3.3. Documentation

Documentation renders the skin of software development. Every creature needs skin, so does software. In this session, we are going to learn how to use Sphinx to write documents.

Sphinx is a general-purpose documenting system, and provides many useful features for documenting computer programs.

To install Sphinx in Debian, execute the following command:

$ sudo apt-get install python-sphinx

3.3.1. Start a Sphinx Project with sphinx-quickstart

Sphinx provides a command to help us creating a Sphinx project template: sphinx-quickstart. After executed, it will interactively collect information to prepare the template. It starts with the name of your working directory:

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Welcome to the Sphinx 1.1.3 quickstart utility.

Please enter values 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 [.]: sphinx_guide

We then choose to separate the source and build directories of Sphinx:

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You have two options for placing the build directory for Sphinx output.
Either, you use a directory "_build" within the root path, or you separate
"source" and "build" directories within the root path.
> Separate source and build directories (y/N) [n]: y

We want the default prefixes of the template and static files:

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Inside the root directory, two more directories will be created; "_templates"
for custom HTML templates and "_static" for custom stylesheets and other static
files. You can enter another prefix (such as ".") to replace the underscore.
> Name prefix for templates and static dir [_]: _

Then fill the names of the project and author:

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The project name will occur in several places in the built documentation.
> Project name: Sphinx Guide
> Author name(s): Your Name

Specify the current version and release of the project. Since we are starting a new project, let’s use 0.0.0+ for both:

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Sphinx has the notion of a "version" and a "release" for the
software. Each version can have multiple releases. For example, for
Python the version is something like 2.5 or 3.0, while the release is
something like 2.5.1 or 3.0a1.  If you don't need this dual structure,
just set both to the same value.
> Project version: 0.0.0+
> Project release [0.0.0]: 0.0.0+

Choose the source file suffix to be .rst:

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The file name suffix for source files. Commonly, this is either ".txt"
or ".rst".  Only files with this suffix are considered documents.
> Source file suffix [.rst]: .rst

Set the top-level document to “index”:

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One document is special in that it is considered the top node of the
"contents tree", that is, it is the root of the hierarchical structure
of the documents. Normally, this is "index", but if your "index"
document is a custom template, you can also set this to another filename.
> Name of your master document (without suffix) [index]: index

Opt out the epub builder (we don’t need this in our test project):

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Sphinx can also add configuration for epub output:
> Do you want to use the epub builder (y/N) [n]: n

Many Sphinx features are implemented as Sphinx extensions. Here we will enable autodoc and pngmath:

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Please indicate if you want to use one of the following Sphinx extensions:
> autodoc: automatically insert docstrings from modules (y/N) [n]: y
> doctest: automatically test code snippets in doctest blocks (y/N) [n]: n
> intersphinx: link between Sphinx documentation of different projects (y/N) [n]: n
> todo: write "todo" entries that can be shown or hidden on build (y/N) [n]: n
> coverage: checks for documentation coverage (y/N) [n]: n
> pngmath: include math, rendered as PNG images (y/N) [n]: y
> mathjax: include math, rendered in the browser by MathJax (y/N) [n]: n
> ifconfig: conditional inclusion of content based on config values (y/N) [n]: n
> viewcode: include links to the source code of documented Python objects (y/N) [n]: n

In Unix-like Sphinx uses make to control the document generation, and in Windows it uses Windows batch file:

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A Makefile and a Windows command file can be generated for you so that you
only have to run e.g. `make html' instead of invoking sphinx-build
directly.
> Create Makefile? (Y/n) [y]: y
> Create Windows command file? (Y/n) [y]: y
Creating file sphinx_guide/source/conf.py.
Creating file sphinx_guide/source/index.rst.
Creating file sphinx_guide/Makefile.
Creating file sphinx_guide/make.bat.

As such, we finished all steps to create a Sphinx project.

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Finished: An initial directory structure has been created.

You should now populate your master file sphinx_guide/source/index.rst and create other documentation
source files. Use the Makefile to build the docs, like so:
   make builder
where "builder" is one of the supported builders, e.g. html, latex or linkcheck.

3.3.2. Results of sphinx-quickstart

After the above process, we will see a directory sphinx_guide in the current working directory:

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$ tree sphinx_guide/
sphinx_guide/
├── build
├── make.bat
├── Makefile
└── source
    ├── conf.py
    ├── index.rst
    ├── _static
    └── _templates

4 directories, 4 files

3.3.3. Build the Document Project to HTML

The document project is now ready to be build. Run:

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$ make -C sphinx_guide/ html
make: Entering directory `/home/yungyuc/work/writing/pyengr/examples/sphinx/stage0/sphinx_guide'
sphinx-build -b html -d build/doctrees   source build/html
Making output directory...
Running Sphinx v1.1.3
loading pickled environment... not yet created
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
writing additional files... genindex search
copying static files... done
dumping search index... done
dumping object inventory... done
build succeeded.

Build finished. The HTML pages are in build/html.
make: Leaving directory `/home/yungyuc/work/writing/pyengr/examples/sphinx/stage0/sphinx_guide'

Our document is now built and placed at sphinx_guide/build/html:

$ chrome sphinx_guide/build/html/index.html
_images/sphinx_just_created.png

3.3.4. reStructuredText

reStructuredText (usually short-handed as “reST” or “rst”) is the fundamental language that Sphinx uses for composition. The syntax of rst is designed to extend, and Sphinx uses the syntax to support a wide range of contents.

