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
The documentation sources are found in the doc/
directory in the trunk.
The output produced by Sphinx can be configured by editing the conf.py
file located in the 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 doc
. The main
entry point is doc/index.rst
, which pulls in the
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¶
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.
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: , and:.. math:: \int_{-\infty}^{\infty}\frac{e^{i\phi}}{1+x^2\frac{e^{i\phi}}{1+x^2}}
yields:
Footnotes [1] can be added using
[#]_
, followed later by:.. rubric:: Footnotes .. [#]
Footnotes
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 since version 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.
New in version 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:
See also
- Using ResT Emacs helpers:
One example
- A bit about Referring to quantities documents:
One more
The autodoc extension will handle index entries for the API, but additional entries in the index need to be explicitly added.
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 doc
dir has a folder called 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 (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 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 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 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¶
There is an emacs mode 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