Writing Documentation

In this section you will:

  • Generate HTML documentation using Sphinx, starting from a working example provided by the cookiecutter template.

  • Edit usage.rst to add API documentation and narrative documentation.

  • Learn how to incorporate code examples, IPython examples, matplotlib plots, and typeset math.

Build the docs

Almost all scientific Python projects use the Sphinx documentation generator. The cookiecutter template provided a working example with some popular extensions installed and some sample pages.

example/
(...)
├── docs
│   ├── Makefile
│   ├── build
│   ├── make.bat
│   └── source
│       ├── _static
│       │   └── .placeholder
│       ├── _templates
│       ├── conf.py
│       ├── index.rst
│       ├── installation.rst
│       ├── release-history.rst
│       └── usage.rst
(...)

The .rst files are source code for our documentation. To build HTML pages from this source, run:

make -C docs html

You should see some log message ending in build succeeded.

This output HTML will be located in docs/build/html. In your Internet browser, open file://.../docs/build/html/index.html, where ... is the path to your project directory. If you aren’t sure sure where that is, type pwd.

Update the docs

The source code for the documentation is located in docs/source/. Sphinx uses a markup language called ReStructured Text (.rst). We refer you to this primer to learn how to denote headings, links, lists, cross-references, etc.

Sphinx formatting is sensitive to whitespace and generally quite picky. We recommend running make -C docs html often to check that the documentation builds successfully. Remember to commit your changes to git periodically.

Good documentation includes both:

  • API (Application Programming Interface) documentation, listing every public object in the library and its usage

  • Narrative documentation interleaving prose and code examples to explain how and why a library is meant to be used

API Documentation

Most the work of writing good API documentation goes into writing good, accurate docstrings. Sphinx can scrape that content and generate HTML from it. Again, most scientific Python libraries use the numpydoc standard, which looks like this:

# example/refraction.py

import numpy as np


def snell(theta_inc, n1, n2):
    """
    Compute the refraction angle using Snell's Law.

    See https://en.wikipedia.org/wiki/Snell%27s_law

    Parameters
    ----------
    theta_inc : float
        Incident angle in radians.
    n1, n2 : float
        The refractive index of medium of origin and destination medium.

    Returns
    -------
    theta : float
        refraction angle

    Examples
    --------
    A ray enters an air--water boundary at pi/4 radians (45 degrees).
    Compute exit angle.

    >>> snell(np.pi/4, 1.00, 1.33)
    0.5605584137424605
    """
    return np.arcsin(n1 / n2 * np.sin(theta_inc))

Autodoc

In an rst file, such as docs/source/usage.rst, we can write:

.. autofunction:: example.refraction.snell

which renders in HTML like so:

example.refraction.snell(theta_inc, n1, n2)[source]

Compute the refraction angle using Snell’s Law.

See https://en.wikipedia.org/wiki/Snell%27s_law

Parameters
theta_incfloat

Incident angle in radians.

n1, n2float

The refractive index of medium of origin and destination medium.

Returns
thetafloat

refraction angle

Examples

A ray enters an air–water boundary at pi/4 radians (45 degrees). Compute exit angle.

>>> snell(np.pi/4, 1.00, 1.33)
0.5605584137424605

From here we refer you to the sphinx autodoc documentation.

Autosummary

If you have many related objects to document, it may be better to display them in a table. Each row will include the name, the signature (optional), and the one-line description from the docstring.

In rst we can write:

.. autosummary::
   :toctree: generated/

   example.refraction.snell

which renders in HTML like so:

example.refraction.snell(theta_inc, n1, n2)

Compute the refraction angle using Snell’s Law.

It links to the full rendered docstring on a separate page that is automatically generated.

From here we refer you to the sphinx autosummary documentation.

Narrative Documentation

Code Blocks

Code blocks can be interspersed with narrative text like this:

Scientific libraries conventionally use radians. Numpy provides convenience
functions for converting between radians and degrees.

.. code-block:: python

   import numpy as np


   np.deg2rad(90)  # pi / 2
   np.rad2deg(np.pi / 2)  # 90.0

which renders in HTML as:

Scientific libraries conventionally use radians. Numpy provides convenience functions for converting between radians and degrees.

import numpy as np


np.deg2rad(90)  # pi / 2
np.rad2deg(np.pi / 2)  # 90.0

To render short code expressions inline, surround them with back-ticks. This:

Try ``snell(0, 1, 1.33)``.

renders in HTML as:

Try snell(0, 1, 1.33).

From here we refer you to the sphinx code example documentation.

IPython Examples

IPython’s sphinx extension, which is included by the cookiecutter template, makes it possible to execute example code and capture its output when the documentation is built. This rst code:

.. ipython:: python

   1 + 1

renders in HTML as:

In [1]: 1 + 1
Out[1]: 2

From here we refer you to the IPython sphinx directive documentation.

Plots

Matplotlib’s sphinx extension, which is included by the cookiecutter template, makes it possible to display matplotlib figures in line. This rst code:

.. plot::

   import matplotlib.pyplot as plt
   fig, ax = plt.subplots()
   ax.plot([1, 1, 2, 3, 5, 8])

renders in HTML as:

_images/writing-docs-1.png

From here we refer you to the matplotlib plot directive documentation.

Math (LaTeX)

Sphinx can render LaTeX typeset math in the browser (using MathJax). This rst code:

.. math::

    \int_0^a x\,dx = \frac{1}{2}a^2

renders in HTML as:

\[\int_0^a x\,dx = \frac{1}{2}a^2\]

This notation can also be used in docstrings. For example, we could add the equation of Snell’s Law to the docstring of snell().

Math can also be written inline. This rst code:

The value of :math:`\pi` is 3.141592653....

renders in HTML as:

The value of \(\pi\) is 3.141592653….

Referencing Documented Objects

You can create links to documented functions like so:

The :func:`example.refraction.snell` function encodes Snell's Law.

The example.refraction.snell() function encodes Snell’s Law.

Adding a ~ omits the module path from the link text.

The :func:`~example.refraction.snell` function encodes Snell's Law.

The snell() function encodes Snell’s Law.

See the Sphinx documentation for more.