[vissi]

Which languages do you use? There's a wide variety of options: Doxygen for C, PHPDocumentor for PHP, literate tools for Ruby and Coffee, etc. If you describe your software using email, why can't you write the same docs on github using Markdown?

[afshinmeh]

Usually I use JavaScript and Python. I don't have problem with software, I know the correct tools for generating the doc from my code as well. But the problem is that HOW can I integrate it with Github so after each sync/push on the Github repository, document generated automatically from code also?

[globalpanic]

What about generating a wiki from the code documentation, and then uploading that to the Wiki section of your Git repository?