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After having written some python scripts with comments for documentation inside, is it a good idea and possible to aggregate the documentation comments from multiple scripts into some standalone documentation file such as README?

Furthermore, is it possible to aggregate them in some markup format such as Markdown?

Thanks.

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I would highly recommend looking into Epydoc and also Sphinx-Doc.

Epydoc especially does exactly what you are asking for as stated on their website and as per my experience working with it:

Epydoc is a tool for generating API documentation for Python modules, based on their docstrings.

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