[Biopython-dev] test_PhyloXML.py on Python 3
Peter
biopython at maubp.freeserve.co.uk
Thu Aug 12 12:37:14 EDT 2010
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
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