In order to build the documentation you need to install the requirements via the following command:
pip install -r requirements-build-doc.txt
This will mainly drag in sphinx, matplotlib, jupyter notebooks and some small utilities.
After you have successfully installed these dependencies, you can invoke:
make ipython-rst
to execute and convert the notebooks found in ../pyemma-ipython
After this step you are ready to convert the generated RST files to HTML via:
make html
Note that for a quick build you can safely omit the ipython-rst step.