update models to correctly handle ElementIdentifiers

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -430,6 +430,10 @@ class MapArrayLikeAttributes(DatasetMap):
     The most general case - treat everything that isn't handled by one of the special cases
     as an array!
 
+    We specifically include classes that have no attributes but also don't have a name,
+    as they still require their own class (unlike :class:`.MapArrayLike` above, where we
+    just generate an anonymous slot.)
+
     Examples:
 
         .. adapter:: DatasetAdapter
@@ -525,7 +529,7 @@ class MapArrayLikeAttributes(DatasetMap):
         return (
             all([cls.dims, cls.shape])
             and cls.neurodata_type_inc != "VectorData"
-            and has_attrs(cls)
+            and (has_attrs(cls) or not cls.name)
             and not is_compound(cls)
             and (dtype == "AnyType" or dtype in flat_to_linkml)
         )

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -56,6 +56,8 @@ class NamespacesAdapter(Adapter):
                 needed_adapter = NamespacesAdapter.from_yaml(needed_source_ns)
                 ns_adapter.imported.append(needed_adapter)
 
+        ns_adapter.populate_imports()
+
         return ns_adapter
 
     def build(
@@ -176,7 +178,6 @@ class NamespacesAdapter(Adapter):
         else:
             raise KeyError(f"No schema found that define {name}")
 
-    @model_validator(mode="after")
     def populate_imports(self) -> "NamespacesAdapter":
         """
         Populate the imports that are needed for each schema file

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -131,6 +131,8 @@ def load_namespace_adapter(
     else:
         adapter = NamespacesAdapter(namespaces=namespaces, schemas=sch)
 
+    adapter.populate_imports()
+
     return adapter
 
 

nwb_linkml/src/nwb_linkml/providers/linkml.py

@@ -127,6 +127,7 @@ class LinkMLProvider(Provider):
             for schema_needs in adapter.needed_imports.values():
                 for needed in schema_needs:
                     adapter.imported.append(ns_adapters[needed])
+            adapter.populate_imports()
 
         # then do the build
         res = {}

nwb_linkml/src/nwb_linkml/providers/pydantic.py

@@ -278,7 +278,7 @@ class PydanticProvider(Provider):
             nwb_models.models.pydantic.{namespace}.{version}
         """
         name_pieces = [
-            "nwb_linkml",
+            "nwb_models",
             "models",
             "pydantic",
             module_case(namespace),

nwb_linkml/src/nwb_linkml/providers/schema.py

@@ -131,7 +131,7 @@ class SchemaProvider(Provider):
         results = {}
         for ns, ns_result in linkml_res.items():
             results[ns] = pydantic_provider.build(
-                ns_result["namespace"], versions=self.versions, **pydantic_kwargs
+                ns_result.namespace, versions=self.versions, **pydantic_kwargs
             )
         return results
 

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_1_0/hdmf_common_table.py

@@ -866,6 +866,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_1_2/hdmf_common_table.py

@@ -866,6 +866,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_1_3/hdmf_common_table.py

@@ -877,6 +877,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_2_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_2_1/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_3_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_4_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_5_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_5_1/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_6_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_7_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/models/pydantic/hdmf_common/v1_8_0/hdmf_common_table.py

@@ -858,6 +858,10 @@ class ElementIdentifiers(Data):
     name: str = Field(
         "element_id", json_schema_extra={"linkml_meta": {"ifabsent": "string(element_id)"}}
     )
+    value: Optional[NDArray[Shape["* num_elements"], int]] = Field(
+        None,
+        json_schema_extra={"linkml_meta": {"array": {"dimensions": [{"alias": "num_elements"}]}}},
+    )
 
 
 class DynamicTableRegion(DynamicTableRegionMixin, VectorData):

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_1_0/hdmf-common.table.yaml

@@ -86,6 +86,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_1_2/hdmf-common.table.yaml

@@ -86,6 +86,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_1_3/hdmf-common.table.yaml

@@ -114,6 +114,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_2_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_2_1/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_3_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_4_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_5_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_5_1/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_6_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_7_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

nwb_models/src/nwb_models/schema/linkml/hdmf_common/v1_8_0/hdmf-common.table.yaml

@@ -87,6 +87,12 @@ classes:
         ifabsent: string(element_id)
         range: string
         required: true
+      value:
+        name: value
+        array:
+          dimensions:
+          - alias: num_elements
+        range: int
     tree_root: true
   DynamicTableRegion:
     name: DynamicTableRegion

scripts/generate_core.py

@@ -171,17 +171,11 @@ def generate_versions(
             shutil.rmtree(tmp_dir / "linkml")
             shutil.rmtree(tmp_dir / "pydantic")
 
-            # import the most recent version of the schemaz we built
-            latest_version = sorted((pydantic_path / "core").glob("v*"), key=os.path.getmtime)[-1]
-
             # make inits to use the schema! we don't usually do this in the
             # provider class because we directly import the files there.
             with open(pydantic_path / "__init__.py", "w") as initfile:
                 initfile.write(" ")
 
-            with open(pydantic_path / "__init__.py", "w") as initfile:
-                initfile.write(f"from .pydantic.core.{latest_version.name}.namespace import *")
-
             subprocess.run(["black", "."])
 
     finally: