Fixing travis failures

@tanaes, @nbresnick, I've fixed some of the issues that were raised with the Travis builds, you can find a summary in the commit log, bug I'm adding it to this message for convenience:

If you guys decide to merge these commits into this branch, these changes will be reflected in the open pull request over at biocore/scikit-bio and a new Travis build will be triggered, which should pass this time.

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Fix a few stylistic issues
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Some of the errors being raised by flake8 have been fixed here:

- hommola_cospeciation had an unused import, this has been fixed by
  adding the function to the __all__ variable which was previously
  missing.
- Unused math and assert_raises imports in the hommola and
  test_hommola.py files.

Python 3 Related
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The code used a range call to generate a list of elements, and then
access elements from that list. Changing from python 2.7.x to 3.x you
cannot do this as range becomes a generator, thus I've added a cast to a
list.

Testing
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Using the built-in seed function from the random library would generate
different values between python 2.7 and py3k. Thus I've changed the
seeding and random operations to use numpy's which is consistent across
python versions.

Note that along with this I had to change the results of the tests,
however these will be consistent now.