Large changes to the interface, code, and capabilities of compare_alpha_diversities.py. Addresses issue #498 as well as a bug fix for multiple comparisons.
Removed print statements and updated documentation.
Added pycogent_backports/alpha_diversity.py to incorporate the Gini index, Good's coverage, and the conditional_uncovered_probability.py stuff that was formerly in qiime/qiime. Added the test file as well. Modified All added files to remove redundant imports, a circular import that was causing an error, and changed the distribution of functions in the files to better reflect what each does.
Removed the files which have been incorporated into the backport or alpha_diversity.py
Modified files to update calls so that tests weren't failing.
More modifications to ensure that both scripts/conditional_unocovered_probability.py and scripts/alpha_diversity.py work as expected and each have the correct metrics.
Modified the documentation of alpha_diversity_metrics.rst to reflect additions.
minor updates to fix errors

this script could use a major refactoring (e.g., the monster try/except block is scary)
minor updates to fix errors

this script could use a major refactoring (e.g., the monster try/except block is scary)
fixed typo
Merge branch 'make_qiime_rst_file-updates' of github.com:gregcaporaso/qiime into make_qiime_rst_file-updates

Conflicts:
	scripts/make_qiime_rst_file.py
Merge pull request #569 from gregcaporaso/make_qiime_rst_file-updates

Make qiime rst file updates
Updated install docs to reference current dep versions; updated pynast urls; added gdata test to print_qiime_config.py.
Merge pull request #572 from jrrideout/pynast_links

Updated install docs to reference current dep versions; updated pynast u...
Updated the library and tests with the discussed changes.
Modified the results writing component of the compare_alpha_diversity.py script so that it correctly writes the reduced results.
Modified the documentation of the script to update to the new way of doing multiple comparison correction etc.
Modified the documentation as suggested by Jens.
Merge pull request #523 from wdwvt1/alpha_diversity_changes

Alpha diversity changes
re-organized the layout of the QIIME tutorials

we've got a lot of them now, so makes sense to break them apart a little bit. i'd really like to have a catch-all glob under "Other", but putting a glob in there gets all of the pages since I the layout involves multiple :toc:s. I could figure out how to add subheadings in the :toc:s,which would likely be a better solution.