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: Update emperor requirement

Previously was pointing to 0.9.3 and 0.9.4-dev, now states it needs
a version greater than 0.9.5 and lesser than 1.0.0.

I also updated a link for scikit-bio.

Related to #1716
Merge pull request #1720 from ElDeveloper/emperor-0.9.5

MAINT: Update emperor requirement
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