wrapping type to a type annotation string,
@@ -401,7 +388,5 @@ def wrap_preserving_optional(annotation: str, wrap: str) -> str:
         annotation = is_optional.groups()[0]
         annotation = f"Optional[{wrap}[{annotation}]]"
     else:
-        if "Optional" in annotation:
-            pdb.set_trace()
         annotation = f"{wrap}[{annotation}]"
     return annotation

nwb_linkml/src/nwb_linkml/types/hdf5.py

@@ -1,20 +0,0 @@
-"""
-Types used with hdf5 io
-"""
-
-from typing import Any
-
-from pydantic import GetCoreSchemaHandler
-from pydantic_core import CoreSchema, core_schema
-
-
-class HDF5_Path(str):
-    """
-    Trivial subclass of string to indicate that it is a reference to a location within an HDF5 file
-    """
-
-    @classmethod
-    def __get_pydantic_core_schema__(
-        cls, source_type: Any, handler: GetCoreSchemaHandler
-    ) -> CoreSchema:
-        return core_schema.no_info_after_validator_function(cls, handler(str))

nwb_linkml/tests/test_generators/test_generator_pydantic.py

@@ -5,6 +5,8 @@ Note that since this is largely a subclass, we don't test all of the functionali
 because it's tested in the base linkml package.
 """
 
+# ruff: noqa: F821 - until the tests here settle down
+
 import re
 import sys
 import typing
@@ -16,7 +18,7 @@ import pytest
 from numpydantic.ndarray import NDArrayMeta
 from pydantic import BaseModel
 
-from nwb_linkml.generators.pydantic import NWBPydanticGenerator, compile_python
+from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 
 from ..fixtures import (
     TestSchemas,