Fix default .charges

[mattwthompson]

Description

Resolves #1052 ... mostly

Checklist

• Add tests
• Lint
• Update docstrings

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Attention: Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.

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Additional details and impacted files

[mattwthompson]

A major source of confusion for me - for whatever reason, having this code in breaks the test which checks that the .charges property is non-empty. It's not clear to me why, and I don't see the same behavior in my best attempt at stripping it out into a MWE. I don't know if I'm doing something wrong with Pydantic magic, the typing machinery, or I just misunderstand something more basic about how classes and attributes work in Python

from typing import Annotated, Any

import numpy
from openff.toolkit import Quantity
from pydantic import BaseModel, ConfigDict, PrivateAttr, WrapSerializer, computed_field


def quantity_json_serializer(
    quantity: Quantity,
    nxt,
) -> dict:
    """Serialize a Quantity to a JSON-compatible dictionary."""
    magnitude = quantity.m

    if isinstance(magnitude, numpy.ndarray):
        magnitude = magnitude.tolist()

    return {
        "val": magnitude,
        "unit": str(quantity.units),
    }


_DistanceQuantity = Annotated[
    Quantity,
    WrapSerializer(quantity_json_serializer),
]


class _BaseModel(BaseModel):
    """A custom Pydantic model used by other components."""

    model_config = ConfigDict(
        validate_assignment=True,
        arbitrary_types_allowed=True,
    )

    def model_dump(self, **kwargs) -> dict[str, Any]:
        return super().model_dump(serialize_as_any=True, **kwargs)

    def model_dump_json(self, **kwargs) -> str:
        return super().model_dump_json(serialize_as_any=True, **kwargs)


class Example(_BaseModel):
    greeting: str = "Hello"
    _secret: dict[int, _DistanceQuantity] = PrivateAttr(default_factory=dict)

    def _build_secret(self):
        self._secret = {0: Quantity(
            numpy.random.random((3, 3)),
            "nanometer",
        )}

    @computed_field
    @property
    def secret(self) -> _DistanceQuantity:
        self._build_secret()

        return self._secret

assert len(Example().secret) > 0  # runs without error

[ntBre]

LGTM! Not sure about the pydantic magic either, but I can vouch for the tests failing when the definitions are included in the model.

[mattwthompson]

Thanks!