Update GMSO to work with pydantic 2.0 (#745)

* first pass using bump-pydantic per https://docs.pydantic.dev/2.0/migration/

* Further update syntax in abc and core

* checkpoint

* checkpoint

* rip out json_encoder since it iss being deprecated, will need to fix serialization related functions later

* fix up atom related files and tests

* fix bond.py

* fix up dihedral and improper

* fix various import in tests, removed json handler import

* re-add __hash__ method for atom type and parametric potential

* replace parse_obj with model_validate

* add serializer for several fields, fix everything but test_serialization and test_xml_handling

* fix some of the serialization test

* reimplement json_dict, parse_raw (since model_validate_json raised unimplemeted error), all serialization tests fixed

* found workaround to avoid using parse_raw

* fix remainder of xml handling test by change atom_type._etree_attrib to be consistent previous version

* update potential templates to use expected_parameters_dimensions_ for consistency

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* fix typo

* add the missing alias key

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* udpate env yml

* remove pydantic from matrx in CI

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/CI.yaml

@@ -20,7 +20,6 @@ jobs:
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: ["3.9", "3.10", "3.11"]
-        pydantic-version: ["2"]
 
     defaults:
       run:
@@ -36,7 +35,6 @@ jobs:
           environment-file: environment-dev.yml
           create-args: >-
             python=${{ matrix.python-version }}
-            pydantic=${{ matrix.pydantic-version }}
 
       - name: Install Package
         run: python -m pip install -e .

environment-dev.yml

@@ -9,7 +9,7 @@ dependencies:
   - unyt>=2.9.5
   - boltons
   - lxml
-  - pydantic
+  - pydantic>=2
   - networkx
   - pytest
   - mbuild>=0.11.0

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - unyt>=2.9.5
   - boltons
   - lxml
-  - pydantic
+  - pydantic>=2
   - networkx
   - ele>=0.2.0
   - foyer>=0.11.3

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_connection.py

@@ -1,14 +1,11 @@
 from typing import Optional, Sequence
 
+from pydantic import ConfigDict, Field, model_validator
+
 from gmso.abc.abstract_site import Site
 from gmso.abc.gmso_base import GMSOBase
 from gmso.exceptions import GMSOError
 
-try:
-    from pydantic.v1 import Field, root_validator
-except ImportError:
-    from pydantic import Field, root_validator
-
 
 class Connection(GMSOBase):
     __base_doc__ = """An abstract class that stores data about connections between sites.
@@ -18,12 +15,21 @@ class Connection(GMSOBase):
     """
 
     name_: str = Field(
-        default="", description="Name of the connection. Defaults to class name"
+        default="",
+        description="Name of the connection. Defaults to class name.",
+        alias="name",
     )
 
     connection_members_: Optional[Sequence[Site]] = Field(
         default=None,
         description="A list of constituents in this connection, in order.",
+        alias="connection_members",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "connection_members": "connection_members_",
+        }
     )
 
     @property
@@ -37,12 +43,12 @@ def name(self):
     @property
     def member_types(self):
         """Return the atomtype of the connection members as a list of string."""
-        return self._get_members_types_or_classes("member_types_")
+        return self._get_members_types_or_classes("member_types")
 
     @property
     def member_classes(self):
         """Return the class of the connection members as a list of string."""
-        return self._get_members_types_or_classes("member_classes_")
+        return self._get_members_types_or_classes("member_classes")
 
     def _has_typed_members(self):
         """Check if all the members of this connection are typed."""
@@ -53,7 +59,7 @@ def _has_typed_members(self):
 
     def _get_members_types_or_classes(self, to_return):
         """Return types or classes for connection members if they exist."""
-        assert to_return in {"member_types_", "member_classes_"}
+        assert to_return in {"member_types", "member_classes"}
         ctype = getattr(self, "connection_type")
         ctype_attr = getattr(ctype, to_return) if ctype else None
 
@@ -62,15 +68,18 @@ def _get_members_types_or_classes(self, to_return):
         elif self._has_typed_members():
             tc = [
                 member.atom_type.name
-                if to_return == "member_types_"
+                if to_return == "member_types"
                 else member.atom_type.atomclass
                 for member in self.__dict__.get("connection_members_")
             ]
             return tc if all(tc) else None
 
-    @root_validator(pre=True)
+    @model_validator(mode="before")
     def validate_fields(cls, values):
-        connection_members = values.get("connection_members")
+        if "connection_members" in values:
+            connection_members = values.get("connection_members")
+        else:
+            connection_members = values.get("connection_members_")
 
         if all(isinstance(member, dict) for member in connection_members):
             connection_members = [
@@ -103,11 +112,3 @@ def __repr__(self):
 
     def __str__(self):
         return f"<{self.__class__.__name__} {self.name}, id: {id(self)}> "
-
-    class Config:
-        fields = {"name_": "name", "connection_members_": "connection_members"}
-
-        alias_to_fields = {
-            "name": "name_",
-            "connection_members": "connection_members_",
-        }

gmso/abc/abstract_potential.py

@@ -2,14 +2,13 @@
 from abc import abstractmethod
 from typing import Any, Dict, Iterator, List
 
