I do not think this is related to your changes, but this test periodically fails for me, and look like it is the order of the list (both are NOT sorted), but it is random. One time it passes, another it fails

Here is the traceback
FAIL: Test the GraphPartition operation that splits modules so that it returns
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/epd/lib/python2.7/site-packages/nose-1.3.0-py2.7.egg/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/jagust/cindeem/CODE/brainx/brainx/tests/test_modularity.py", line 637, in test_apply_module_split
    npt.assert_equal(np.sort(list(n1)), n1_new)
  File "/usr/local/epd/lib/python2.7/site-packages/numpy/testing/utils.py", line 256, in assert_equal
    return assert_array_equal(actual, desired, err_msg, verbose)
  File "/usr/local/epd/lib/python2.7/site-packages/numpy/testing/utils.py", line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File "/usr/local/epd/lib/python2.7/site-packages/numpy/testing/utils.py", line 636, in assert_array_compare
    raise AssertionError(msg)
AssertionError: 
Arrays are not equal

(mismatch 100.0%)
 x: array([2, 8])
 y: array([8, 2])