.. _documenting-matplotlib:

**********************
Documenting matplotlib
**********************

Getting started
===============

The documentation for matplotlib is generated from ReStructured Text
using the Sphinx_ documentation generation tool. Sphinx-1.0 or later
is required.

The documentation sources are found in the :file:`doc/` directory in
the trunk.  To build the users guide in html format, cd into
:file:`doc/` and do::

  python make.py html

or::

  ./make.py html

you can also pass a ``latex`` flag to make.py to build a pdf, or pass no
arguments to build everything.

The output produced by Sphinx can be configured by editing the :file:`conf.py`
file located in the :file:`doc/`.


Organization of matplotlib's documentation
==========================================

The actual ReStructured Text files are kept in :file:`doc/users`,
:file:`doc/devel`, :file:`doc/api` and :file:`doc/faq`. The main entry point is
:file:`doc/index.rst`, which pulls in the :file:`index.rst` file for the users
guide, developers guide, api reference, and faqs. The documentation suite is
built as a single document in order to make the most effective use of cross
referencing, we want to make navigating the Matplotlib documentation as easy as
possible.

Additional files can be added to the various guides by including their base
file name (the .rst extension is not necessary) in the table of contents.
It is also possible to include other documents through the use of an include
statement, such as::

  .. include:: ../../TODO


.. _formatting-mpl-docs:

Formatting
==========

The Sphinx website contains plenty of documentation_ concerning ReST markup and
working with Sphinx in general. Here are a few additional things to keep in mind:

* Please familiarize yourself with the Sphinx directives for `inline
  markup`_. Matplotlib's documentation makes heavy use of cross-referencing and
  other semantic markup. For example, when referring to external files, use the
  ``:file:`` directive.

* Function arguments and keywords should be referred to using the *emphasis*
  role. This will keep matplotlib's documentation consistant with Python's
  documentation::

    Here is a description of *argument*

  Please do not use the `default role`::

    Please do not describe `argument` like this.

  nor the ``literal`` role::

    Please do not describe ``argument`` like this.

* Sphinx does not support tables with column- or row-spanning cells for
  latex output. Such tables can not be used when documenting matplotlib.

* Mathematical expressions can be rendered as png images in html, and in the
  usual way by latex. For example:

  ``:math:`\sin(x_n^2)``` yields: :math:`\sin(x_n^2)`, and::

    .. math::

      \int_{-\infty}^{\infty}\frac{e^{i\phi}}{1+x^2\frac{e^{i\phi}}{1+x^2}}

  yields:

  .. math::

    \int_{-\infty}^{\infty}\frac{e^{i\phi}}{1+x^2\frac{e^{i\phi}}{1+x^2}}

* Interactive IPython sessions can be illustrated in the documentation using
  the following directive::

    .. sourcecode:: ipython

      In [69]: lines = plot([1,2,3])

  which would yield:

  .. sourcecode:: ipython

    In [69]: lines = plot([1,2,3])

* Footnotes [#]_ can be added using ``[#]_``, followed later by::

    .. rubric:: Footnotes

    .. [#]

  .. rubric:: Footnotes

  .. [#] For example.

* Use the *note* and *warning* directives, sparingly, to draw attention to
  important comments::

    .. note::
       Here is a note

  yields:

  .. note::
     here is a note

  also:

  .. warning::
     here is a warning

* Use the *deprecated* directive when appropriate::

    .. deprecated:: 0.98
       This feature is obsolete, use something else.

  yields:

  .. deprecated:: 0.98
     This feature is obsolete, use something else.

* Use the *versionadded* and *versionchanged* directives, which have similar
  syntax to the *deprecated* role::

    .. versionadded:: 0.98
       The transforms have been completely revamped.

  .. versionadded:: 0.98
     The transforms have been completely revamped.

