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

[Peter]

This is about three Biopython "support" modules: Bio.mathfns,
Bio.listfns, Bio.stringfns, each of which has its own C implementation
for speed.  These haven't been touched for 6 years (which suggests
they are stable and well tested), but they are now hardly used in
Biopython.

By removing these we not only reduce the amount of C code in Biopython
(although here it is optional) which is a good thing for portability
and supporting other python variants, but we also can reduce the
"clutter" under the Bio.* namespace, e.g.
>>> import Bio
>>> help(Bio)

On 9th Oct I wrote:
> Until recently Bio.mathfns was used in Bio/NaiveBayes.py but that now
> uses numpy more heavily instead.  I think that Bio.mathfns (and its C
> implementation) are no longer used anywhere in Biopython (and I would
> be surprised if anyone else is using this module).  I'm suggesting
> deprecating Bio.mathfns and Bio.cmathfns for the next release.

Any objections to deprecating Bio.mathfns and Bio.cmathfns?

On 9th Oct I wrote:
> I think Bio.stringfns and its C implementation Bio.cstringfns are also
> now unused in Biopython, and like Bio.mathfns and Bio.cmathfns
> should be deprecated for the next release.

Any objections to deprecating Bio.stringfns and Bio.cstringfns?

On 9th Oct I wrote:
> Similarly, Bio.listfns and its C implementation Bio.clistfns might
> also be deprecated with a little effort ... only three modules
> currently use Bio.listfns

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.

Peter