[Biopython-dev] Minor buildbot issues from SearchIO

[Peter Cock]

On Wed, Dec 5, 2012 at 11:41 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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

OK, the buildbot looks happy now from the SearchIO work.

There is one issue under Python 3.1.5 on a 64 bit Linux server,
which I suspect is down to the Python version (this buildslave
used to run an older version - Python 3.1.3 (separate email
to follow).

Regards,

Peter