[Biopython-dev] PAML unit test failure

[Peter Cock]

Hi guys,

We're seeing new failures on the buildbot under Python 3, e.g.
http://testing.open-bio.org/biopython/builders/Linux%20-%20Python%203.2/builds/147/steps/shell/logs/stdio

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ERROR: testOptionExists (test_Baseml.ModTest)
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Traceback (most recent call last):
  File "/home/pjcock/repositories/BuildBot/lin32/build/build/py3.2/Tests/test_Baseml.py",
line 94, in testOptionExists
    self.bml.set_option, "xxxx", 1)
AttributeError: 'Baseml' object has no attribute 'set_option'

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ERROR: testOptionExists (test_Codeml.ModTest)
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Traceback (most recent call last):
  File "/home/pjcock/repositories/BuildBot/lin32/build/build/py3.2/Tests/test_Codeml.py",
line 92, in testOptionExists
    self.cml.set_option, "xxxx", 1)
AttributeError: 'Codeml' object has no attribute 'set_option'

======================================================================
ERROR: testOptionExists (test_Yn00.ModTest)
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Traceback (most recent call last):
  File "/home/pjcock/repositories/BuildBot/lin32/build/build/py3.2/Tests/test_Yn00.py",
line 67, in testOptionExists
    self.yn00.set_option, "xxxx", 1)
AttributeError: 'Yn00' object has no attribute 'set_option'

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Caused by this commit,

https://github.com/biopython/biopython/tree/de671e1baf3faa0ed8c10835397e308b1cf1b59d

I couldn't see a matching change to the unit tests on Brandon's branch
to apply, so I just fixed it:

https://github.com/biopython/biopython/commit/145fe2a01afb4092cb2e862142dd04234410b74f

Peter