Documentation is hard

  • Good documentation is hard, and very expensive.
  • Bad documentation is detrimental.
  • Good documentation quickly becomes bad if not kept up-to-date with code changes.
  • Professional companies pay large teams of documentation writers.

Prefer readable code with tests and vignettes

If you don't have the capacity to maintain great documentation, focus on:

  • Readable code
  • Automated tests
  • Small code samples demonstrating how to use the api

Comment-based Documentation tools

Documentation tools can produce extensive documentation about your code by pulling out comments near the beginning of functions, together with the signature, into a web page.

The most popular is Doxygen

Have a look at an example of some Doxygen output

Sphinx is nice for Python, and works with C++ as well. Here's some Sphinx-generated output and the corresponding source code Breathe can be used to make Sphinx and Doxygen work together.

Roxygen is good for R.

Example of using Sphinx

Write some docstrings

We're going to document our "greeter" example using docstrings with Sphinx.

There are various conventions for how to write docstrings, but the native sphinx one doesn't look nice when used with the built in help system.

In writing Greeter, we used the docstring conventions from NumPy. So we use the numpydoc sphinx extension to support these.

Generate a greeting string for a person.

personal: str
    A given name, such as Will or Jean-Luc

family: str
    A family name, such as Riker or Picard
title: str
    An optional title, such as Captain or Reverend
polite: bool
    True for a formal greeting, False for informal.

    An appropriate greeting

Set up sphinx

Invoke the sphinx-quickstart command to build Sphinx's configuration file automatically based on questions at the command line:


Which responds:

Welcome to the Sphinx 1.2.3 quickstart utility.

Please enter avalues for the following settings (just press Enter to
accept a default value, if one is given in brackets).

Enter the root path for documentation.
> Root path for the documentation [.]:

and then look at and adapt the generated config, a file called conf.py in the root of the project. This contains the project's Sphinx configuration, as Python variables:

#Add any Sphinx extension module names here, as strings. They can be
#extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    'sphinx.ext.autodoc',  # Support automatic documentation
    'sphinx.ext.coverage', # Automatically check if functions are documented
    'sphinx.ext.mathjax',  # Allow support for algebra
    'sphinx.ext.viewcode', # Include the source code in documentation
    'numpydoc'             # Support NumPy style docstrings

To proceed with the example, we'll copy a finished conf.py into our folder, though normally you'll always use sphinx-quickstart

In [1]:
%%writefile greetings/conf.py

import sys
import os

extensions = [
    'sphinx.ext.autodoc',  # Support automatic documentation
    'sphinx.ext.coverage', # Automatically check if functions are documented
    'sphinx.ext.mathjax',  # Allow support for algebra
    'sphinx.ext.viewcode', # Include the source code in documentation
    'numpydoc'             # Support NumPy style docstrings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
project = u'Greetings'
copyright = u'2014, James Hetherington'
version = '0.1'
release = '0.1'
exclude_patterns = ['_build']
pygments_style = 'sphinx'
htmlhelp_basename = 'Greetingsdoc'
latex_elements = {

latex_documents = [
  ('index', 'Greetings.tex', u'Greetings Documentation',
   u'James Hetherington', 'manual'),

man_pages = [
    ('index', 'greetings', u'Greetings Documentation',
     [u'James Hetherington'], 1)

texinfo_documents = [
  ('index', 'Greetings', u'Greetings Documentation',
   u'James Hetherington', 'Greetings', 'One line description of project.',
Overwriting greetings/conf.py

Define the root documentation page

Sphinx uses RestructuredText another wiki markup format similar to Markdown.

You define an "index.rst" file to contain any preamble text you want. The rest is autogenerated by sphinx-quickstart

In [2]:
%%writefile greetings/index.rst
Welcome to Greetings's documentation!

Simple "Hello, James" module developed to teach research software engineering.

.. autofunction:: greetings.greeter.greet
Overwriting greetings/index.rst

 Run sphinx

We can run Sphinx using:

In [3]:
cd greetings/
sphinx-build . doc
Running Sphinx v1.8.3
loading pickled environment... failed: build environment version not current
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 1 source files that are out of date
updating environment: 1 added, 0 changed, 0 removed
reading sources... [100%] index

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] index

generating indices... genindex
highlighting module code... [100%] greetings.greeter

writing additional pages... search
copying static files... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded.

The HTML pages are in doc.

Sphinx output

Sphinx's output is html. We just created a simple single function's documentation, but Sphinx will create multiple nested pages of documentation automatically for many functions.

In [ ]: