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.
Adding functionality to calculate linear distance from a latitute/longitud point
Fixing a missing credit
Partial support for variable-sized bins in MantelCorrelogram class.
Fixing issues from pull request
Fixing wrong evaluation of max/min lat/long
Fixing error message for lat/long evaluation
Backported changes to rdp_classifier.py in PyCogent
Merge pull request #602 from antgonza/lat_long_distance

Adding functionality to calculate linear distance from Latitude/Longitude point
Fixing error with distance_matrix_from_mapping.py in Clout
Merge pull request #607 from antgonza/fix_for_distance_matrix_from_mapping_in_clout

Fixing error with distance_matrix_from_mapping.py in Clout
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.