Modified add_qiime_labels.py script to use a standard metadata mapping file instead of custom mapping file to be more intuitive to use with the rest of QIIME.  Updated unit tests.
Partial support for variable-sized bins in MantelCorrelogram class.
Backported changes to rdp_classifier.py in PyCogent
Add is_valid_git_refname and is_valid_git_sha1

Given the great variability that exists between versions of git, this
functions validate the output returned from the git commands used to
retrieve the current branch name (refname) and the current SHA.

The function get_qiime_library_version was updated to make use of these
functions.

The module was updated accordingly.

This should fix issue #603.
Modified the compare_alpha_diversity library, script, and tests to resolve issue #597.
Backported changes to rdp_classifier.py in PyCogent
Merge branch 'backport-rdp-classifier' of github.com:kylebittinger/qiime into backport-rdp-classifier
Backported PyCogent commit fec2a29
Merge branch 'master' into mantel_correlogram_bins
Added MantelCorrelogram._find_row_col_indices(), which is necessary for variable-sized bins.
Added variable-size bin support to MantelCorrelogram._find_distance_classes().
Added --variable_size_distance_classes option to compare_distance_matrices.py script.
Fixed a couple of border-case bugs and added tests for them.
Merge pull request #606 from kylebittinger/backport-rdp-classifier

Backported changes to rdp_classifier.py in PyCogent
Added notes to changelog; reverted a few comments I didn't mean to add.
The coverage_category states are returned instead of their number.
Updated tests to work with new function signature.
Added optional splitter_category parameter.

Partial support for (optional) splitting of mapping file prior to filtering.
Added some preliminary error handling unit tests and pulled the "meaty" code
into a "private" function ```__filter_sample_ids_from_category_state_coverage()```.
Finished implementation of splitter_category.

Still need to add more unit tests.
Merge pull request #612 from wdwvt1/compare_alpha_diversity_fixes

Modified the compare_alpha_diversity library, script, and tests to resol...