Updated documentation, includes input / output file descriptions
Remove qiime.util.DistanceMatrix and unit tests
Remove DistanceMatrix usage from test_format.py

Also cleaned up related test code so that it uses mock stats results dictionaries. This makes the test code much simpler and decouples it from qiime.stats.
Merge branch 'master' into issue-829
Update stats.py, test_stats.py

Now uses SymmetricDistanceMatrix.
update compare_categories.py lib code
update compare_distance_matrices.py lib code
relax print_qiime_config.py python version check

Is now okay with any python versions >= 2.7.0 and < 3.0.0. Also supports python
version strings like the kind found in Miniconda's python, e.g.:

Python 2.7.6 :: Continuum Analytics, Inc.

Fixes #1391.
Clean up

I find myself making these changes every time I use this script to make a new
QIIME-style py file.
Change error type to option_parser.error
Address comments from @ElDeveloper

Also fixes up various other parts of the script
Merge pull request #1393 from adamrp/make_qiime_file

Clean up make_qiime_py_file.py
Merge pull request #1390 from jrrideout/issue-829

Replace qiime.util.DistanceMatrix with bipy.core.distance.SymmetricDistanceMatrix
Merge pull request #1392 from jrrideout/issue-1391

relax print_qiime_config.py python version check
Addressed @gregcaporaso comments for clarity
Address @gregcaporaso comments
Changed command line flags refs in documentation
Merge pull request #1372 from lkursell/improve_openref_doc

Update documentation for pick_open_reference_otus.py - #1296
fixes #1400
this test file isn't used anymore