[#161] fixing some returns and type hints

[angeloprobst]

Progress on ticket #161

• Created some Type Aliases, like AtomT: TypeAlias = dict[str, Any], similarly for NodeT, NodeParamsT, LinkT and LinkParamsT.
• Used the new type aliases for annotations on all over the code.
• Revisited and fixed all type hints with the help of mypy.
• Left some TODOs for future evaluation.
• Ensured that the entire repo passes green through flake8 + pylint + mypy.
• Fixed a unit test.
• Improved docstrings.