[Biopython-dev] Biopython 1.56 release plans

[Peter]

On Fri, Nov 12, 2010 at 5:47 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Nov 4, 2010 at 5:13 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> Hi all,
>>
>> I've mentioned in recent threads that I think we should try and
>> release Biopython 1.56 this month (November 2010).
>>
>> ...
>
> As people will have noticed, the release didn't happen this week.
>
> ...
>
> Unfortunately running under Jython on Windows XP has
> revealed several new problems, e.g.
> http://lists.open-bio.org/pipermail/biopython-dev/2010-November/008431.html
>
> ...
>
> Hopefully we can address these three test failures (or
> at least understand them) and do Biopython 1.56 at
> the end of next week instead.

Two of the problems on Jython on Windows were down
to the Windows specific command line tool detection
not being used, now fixed:

https://github.com/biopython/biopython/commit/db41d7e4bfd8f5d4ea44bf8254334fcd7b76474f
https://github.com/biopython/biopython/commit/7e5b71093c8408de140de1937480e26aaaa5daf1

There was also a heap space problem solved by a
more memory efficient __getitem__ method for the
UnknownSeq object (still room for improvement here).

https://github.com/biopython/biopython/commit/125d8d31d07f57628c231286afae99a178e6f2c5

So, we now have a clean bill of health from the offline
tests run on the buildslaves (apart from the occasional
GenePop failure where retesting can make it work).

I still want to look at the SeqIO/AlignIO handle issue,
http://lists.open-bio.org/pipermail/biopython-dev/2010-November/008431.html
and also the UniProt XML issue,
http://lists.open-bio.org/pipermail/biopython-dev/2010-November/008440.html

Peter