Use model_config instead of class Config

src/metldata/builtin_transformations/add_accessions/config.py

@@ -17,21 +17,18 @@
 """Config parameters and their defaults."""
 
 from pydantic import Field
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class AccessionAdditionConfig(BaseSettings):
     """Config to add accessions to a model and associated metadata."""
 
+    model_config = SettingsConfigDict(extra="forbid")
+
     accession_slot_name: str = Field(
         "accession", description="The name of the slot to contain the accessions to."
     )
     accession_slot_description: str = Field(
         "The accession for an entity.",
         description="The description of the slot to contain the accessions to.",
     )
-
-    class Config:
-        """Pydantic config."""
-
-        extra = "forbid"

src/metldata/builtin_transformations/custom_embeddings/config.py

@@ -17,7 +17,7 @@
 """Models used to describe embedding profiles."""
 
 from pydantic import Field, field_validator
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from metldata.builtin_transformations.custom_embeddings.embedding_profile import (
     EmbeddingProfile,
@@ -43,6 +43,8 @@ class CustomEmbeddingConfig(BaseSettings):
     model.
     """
 
+    model_config = SettingsConfigDict(extra="forbid")
+
     embedding_profiles: list[EmbeddingProfile] = Field(
         ...,
         description=(
@@ -67,8 +69,3 @@ def check_embedding_profiles_unique(
             raise ValueError("Names for embedded classes must be unique.")
 
         return value
-
-    class Config:
-        """Pydantic config."""
-
-        extra = "forbid"

src/metldata/builtin_transformations/delete_slots/config.py

@@ -17,12 +17,14 @@
 """Config parameters and their defaults."""
 
 from pydantic import Field
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class SlotDeletionConfig(BaseSettings):
     """Config containing slots to be deleted from models and associated metadata."""
 
+    model_config = SettingsConfigDict(extra="forbid")
+
     slots_to_delete: dict[str, list[str]] = Field(
         ...,
         description=(
@@ -38,8 +40,3 @@ class SlotDeletionConfig(BaseSettings):
             }
         ],
     )
-
-    class Config:
-        """Pydantic config."""
-
-        extra = "forbid"

src/metldata/builtin_transformations/infer_references/config.py

@@ -17,7 +17,7 @@
 """Models used to describe all inferred references based on existing references."""
 
 from pydantic import Field
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from metldata.builtin_transformations.infer_references.reference import (
     InferredReference,
@@ -31,6 +31,8 @@ class ReferenceInferenceConfig(BaseSettings):
     a list of InferredReferences.
     """
 
+    model_config = SettingsConfigDict(extra="forbid")
+
     inferred_ref_map: dict[str, dict[str, ReferenceDetails]] = Field(
         ...,
         description=(
@@ -81,8 +83,3 @@ def inferred_references(self) -> list[InferredReference]:
                 )
 
         return inferred_refs
-
-    class Config:
-        """Pydantic config."""
-
-        extra = "forbid"

src/metldata/builtin_transformations/infer_references/reference.py

@@ -16,7 +16,7 @@
 
 """Reference models."""
 
-from pydantic import BaseModel, Field, model_validator
+from pydantic import BaseModel, ConfigDict, Field, model_validator
 
 from metldata.builtin_transformations.infer_references.path.path import ReferencePath
 
@@ -40,6 +40,8 @@ class InferredReference(ReferenceDetails):
     references.
     """
 
+    model_config = ConfigDict(frozen=True)
+
     source: str = Field(
         ..., description="The source class to which this reference should be added."
     )
@@ -66,8 +68,3 @@ def validate_source_and_target(cls, values):
             )
 
         return values
-
-    class Config:
-        """Config for this model."""
-
-        frozen = True

src/metldata/builtin_transformations/merge_slots/config.py

@@ -17,14 +17,16 @@
 """Config parameters and their defaults."""
 
 from pydantic import Field, field_validator
-from pydantic_settings import BaseSettings
+from pydantic_settings import BaseSettings, SettingsConfigDict
 
 from metldata.builtin_transformations.merge_slots.models import SlotMergeInstruction
 
 
 class SlotMergingConfig(BaseSettings):
     """Config containing slots to be deleted from models and associated metadata."""
 