+import unyt as u
+from pydantic import ConfigDict, Field, field_serializer, field_validator
+
 from gmso.abc.gmso_base import GMSOBase
+from gmso.abc.serialization_utils import unyt_to_dict
 from gmso.utils.expression import PotentialExpression
 
-try:
-    from pydantic.v1 import Field, validator
-except ImportError:
-    from pydantic import Field, validator
-
 
 class AbstractPotential(GMSOBase):
     __base_doc__ = """An abstract potential class.
@@ -24,16 +23,28 @@ class AbstractPotential(GMSOBase):
     """
 
     name_: str = Field(
-        "", description="The name of the potential. Defaults to class name"
+        "",
+        description="The name of the potential. Defaults to class name",
+        alias="name",
     )
 
     potential_expression_: PotentialExpression = Field(
         PotentialExpression(expression="a*x+b", independent_variables={"x"}),
         description="The mathematical expression for the potential",
+        alias="potential_expression",
     )
 
     tags_: Dict[str, Any] = Field(
-        {}, description="Tags associated with the potential"
+        {},
+        description="Tags associated with the potential",
+        alias="tags",
+    )
+    model_config = ConfigDict(
+        alias_to_fields={
+            "name": "name_",
+            "potential_expression": "potential_expression_",
+            "tags": "tags_",
+        }
     )
 
     def __init__(
@@ -72,12 +83,12 @@ def name(self):
     @property
     def independent_variables(self):
         """Optional[Union[set, str]]\n\tThe independent variables in the `Potential`'s expression."""
-        return self.potential_expression_.independent_variables
+        return self.potential_expression.independent_variables
 
     @property
     def expression(self):
         """Optional[Union[str, sympy.Expr]]\n\tThe mathematical expression of the functional form of the potential."""
-        return self.potential_expression_.expression
+        return self.potential_expression.expression
 
     @property
     def potential_expression(self):
@@ -96,6 +107,34 @@ def tag_names(self) -> List[str]:
     def tag_names_iter(self) -> Iterator[str]:
         return iter(self.__dict__.get("tags_"))
 
+    @field_serializer("potential_expression_")
+    def serialize_expression(self, potential_expression_: PotentialExpression):
+        expr = str(potential_expression_.expression)
+        ind = sorted(
+            list(
+                str(ind) for ind in potential_expression_.independent_variables
+            )
+        )
+        params = {
+            param: unyt_to_dict(val)
+            for param, val in potential_expression_.parameters.items()
+        }
+        return {
+            "expression": expr,
+            "independent_variables": ind,
+            "parameters": params,
+        }
+
+    @field_serializer("tags_")
+    def serialize_tags(self, tags_):
+        return_dict = dict()
+        for key, val in tags_.items():
+            if isinstance(val, u.unyt_array):
+                return_dict[key] = unyt_to_dict(val)
+            else:
+                return_dict[key] = val
+        return return_dict
+
     def add_tag(self, tag: str, value: Any, overwrite=True) -> None:
         """Add metadata for a particular tag"""
         if self.tags.get(tag) and not overwrite:
@@ -118,7 +157,8 @@ def delete_tag(self, tag: str) -> None:
     def pop_tag(self, tag: str) -> Any:
         return self.tags.pop(tag, None)
 
-    @validator("potential_expression_", pre=True)
+    @field_validator("potential_expression_", mode="before")
+    @classmethod
     def validate_potential_expression(cls, v):
         if isinstance(v, dict):
             v = PotentialExpression(**v)
@@ -132,9 +172,9 @@ def set_expression(self):
     def __setattr__(self, key: Any, value: Any) -> None:
         """Set attributes of the potential."""
         if key == "expression":
-            self.potential_expression_.expression = value
+            self.potential_expression.expression = value
         elif key == "independent_variables":
-            self.potential_expression_.independent_variables = value
+            self.potential_expression.independent_variables = value
         elif key == "set_ref_":
             return
         else:
@@ -156,18 +196,3 @@ def __str__(self):
             f"expression: {self.expression}, "
             f"id: {id(self)}>"
         )
-
-    class Config:
-        """Pydantic configuration for the potential objects."""
-
-        fields = {
-            "name_": "name",
-            "potential_expression_": "potential_expression",
-            "tags_": "tags",
-        }
-
-        alias_to_fields = {
-            "name": "name_",
-            "potential_expression": "potential_expression_",
-            "tags": "tags_",
-        }