How is better for Documentation in Python ?
I think pydocs and mkdocs serve different purpose. Pydocs is able to extract docstring comments from your codebase. If you follow the PEP257 guideline to carefully comment your code, then basically your documentation will write itself. https://www.python.org/dev/peps/pep-0257/ Mkdocs can be used to write up some user guide or tutorial for your program in wiki-like markdown syntax. This is not strictly related to your code structure, more like usage instructions.