neurobagel / bagel-cli / 11849811079

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[REF] Upgrade codebase to Pydantic>2 (#389)

* update extra fields config, regex validation

* replace conlist with List and custom AfterValidator

* add type annotation to all schemaKey fields
- now required to prevent error: pydantic.errors.PydanticUserError: Field 'schemaKey' defined on a base class was overridden by a non-annotated attribute. All field definitions, including overrides, require a type annotation.

* use pydantic.RootModel instead of deprecated __root__

* update pydantic model method names

* update generate_context to better accommodate changes to Pydantic internals

* update URL type annots and notes re: deprecation of str inheriting

* remove example portal URL missing TLD
- pydantic v2 HttpUrl no longer requires it

* shorten test name

* update dependencies including pydantic>2

* replace deprecated DataFrame.applymap call

* require python>=3.10 for package and test 3.11

* add python versions badge

* add README note about pip-compile's Python version awareness

* test validate_unique_list() in pydantic model instance

* remove seemingly unnecessary Optional type hint

* raise explicit exception for non-unique missing value list

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Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

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