enhancement(msgspec): create BaseStruct with __get_pydantic_core_schema__ class method and refactor MCP msgspec.Struct types to use it

[bjoaquinc]

📝 Summary

Create BaseStruct to make msgspec.Struct types compatible with pydantic typechecking (for MCP Server tools). Update old code to now use this and remove redundant types.

This PR reverses the temporary fix implemented in #6265

🔍 Description of Changes

• Create BaseStruct with get_pydantic_core_schema in marimo/_utils/msgspec_basestruct.py
• Update datatypes in marimo/_data/models.py to use BaseStruct for marimo/_ai/_tools/tools/tables_and_variables.py tool
• Update CellVariableValue -> VariableValue(BaseStruct) in tables_and_variables.py and cells.py
• Update tests to use VariableValue, inherit Session for type saftey, and use correct DataType enums
• Add pydantic >2 as mcp dependency in pyproject.toml
• Add test that checks if all exposed msgspec.Struct classes exposed to tools Args or Output use BaseStruct

📋 Checklist

• I have read the contributor guidelines.
• For large changes, or changes that affect the public API: this change was discussed or approved through an issue, on Discord, or the community discussions (Please provide a link if applicable).
• I have added tests for the changes made.
• I have run the code and verified that it works as expected.

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Project	Deployment	Preview	Comments	Updated (UTC)
marimo-docs	Ready	Preview	Comment	Sep 26, 2025 3:26pm

[mscolnick]

could this just be cell_variables[var_name] = var_value

[bjoaquinc]

Yeah that makes sense. Done!