[Biopython-dev] Deprecating Bio.mathfns, Bio.stringfns and their C code?
biopython at maubp.freeserve.co.uk
Thu Oct 23 12:48:23 EDT 2008
>> Any objections to deprecating Bio.mathfns and Bio.cmathfns?
> Nope, the functions used by Bio/NaiveBayes.py are ...
You must be looking at Bio/NaiveBayes.py an older CVS checkout - it
doesn't use Bio.mathfns at all now, but rather makes more use of
>> We could just label Bio.listfns (and Bio.clistfns) as obsolete for the
>> next release, or just add a note in the docstring that this might be
>> deprecated shortly.
> Used by:
> Functions directly used:
> At present I do not know enough about Bio/MaxEntropy.py, Bio/NaiveBayes.py,
> and Bio/MarkovModel.py to indicate if Bio.listfns functions are really
> required or to port them to numpy. (I may try look at trying to port them
> but not soon.)
I haven't dug too deeply either - which is why I wasn't going to push
to deprecate Bio.listfns yet.
I did mention some of this in the earlier email, but you have gone
into more detail.
As you will have noticed, many of the things in Bio.listfns could
nowadays be done in pure python with a set.
> Also Bio.listfns used by pairwise2.py which also has a c implementation
> (cpairwise2) that I would also suggest is a candidate for removal.
I think Bio.pairwise2 is actually potentially quite useful. It could
do with a little documentation love - even a short "cookbook" entry
for the Tutorial would help.
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