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

[Peter]

Bruce:
>Peter:
>> 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
numpy.

>> 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:
> Bio/MaxEntropy.py
> Bio/NaiveBayes.py
> Bio/MarkovModel.py
> Bio/pairwise2.py
>
> 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.
http://lists.open-bio.org/pipermail/biopython-dev/2008-October/004406.html

As you will have noticed, many of the things in Bio.listfns could
nowadays be done in pure python with a set.

Bruce wrote:
> 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.

Peter