test_geometry_engine nosetest failure about perses HOT 3 CLOSED

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FAIL: Doctest: perses.annihilation.alchemical_engine.AlchemicalEliminationEngine
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Traceback (most recent call last):
  File "/Users/choderaj/anaconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for perses.annihilation.alchemical_engine.AlchemicalEliminationEngine
  File "/Users/choderaj/anaconda/lib/python2.7/site-packages/perses-0.1-py2.7.egg/perses/annihilation/alchemical_engine.py", line 8, in AlchemicalEliminationEngine

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File "/Users/choderaj/anaconda/lib/python2.7/site-packages/perses-0.1-py2.7.egg/perses/annihilation/alchemical_engine.py", line 26, in perses.annihilation.alchemical_engine.AlchemicalEliminationEngine
Failed example:
    topology_proposal = topology_proposal.TopologyProposal(old_topology=testsystem.topology, new_topology=testsystem.topology, logp=0.0, new_to_old_atom_map=new_to_old_atom_map, metadata=dict())
Exception raised:
    Traceback (most recent call last):
      File "/Users/choderaj/anaconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest perses.annihilation.alchemical_engine.AlchemicalEliminationEngine[4]>", line 1, in <module>
        topology_proposal = topology_proposal.TopologyProposal(old_topology=testsystem.topology, new_topology=testsystem.topology, logp=0.0, new_to_old_atom_map=new_to_old_atom_map, metadata=dict())
    TypeError: __new__() got an unexpected keyword argument 'old_topology'
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File "/Users/choderaj/anaconda/lib/python2.7/site-packages/perses-0.1-py2.7.egg/perses/annihilation/alchemical_engine.py", line 30, in perses.annihilation.alchemical_engine.AlchemicalEliminationEngine
Failed example:
    alchemical_system_insert = make_alchemical_system(testsystem.system, topology_proposal, direction='create')
Exception raised:
    Traceback (most recent call last):
      File "/Users/choderaj/anaconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest perses.annihilation.alchemical_engine.AlchemicalEliminationEngine[5]>", line 1, in <module>
        alchemical_system_insert = make_alchemical_system(testsystem.system, topology_proposal, direction='create')
    NameError: name 'make_alchemical_system' is not defined
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File "/Users/choderaj/anaconda/lib/python2.7/site-packages/perses-0.1-py2.7.egg/perses/annihilation/alchemical_engine.py", line 31, in perses.annihilation.alchemical_engine.AlchemicalEliminationEngine
Failed example:
    alchemical_system_delete = make_alchemical_system(testsystem.system, topology_proposal, direction='delete')
Exception raised:
    Traceback (most recent call last):
      File "/Users/choderaj/anaconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest perses.annihilation.alchemical_engine.AlchemicalEliminationEngine[6]>", line 1, in <module>
        alchemical_system_delete = make_alchemical_system(testsystem.system, topology_proposal, direction='delete')
    NameError: name 'make_alchemical_system' is not defined