rip out json_encoder since it iss being deprecated, will need to fix …

…serialization related functions later

gmso/abc/__init__.py

@@ -1 +1 @@
-from gmso.abc.serialization_utils import GMSOJSONHandler, unyt_to_dict
+from gmso.abc.serialization_utils import unyt_to_dict

gmso/abc/abstract_potential.py

@@ -28,10 +28,10 @@ class AbstractPotential(GMSOBase):
         PotentialExpression(expression="a*x+b", independent_variables={"x"}),
         description="The mathematical expression for the potential",
     )
-    # expected_parameters_dimensions: Dict[str, Any] = Field(
-    #     dict(),
-    #     description="The expected unit dimensions of all the parameters",
-    # )
+    expected_parameters_dimensions: Dict[str, Any] = Field(
+        dict(),
+        description="The expected unit dimensions of all the parameters",
+    )
     tags: Dict[str, Any] = Field(
         {}, description="Tags associated with the potential"
     )

gmso/abc/abstract_site.py

@@ -33,10 +33,12 @@ def default_position():
 
 class Site(GMSOBase):
     __iterable_attributes__: ClassVar[set] = {
-        "label",
+        "name" "label",
         "group",
         "molecule",
         "residue",
+        "position",
+        "model_config",
     }
 
     __base_doc__: ClassVar[
@@ -57,9 +59,9 @@ class Site(GMSOBase):
 
     name: str = Field(
         "",
+        validate_default=True,
         description="Name of the site, defaults to class name",
     )
-
     label: str = Field("", description="Label to be assigned to the site")
 
     group: Optional[StrictStr] = Field(
@@ -86,36 +88,6 @@ class Site(GMSOBase):
         validate_assignment=True,
     )
 
-    @property
-    def name(self) -> str:
-        """Return the name of the site."""
-        return self.__dict__.get("name_")
-
-    @property
-    def position(self) -> u.unyt_array:
-        """Return the 3D Cartesian coordinates of the site."""
-        return self.__dict__.get("position_")
-
-    @property
-    def label(self) -> str:
-        """Return the label assigned to the site."""
-        return self.__dict__.get("label_")
-
-    @property
-    def group(self) -> str:
-        """Return the group of the site."""
-        return self.__dict__.get("group_")
-
-    @property
-    def molecule(self) -> tuple:
-        """Return the molecule of the site."""
-        return self.__dict__.get("molecule_")
-
-    @property
-    def residue(self):
-        """Return the residue assigned to the site."""
-        return self.__dict__.get("residue_")
-
     def __repr__(self):
         """Return the formatted representation of the site."""
         return (

gmso/abc/auto_doc.py

@@ -4,10 +4,7 @@
 from copy import deepcopy
 from typing import Any, Dict, List, Optional, Tuple, Type, Union
 
-try:
-    from pydantic.v1 import BaseModel
-except ImportError:
-    from pydantic import BaseModel
+from pydantic import BaseModel
 
 BASE_DOC_ATTR = "__base_doc__"
 FIELDS_IN_DOCSTRING = "__alias_to_fields__"

gmso/abc/gmso_base.py

@@ -6,7 +6,6 @@
 
 from pydantic import BaseModel, ConfigDict, validators
 
-from gmso.abc import GMSOJSONHandler
 from gmso.abc.auto_doc import apply_docs
 from gmso.abc.serialization_utils import dict_to_unyt
 
@@ -26,9 +25,7 @@ class GMSOBase(BaseModel, ABC):
     # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information.
     model_config = ConfigDict(
         arbitrary_types_allowed=True,
-        alias_to_fields=dict(),
         extra="forbid",
-        json_encoders=GMSOJSONHandler.json_encoders,
         populate_by_name=True,
     )
 
@@ -90,18 +87,6 @@ def _iter(self, **kwargs) -> "TupleGenerator":
 
         yield from super()._iter(**kwargs)
 
-    def json(self, **kwargs):
-        kwargs["by_alias"] = True
-        # FIXME: Pydantic>1.8 doesn't recognize json_encoders without this update
-        self.__config__.json_encoders.update(GMSOJSONHandler.json_encoders)
-
-        return super(GMSOBase, self).json(**kwargs)
-
-    def json_dict(self, **kwargs):
-        """Return a JSON serializable dictionary from the object"""
-        raw_json = self.json(**kwargs)
-        return json.loads(raw_json)
-
     @classmethod
     def validate(cls, value):
         """Ensure that the object is validated before use."""

gmso/abc/serialization_utils.py

@@ -33,21 +33,3 @@ def dict_to_unyt(dict_obj) -> None:
                     unyt_func = u.unyt_array
 
                 dict_obj[key] = unyt_func(np_array, value["unit"])
-
-
-class JSONHandler:
-    def __init__(self):
-        self.json_encoders = {}
-
-    def register(self, type_, callable_, override=False):
-        """Register a new JSON encoder for an object for serialization in GMSO"""
-        if type_ not in self.json_encoders:
-            self.json_encoders[type_] = callable_
-        else:
-            if override:
-                warn(f"Overriding json serializer for {type_}")
-                self.json_encoders[type_] = callable_
-
-
-GMSOJSONHandler = JSONHandler()
-GMSOJSONHandler.register(u.unyt_array, unyt_to_dict)

gmso/utils/decorators.py

@@ -2,21 +2,6 @@
 import functools
 import warnings
 
-from gmso.abc import GMSOJSONHandler
-
-
-class register_pydantic_json(object):
-    """Provides a way to register json encoders for a non-JSON serializable class."""
-
-    def __init__(self, method="json"):
-        self.method = method
-
-    def __call__(self, cls):
-        """Register this class's json encoder method to GMSOJSONHandler."""
-        json_method = getattr(cls, self.method)
-        GMSOJSONHandler.register(cls, json_method)
-        return cls
-
 
 def deprecate_kwargs(deprecated_kwargs=None):
     """Decorate functions with deprecated/deprecating kwargs."""

gmso/utils/expression.py

@@ -7,8 +7,6 @@
 import sympy
 import unyt as u
 
-from gmso.utils.decorators import register_pydantic_json
-
 __all__ = ["PotentialExpression"]
 
 
@@ -30,7 +28,6 @@ def _are_equal_parameters(u1, u2):
         return True
 
 
-@register_pydantic_json(method="json")
 class PotentialExpression:
     """A general Expression class with parameters.