[Biopython-dev] New Biopython release coming up

[Peter]

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
http://bugzilla.open-bio.org/show_bug.cgi?id=1997
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
http://bugzilla.open-bio.org/show_bug.cgi?id=1987
I have attached a suggested patch, second opinion welcome

Bugzilla Bug 1981 GenBank parser generates unusual feature qualifiers.
http://bugzilla.open-bio.org/show_bug.cgi?id=1981
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 
error
http://bugzilla.open-bio.org/show_bug.cgi?id=1936
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?

Peter