* Use the *seealso* directive, for example::

    .. seealso::

       Using ReST :ref:`emacs-helpers`:
          One example

       A bit about :ref:`referring-to-mpl-docs`:
          One more

  yields:

  .. seealso::

     Using ResT :ref:`emacs-helpers`:
        One example

     A bit about :ref:`referring-to-mpl-docs`:
        One more

* Please keep the :ref:`glossary` in mind when writing documentation. You can
  create a references to a term in the glossary with the ``:term:`` role.

* The autodoc extension will handle index entries for the API, but additional
  entries in the index_ need to be explicitly added.

.. _Sphinx: http://sphinx.pocoo.org
.. _documentation: http://sphinx.pocoo.org/contents.html
.. _`inline markup`: http://sphinx.pocoo.org/markup/inline.html
.. _index: http://sphinx.pocoo.org/markup/para.html#index-generating-markup

Docstrings
----------

In addition to the aforementioned formatting suggestions:

* Please limit the text width of docstrings to 70 characters.

* Keyword arguments should be described using a definition list.

  .. note::
     matplotlib makes extensive use of keyword arguments as pass-through
     arguments, there are a many cases where a table is used in place of a
     definition list for autogenerated sections of docstrings.


Figures
=======

Dynamically generated figures
-----------------------------

Figures can be automatically generated from scripts and included in
the docs.  It is not necessary to explicitly save the figure in the
script, this will be done automatically at build time to ensure that
the code that is included runs and produces the advertised figure.

The path should be relative to the ``doc`` directory.  Any plots
specific to the documentation should be added to the ``doc/pyplots``
directory and committed to git.  Plots from the ``examples`` directory
may be referenced through the symlink ``mpl_examples`` in the ``doc``
directory.  e.g.::

  .. plot:: mpl_examples/pylab_examples/simple_plot.py

The ``:scale:`` directive rescales the image to some percentage of the
original size, though we don't recommend using this in most cases
since it is probably better to choose the correct figure size and dpi
in mpl and let it handle the scaling.

Plot directive documentation
''''''''''''''''''''''''''''

.. automodule:: matplotlib.sphinxext.plot_directive

Static figures
--------------

Any figures that rely on optional system configurations need to be handled a
little differently. These figures are not to be generated during the
documentation build, in order to keep the prerequisites to the documentation
effort as low as possible. Please run the :file:`doc/pyplots/make.py` script
when adding such figures, and commit the script **and** the images to
git. Please also add a line to the README in doc/pyplots for any additional
requirements necessary to generate a new figure. Once these steps have been
taken, these figures can be included in the usual way::

   .. plot:: pyplots/tex_unicode_demo.py
      :include-source:

Examples
--------

The source of the files in the ``examples`` directory are
automatically included in the HTML docs.  An image is generated and
included for all examples in the ``api`` and ``pylab_examples``
directories.  To exclude the example from having an image rendered,
insert the following special comment anywhere in the script::

  # -*- noplot -*-

Animations
----------

We have a matplotlib google/gmail account with username ``mplgithub``
which we used to setup the github account but can be used for other
purposes, like hosting google docs or youtube videos.  You can embed a
matplotlib animation in the docs by first saving the animation as a
movie using :meth:`matplotlib.animation.Animation.save`, and then
uploading to `matplotlib's youtube
channel <http://www.youtube.com/user/matplotlib>`_ and inserting the
embedding string youtube provides like::

  .. raw:: html

     <iframe width="420" height="315"
       src="http://www.youtube.com/embed/32cjc6V0OZY"
       frameborder="0" allowfullscreen>
     </iframe>

An example save command to generate a movie looks like this

.. sourcecode:: python

    ani = animation.FuncAnimation(fig, animate, np.arange(1, len(y)),
        interval=25, blit=True, init_func=init)

    ani.save('double_pendulum.mp4', fps=15)

Contact John Hunter for the login password to upload youtube videos of
google docs to the mplgithub account.

