[Biopython-dev] Next release?

Peter biopython at maubp.freeserve.co.uk
Wed May 21 09:21:51 UTC 2008


>From the discussion list, quite a few people have suffered from the
NCBI tweaking the online Blast XML format with 2.2.18+ (bug 3499), so
it would be nice to get a new release out soon to address this.  See
http://bugzilla.open-bio.org/show_bug.cgi?id=2499

How do the other modules stand at the moment?

Bio.PopGen (Tiago). Is this currently stable, or are you in the middle
of adding more features?

Bio.Entrez (Michiel). I see you've been very busy with the new
simplified XML parsers (see bug 2488).  This looks like a big
improvement on the rather repetitive coding needed in the first draft.
 Are you still actively making further refinements?  How many Entrez
XML file formats are still needed?
http://bugzilla.open-bio.org/show_bug.cgi?id=2488

Bio.AlignIO - this is new, but has a reasonable amount of
documentation and a small unit test (see bug 2285).  If we did do a
release soon, it could be announced as "in beta", and subject to
change, but feedback welcomed.
http://bugzilla.open-bio.org/show_bug.cgi?id=2285

In terms of the unit tests, I haven't run them on Windows recently
(internet access issues, hopefully resolved now), but on Linux things
looks fine.

Peter



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