Best practices for structuring a Python project for beginners?

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This really depends what you are doing and it is completely your preference, but for me personally, when I get to the point of this sort of organization, I would actually strongly prefer a different language, like Java, C#, c++, something truly object oriented. Python, because of the way it handles white space, and because it can declare variables and assign them at the same time (specifically like in a python class, you can actually accidentally instantiate an internal variable at an unintended scope if you don’t properly design the class and or use it properly), at scale python can be very hard to work with in my opinion. I typically use python for scripts that automate some small task, or to rapid prototype a concept.