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How to generate beautiful technical documentation

In the previous post I gave some motivational tips to inspire you to document your coding project. In this post I will illustrate how you can convert documentation written as plain text files into beautiful HTML documentation using a tool called Sphinx.

Installing Sphinx

Sphinx is a documentation generation tool written in Python and it can be installed using pip. If you do not yet have pip installed on your system please have a look at the pip installation notes.

Let us install Sphinx.

$ sudo pip install -U Sphinx

Generating boilerplate files for the documentation

Suppose that we are at the early stages of our project. All we have is a README file with the content below.

README
======

This project aims to inspire people to write more and better documentation.

However, we know that we want to store more extensive documentation in a subdirectory named docs. Let us create that directory and add some Sphinx boilerplate files to it.

$ mkdir docs
$ cd docs
$ sphinx-quickstart

The last command will prompt you for answers to a bunch of questions on how you want to setup your documentation and what extensions you want to enable. I tend to accept the defaults for everything except the question on whether or not I want to separate the source and build directories.

> Separate source and build directories (y/n) [n]: y

The input fields for project name, author name(s) and project version require you to provide some information. Below are the answers that I gave to these questions in this instance.

> Project name: Better documentation
> Author name(s): Tjelvar Olsson
> Project version: 0.0.1

Let’s see what was generated.

