Fix pr 345

.github/workflows/main.yaml

@@ -12,10 +12,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.12"]
+        python-version: ["3.9", "3.10", "3.12", "3.13"]
         exclude:
         - os: windows-latest
-          python-version: "3.8"
+          python-version: "3.10"
+        - os: windows-latest
+          python-version: "3.12"
 
     runs-on: ${{ matrix.os }}
 
@@ -34,7 +36,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'poetry'

.github/workflows/pypi-publish.yaml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python
       uses: actions/[email protected]
       with:
-        python-version: 3.8
+        python-version: 3.12
 
     - name: Install Poetry
       run: pipx install poetry

.github/workflows/test-upstream.yaml

@@ -20,14 +20,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, windows-latest ]
-        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12" ]
+        python-version: [ "3.9", "3.10", "3.11", "3.12", "3.13" ]
         exclude:
-          - os: windows-latest
-            python-version: "3.9"
           - os: windows-latest
             python-version: "3.10"
           - os: windows-latest
             python-version: "3.11"
+          - os: windows-latest
+            python-version: "3.12"
     runs-on: ${{ matrix.os }}
     env:
       POETRY_VIRTUALENVS_IN_PROJECT: true

linkml_runtime/__init__.py

@@ -3,6 +3,10 @@
 from linkml_runtime.utils.schemaview import SchemaView
 from rdflib import RDF, RDFS, SKOS, XSD, OWL
 
+__all__ = [
+    "SchemaView",
+]
+
 # use importlib.metadata to read the version provided
 # by the package during installation. Do not hardcode
 # the version in the code

linkml_runtime/dumpers/delimited_file_dumper.py

@@ -1,17 +1,17 @@
 import io
-import yaml
 import json
 from abc import ABC, abstractmethod
 from typing import Union
 from pydantic import BaseModel
+from json_flattener import GlobalConfig
 
 from linkml_runtime.dumpers.dumper_root import Dumper
 from linkml_runtime.dumpers.json_dumper import JSONDumper
 from linkml_runtime.utils.yamlutils import YAMLRoot
 from linkml_runtime.linkml_model.meta import SlotDefinitionName, SchemaDefinition
 from linkml_runtime.utils.schemaview import SchemaView
 
-from linkml_runtime.utils.csvutils import GlobalConfig, get_configmap
+from linkml_runtime.utils.csvutils import get_configmap
 from json_flattener import flatten_to_csv
 
 

linkml_runtime/dumpers/json_dumper.py

@@ -1,6 +1,6 @@
 import json
 from decimal import Decimal
-from typing import Dict, Union
+from typing import Union
 from pydantic import BaseModel
 
 from deprecated.classic import deprecated
@@ -30,7 +30,7 @@
             * A list containing elements of any type named above
         """
         if isinstance(element, BaseModel):
-            element = element.dict()
+            element = element.model_dump()
         super().dump(element, to_file, contexts=contexts, **kwargs)
 
     def dumps(self, element: Union[BaseModel, YAMLRoot], contexts: CONTEXTS_PARAM_TYPE = None, inject_type=True) -> str:
@@ -50,7 +50,7 @@
 
         def default(o):
             if isinstance(o, BaseModel):
-                return remove_empty_items(o.dict(), hide_protected_keys=True)
+                return remove_empty_items(o.model_dump(), hide_protected_keys=True)
             if isinstance(o, YAMLRoot):
                 return remove_empty_items(o, hide_protected_keys=True)
             elif isinstance(o, Decimal):
@@ -59,15 +59,15 @@
             else:
                 return json.JSONDecoder().decode(o)
         if isinstance(element, BaseModel):
-            element = element.dict()
+            element = element.model_dump()
         return json.dumps(as_json_object(element, contexts, inject_type=inject_type),
                           default=default,
                           ensure_ascii=False,
                           indent='  ')
 
     @staticmethod
     @deprecated("Use `utils/formatutils/remove_empty_items` instead")
-    def remove_empty_items(obj: Dict) -> Dict:
+    def remove_empty_items(obj: dict) -> dict:
         """
         Remove empty items from obj
         :param obj:

linkml_runtime/dumpers/rdf_dumper.py

@@ -79,7 +79,7 @@
         :param fmt: RDF format
         """
         if isinstance(element, BaseModel):
-            element = element.dict()
+            element = element.model_dump()
         super().dump(element, to_file, contexts=contexts, fmt=fmt)
 
