.. _documenting-phynx:

*****************
Documenting Phynx
*****************

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

The documentation for Phynx is generated from ReStructured Text
using the Sphinx_ documentation generation tool. Sphinx-0.6.3 or later
is required. Sphinx can be obtained through your package manager or by
doing::

  easy_install sphinx

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 phynx
directory::

  python setup.py build_sphinx

and the html will be produced in `build/sphinx/html`. To build the pdf
file, LaTeX_ (preferably TeX-Live_) and dvipng_ are required. Once
these are installed, do::

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

To upload the documentation to the Phynx website::

  cd build/sphinx/html
  zip -r phynx *

Then visit the `Phynx page at the Python Package Index`_ to upload the
documentation.

.. _Sphinx: http://sphinx.pocoo.org/
.. _LaTeX: http://www.latex-project.org/
.. _TeX-Live: http://www.tug.org/texlive/
.. _dvipng: http://sourceforge.net/projects/dvipng/
.. _`Phynx page at the Python Package Index`: http://pypi.python.org/pypi?%3Aaction=pkg_edit&name=phynx

Organization of Phynx'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 Phynx 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-phynx-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`_. Phynx'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 Phynx'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
  Phynx.

* 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-phynx-docs`:
          One more

  yields:

  .. seealso::

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

     A bit about :ref:`referring-to-phynx-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.

.. _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.


.. _referring-to-phynx-docs:

Referring to Phynx documents
============================

In the documentation, you may want to include to a document in the
Phynx 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 hyphen separated, descriptive labels for section references, eg::

    .. _howto-webapp:

and refer to it using  the standard reference syntax::

    See :ref:`howto-webapp`

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 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