[Biopython-dev] test_PhyloXML.py on Python 3

[Eric Talevich]

On Thu, Aug 12, 2010 at 12:37 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> Hi Eric (et al),
>
> Is test_PhyloXML.py working for you under Python 3?
>
> I'm getting the following (both with and without the 2to3 --nofix=long
> option):
>
> $ python3 test_PhyloXML.py
> ...
>  File "/home/xxx/lib/python3.1/site-packages/Bio/Phylo/PhyloXMLIO.py",
> line 298, in __init__
>    event, root = next(context)
>  File "<string>", line 59, in __iter__
> TypeError: invalid event tuple
>
> ----------------------------------------------------------------------
> Ran 47 tests in 0.015s
>
> All the sub-tests in test_PhyloXML.py are failing the same way.
>
> >From memory this was working recently.
>
>
Yeah, it was... it's fixed now/again.

This is the issue with passing byte/unicode strings to cElementTree in
Python 3. I had a check for Python versions 3.0.0 through 3.1.1, where we
need to import ElementTree instead of cElementTree. Apparently Python 3.1.2
still has the bug.

-Eric