[Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?

[Bruce Southey]

Peter wrote:
> Bruce wrote:
>   
>> Personally I would be inclined
>> to incorporate Bio.listfns into each of these and depreciate Bio.listfns. I
>> know this is duplication but hopefully this would be addressed if someone
>> updates the code.
>>     
>
> If it were only pure python, I might agree with you.  But given there
> is C code which might well be worthwhile for speed, I'm not in any
> hurry to remove Bio.listfns until Bio.MaxEntropy.py, Bio.NaiveBayes
> and Bio.MarkovModel don't need it.  Labelling Bio.listfns as likely to
> be deprecated and removed in the future should suffice for the time
> being.
>
> Peter
>
>   
Hi,
Just an update, I think that I have removed the listfns dependency from 
Bio.MaxEntropy.py (Bug 2631 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2631>), Bio.NaiveBayes 
(Bug 2629 <http://bugzilla.open-bio.org/show_bug.cgi?id=2629>)and 
Bio.MarkovModel (Bug 2627 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2627>) - the order is also 
in terms of low to high number of changes that were required. I also 
removed any 'from x import *' as well especially where x=numpy.oldnumeric.

I also added examples that use MaxEntropy and NaiveBayes but these 
should have bioinformatics examples. Note that NaiveBayes is the 
discrete version.

Bruce