Changelog

v3.3 (August 27, 2015)

We’re pleased to announce the release of MSMBuilder v3.3.0. The focus of this release is a completely re-written module for constructing HMMs as well as bug fixes and incremental improvements.

API Changes

  • FeatureUnion is an estimator that deprecates the functionality of UnionDataset. Passing a list of paths to dataset() will no longer automatically yield a UnionDataset. This behavior is still available by specifying fmt="dir-npy-union", but is deprecated (#611).
  • The command line flag for featurizers --out (deprecated in 3.2) now saves the featurizer as a pickle file (#546). Please use --transformed for the old behavior. This is consistent with other command-line commands.
  • The default number of timescales in MarkovStateModel is now one less than the number of states (was 10). This addresses some bugs with implied_timescales and PCCA(+) (#603).

New Features

  • GaussianHMM and VonMisesHMM is rewritten to feature higher code reuse and code quality (#583, #582, #584, #572, #570).
  • KDTree can find n nearest points to e.g. a cluster center (#599).
  • Slicer featurizer can slice feature arrays as part of a pipeline (#567).

Improvements

  • PCCAPlus is compatible with scipy 0.16 (#620).
  • Documentation improvements (#618, #608, #604, #602)
  • Test improvements, especially for Windows (#593, #590, #588, #579, #578, #577, #576)
  • Bug fix: MarkovStateModel.sample() produced trajectories of incorrect length. This function is still deprecated (#556).
  • Bug fix: The muller example dataset did not respect users’ specifications for initial coordinates (#631).
  • MarkovStateModel.draw_samples failed if discrete trajectories did not contain every possible state (#638). Function can now accept a single trajectory, as well as a list of them.
  • SuperposeFeaturizer now respects the topology argument when loading the reference trajectory (#555).

v3.2 (April 14, 2015)

  • tICA ignores too-short trajectories during fitting instead of raising an exception
  • New methods for sampling from MSM models
  • Datasets can be opened in “append” mode
  • Compatibility with scipy 0.16
  • utils.dump saves using the pickle protocol. utils.load is backwards compatible.
  • The command line flag for featurizers --out is deprecated. Use --transformed instead. This is consistent with other command-line commands.
  • Bug fixes

v3.1 (Feb 27, 2015)

  • Numerous improvements to ContinuousTimeMSM optimization
  • Switch ContinuousTimeMSM.score to transmat-style GMRQ
  • New example dataset with Muller potential
  • Assorted bug fixes in the command line layer

v3.0.1 (January 9, 2015)

  • Fix missing file on PyPI.

v3.0.0 (January 9, 2015)

MSMBuilder 3.0 is a complete rewrite of our previous work. The focus is on power and extensibility, with a much wider class of estimators and models supported throughout the codebase. All users are encouraged to switch to MSMBuilder 3.0. Pre-release versions of MSMBuilder 3.0 were called mixtape.

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