[Biopython-dev] Status of the upcoming release

[Michiel De Hoon]

Hi everybody,

Originally I was planning to create a new Biopython release during last
weekend. However, as you have seen from the discussions on the mailing list,
while we were preparing for this new release, we discovered that Biopython
does not work well with the new version of mxTextTools (3.0). This code is
being used by Martel, which is used for various parsers in Biopython. In
particular Peter and I have been trying to find solutions for this problem,
but we're not quite there yet. Currently, I am getting two remaining errors
from the Biopython test suite (I believe there were ten when we started). I
feel that we should postpone the release until we sort this out.

The difficulty of solving these bugs is that they are located in various
interdependent modules. None of the currently active developers are familiar
with this code. To make matters worse, some of the code cannot even be
deprecated without causing spurious deprecation warnings all over Biopython
(even in totally unrelated code).

On the bright side, there seem to be few (if any) users of the code that are
causing the mxTextTools problems. Therefore I think that in practice, few
users will actually run into problems if we remove the offending modules. So
it may not be worth banging our heads over this.

Unfortunately I will be out of town for the next ten days (I had been hoping
to finish the release before), so I'm afraid the next release will have to
wait until after that. In the mean time, feel free to download current
Biopython versions from CVS to see if all your favorite modules are still
there. If not, let us know which module you'd like to retain (and why).

--Michiel.

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032