[Biopython-dev] test_PhyloXML.py on Python 3

[Peter]

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
test_clade_getitem (__main__.MethodTests)
Clade.__getitem__: get sub-clades by extended indexing. ... ERROR
test_clade_to_phylogeny (__main__.MethodTests)
Convert a Clade object to a new Phylogeny. ... ERROR
...
Traceback (most recent call last):
  File "test_PhyloXML.py", line 571, in test_phylo
    'test_Taxonomy',   'test_Uri',
  File "test_PhyloXML.py", line 504, in _rewrite_and_call
    phx = PhyloXMLIO.read(infile)
  File "/home/xxx/lib/python3.1/site-packages/Bio/Phylo/PhyloXMLIO.py",
line 105, in read
    return Parser(file).read()
  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.

Peter