BUGFIX in tpt.py which resulted in repeated paths in find_top_paths whenever the 'sinks' had more than one entry. Also  fixed tests/test_tpt.py to actually test whether the paths are correct. We need to add a test for multiple sinks/sources as well to avoid these types of bugs in the future.
Changed Flux to flux in tpt._backtrack
Added a test for multiple states/sinks in FindPaths.
Changed eigendecomposition in msm_analysis.calc_expectation_timeseries to use msm_analysis.get_eigenvectors rather than scipy.sparse.linalg.eigs. The reason I think this is necessary is I was having issues calculating eigenvalues using eigs directly. For instance on one MSM, I was calculating the top 250, but the stationary eigenvector did not end up in the returned set. I  do not understand why, and could not repeat it with a smaller MSM (mine was 19k states). Secondly, however, it is better practice to reuse our own eigendecomposition code anyway, so from a purely engineering perspective this is the right way to do it anyway. I also added a check to remove negative eigenvalues. Numerically this can happen, but they have no physical meaning, and so we should ignore them when calculating observables.
uppercase the M in AssignHierarchical's zmatrix input
Merge pull request #198 from rmcgibbo/zmatrixtypo

Uppercase the M in AssignHierarchical's ZMatrix input arg
Merge pull request #178 from schwancr/fix_tpt

Fix tpt bug where the paths were not output correctly due to issues in tpt._backtrack
Merge pull request #182 from schwancr/expec_time_fix

(Bug?)fix in msm_analysis.calc_expectation_timeseries

Calculated the eigenvectors with msm_analysis.get_eigenvectors rather than scipy.linalg.eigs directly
Added functionality to use CLoader / CDumper from yaml to load and save yaml files. This takes advantage of a c-library (libyaml) if its available for faster loads and saves.
Merge pull request #199 from schwancr/libyaml

Added functionality to use CLoader / CDumper from yaml
Merge branch 'master' of github.com:SimTk/msmbuilder into tica_mle