Development release

This version contains updated examples.

Updated development version

A number of fixes and improvements to the development version.

Major changes in the code:

New features:

• Offering useful functions in a user API (bhmm/api.py). The old api objects (HMM, BHMM, MLHMM) are still available.
• Extended HMM to compute various useful properties.
• Extended MLHMM (MaximumLikelihoodEstimator) to provide various useful properties.
• New SampledHMM object that encapsulates a list of sampled HMMs and can provide various statistical quantities (means, stds, confidence intervals)
• New HMM subclasses to provide convenient access to special HMM types (Gaussian, Discrete)

Testing and docs:

• Added extensive Tests for MLHMM and BHMM
• Removed verbosity in tests
• Improved API docs

Refactoring:

• HMM now has an update option to set new transition matrix. Avoids inconsistencies and removes inconsistency errors previous created by directly setting attributes
• HMM, BHMM and MLHMM have all their attributes hidden, and have property getters to avoid undesired write access.
• Moved general settings (kernel, dtype and verbose) to bhmm.config and set to reasonable defaults
• Refactored various internal implementation details and moved all python files into packages.
• Moved plots module to examples directory and thus out of the install directory. Consequently removed the dependencies to matplotlib and seaborn.

Examples for paper

• Made example scripts more general and simpler
• Fixed LaTeX table generation for BHMM data
• Removed generated files from git

Bugfixes

• Fixed: initialization problems with discrete and Gaussian HMMs
• Fixed: Using pyEMMA>=1.2, should fix previous dependency problems
• Countless small bugfixes

Initial development release

This is a first development release to facilitate creating the conda packaging and release infrastructure.