Fix problem with plot_semivariogram.py

This is a quick fix for the fact that plot_semivariogram.py would fail
when the inputed mapping file contains more categories than the ones in
the distance matrix.

Fixes #1378
Addressing comments
Addressing comments
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Merge branch 'master' of github.com:antgonza/qiime into join_pair_one_file
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
Modified split_libraries.py to handle case of not finding a reverse primer (with truncate_remove option) and a low quality window, which was causing an error. This is to address issue #1336
Merge branch 'master' of https://github.com/qiime/qiime into join_pair_one_file
addressing @gregcaporaso comments
MAINT: removed dependencies that are not directly imported in QIIME
MAINT: added note on this change, fixes #1719
MAINT: clarified text
MAINT: fixed typo
MAINT: removed changelog lines regarding changes that only occurred in the 1.8.0-dev cycle (i.e., never made it to a relase)
Merge pull request #1722 from gregcaporaso/issue-1719

update dependencies in setup.py
MAINT: updated biom requirement, partial fix for #1716
Merge pull request #1727 from gregcaporaso/issue-1716

updated biom requirement in prep for QIIME 1.9.0
BUG: Update summarize_otu_by_cat.py to BIOM 2.x

This one slipped through the cracks, I have added an extra script usage
case to test for this.

Fixes #1713
Allows group_signifigance to skip rows

if a group row would cause an error in kruskal wallis, the p_val and
test stat are returned as nan