The MDTraj documentation is built using sphinx and requires a few dependencies like ipython and matplotlib that you probably already have installed. We use travis-ci for continuous integration (running the tests), and also for building the documentation, which is built and pushed directly to Amazon S3 after every successful build.
Although readthedocs is a great tool, it doesn’t have the flexibility we need for this project. We use sphinx’s autodoc feature to generate documentation from docstrings, many of which are in compiled cython code. This means that building the documentation requires having a fully compiled version of MDTraj, which is not supported on readthedoc’s servers. Furthermore, our documentation includes examples (with plots!) which are built directly with the documentation, and requires a fully functional MDTraj environment.
If you’d like to build the docs on your machine, you’ll first need to install sphinx and numpydoc
pip install sphinx numpydoc
You’ll also need IPython, pandoc and runipy for the example notebooks
sudo apt-get install pandoc pip install ipython runipy
Now, go back to the docs subdirectory in the main repository. The documentation will be built in the docs/_build subdirectory
cd docs make html