How to Document PyNE

Documentation takes many forms. This will guide you through the steps of successful documentation.


No matter what language you are writing in, you should always have documentation strings along with you code. This is so important that it is part of the style guide. When writing in Python or Cython, your docstrings should be in reStructured Text using the numpydoc format. When writing in C, C++, or Fortran you should write your docstrings in Doxygen.

Auto-Documentation Hooks

The docstrings that you have written will automatically be connected to the website, once the appropriate hooks have been setup. At this stage, all documentation lives within pyne’s top-level docs directory. PyNE uses the sphinx tool to manage and generate the documentation, which you can learn about from the sphinx website. If you want to generate the documentaion, first pyne itself must be installed and then you may run the following command from the docs dir:

~/pyne/docs $ make html

For each new module, you will have to supply the appropriate hooks. This should be done the first time that the module appears in a pull request. From here, call the new module mymod. The following explains how to add hooks based on language:

Python & Cython Hooks

Python and Cython documentation lives in the docs/pyapi directory. First create a file in this directory that represents the new module called mymod.rst. The docs/pyapi directory matches the structure of the pyne directory. So if your module is in a sub-package, you’ll need to go into the sub-package’s directory before creating mymod.rst. The contents of this file should be as follows:


.. _pyne_mymod:

My Awesome Module -- :mod:`pyne.mymod`

.. currentmodule:: pyne.mymod

.. automodule:: pyne.mymod

This will discover all of the docstrings in mymod and create the appropriate webpage. Now, you need to hook this page up to the rest of the website.

Go into the index.rst file in docs/pyne or other subdirectory and add mymod to the appropriate toctree (which stands for table-of-contents tree). Note that every sub-package has its own index.rst file.

C++ et al. Hooks

This is very similar to the Python hooks except that all of the pages live in the docs/cppapi directory. Again, create a mymod.rst file in the appropriate place. This file will have contents as follows:


My Awesome Module

.. autodoxygenindex:: mymod.h
    :source: pyne_mymod

This must be performed for every header file. Again, open up the index.rst file edit the toctree to indclue mymod where appropriate.

User’s Guide

The user’s guide is available for additions via the docs/usersguide directory. This is a more free-form and high-level introduction to pyne topics than anywhere else. Simply write rst files and add them to the index.rst.

Theory Manual

The theory manual is a required document for our quality assurance. These documents have a well defined structure that you may see in the docs/theorymanual/theory_template.rst.t file.