IPython directive is a very handy Sphinx extension for writing tutorials and documentation. In fact, I used it extensively when developing ProDy tutorials. With this directive, you just let Sphinx run a piece of code and incorporate output into the output HTML. It even allows for making plots and saving image files automatically. This post shows how to use it via Meze.
I have been using Sphinx for documenting my open-source Python packages and also maintaining a personal site. It is a great tool that handles code highlighting, cross-referencing, and hierarchical structures, and conversion of content in reStructuredText to HTML, PDF, and other formats. For documenting ProDy package, it has been extremely useful, but for my personal site, I thought, time has come for a change.