apply ruff safe fixes

Author: sneakers-the-rat

linkml_runtime/__init__.py

@@ -1,7 +1,9 @@
 from pathlib import Path
+
+from rdflib import OWL, RDF, RDFS, SKOS, XSD
+
 from linkml_runtime.utils.curienamespace import CurieNamespace
 from linkml_runtime.utils.schemaview import SchemaView
-from rdflib import RDF, RDFS, SKOS, XSD, OWL
 
 __all__ = [
     "SchemaView",

linkml_runtime/dumpers/__init__.py

@@ -1,9 +1,9 @@
+from linkml_runtime.dumpers.csv_dumper import CSVDumper
 from linkml_runtime.dumpers.json_dumper import JSONDumper
 from linkml_runtime.dumpers.rdf_dumper import RDFDumper
 from linkml_runtime.dumpers.rdflib_dumper import RDFLibDumper
 from linkml_runtime.dumpers.tsv_dumper import TSVDumper
 from linkml_runtime.dumpers.yaml_dumper import YAMLDumper
-from linkml_runtime.dumpers.csv_dumper import CSVDumper
 
 json_dumper = JSONDumper()
 rdf_dumper = RDFDumper()

linkml_runtime/dumpers/dumper_root.py

@@ -1,9 +1,10 @@
 from abc import ABC, abstractmethod
 from typing import Union
 
-from linkml_runtime.utils.yamlutils import YAMLRoot
 from pydantic import BaseModel
 
+from linkml_runtime.utils.yamlutils import YAMLRoot
+
 
 class Dumper(ABC):
     """Abstract base class for all dumpers"""

linkml_runtime/dumpers/json_dumper.py

@@ -2,16 +2,16 @@
 from datetime import datetime, date
 from decimal import Decimal
 from typing import Union
-from pydantic import BaseModel
 
 from deprecated.classic import deprecated
+from jsonasobj2 import JsonObj
+from pydantic import BaseModel
 
 from linkml_runtime.dumpers.dumper_root import Dumper
 from linkml_runtime.utils import formatutils
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE
 from linkml_runtime.utils.formatutils import remove_empty_items
 from linkml_runtime.utils.yamlutils import YAMLRoot, as_json_object
-from jsonasobj2 import JsonObj
 
 
 class JSONDumper(Dumper):

linkml_runtime/dumpers/rdf_dumper.py

@@ -1,13 +1,12 @@
 import json
 from typing import Optional, Union
-from pydantic import BaseModel
 
 from hbreader import hbread
+from pydantic import BaseModel
 from rdflib import Graph
 
-
 from linkml_runtime.dumpers.dumper_root import Dumper
-from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE, CONTEXT_TYPE
+from linkml_runtime.utils.context_utils import CONTEXT_TYPE, CONTEXTS_PARAM_TYPE
 from linkml_runtime.utils.formatutils import remove_empty_items
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
@@ -31,7 +30,7 @@ def as_rdf_graph(
         :return: rdflib Graph containing element
         """
         if contexts is None:
-            raise Exception(f"Must pass in JSON-LD context via contexts parameter")
+            raise Exception("Must pass in JSON-LD context via contexts parameter")
         if isinstance(contexts, list):
             inp_contexts = [json.loads(hbread(c)) for c in contexts]
         else:

linkml_runtime/dumpers/rdflib_dumper.py

@@ -1,17 +1,16 @@
 import logging
 import urllib
-from typing import Optional, Any, Union
-from pydantic import BaseModel
+from typing import Any, Optional, Union
 
 from curies import Converter
-from rdflib import Graph, URIRef, XSD
-from rdflib.term import Node, BNode, Literal
+from pydantic import BaseModel
+from rdflib import XSD, Graph, URIRef
 from rdflib.namespace import RDF
-
+from rdflib.term import BNode, Literal, Node
 
