Remove deprecated json_encoder from ConfigDict for serializing SympyE…

…xprStr objects. Use updated field serializer decorator

mira/metamodel/comparison.py

@@ -74,14 +74,8 @@ class IntraModelEdge(DataEdge):
 
 class ModelComparisonGraphdata(BaseModel):
     """A data structure holding a graph representation of TemplateModel delta"""
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(arbitrary_types_allowed=True, json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={
-        SympyExprStr: lambda e: safe_parse_expr(e),
-        Template: lambda t: Template.from_json(data=t),
-    })
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     template_models: Dict[int, TemplateModel] = Field(
         ..., description="A mapping of template model keys to template models"

mira/metamodel/template_model.py

@@ -20,7 +20,7 @@
 import networkx as nx
 import sympy
 import mira.metamodel.io
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, field_serializer
 from .templates import *
 from .units import Unit
 from .utils import safe_parse_expr, SympyExprStr
@@ -36,11 +36,8 @@ class Initial(BaseModel):
     expression: SympyExprStr = Field(
         description="The expression for the initial."
     )
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(arbitrary_types_allowed=True, json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={SympyExprStr: lambda e: sympy.parse_expr(e)})
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     @classmethod
     def from_json(cls, data: Dict[str, Any], locals_dict=None) -> "Initial":
@@ -68,6 +65,10 @@ def from_json(cls, data: Dict[str, Any], locals_dict=None) -> "Initial":
         expression = safe_parse_expr(expression_str, local_dict=locals_dict)
         return cls(concept=concept, expression=SympyExprStr(expression))
 
+    @field_serializer('expression')
+    def serialize_expression(self, expression):
+        return str(expression)
+
     def substitute_parameter(self, name, value):
         """
         Substitute a parameter value into the initial expression.
@@ -135,16 +136,17 @@ class Observable(Concept):
     readout is not defined as a state variable but is rather a function of
     state variables.
     """
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(arbitrary_types_allowed=True, json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={SympyExprStr: lambda e: safe_parse_expr(e)})
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     expression: SympyExprStr = Field(
         description="The expression for the observable."
     )
 
+    @field_serializer('expression')
+    def serialize_expression(self, expression):
+        return str(expression)
+
     def substitute_parameter(self, name, value):
         """
         Substitute a parameter value into the observable expression.
@@ -367,11 +369,6 @@ class TemplateModel(BaseModel):
         description="A structure containing time-related annotations. "
         "Note that all annotations are optional.",
     )
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={SympyExprStr: lambda e: safe_parse_expr(e)})
 
     def get_parameters_from_rate_law(self, rate_law) -> Set[str]:
         """Given a rate law, find its elements that are model parameters.

mira/metamodel/templates.py

@@ -62,7 +62,7 @@
 import networkx as nx
 import pydantic
 import sympy
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, field_serializer
 
 try:
     from typing import Annotated  # py39+
@@ -128,13 +128,8 @@ class Concept(BaseModel):
         None, description="The units of the concept."
     )
     _base_name: str = pydantic.PrivateAttr(None)
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(arbitrary_types_allowed=True, json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={
-        SympyExprStr: lambda e: sympy.parse_expr(e)
-    })
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     def __eq__(self, other):
         if isinstance(other, Concept):
@@ -399,13 +394,8 @@ def from_json(cls, data) -> "Concept":
 
 class Template(BaseModel):
     """The Template is a parent class for model processes"""
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(arbitrary_types_allowed=True, json_encoders={
-        SympyExprStr: lambda e: str(e),
-    }, json_decoders={
-        SympyExprStr: lambda e: safe_parse_expr(e)
-    })
+
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     rate_law: Optional[SympyExprStr] = Field(
         default=None, description="The rate law for the template."
@@ -466,6 +456,10 @@ def from_json(cls, data, rate_symbols=None) -> "Template":
                            if k not in {'rate_law', 'type'}},
                         rate_law=rate)
 
+    @field_serializer('rate_law')
+    def serialize_expression(self, rate_law):
+        return str(rate_law)
+
     def is_equal_to(self, other: "Template", with_context: bool = False,
                     config: Config = None) -> bool:
         """Check if this template is equal to another template

mira/metamodel/units.py

@@ -14,7 +14,7 @@
 from typing import Dict, Any
 
 import sympy
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, field_serializer
 from .utils import SympyExprStr
 
 
@@ -34,17 +34,7 @@ def load_units():
 
 class Unit(BaseModel):
     """A unit of measurement."""
-    # TODO[pydantic]: The following keys were removed: `json_encoders`.
-    # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
-    model_config = ConfigDict(
-        arbitrary_types_allowed=True,
-        json_encoders={
-            SympyExprStr: lambda e: str(e),
-        },
-        #json_decoders={
-        #    SympyExprStr: lambda e: sympy.parse_expr(e)
-        #}
-    )
+    model_config = ConfigDict(arbitrary_types_allowed=True)
 
     expression: SympyExprStr = Field(
         description="The expression for the unit."
@@ -66,6 +56,10 @@ def model_validate(cls, obj):
             obj['expression'] = SympyExprStr(obj['expression'])
         return super().model_validate(obj)
 
+    @field_serializer('expression')
+    def serialize_expression(self, expression):
+        return str(expression)
+
 
 person_units = Unit(expression=sympy.Symbol('person'))
 day_units = Unit(expression=sympy.Symbol('day'))

tests/test_model_api.py

@@ -586,16 +586,18 @@ def test_n_way_comparison_askenet(self):
             "exclude_defaults": True,
             "exclude_unset": True,
             "exclude_none": True,
+            # This key is outdated in Pydantic2
             # "skip_defaults": True,
         }
         # Compare the ModelComparisonResponse models
-        assert local_response == resp_model  # If assertion fails the diff is printed
+        # If assertion fails the diff is printed
+        assert local_response.model_dump() == resp_model.model_dump()
         local_sorted_str = sorted_json_str(
-            json.loads(local_response.model_dump_json(**dict_options)),
+            json.loads(local_response.model_dump_json()),
             skip_empty=True
         )
         resp_sorted_str = sorted_json_str(
-            json.loads(resp_model.model_dump_json(**dict_options)),
+            json.loads(resp_model.model_dump_json()),
             skip_empty=True
         )
         self.assertEqual(local_sorted_str, resp_sorted_str)