[Biopython-dev] Removing Bio.Mindy and Martel

[Peter]

Hi all,

Bio.Mindy and Martel are the old "regular expressions on steroids"
parsing framework we used to use in Biopython, which needed the
external dependency mxTextTools (v2, we never got things to work fully
with v3).  These modules were deprecated in Biopython 1.48  (Sept
2008), and I explicitly wrote in the release announcements for
Biopython 1.50 (and its beta) that this would be the final release to
include them.

I decided to do this in two steps (partly because of the number of
files involved).  I've just removed Mindy and associated bits in CVS,
and everything looks fine from a setup and unit test point of view.
Next comes Martel and its remaining dependent modules.  Martel is
still used in the following modules, which were also deprecated in
Biopython 1.48 (Sept 2008):

Bio.MetaTool (parser for output from an obsolete version of MetaTool)
Bio.Saf (an obscure alignment format)
Bio.NBRF (replaced with "pir" format in Bio.SeqIO)
Bio.IntelliGenetics (replaced with "ig" format in Bio.SeqIO)

We've actually had three releases where these modules have had a
deprecation warning in place, but not quite the full year as stated in
the written policy: http://biopython.org/wiki/Deprecation_policy

Does anyone have any objections about us pressing ahead with removing
Martel and these modules now?

Peter