RevisionHistory.txt

MSMBuilder 2.6.dev # the current development version: work so far
1. Migrate from SVN to Github for version control
2. Rename all the functions on MSMLib to be pep8 compliant. Aliases have been added for the old names
3. Split MSMLib into 2 files: MSMLib and msm_analysis. msm_analysis contains all the code
   for eigenvectors, sampling from models, etc. MSMLib contains code for building models
4. Removed AssignMPI.py, and added a new SimTk project -- msmbuilder.parallel_assign
   with better code.
5. Added more unit tests
6. Various pep8 fixes

MSMBuilder 2.5.1
1.  Fixes to Tutorials
2.  Moved Ward and SCRE to AdvancedMethods tutorial

MSMBuilder 2.5.0
1. The libraries are distance metric agnostic, you can use your own new distance metric
without having to change the clustering/assignment code
2. Dihedral, Contact (residues and/or atoms), hybrid distance metric code
3. New clustering algorithms (CLARANS / subsampled CLARANS)
4. Flux-based PCCA+.
5. Hierarchical Clustering.
6. SCRE rate matrix estimation.

MSMBuilder 2.0.4
1.  Improvements in PCCA, PCCA+ lead to better macrostate definition.

MSMBuilder 2.0.3
1.  BugFix: In ConvertDataToHDF, the Stride option was not being used for non-FAH style datasets. 
2.  Fixed unicode strings were causing scipy issues on certain platforms.

MSMBuilder 2.0.2

1.  Fixed issue with AtomIndices in UpdateProjectToHDF
2.  Using dtype='int' for Assignments, consistent throughout MSMBuilder.
3.  CalculateImpliedTimescales now allows users to exit through control+C
4.  Fixed some tabbing issues in MSMLib.py

MSMBuilder 2.0.1

1. Fixed a bug in ConvertProjectToHDF that prevented MSMBuilder from seeing multiple XTC files in a single directory. 
2. Fixed carriage return issues in UpdateProjectToHDF 
3. Fixed minor bugs in Project class. 
4. If Project cannot find its PDB, it also will look in the current directory. This helps when the absolute path of a Project changes. 
5. Unit tests. 
6. Removed unnecessary files, reducing the package size to 10MB.