.. _documenting-quantities:

**********************
Documenting Quantities
**********************

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

The documentation for Quantities is generated from ReStructured Text
using the Sphinx_ documentation generation tool and the numpydoc_
Sphinx extension. Sphinx-0.6.3 or later is required. You can obtain
Sphinx and numpydoc from the `Python Package Index`_ or
by doing::

  pip install sphinx

.. _Sphinx: http://sphinx.pocoo.org/
.. _numpydoc: http://pypi.python.org/pypi/numpydoc
.. _`Python Package Index`: http://pypi.python.org/pypi

The documentation sources are found in the :file:`doc/` directory in the trunk.
The output produced by Sphinx can be configured by editing the :file:`conf.py`
file located in the :file:`doc/` directory. To build the users guide in html
format, run from the main quantities directory::

  python setup.py build_sphinx

and the html will be produced in `build/sphinx/html`. To build the pdf file::

  python setup.py build_sphinx -b latex
  cd build/sphinx/latex
  make all-pdf


Organization of Quantities' documentation
==========================================

The actual ReStructured Text files are kept in :file:`doc`. The main
entry point is :file:`doc/index.rst`, which pulls in the
:file:`index.rst` file for the user guide and the developers guide.
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 Quantities 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-quantities-docs:

Formatting
==========

The Sphinx website contains plenty of documentation_ concerning ReST markup and
working with Sphinx in general. Since quantities is so closely coupled with the
numpy package, quantities will conform to numpy's documentation standards and
use numpy's documentation tools. Please familiarize yourself with the `docstring
standard`_ and the examples_ `like these`_.

.. _`docstring standard`: http://projects.scipy.org/scipy/numpy/wiki/CodingStyleGuidelines#docstring-standard
.. _examples: http://projects.scipy.org/scipy/numpy/browser/trunk/doc/example.py#L37
.. _`like these`: http://projects.scipy.org/scipy/numpy/browser/trunk/doc/EXAMPLE_DOCSTRING.txt

Here are a few additional things to keep in
mind:

* Please familiarize yourself with the Sphinx directives for `inline
  markup`_. Quantities' 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 Quantities' 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 Quantities.

* 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}}

* 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-quantities-docs`:
          One more

  yields:

  .. seealso::

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

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

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

.. _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.

Figures
=======

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

The top level :file:`doc` dir has a folder called :file:`pyplots` in
which you should include any pyplot plotting scripts that you want to
generate figures for the documentation.  It is not necessary to
explicitly save the figure in the script, this will be done
automatically at build time to insure that the code that is included
runs and produces the advertised figure.  Several figures will be
saved with the same basnename as the filename when the documentation
is generated (low and high res PNGs, a PDF).  Quantities includes a
Sphinx extension (:file:`sphinxext/plot_directive.py`) for generating
the images from the python script and including either a png copy for
html or a pdf for latex::

   .. plot:: pyplot_simple.py
      :include-source:

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. ``:include-source:`` will
present the contents of the file, marked up as source code.

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
svn. 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:: tex_unicode_demo.py
      :include-source


.. _referring-to-quantities-docs:

Referring to quantities documents
=================================

In the documentation, you may want to include to a document in the Quantities
src, e.g. a license file or an example.  When you include these files,
include them using the ``literalinclude`` directive::

   .. literalinclude:: ../examples/some_example.py


.. _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 necessary, 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``


.. _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 updating
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