Building the documentation

The YANK documentation system is modeled after the MDTraj documentation system.

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

To view the output of your build, go into the docs/_build directory and open up index.html to see how it rendered in your local browser.