.. _referring-to-mpl-docs:

Referring to mpl documents
==========================

In the documentation, you may want to include to a document in the
matplotlib src, e.g. a license file or an image file from `mpl-data`,
refer to it via a relative path from the document where the rst file
resides, eg, in :file:`users/navigation_toolbar.rst`, we refer to the
image icons with::

    .. image:: ../../lib/matplotlib/mpl-data/images/subplots.png

In the `users` subdirectory, if I want to refer to a file in the mpl-data
directory, I use the symlink directory.  For example, from
`customizing.rst`::

    .. literalinclude:: ../../lib/matplotlib/mpl-data/matplotlibrc

One exception to this is when referring to the examples dir.  Relative
paths are extremely confusing in the sphinx plot extensions, so
without getting into the dirty details, it is easier to simply include
a symlink to the files at the top doc level directory.  This way, API
documents like :meth:`matplotlib.pyplot.plot` can refer to the
examples in a known location.

In the top level doc directory we have symlinks pointing to
the mpl `examples`::

    home:~/mpl/doc> ls -l mpl_*
    mpl_examples -> ../examples

So we can include plots from the examples dir using the symlink::

    .. plot:: mpl_examples/pylab_examples/simple_plot.py


We used to use a symlink for :file:`mpl-data` too, but the distro
becomes very large on platforms that do not support links (eg the font
files are duplicated and large)

.. _internal-section-refs:

Internal section references
===========================

To maximize internal consistency in section labeling and references,
use hypen separated, descriptive labels for section references, eg::

    .. _howto-webapp:

and refer to it using  the standard reference syntax::

    See :ref:`howto-webapp`

Keep in mind that we may want to reorganize the contents later, so
let's avoid top level names in references like ``user`` or ``devel``
or ``faq`` unless necesssary, because for example the FAQ "what is a
backend?" could later become part of the users guide, so the label::

    .. _what-is-a-backend

is better than::

    .. _faq-backend

In addition, since underscores are widely used by Sphinx itself, let's prefer
hyphens to separate words.



Section names, etc
==================

For everything but top level chapters, please use ``Upper lower`` for
section titles, eg ``Possible hangups`` rather than ``Possible
Hangups``

Inheritance diagrams
====================

Class inheritance diagrams can be generated with the
``inheritance-diagram`` directive.  To use it, you provide the
directive with a number of class or module names (separated by
whitespace).  If a module name is provided, all classes in that module
will be used.  All of the ancestors of these classes will be included
in the inheritance diagram.

A single option is available: *parts* controls how many of parts in
the path to the class are shown.  For example, if *parts* == 1, the
class ``matplotlib.patches.Patch`` is shown as ``Patch``.  If *parts*
== 2, it is shown as ``patches.Patch``.  If *parts* == 0, the full
path is shown.

Example::

    .. inheritance-diagram:: matplotlib.patches matplotlib.lines matplotlib.text
       :parts: 2

.. inheritance-diagram:: matplotlib.patches matplotlib.lines matplotlib.text
   :parts: 2


.. _emacs-helpers:

Emacs helpers
=============

There is an emacs mode `rst.el
<http://docutils.sourceforge.net/tools/editors/emacs/rst.el>`_ which
automates many important ReST tasks like building and updateing
table-of-contents, and promoting or demoting section headings.  Here
is the basic ``.emacs`` configuration::

    (require 'rst)
    (setq auto-mode-alist
          (append '(("\\.txt$" . rst-mode)
                    ("\\.rst$" . rst-mode)
                    ("\\.rest$" . rst-mode)) auto-mode-alist))


Some helpful functions::

    C-c TAB - rst-toc-insert

      Insert table of contents at point

    C-c C-u - rst-toc-update

        Update the table of contents at point

    C-c C-l rst-shift-region-left

        Shift region to the left

    C-c C-r rst-shift-region-right

        Shift region to the right

.. TODO: Add section about uploading docs