[Biopython-dev] Minor buildbot issues from SearchIO

[Peter Cock]

On Fri, Nov 30, 2012 at 2:35 AM, Wibowo Arindrarto
<w.arindrarto at gmail.com> wrote:
> Hi everyone,
>
> I've done some digging around to see how to deal with these issues.
> Here's what I found:
>
>> The BuildBot flagged two new issues overnight,
>> http://testing.open-bio.org/biopython/tgrid
>>
>> Python 2.5 on Windows - doctests are failing due to floating point decimal place
>> differences in the exponent (down to C library differences, something fixed in
>> later Python releases). Perhaps a Python 2.5 hack is the way to go here?
>> http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%202.5/builds/664/steps/shell/logs/stdio
>
> I've submitted a pull request to fix this here:
> https://github.com/biopython/biopython/pull/98

The Windows detection wasn't quite right, it should now match
how we look for Windows elsewhere in Biopython:
https://github.com/biopython/biopython/commit/fc24967b89eda56675e67824a4a57a6059650636

>> There is a separate cross-platform issue on Python 3.1, "TypeError:
>> invalid event tuple" again with XML parsing. Curiously this had started
>> a few days back in the UniprotIO tests on one machine, pre-dating the
>> SearchIO merge. I'm not sure what triggered it.
>> http://testing.open-bio.org/biopython/builders/Linux%20-%20Python%203.1/builds/767
>> http://testing.open-bio.org/biopython/builders/Linux%2064%20-%20Python%203.1/builds/766/steps/shell/logs/stdio
>> http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%203.1/builds/648/steps/shell/logs/stdio
>
> As for this one, it seems that it's caused by a bug in Python3.1
> (http://bugs.python.org/issue9257) due to the way
> `xml.etree.cElemenTree.iterparse` accepts the `event` argument.

Ah - I remember that bug now, we have a hack in place elsewhere
to try and avoid that - seems it won't be fixed in Python 3.1.x now
so I've relaxed the version check here:
https://github.com/biopython/biopython/commit/52fdd0ed7fa576494005e635b6a6610daab2ab0e

Hopefully that will bring the buildbot back to all green tonight.
(TravisCI has now dropped their Python 3.1 support, but they
should have Python 3.3 with NumPy working soon).

Peter