Minor cleanup
-q
Change bucket name for S3 docs in preparation for new domain name
Merge pull request #327 from rmcgibbo/cleanup

Minor cleanup
Check for mle and not ergodic trimming
Merge pull request #329 from mpharrigan/fix

Check for mle and not ergodic trimming
Minor fix
Merge pull request #331 from SimTk/check-empty

Checking for empty states
Cleaned up __init__.py
Merge pull request #333 from SimTk/clustering_namespace

Cleaned up __init__.py
reworked (copied) sphinx-rtd-theme to include our new logo instead of just MSMBuilder at the top left of the docs. Also added the new logo in bold.
Merge pull request #336 from SimTk/logo

New logo