     def dumps(self, element: Union[BaseModel, YAMLRoot], contexts: CONTEXTS_PARAM_TYPE = None, fmt: Optional[str] = 'turtle') -> str:
@@ -91,6 +91,6 @@
         :return: rdflib Graph containing element
         """
         if isinstance(element, BaseModel):
-            element = element.dict()
+            element = element.model_dump()
         return self.as_rdf_graph(remove_empty_items(element, hide_protected_keys=True), contexts).\
             serialize(format=fmt)

linkml_runtime/dumpers/rdflib_dumper.py

@@ -1,7 +1,6 @@
 import logging
 import urllib
-from abc import abstractmethod
-from typing import Optional, Any, Dict, Union
+from typing import Optional, Any, Union
 from pydantic import BaseModel
 
 from curies import Converter
@@ -31,7 +30,7 @@ def as_rdf_graph(
         self,
         element: Union[BaseModel, YAMLRoot],
         schemaview: SchemaView,
-        prefix_map: Union[Dict[str, str], Converter, None] = None,
+        prefix_map: Union[dict[str, str], Converter, None] = None,
     ) -> Graph:
         """
         Dumps from element to an rdflib Graph,
@@ -154,7 +153,7 @@ def dump(
         to_file: str,
         schemaview: SchemaView = None,
         fmt: str = 'turtle',
-        prefix_map: Union[Dict[str, str], Converter, None] = None,
+        prefix_map: Union[dict[str, str], Converter, None] = None,
         **args,
     ) -> None:
         """
@@ -174,7 +173,7 @@ def dumps(
         element: Union[BaseModel, YAMLRoot],
         schemaview: SchemaView = None,
         fmt: Optional[str] = 'turtle',
-        prefix_map: Union[Dict[str, str], Converter, None] = None,
+        prefix_map: Union[dict[str, str], Converter, None] = None,
     ) -> str:
         """
         Convert element into an RDF graph guided by the schema

linkml_runtime/index/object_index.py

@@ -10,7 +10,8 @@
 """
 import logging
 import inspect
-from typing import Mapping, Any, Optional, Tuple, List, Iterator, Union
+from typing import Any, Union
+from collections.abc import Mapping, Iterator
 
 from linkml_runtime import SchemaView
 from linkml_runtime.utils import eval_utils
@@ -54,8 +55,8 @@ def __init__(self, obj: YAMLRoot, schemaview: SchemaView):
         self._schemaview = schemaview
         self._class_map = schemaview.class_name_mappings()
         self._source_object_cache: Mapping[str, Any] = {}
-        self._proxy_object_cache: Mapping[str, "ProxyObject"] = {}
-        self._child_to_parent: Mapping[str, List[Tuple[str, str]]] = {}
+        self._proxy_object_cache: Mapping[str, ProxyObject] = {}
+        self._child_to_parent: Mapping[str, list[tuple[str, str]]] = {}
         self._index(obj)
 
     def _index(self, obj: Any, parent_key=None, parent=None):
@@ -112,7 +113,7 @@ def bless(self, obj: Any) -> "ProxyObject":
         else:
             return ProxyObject(obj, _db=self)
 
-    def _key(self, obj: Any) -> Tuple[Union[str, YAMLRoot], str]:
+    def _key(self, obj: Any) -> tuple[Union[str, YAMLRoot], str]:
         """
         Returns primary key value for this object.
 
@@ -265,6 +266,6 @@ def _map(self, obj: Any, in_range: str) -> Any:
                 return cls(obj)
         return obj
 
-    def _attributes(self) -> List[str]:
+    def _attributes(self) -> list[str]:
         return list(vars(self._shadowed).keys())
 

linkml_runtime/linkml_model/__init__.py

@@ -8,3 +8,49 @@
     Definition, EnumDefinition, SlotDefinition, ClassDefinition, Prefix, LocalName, Example, AltDescription, \
     PermissibleValue, PvFormulaOptions
 
+__all__ = [
+    "String",
+    "Integer",
+    "Boolean",
+    "Float",
+    "Double",
+    "Decimal",
+    "Time",
+    "Date",
+    "Datetime",
+    "Uriorcurie",
+    "Uri",
+    "Ncname",
+    "Objectidentifier",
+    "Nodeidentifier",
+    "Extension",
+    "Extensible",
+    "Annotation",
+    "Annotatable",
+    "ElementName",
+    "SchemaDefinitionName",
+    "TypeDefinitionName",
+    "SubsetDefinitionName",
+    "DefinitionName",
+    "EnumDefinitionName",
+    "SlotDefinitionName",
+    "ClassDefinitionName",
+    "PrefixPrefixPrefix",
+    "LocalNameLocalNameSource",
+    "AltDescriptionSource",
+    "PermissibleValueText",
+    "Element",
+    "SchemaDefinition",
+    "TypeDefinition",
+    "SubsetDefinition",
+    "Definition",
+    "EnumDefinition",
+    "SlotDefinition",
+    "ClassDefinition",
+    "Prefix",
+    "LocalName",
+    "Example",
+    "AltDescription",
+    "PermissibleValue",
+    "PvFormulaOptions",
+]

