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Documentation¶
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.
Parameters
----------
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.
Returns
-------
string
An appropriate greetingSet up sphinx¶
Invoke the sphinx-quickstart command to build Sphinx's configuration file automatically based on questions at the command line:
sphinx-quickstart
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
%%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.',
'Miscellaneous'),
]
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
%%writefile greetings/index.rst
Welcome to Greetings's documentation!
=====================================
Simple "Hello, James" module developed to teach research software engineering.
.. autofunction:: greetings.greeter.greet
Run sphinx¶
We can run Sphinx using:
%%bash
cd greetings/
sphinx-build . 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.