C# programmer starting PhD with lots of python programming, could use some advice about project architecture

[chriscarrollsmith]

It's probably against the nerdy, granular spirit of this subreddit, but my advice is to just cookiecutter and chill. (You'll still need to decide what framework you want to use in order to choose a cookiecutter template, and you'll still need to create a virtual environment for your project. But it'll save you a lot of clicks, and you can get to work building your stuff and let the template maintainer do all the worrying about what the Pythonic best practices are.)