[Biopython-dev] New Biopython release coming up

Peter biopython-dev at maubp.freeserve.co.uk
Sun Jul 2 18:11:47 UTC 2006

Michiel de Hoon wrote:
> Hi everybody,
> The next Biopython release (1.42, code-named "Brooklyn") is coming up. 
> I'm planning to finish this release about two weeks from now. The tests 
> of Biopython in CVS all pass, so we are doing well. However, there are 
> 25 bugs listed in Bugzilla, so please have a look to see if there's 
> something we can do about them. If you have some code sitting around, 
> now would be a good time to commit it to CVS. However, if you are not 
> sure if your code is ready for prime time, please hold off until after 
> this release. Also, if you have a cvs checkout of Biopython, please make 
> sure to update it before doing any commits to avoid overwriting.
> Thanks everybody for your contributions to Biopython.
> --Michiel.

Sounds like a good plan Michiel

Did anyone get back to you about the NBCI Blast XML format?  I would say 
parsing blast output is a fairly important feature to a lot of users (I 
may of course be biased)...

Getting down to specifics:

Bugzilla Bug 1997 VARCHAR too small in SCOP tables
Suggested fix looked OK to me, but as I've never used SCOP as second 
opinion would be wise.

Bugzilla Bug 1987 Alphabet.Gapped does not retain gap character
I have attached a suggested patch, second opinion welcome

Bugzilla Bug 1981 GenBank parser generates unusual feature qualifiers.
A question about the white space in GenBank comments etc.  Changing this 
is probably harmless but we are already making a big change internally 
with the move away from Martel, I would rather post pone any further 
change until after the next release.

Bugzilla Bug 1936 Bio.PDB.PDBParser throws PDBException, 'No parent' in 
One for Thomas Hamelryck which on the face of it looks fairly simple.

Bugzilla Bug 1946 Parsing GenBank Files - unknown line type PROJECT
Does anyone use the new project line?  Would a simple string be enough 
to store this?


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