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It really depends on how you plan to use your projects: Is it for personal use only? Do you want to use it as a cli application or a standalone package or just some loose script collection? If you want to get an idea of how to structure bigger projects, I recommend you to take a look at https://github.com/cookiejar/cookietemple. (Disclaimer: I'm one of its developers). The cli-python template there should give you a good idea of how a project could actually look like.
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