This PR updates the codebase following the end of life for Python 3.9.

Reference: https://devguide.python.org/versions/

- Updated type annotations to Python 3.10+ style, replacing deprecated ``List``, ``Set``, etc., with built-in ``list``, ``set``, and related types.
- Refactored code by simplifying nested ``if`` expressions.
- Updated several dependencies, including security-related upgrades.