[Biopython-dev] New Biopython release

[Peter]

Michiel de Hoon wrote:
> Hi everybody,
> 
> Let's make a new release (1.44) of Biopython. Biopython has received
> a lot of improvements and bug fixes in recent months, and the current
>  (1.43) release hangs on some platforms during the Biopython tests
> (due to a bug in my own Bio.Cluster module, ahem). I am planning to
> make a new release during the next weekend (around 9/15).

Good idea - I was wondering about suggesting this.  By the way, I
updated the NEWS file fairly recently.

> A number of bugs in Bugzilla currently have a partial solution that
> has not yet made it into CVS. I suggest to commit those partial
> solutions to CVS if possible so that they can be included in the next
> release.

Some of those are enhancement bugs where things are still a little
undecided.  I'm fairly happy with the __getitem__ method for the
alignment, but would want to change it slightly if we added a
__getitem__ to the SeqRecord itself.

> On my machine, only test_SeqIO fails its test. The error seems to be
> trivial, but we should fix it before making the next release.

It was trivial ;)
I had forgotten to check in a SwissProt test case. Sorry.

We should get Tiago's input before making a release - see if he's happy
for his initial Bio.PopGen code to be released yet.  If not, then it
shouldn't be too hard to removed that module, its test cases, and
section in the tutorial.  Just a little fiddly...

I've also done a little work on writing EMBL and GenBank files (based in
part on Howard Salis' patches on Bug 2294) but I don't think they are
ready yet.  As part of this I am planning to making some small changed
to the EMBL and GenBank parsers to record a few more bits of annotation.
Rather than rush this I'll hold back until after release 1.44 is done.

Peter