Fix some Pydantic V2 deprecations

[mattwthompson]

Holding off on this one briefly until I can be sure that pydantic =2 constraints in new releases are okay. I will update this top-level comment as the source of truth

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Fixes #2233

I couldn't find any other usages such as .json(). When I run tests locally, no Pydantic-related deprecation warnings are thrown

• Tag issue being addressed
• Add tests
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog

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[Copilot]

🟡 Changes recommended

The switch to model_dump() introduces a compatibility regression for inputs that only implement .dict() (e.g., Pydantic v1 / pydantic.v1 models), so a fallback is needed to preserve prior behavior.

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Pull request overview

This PR addresses deprecation warnings under Pydantic v2 by replacing usages of .dict() with .model_dump() when converting QCArchive/QCSchema model objects into plain dictionaries.

Changes:

• Updated Molecule.from_qcschema() to call model_dump() when converting non-dict inputs to dicts.
• Updated a molecule round-trip test to use model_dump() when mutating the returned QCSchema object as a dict.
• Updated the QCArchive interface example notebook to use model_dump() in demonstration code.

File summaries

File	Description
openff/toolkit/topology/molecule.py	Updates QCSchema input normalization to use model_dump() to avoid Pydantic v2 deprecation warnings.
openff/toolkit/_tests/test_molecule.py	Updates test dict conversion to use model_dump() to avoid deprecation warnings.
examples/QCArchive_interface/QCarchive_interface.ipynb	Updates example cells to demonstrate model_dump() instead of deprecated .dict().

Review details

Suppressed comments (2)

openff/toolkit/topology/molecule.py:4712

• Switching to model_dump() removes the Pydantic v2 deprecation, but it also stops accepting objects that only implement .dict() (including Pydantic v1 models or pydantic.v1.BaseModel). This is a behavioral regression from the previous implementation and can cause from_qcschema to raise even though the input is convertible. Consider falling back to .dict() when .model_dump() is not available, and fix the grammar in the error message while touching this block.

                qca_object = qca_object.model_dump()
            except AttributeError:
                raise AttributeError(
                    f"The input object (type {type(qca_object)=} "
                    "passed is not and a dict and could not be converted to a dict."

examples/QCArchive_interface/QCarchive_interface.ipynb:593

• Same as above: calling entry.model_dump() directly may break this example for QCArchive objects that only support .dict(). Consider a small compatibility fallback.

    "molecule_from_dict = Molecule.from_qcschema(entry.model_dump())\n",

• Files reviewed: 3/3 changed files
• Comments generated: 2
• Review effort level: Lite

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