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How to set up the documentation

Part one of this procedure sets up a documentation framework using Sphinx. Part two explains how you can use readthedocs.org to build your documentation automatically, and how to use conda to install the dependencies on the readthedocs server.

Set up sphinx

  1. Run sphinx-quickstart and follow instructions to set up your documentation. If you run this in a docs subdirectory, you can prevent it from cluttering up your code directories. Autodoc is recommended for python projects. You can also enable mathjax for displaying math. Be sure to generate a MakeFile and a make batch file for windows, since you'll need these to build your documentation.
  2. Modify conf.py to add your library to the path of the script, for instance if your documentation lives in a docs subdirectory of the project.

Example:

# If extensions (or modules to document with autodoc) are in another directory,``
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
  sys.path.insert(0, os.path.abspath('..'))
  1. Adjust themes, and other options that you like in conf.py.
  2. You can add documentation by editing index.rst, which uses reST. Please read the sphinx documentation for further instructions on how to write your docs.
  1. Test your docs using make html as a command. Depending on what build directory you specified (default _build), you will find the html documentation there. There is no need to commit this. You may wish to add the directory to your .gitignore file.
  2. Fix any errors or warnings that may pop up. Common errors are docstrings including rst syntax errors, and missing python dependencies.

Read the docs!

Next, the documentation needs to be built on www.readthedocs.org. This next section is important if you use conda packages to run your code and build your docs.

Enable a conda environment for ReadTheDocs

  1. Describe the necessary conda environment in a yml file, including the channels from which to download packages.

Example:

name: constph
channels:
    - omnia
dependencies:
    - python
    - openmm ==7.0rc1
    - numpy >=1.10
    - scipy >=0.17.0
    - openmmtools ==0.7.5
    - pymbar
    - openmoltools ==0.7.0
    - ambermini
    - joblib
    - lxml
  1. In the top level directory of the repository, place a file called readthedocs.yml that links to it.

Example:

conda:
    file: docs/environment.yml

Website settings

  1. Enable the repository on ReadTheDocs. Now, everytime code is pushed to master, or a release is made, new docs are automatically built.
  2. While writing documentation, you can use make html to build it locally to see a preview. If all goes well, your docs should look exactly the same on ReadTheDocs.

Disclaimer

Note that conda is currently a beta feature of readthedocs. The exact way this will work might change.

Happy documenting!

Author: Bas Rustenburg