Clean Graph layouts and increase flexibility (#3434)

* allow user-defined layout functions for Graph
+ fixup type annotations

* only pass relevant args

* write tests

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* change_layout forward root_vertex and partitions
- deduplicated layout code in __init__ and change_layout
- fixed change_layout backwards compatibility

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* add test for change_layout

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* fix copy/paste error

* fix

* fixup types for CodeQL

* static type the Layout Names

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* fix dynamic union type for Python 3.9

* add example scenes to LayoutFunction protocol documentation

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* Replace references to np.ndarray with standard Manim types

* Label NxGraph as a TypeAlias

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Tristan Schulz <mrdiverlp@gmail.com>
Co-authored-by: Benjamin Hackl <devel@benjamin-hackl.at>

Author: 4 people