[Biopython] Biopython on Jython

[Peter]

On Thu, Oct 22, 2009 at 10:15 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all,
>
> On Thu, Oct 22, 2009 at 5:47 AM, Kyle Ellrott <kellrott at gmail.com> wrote:
>>> You probably noticed I merged some of your fixes to get (the non C and
>>> non NumPy bits of) Biopython to work on Jython, but not all. Could you
>>> update your github branch to the trunk at some point? That would help
>>> in picking up more of your fixes.
>>
>> I've tried to keep my branch up to speed with the mainline.  But I didn't
>> branch my work from master, so it may harder to extract...
>
> True, but I can probably manage.

Thanks for updating your branch to the trunk.

I've grabbed the BLAST XML fix (and tweaked it) - thanks.

I also made test_Entrez.py get skipped on Jython (although
I just reused the missing dependency trick). See:
http://bugzilla.open-bio.org/show_bug.cgi?id=2918
http://bugs.jython.org/issue1447

>>> Many of the issues related to large python methods exceeding JVM size
>>> restrictions, something which Jython was going to try and fix in 2.5.1
>>> (but didn't seem to be solved in the release candidate I was trying),
>>> see e.g. http://bugs.jython.org/issue527524
>>> ...

This single issue covers the remaining test failures, and persists
on Jython 2.5.1 (final). They may solve it in the next release,
or I can look again at the work arounds on your branch.

We must of course skip anything requiring C code, or NumPy,
but most of Biopython is looking pretty good on Jython now.
Good work Kyle :)

Peter