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root/osprai/osprai/trunk/sphinx/index.rst
Revision: 42
Committed: Tue Feb 1 08:07:06 2011 UTC (8 years, 4 months ago) by clausted
File size: 1944 byte(s)
Log Message:
Begin to use Sphinx and reStructuredText for documentation.  This provides comprehensive documentation as well as automatic API documentation.  This does not preclude the use of Epydoc, another simple autodocumentation tool.
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1 clausted 42 .. osprai-doc documentation master file, created by
2     sphinx-quickstart on Mon Jan 31 23:07:52 2011.
3     You can adapt this file completely to your liking, but it should at least
4     contain the root `toctree` directive.
5    
6     Welcome to the OSPRAI documentation!
7     ====================================
8    
9     Contents:
10    
11     .. toctree::
12     :maxdepth: 2
13    
14    
15     Overview
16     ========
17    
18     OSPRAI is Open-source SPR Analysis and Integration software.
19     Its aim is to provide a set of command-line tools for processing high-throughput biosensor data.
20     With OSPRAI, you can import and export common formats, annotate sensorgrams, and perform calibration, background subtraction, and curvefitting.
21    
22    
23     Software installation
24     =====================
25    
26     OSPRAI is written in Python so as to run on all popular platforms, including Linux, Windows, and Macintosh.
27     Install Python 2.4 (or newer) and the following libraries: python-tk, matplotlib, and scipy.
28     Additionally, it is useful to install IPython, the interaction Python shell, as well as a good python-aware text editor, such as Scite or gedit.
29     OSPRAI is hosted by Bioinformatics.org and managed using the Subversion version control system.
30     It can be obtained from the website or by using a Subversion client such as `Svn <http://subversion.apache.org>`_, `RapidSVN <http://rapidsvn.tigris.org>`_, or `TortoiseSVN <http://tortoisesvn.tigris.org>`_.
31     Windows users can install all of the necessary prerequisites by installing `PythonXY <http://www.pythonxy.com>`_, while Ubuntu Linux users can find everything they need in the Ubuntu repositories.
32     An example for Ubuntu users follows::
33    
34     $ sudo aptitude install python-tk python-matplotlib scipy ipython scite
35     $ svn checkout svn://bioinformatics.org/svnroot/osprai
36    
37    
38     API
39     ===
40    
41     .. automodule:: ba_class
42     :members:
43    
44     .. automodule:: vu_module
45     :members:
46    
47     .. automodule:: io_module
48     :members:
49    
50    
51     Indices and tables
52     ==================
53    
54     * :ref:`genindex`
55     * :ref:`modindex`
56     * :ref:`search`