.. reproducible-research Version Control file, created by ARichards


Documentation
=============

The ability to reproduce a given experiment or analysis depends heavily on the level of and care given to documentation.  Fortunately,
there exist documentation tools and philosophies that can aid scientists in this often time-consuming endeavor.

For the laboratory, there are electronic notebooks and wikis that may serve as documentation aids.  For the side of reproducible analysis
the principals of :doc:`LiterateProgramming` are central to good reproducible practices.


Notable documentation software
---------------------------------

There are widely used tools like `Sphinx <http://sphinx-doc.org>`_ and `Doxygen <http://www.stack.nl/~dimitri/doxygen>`_ for document generation.  Wiki maintains a table comparison of `document generation tools <http://en.wikipedia.org/wiki/Comparison_of_documentation_generators>`_. :doc:`lpEdit` gives users the option to use :doc:`Latex` or `reStructuredText <http://docutils.sourceforge.net/rst.html>`_. lpEdit is not targeting the automatic generation of documention, however the autodoc tools that come with Sphinx can be easily integrated into a project.