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MAINT: various changes to fix build/test failures (#1546)

Made the following changes to fix build/test failures:

- scikit-bio now depends on `numpy >= 1.9.2, < 1.14.0` for compatibility with Python 3.4, 3.5, and 3.6 and the available numpy conda packages in `defaults` and `conda-forge` channels.
- Use latest Sphinx release (1.6) instead of Sphinx master branch.
- Fix flake8 errors related to updated flake8 package.
- Fix unit test for beta_diversity error message to work across supported Python 3 versions.

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