[Biopython-dev] Minor buildbot issues from SearchIO

Wibowo Arindrarto w.arindrarto at gmail.com
Fri Nov 30 02:35:25 UTC 2012

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:

> Python 3.2 and 3.3 on Windows are showing some XML character encoding oddity.
> Perhaps there is some encoding setting needed under Python 3 for the BLAST
> XML files?
> http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%203.2/builds/512/steps/shell/logs/stdio
> http://testing.open-bio.org/biopython/builders/Windows%20XP%20-%20Python%203.3/builds/29/steps/shell/logs/stdio

I've also addressed these failures here:

> 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. I
haven't submitted any pull request for this bug, since the fix looks
quite messy. Should we try to address this or simply make note that
XML parsing in Python3.1 will not work? Like Peter noted, currently
this bug involves Bio.SearchIO blast xml parsing, SeqIO.UniprotIO, and


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