Building the documentation

The YANK documentation system is modeled after the MDTraj documentation system and runs on Sphinx with Read The Docs styling.

The YANK documentation is built using sphinx and requires a few dependencies like Jupyter 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 formated from NumPy docstring processing. We also have custom formatting for our detailed YAML options lists.

If you’d like to build the docs on your machine, you’ll first need to install sphinx and numpydoc:

$ conda install sphinx numpydoc

You may also need Jupyter notebooks and matplotlib:

$ conda install jupyter matplotlib

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.