added dependencies
typo
manually install dependencies in travis env in quiet mode, but then do the tests verbosely so its easier to find the error
insiginficant
removed -qq for statsmodels
remove statsmodels from .travis list
Added fix to Cluster.py that removes the assignments, generators, and distances options and adds the output_dir option. The Assignments, etc. are therefore named in a regular manner but to the output_dir. Additionally, I removed the output for Ward's method (output_zmatrix). It behaves in the same way as the assignments. It ends up saved to output_dir.
Fixed typo in Cluster.py.
I hadn't removed the zmatrix output argument from Cluster.py yet. I just removed it now.
Cluster.py now only has the output filenames hardcoded once. I removed the check_paths function, and essentially put it in the main function. In order to get the zmatrix_fn to the cluster function, I created an empty dictionary in main (extra_kwargs) that can house any additional data necessary for the clustering step. This is then passed as kwargs to cluster. This addresses issue #127. How's this @rmcgibbo?
Merge pull request #119 from SimTk/new_mle

New mle code
Added 'import warnings' to CalculateProjectRMSD.py. This has been broken for a while I guess, but maybe people stopped using it since CalculateProjectDistance.py is the better version...
Merge branch 'master' of github.com:SimTk/msmbuilder
Changing the parser arguments broke the Cluster.py tests. This commit fixes them so that the correct options are passed to the script. Also changed the Assignments.h5.distances name from Assignments.h5.dist.
Minor changes to Tutorial; SaveStructures instead of SavePDBs
trigger build
trigger
new travis yaml
change lang
fix