linkml_runtime/linkml_model/annotations.py

@@ -6,30 +6,19 @@
 # description: Annotations mixin
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
-import dataclasses
-import re
-from jsonasobj2 import JsonObj, as_dict
-from typing import Optional, List, Union, Dict, ClassVar, Any
+from typing import Optional, Union, ClassVar, Any
 from dataclasses import dataclass
 
 from linkml_runtime.utils.slot import Slot
-from linkml_runtime.utils.metamodelcore import empty_list, empty_dict, bnode
-from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str, extended_float, extended_int
-from linkml_runtime.utils.dataclass_extensions_376 import dataclasses_init_fn_with_kwargs
-from linkml_runtime.utils.formatutils import camelcase, underscore, sfx
-from linkml_runtime.utils.enumerations import EnumDefinitionImpl
-from rdflib import Namespace, URIRef
+from linkml_runtime.utils.metamodelcore import empty_dict
+from linkml_runtime.utils.yamlutils import YAMLRoot
+from rdflib import URIRef
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from .extensions import AnyValue, Extension, ExtensionTag
-from .types import Uriorcurie
-from linkml_runtime.utils.metamodelcore import URIorCURIE
 
 metamodel_version = "1.7.0"
 version = "2.0.0"
 
-# Overwrite dataclasses _init_fn to add **kwargs in __init__
-dataclasses._init_fn = dataclasses_init_fn_with_kwargs
-
 # Namespaces
 LINKML = CurieNamespace('linkml', 'https://w3id.org/linkml/')
 DEFAULT_ = LINKML
@@ -47,16 +36,16 @@ class Annotatable(YAMLRoot):
     """
     mixin for classes that support annotations
     """
-    _inherited_slots: ClassVar[List[str]] = []
+    _inherited_slots: ClassVar[list[str]] = []
 
     class_class_uri: ClassVar[URIRef] = LINKML["Annotatable"]
     class_class_curie: ClassVar[str] = "linkml:Annotatable"
     class_name: ClassVar[str] = "annotatable"
     class_model_uri: ClassVar[URIRef] = LINKML.Annotatable
 
-    annotations: Optional[Union[Dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], List[Union[dict, "Annotation"]]]] = empty_dict()
+    annotations: Optional[Union[dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], list[Union[dict, "Annotation"]]]] = empty_dict()
 
-    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+    def __post_init__(self, *_: list[str], **kwargs: dict[str, Any]):
         self._normalize_inlined_as_dict(slot_name="annotations", slot_type=Annotation, key_name="tag", keyed=True)
 
         super().__post_init__(**kwargs)
@@ -67,7 +56,7 @@ class Annotation(Extension):
     """
     a tag/value pair with the semantics of OWL Annotation
     """
-    _inherited_slots: ClassVar[List[str]] = []
+    _inherited_slots: ClassVar[list[str]] = []
 
     class_class_uri: ClassVar[URIRef] = LINKML["Annotation"]
     class_class_curie: ClassVar[str] = "linkml:Annotation"
@@ -76,9 +65,9 @@ class Annotation(Extension):
 
     tag: Union[str, AnnotationTag] = None
     value: Union[dict, AnyValue] = None
-    annotations: Optional[Union[Dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], List[Union[dict, "Annotation"]]]] = empty_dict()
+    annotations: Optional[Union[dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], list[Union[dict, "Annotation"]]]] = empty_dict()
 
-    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+    def __post_init__(self, *_: list[str], **kwargs: dict[str, Any]):
         if self._is_empty(self.tag):
             self.MissingRequiredField("tag")
         if not isinstance(self.tag, AnnotationTag):
@@ -97,4 +86,4 @@ class slots:
     pass
 
 slots.annotations = Slot(uri=LINKML.annotations, name="annotations", curie=LINKML.curie('annotations'),
-                   model_uri=LINKML.annotations, domain=None, range=Optional[Union[Dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], List[Union[dict, "Annotation"]]]])
+                   model_uri=LINKML.annotations, domain=None, range=Optional[Union[dict[Union[str, AnnotationTag], Union[dict, "Annotation"]], list[Union[dict, "Annotation"]]]])