In this documentation I collect everything related to my work. The Repo language is english e.g. to keep it accessible for other people.
You need to install pandoc, pip install sphinx, pip install sphinx_rtd_theme and pip install nbsphinx and then you can simply execute make html in the main repo directory.
The source files are in the source folder, the build files are in build/html. To view the documentation open the index.html inside this folder.
Every script or script collection should have its own doc page describing what it does and how it works. Doc pages are written in ReStructured Text markup language and can contain python code. You can even create plots directly in the rst structure. More information on how to use rst and python inside sphinx is available in the matplotlib primer or in the sphinx sampledoc. Also it can be a good idea to just look at existing files in this repo if something doesn't work at first try.
In general the documentation is logically grouped in folders in the source/doc folder. Scripts are in the same structure in the source/_pyplots folder and can be called from the documentation. The same goes for static content like images which are inside source/_static. The source/_pymodules folder contains extension modules that are already added in the source/config.py file.
Instead of using rst files you can directly use iPython notebooks. Currently you can't mix rst and ipynb files in one subdirectory because it messes up the navigation Just look in the existing notebooks for further infos. So you need to convert your ipynb to rst or make all rst files to notebooks. In doubt just rewrite your notebook cells (by copy & paste) to rst which only takes a few minutes.