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

4 directories, 4 files
 ```

Let us go through the files one by one. The ``Makefile`` allows us to build the
documentation using ``make``. The ``make.bat`` file allows us to build the documentation
on Windows based systems. The ``source/conf.py`` file contains configurations for building
the documentation (we will edit this later). The ``index.rst`` file is the root file of
the documentation we are about to write. 

## Let's build some documentation

Before we do anything else let us see what we get when we build the documentation.

$ make html ```

This will create output in the directory build/html, open the build/html/index.html file in your browser of choice. You should see something along the lines of the below.

Sphinx default look

Now have a look at the content of the source/index.rst file.

.. Better documentation documentation master file, created by
   sphinx-quickstart on Mon Jun 29 11:00:21 2015.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to Better documentation's documentation!
================================================

Contents:

.. toctree::
   :maxdepth: 2



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

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

The first section is a comment (the section starting with ..). This is followed by a header (denoted by the = underline). The .. toctree:: section is Sphinx’s way of denoting that a list of other files should be included (at the moment we have none). Finally, in the Indices and tables section there are links to index, module and search pages. If you are documenting a Python package the module page will contain links to the modules in your package.

Adding some more content

Let us add some more content. Create the file source/intro.rst and copy and paste the text below into it.

Introduction
============

The purpose of this project is to help scientists write better documentation.

Now add a link to it in source/index.rst.

Contents:

.. toctree::
   :maxdepth: 2

   intro

Note that the reference of the file to be included does not need the .rst extension. Furthermore it needs to be indented to the same level as :maxdepth: (by default this is three spaces). The latter has caught me out many times as I tend to indent four spaces.

If you rebuild the documentation using make html you will see the content of the source/intro.rst file included in the documentation.

reStructuredText markup

You may have noticed that we can create headers by underlining them with special characters. Sphinx uses reStructuredText as a markup language. For a quick introduction to the reStructuredText syntax have a look at A ReStructuredText Primer followed by Quick reStructuredText. Another good source is Sphinx’s ReStructuredText Primer.

Including code snippets in the documentation

Sphinx has taken advantage of the fact that reStructuredText is extensible and has added directives of its own. We have already seen one of these: the toctree directive.

Let us have a look at the code-block directive, which can be used to include code snippets. Create the file source/code_example.rst and add the text below to it.

Code example
============

Here is a Python function.

.. code-block:: python

    def greet(name):
        print("Hello {}".format(name))

Here is a C function.

.. code-block:: C

    int add(int a, int b) {
        return a + b;
    }

Remember to include the file into the toctree of source/index.rst.

.. toctree::
   :maxdepth: 2

   intro
   code_example

Use make html to build the documentation and behold the beautifully generated code snippets included in your documentation.

It is also possible to include whole files of source code in your documentation. Copy and paste the text below into a file named source/example_script.py.

"""This is an example script."""
import sys

def greet(name):
    """Return greeting."""
    return "Hello {}!".format(name)

if __name__ == "__main__":
    name = sys.argv[1]
    print(greet(name))

Now we will use Sphinx’s include directive to include the content of this script into the “Code example” page. Add the lines below to the end of the source/code_example.rst file.

Below is the content of a Python sample script.

.. literalinclude:: example_script.py
   :language: python

Sphinx also has several options for styling the display of your code snippets. For example you can add line numbers and emphasize particular lines. For more inspiration on how to include code snippets in your documentation have a look at Showing code examples in the Sphinx documentation.

Generating API documentaiton for Python projects

Sphinx has got particularly good support for documenting Python projects.

Let us create a module named chemistry for us to document at the root level of the project .

$ cd ../
$ mkdir chemistry
$ ls
README
docs
chemistry

Create the file chemistry/__init__.py and add the code below to it.

"""Basic chemistry module.

The :mod:`chemistry` module contains three classes:

- :class:`chemistry.Atom`
- :class:`chemistry.Bond`
- :class:`chemistry.Molecule`

One can use the :func:`chemistry.Molecule.add_atom` and
:func:`chemsitry.Molecule.add_bond` functions to build up a molecule.

Example illustrating how to create a methane molecule.

>>> from chemistry import Molecule
>>> mol = Molecule('Methane')
>>> carbon_index = mol.add_atom(atomic_number=6)
>>> hydrogen1_index = mol.add_atom(atomic_number=1)
>>> hydrogen2_index = mol.add_atom(atomic_number=1)
>>> hydrogen3_index = mol.add_atom(atomic_number=1)
>>> hydrogen4_index = mol.add_atom(atomic_number=1)
>>> bond1_index = mol.add_bond(carbon_index, hydrogen1_index)
>>> bond2_index = mol.add_bond(carbon_index, hydrogen2_index)
>>> bond3_index = mol.add_bond(carbon_index, hydrogen3_index)
>>> bond4_index = mol.add_bond(carbon_index, hydrogen4_index)
"""

class Atom(object):
    """Class representing an atom."""

    def __init__(self, atomic_number):
        self.atomic_number = atomic_number
        self.bonds = []

    def bond_to(self, other_atom):
        """Return the :class:`chemistry.Bond` formed between the two atoms.

        :param other_atom: :class:`chemistry.Atom` to form :class:`chemistry.Bond` to
        :returns: :class:`chemistry.Bond`
        """
        bond = Bond(self, other_atom)
        self.bonds.append(bond)
        other_atom.bonds.append(bond)
        return bond

class Bond(object):
    """Class representing a bond between two atoms."""
    
    def __init__(self, atom1, atom2):
        self.atoms = (atom1, atom2)

class Molecule(object):
    """Class representing a molecule consisting of atoms and bonds."""

    def __init__(self, identifier):
        self.identifier = identifier
        self.atoms = []
        self.bonds = []

    def add_atom(self, atomic_number):
        """Return the list index of the atom added to the molecule.

        :param atomic_number: atomic number of the atom to be added
        :returns: index of the atom in the molecule
        """
        atom = Atom(atomic_number)
        self.atoms.append(atom)
        return len(self.atoms) - 1

    def add_bond(self, atom1_index, atom2_index):
        """Return the list index of the bond added to the molecule.

        :param atom1_index: atom's index in molecule
        :param atom2_index: atom's index in molecule
        :returns: index of the bond in the molecule
        """
        atom1 = self.atoms[atom1_index]
        atom2 = self.atoms[atom2_index]
        bond = atom1.bond_to(atom2)
        self.bonds.append(bond)
        return len(self.bonds) - 1

We will now use Sphinx’s autodoc functionality to generate API documentation for this module. First of all we need to add the sphinx.ext.autodoc extension to the docs/source/conf.py file.

# 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']

In the same file we also need to specify the path to the module that we want to generate documentation for.

# 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('../../'))

Now create the file docs/source/api.rst and copy and paste the text below into it.

API documentaiton
=================

.. automodule:: chemistry
   :members:

We also need to remember to include the api.rst file in the toctree. Edit the docs/source/index.rst file to match the below.

.. toctree::
   :maxdepth: 2

   intro
   code_example
   api

Finally, regenerate the documentation by running make html in the docs directory and behold the beautifully generated API documentation.

If you interact with the generated HTML documentation you will note that the constructs following the pattern below have been converted into hyperlinks.

:mod:`chemistry`
:class:`chemistry.Molecule`
:func:`chemistry.Molecule.add_atom`

These directives can be used anywhere in your documentation to link to the relevant section in the API documentation. Having descriptive documentation that contains links to the more technical API documentation is very pleasant and these directives make it very easy to do so.

It is also worth commenting on the :param: and :returns: directives used in the docstrings. These are part of a larger set of description directives that are formatted nicely by Sphinx. For more information have a look at the info field list section in the Sphinx documentation.

What about the original README file?

Let us finish off by including the content of the original README file into the generated HTML documenation.

Create the file docs/source/README.rst and copy and paste the text below into it.

.. include:: ../../README

This will include the content of the top level README file into the documentation.

Styling the documentaiton

The default theme of Sphinx is currently Alabaster. It is very beautiful. However, personally I prefer the Sphinx ReadTheDocs theme. In particular because of its left hand side navigation bar. Let’s check it out.

First of all we install the theme using pip.

$ pip install sphinx_rtd_theme

Now we need to edit theme section in docs/source/conf.py to look like the below.

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#html_theme = 'alabaster'

# on_rtd is whether we are on readthedocs.org
on_rtd = os.environ.get('READTHEDOCS', None) == 'True'

if not on_rtd:  # only import and set the theme if we're building docs locally
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

# otherwise, readthedocs.org uses their theme by default, so no need to specify it

Note that the code above includes some logic for handling the cases where one hosts the documentation on readthedocs.

Regenerate the documentation by running make html in the docs directory and explore the look and feel of this new theme. Note in particular the behaviour of the left hand side navigation bar and the clear “next” and “previous” buttons at the bottom of each page.

Sphinx rdt theme

For more information on the ReadTheDocs theme have a look here.

ReadTheDocs

Whilst on the subject it is worth mentioning the ability to host your documentation on readthedocs. Simply sign-up for an account, link your GitHub/BitBucket account and then you can select the projects that you want to host on readthedocs. It is great!

It is worth noting that if your project documentation includes links to packages such as numpy and scipy you will need to mock these out in the conf.py file. For more information have a look at this readthedocs faq. For a real life example have a look at this conf.py.

Further reading

I hope this post has inspired you to try out Sphinx. It is a wonderful tool for generating beautiful documentation!

Below are a couple links to other resources on how to use Sphinx.