Checking in fixed changes for TopiaryExplorer 1.0
Merge pull request #675 from meganap/master

Fixed changes for TE 1.0
I changed the behavior of beta_diversity.py -r xxx using unifrac-like measures to now only warn the user when there's no information on a sample (no counts in an otu table, or none that match the phylogenetic tree. Those comparisons are meaningless, but when two samples are absent any information, they now return a distance of 1 with -r, but 0 without the -r flag (i.e., computing the whole matrix). This is tricky to change, and I think since we clearly list those distances as meaningless, it's a non-ideal but ok approach.
Merge pull request #682 from justin212k/676

fixing issue #676.  beta_diversity.py -r now only warns when run on samples with no data
Merge branch 'master' into issue-477
updated test code to suppress stderr

one of the samples in this test data set is composed of all non-16S sequences, and thus has no tips in the tree. unifrac raises a warning as a result, but because that warning is raised from within a beta_diversity.py system call, we can't suppress it with warnings.filterwarnings(). to get around this, we're essentially redirecting stderr temporarily during each test.