[Biopython-dev] Issue with test_Phylo_CDAO

[Tiago Antão]

Dear all,

I am trying to release 1.63 and I am getting a strange problem with the
test_Python_CDAO module:

If we run the test on a recent Ubuntu Linux Machine the following error
occurs (Python 2.7, rdflib 2.4.2):

ERROR: test_parse_0 (__main__.ParseTests)
Parse the phylogenies in test.cdao.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Phylo_CDAO.py", line 43, in test_parse
    trees = list(bp._io.parse(filename, 'cdao'))
  File
"/home/tiago/Dropbox/soft/bp-release/release/biopython-1.63/Bio/Phylo/_io.py",
line 53, in parse
    for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
  File
"/home/tiago/Dropbox/soft/bp-release/release/biopython-1.63/Bio/Phylo/CDAOIO.py",
line 63, in parse
    return Parser(handle).parse(**kwargs)
  File
"/home/tiago/Dropbox/soft/bp-release/release/biopython-1.63/Bio/Phylo/CDAOIO.py",
line 94, in parse
    self.parse_handle_to_graph(**kwargs)
  File
"/home/tiago/Dropbox/soft/bp-release/release/biopython-1.63/Bio/Phylo/CDAOIO.py",
line 115, in parse_handle_to_graph
    graph.parse(file=self.handle, publicID=base_uri, format=parse_format)
TypeError: parse() takes at least 2 arguments (3 given)


We suspect that the interface to the RDFLib might have changed recently and
that that might have broke the test code. Can someone (Eric, Ben?) that is
more experienced with this code maybe give a suggestion and comment on the
potentially importance of correcting this before releasing 1.63?

Regards,
Tiago

-- 
"The truth may be out there, but the lies are already in your head" - Terry
Pratchett