This is the location for self-contained add-ons that are currently baking.  Please try to organize your buns into rational categories.  Occasionally, I will reorganize items in a logical fashion as the module set grows and my vision develops.

If you want to contribute to the oven, please create a directory with your sourceforge username and put all files in it.


For modifications to the pre-existing code, please continue to use the patch tracker or contact the sourceforge username associated with the files.

Please follow the python style guide
 http://www.python.org/dev/peps/pep-0008/
and document thoroughly.  Modules that deviate from these two commandments will not make it into the core and may result in revocation of svn privileges.


Also, remember the following:
1) Document thoroughly. The world is much bigger than you really seem to think.
2) No camelCase or camelToes no matter who sports them.  The exception: classes must be defined with CamelToeCase.
3) No non-standard lazy abbreviations kegg is acceptable mets, rxns, and
coefs are not.
4) phrasesmusthaveunderscores is bad phrases_must_have_underscores is
good
5) For default values in functions don't put spaces around the =. def
my_cat(color = 'black') is bad. def my_cat(color='black') is good.
6) Also, unless absolutely necessary you should import functions from modules and not use the whole path name.  This allows for faster transitions if we need to change an upstream module or want to maintain python and jython compatibility, or want to test some new package. 

If a function something requires a very specific set of data files then it
is best to make a module.


Happy coding!

Dr. S.