As a beginner you can start with reading the index.rst generated by sphinx-quickstart. It locates at sphinx_guide/source/index.rst:

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.. Sphinx Guide documentation master file, created by
   sphinx-quickstart on Sun Jul 14 14:06:36 2013.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to Sphinx Guide's documentation!
========================================

Contents:

.. toctree::
   :maxdepth: 2

   python
   math

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

We won’t have enough time to cover everything in rst. In the following sections we will demonstrate some important features of the format. You can check reStructuredText primer (at Sphinx) and reStructuredText (at docutils) for detailed description.

Before start, we will create placeholders for the materials to be added. Let’s insert the following at the 14th line of index.rst (at the same indentation level of :maxdepth: 2):

python
math

Also, we create the corresponding files in sphinx_guide/source directory:

$ touch python.rst math.rst

If you rebuild the document now (note, you must build the document in the directory sphinx_guide or the Makefile will be missing), you will find no change in HTML. It’s normal.

3.3.5. Documenting Python

Sphinx extends rst to let us use directives for documenting computer programs. However, by default Sphinx wants to you to write documents outside the source code, and this is what we are going to do now.

Edit the file sphinx_guide/source/python.rst and put in the following text:

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===============
Python Examples
===============

.. py:function:: one_python_function(arg1, arg2)

  This is to demonstrate how to document a Python function with Sphinx.  *arg1*
  and *arg2* are the positional arguments of the function.

.. py:class:: DemonstrativeClass

  This is a Python class.

  .. py:method:: clone_myself(param)

    This is an instance method of :py:class:`DemonstrativeClass`.  Assume the
    only argument *param* is a :py:class:`str`.  The method returns another
    :py:class:`DemonstrativeClass` object.

  .. py:attribute:: settable_value

    This is an instance attribute.  Assume it (:py:attr:`settable_value`) is
    used by :py:meth:`clone_myself`.

In the above example we used the Python domain in Sphinx. You can build the document and get the results (click the newly built Python Examples in the index page):

_images/sphinx_python.png

We used the following directives:

.. py:function:: name(signature)

See http://sphinx-doc.org/domains.html#directive-py:function. This directive allows us to document a Python function.

.. py:class:: name[(signature)]

See http://sphinx-doc.org/domains.html#directive-py:class. This directive allows us to document a Python class. We can put other directives like py:class inside it.

.. py:method:: name(signature)

See http://sphinx-doc.org/domains.html#directive-py:method. This directive allows us to document an instance method.

.. py:attribute:: name

See http://sphinx-doc.org/domains.html#directive-py:attribute. This directive allows use to document an instance attribute.

We also used the following roles to refer to Python objects:

:py:class:

See http://sphinx-doc.org/domains.html#role-py:class. It refers to a Python class.

:py:attr:

See http://sphinx-doc.org/domains.html#role-py:attr. It refers to a Python attribute.

:py:meth:

See http://sphinx-doc.org/domains.html#role-py:meth. It refers to a Python method.

This section is a simple introduction to documenting Python code. To write good documents, you need to familiarize yourself with the vocabulary in the Sphinx Python domain.

3.3.6. Mathematical Formula

Another plausible feature of Sphinx is the ability to connect to LaTeX for mathematical formula. To use this feature we need to install TeXLive:

$ sudo apt-get install texlive

When configuring our test project we’ve enabled the pngmath extension. Simple put the following text in math.rst:

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====================
Mathematical Formula
====================

This is one of my favoriate formula (one-dimensional, first-order hyperbolic
partial differential equation):

.. math::
  :label: e:onedim

  \frac{\partial u}{\partial t} + \frac{\partial f(u)}{\partial x} = 0

We can write virtually any mathematical expresions, like an integral:

.. math::
  :label: e:integral

  F(\omega) \cong \frac{\Delta x}{2}\left[
    g(0) + 2\sum_{n=1}^{N-2}g(x_n) + g(A) \right]

or a matrix:

.. math::
  :label: e:matrix

  A = \left[\begin{array}{ccc}
    a_{11} & a_{12} & a_{13} \\
    a_{21} & a_{22} & a_{23} \\
    a_{31} & a_{32} & a_{33}
  \end{array}\right]

All of Eqs. :eq:`e:onedim`, :eq:`e:integral`, and :eq:`e:matrix` can be
numbered and referred.  Inline mathematics like :math:`e = \sum_{n=0}^{\infty}
\frac{1}{n!}` also works.

The directive and role involved are:

.. math::

See http://sphinx-doc.org/ext/math.html#directive-math.

:math:

See http://sphinx-doc.org/ext/math.html#role-math.

After building the document, you can get the results by clicking the Mathematical Formula in the index page:

_images/sphinx_math.png

3.3.7. Using Third-Party Extensions (Optional)

There are a lot of extensions available to Sphinx. Some of them are organized in https://bitbucket.org/birkenfeld/sphinx-contrib/. Here I am demonstrate how to enable the third-party extension by using sphinx-issuetracker.

sudo apt-get install python-sphinx-issuetracker

For this example we will use pyengr. You need to clone it to your local computer. Right after the extension list of conf.py, add:

try:
    from sphinxcontrib import issuetracker
except ImportError:
    pass
else:
    extensions.append('sphinxcontrib.issuetracker')

Then add the configuration to the extension:

# issuetracker settings.
issuetracker = 'bitbucket'
issuetracker_project = 'yungyuc/pyengr'

After the settings, we can use #1 or #2 to refer to the issues on bitbucket, like: #1 and #2.