restructured text documentation about mdanalysis

[GoogleCodeExporter]

We'll also need to find a place to host the html docs.

Original comment by orbeckst on 24 Sep 2010 at 3:30

[GoogleCodeExporter]

Tyler has started work on documentation using sphinx.

Original comment by orbeckst on 24 Sep 2010 at 5:32

[GoogleCodeExporter]

have docs for MDAnalysis.analysis

Original comment by orbeckst on 3 Oct 2010 at 12:09

• Changed state: Started

[GoogleCodeExporter]

We will serve the docs from the svn repo, e.g. 
http://mdanalysis.googlecode.com/svn/trunk/doc/html/index.html (note the path).

* Check in generated docs.
* Set the svn:mime-type property appropriately on html, css, and images as 
detailed in 
http://code.google.com/p/support/wiki/SubversionFAQ#How_can_I_make_SVN_serve_HTM
L_and_images_with_the_correct_Conten
(Note that this can only be done with a subversion client and the 'svn propset' 
command).
* Whenever a new generated file is added to the documentation one has to 
manually set the mime property, too.

Original comment by orbeckst on 5 Jan 2011 at 7:31

[GoogleCodeExporter]

See also WritingDocumentation

Original comment by orbeckst on 5 Jan 2011 at 10:45

[GoogleCodeExporter]

Paul Rigor reported 
http://groups.google.com/group/mdnalysis-discussion/browse_thread/thread/d5f4615
955c84415 :

Just some notes:
(1) 
http://mdanalysis.googlecode.com/svn/trunk/doc/html/documentation_pages/KDTree/N
eighborSearch.html
    i) New lines are missing or the formatting for the code section doesn't seem right.
    ii) Is the atom_list argument in the constructor for 'AtomNeighborSearch' an AtomGroup type or a python list of AtomGroup objects? What about the type for the 'center' argument in the constructor for  'CoordinateNeighborSearch'?

(2) 
http://mdanalysis.googlecode.com/svn/trunk/doc/html/documentation_pages/core/uti
l.html
    i) There are some inconsistent semi colons between function parameters in the doc strings

Original comment by orbeckst on 6 Jan 2011 at 8:47

[GoogleCodeExporter]

addressed Paul's comments in r578 and r579 (updated online docs)

Original comment by orbeckst on 10 Jan 2011 at 3:17

[GoogleCodeExporter]

Basic online docs are available and will be enhanced in the future. Please file 
new issues for specific problems or shortcomings with the docs. Thanks.

Original comment by orbeckst on 5 Feb 2011 at 11:07

• Changed state: Fixed