+    model_config = SettingsConfigDict(extra="forbid")
+
     merge_instructions: list[SlotMergeInstruction] = Field(
         ...,
         description=(
@@ -83,8 +85,3 @@ def validate_merge_instructions(
                 )
 
         return filtered_merge_instructions
-
-    class Config:
-        """Pydantic config."""
-
-        extra = "forbid"

src/metldata/model_utils/anchors.py

@@ -21,7 +21,7 @@
 
 from linkml_runtime import SchemaView
 from linkml_runtime.linkml_model import SlotDefinition
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 
 from metldata.model_utils.essentials import ROOT_CLASS, MetadataModel
 from metldata.model_utils.identifiers import get_class_identifiers
@@ -42,6 +42,8 @@ class ClassNotAnchoredError(RuntimeError):
 class AnchorPoint(BaseModel):
     """A model for describing an anchor point for the specified target class."""
 
+    model_config = ConfigDict(frozen=True)
+
     target_class: str = Field(..., description="The name of the class to be targeted.")
     identifier_slot: str = Field(
         ...,
@@ -56,11 +58,6 @@ class AnchorPoint(BaseModel):
         ),
     )
 
-    class Config:
-        """Pydantic Configs."""
-
-        frozen = True
-
 
 def check_root_slot(slot: SlotDefinition):
     """Make sure that the given root slot is a valid anchor point. Validates that the

src/metldata/transform/base.py

@@ -22,7 +22,14 @@
 from graphlib import CycleError, TopologicalSorter
 from typing import Callable, Generic, Optional, TypeVar
 
-from pydantic import BaseModel, Field, create_model, field_validator, model_validator
+from pydantic import (
+    BaseModel,
+    ConfigDict,
+    Field,
+    create_model,
+    field_validator,
+    model_validator,
+)
 
 from metldata.custom_types import Json
 from metldata.event_handling.models import SubmissionAnnotation
@@ -114,6 +121,7 @@ class WorkflowConfig(BaseModel, ABC):
 class WorkflowStepBase(BaseModel, ABC):
     """A base class for workflow steps."""
 
+    model_config = ConfigDict(frozen=True)
     description: str = Field(..., description="A description of the step.")
     input: Optional[str] = Field(
         ...,
@@ -123,11 +131,6 @@ class WorkflowStepBase(BaseModel, ABC):
         ),
     )
 
-    class Config:
-        """Config for the workflow step."""
-
-        frozen = True
-
 
 class WorkflowStep(WorkflowStepBase):
     """A single step in a transformation workflow."""
@@ -141,6 +144,7 @@ class WorkflowStep(WorkflowStepBase):
 class WorkflowDefinition(BaseModel):
     """A definition of a transformation workflow."""
 
+    model_config = ConfigDict(frozen=True)
     description: str = Field(..., description="A description of the workflow.")
     steps: dict[str, WorkflowStep] = Field(
         ...,
@@ -240,8 +244,3 @@ def step_order(self) -> list[str]:
             return list(topological_sorter.static_order())
         except CycleError as exc:
             raise RuntimeError("Step definitions imply a circular dependency.") from exc
-
-    class Config:
-        """Config for the workflow step."""
-
-        frozen = True

src/metldata/transform/handling.py

@@ -16,7 +16,7 @@
 
 """Logic for handling Transformation."""
 
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 from metldata.custom_types import Json
 from metldata.event_handling.models import SubmissionAnnotation
@@ -115,13 +115,9 @@ def transform_metadata(
 class ResolvedWorkflowStep(WorkflowStepBase):
     """A resolved workflow step contains a transformation handler."""
 
+    model_config = ConfigDict(arbitrary_types_allowed=True)
     transformation_handler: TransformationHandler
 
-    class Config:
-        """Config for ResolvedWorkflowStep."""
-
-        arbitrary_types_allowed = True
-
 
 class ResolvedWorkflow(WorkflowDefinition):
     """A resolved workflow contains a list of resolved workflow steps."""

tests/test_event_handling.py

@@ -21,7 +21,7 @@
 import pytest
 from hexkit.custom_types import Ascii, JsonObject
 from hexkit.protocols.eventsub import EventSubscriberProtocol
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, ConfigDict, Field
 
 from metldata.event_handling.event_handling import FileSystemEventSubscriber
 from tests.fixtures.event_handling import (
@@ -44,15 +44,11 @@
 class ConsumedEvent(BaseModel):
     """Consumed event without the key."""
 
+    model_config = ConfigDict(frozen=True)
     topic: str
     type_: str
     payload: str = Field(..., description="JSON string of the event payload.")
 
-    class Config:
-        """Pydantic model configuration."""
-
-        frozen = True
-
 
 @pytest.mark.asyncio
 async def test_pub_sub_workflow(