May address issue #16
Added pdf doc regarding MLE code in issue #16
Merge branch 'master' into new_mle
Speed improvements and unit tests for new MLE code
Removed prior option from BuildMSM.py.  Pep8 fixes for MSMLib
Print the current lagtime when calculating implied timescales
Added comments and docstrings addressing roberts comments
Ran autopep8 on MSMLib.py, with max line length of 160 chars
More docstring fixes
Changed variable names in BuildMSM.py for pep8
pep8 fixes in BuildMSM.py
Added convergnece check in MLE BFGS
Fixed BuildMSM test and err checking for MLE
Improved variables names (row and col) for MLE code
Improved latex mle_notes
pep8 fix in MLE MSMLib
Changed C to counts in MLE MSMLib
Changed variable names to row_sums etc
Merge branch 'master' into new_mle
Merge pull request #119 from SimTk/new_mle

New mle code