 from linkml_runtime.dumpers.dumper_root import Dumper
 from linkml_runtime.linkml_model import SlotDefinition
-from linkml_runtime.utils.schemaview import SchemaView, ElementName, PermissibleValue, PermissibleValueText
+from linkml_runtime.utils.schemaview import ElementName, PermissibleValue, PermissibleValueText, SchemaView
 from linkml_runtime.utils.yamlutils import YAMLRoot
 
 logger = logging.getLogger(__name__)

linkml_runtime/dumpers/yaml_dumper.py

@@ -1,5 +1,6 @@
-import yaml
 from typing import Union
+
+import yaml
 from pydantic import BaseModel
 
 from linkml_runtime.dumpers.dumper_root import Dumper

linkml_runtime/index/object_index.py

@@ -9,10 +9,10 @@
    a proxy for a domain object that "knows" its place in the index
 """
 
-import logging
 import inspect
+import logging
+from collections.abc import Iterator, Mapping
 from typing import Any, Union
-from collections.abc import Mapping, Iterator
 
 from linkml_runtime import SchemaView
 from linkml_runtime.utils import eval_utils

linkml_runtime/linkml_model/__init__.py

@@ -1,48 +1,48 @@
-from .types import (
-    String,
-    Integer,
-    Boolean,
-    Float,
-    Double,
-    Decimal,
-    Time,
-    Date,
-    Datetime,
-    Uriorcurie,
-    Uri,
-    Ncname,
-    Objectidentifier,
-    Nodeidentifier,
-)
-from .extensions import Extension, Extensible
-from .annotations import Annotation, Annotatable
+from .annotations import Annotatable, Annotation
+from .extensions import Extensible, Extension
 from .meta import (
-    ElementName,
-    SchemaDefinitionName,
-    TypeDefinitionName,
-    SubsetDefinitionName,
-    DefinitionName,
-    EnumDefinitionName,
-    SlotDefinitionName,
-    ClassDefinitionName,
-    PrefixPrefixPrefix,
-    LocalNameLocalNameSource,
+    AltDescription,
     AltDescriptionSource,
-    PermissibleValueText,
-    Element,
-    SchemaDefinition,
-    TypeDefinition,
-    SubsetDefinition,
+    ClassDefinition,
+    ClassDefinitionName,
     Definition,
+    DefinitionName,
+    Element,
+    ElementName,
     EnumDefinition,
-    SlotDefinition,
-    ClassDefinition,
-    Prefix,
-    LocalName,
+    EnumDefinitionName,
     Example,
-    AltDescription,
+    LocalName,
+    LocalNameLocalNameSource,
     PermissibleValue,
+    PermissibleValueText,
+    Prefix,
+    PrefixPrefixPrefix,
     PvFormulaOptions,
+    SchemaDefinition,
+    SchemaDefinitionName,
+    SlotDefinition,
+    SlotDefinitionName,
+    SubsetDefinition,
+    SubsetDefinitionName,
+    TypeDefinition,
+    TypeDefinitionName,
+)
+from .types import (
+    Boolean,
+    Date,
+    Datetime,
+    Decimal,
+    Double,
+    Float,
+    Integer,
+    Ncname,
+    Nodeidentifier,
+    Objectidentifier,
+    String,
+    Time,
+    Uri,
+    Uriorcurie,
 )
 
 __all__ = [

linkml_runtime/linkml_model/annotations.py

@@ -6,15 +6,16 @@
 # description: Annotations mixin
 # license: https://creativecommons.org/publicdomain/zero/1.0/
 
-import dataclasses
-from typing import Optional, Union, ClassVar, Any
 from dataclasses import dataclass
+from typing import Any, ClassVar, Optional, Union
 
-from linkml_runtime.utils.slot import Slot
-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 linkml_runtime.utils.metamodelcore import empty_dict
+from linkml_runtime.utils.slot import Slot
+from linkml_runtime.utils.yamlutils import YAMLRoot
+
 from .extensions import AnyValue, Extension, ExtensionTag
 
 metamodel_version = "1.7.0"