CHANGELOG

pytram changelog
================

Version 0.1.0 (Alpha):

    Implemented the dTRAM estimator, nosetests, and a dTRAM example (iPython notebook).

Version 0.1.1 (Alpha):

    Added a second example for dTRAM. Added docstrings for DTRAM and the API function.

Version 0.1.2 (Alpha):

    Added the TRAMData class for easy input data preparation. Adapted API and dTRAM example.
    Added new dTRAM API function for simple use of TRAMData. Changed dTRAM dependency from
    reweighting factors to bias energies. Added method for transition matrix of a given
    thermodynamic state.

Version 0.1.3 (Alpha):

    Added the Reader class for easy input data import. Added run script for dTRAM.
    Added u_I_x generators. in TRAMData for use with xTRAM.
    
Version 0.1.4 (Alpha):

    Added xTRAM estimator, API, runscript, tests
    Added documentation.
    Minor bug fixes.
    
Version 0.1.5 (Alpha):

    Preparation for pypi

Version 0.1.6 (Beta)

    Added verbosity to TRAMData. Binning bugfix in xTRAM. Fixed None comparisons in dTRAM.

Version 0.1.7 (Beta)

    Added stationary property getters to Estimator. Removed unsafe setters from Estimator classes.
    Added kT switch in TRAMData. Moved sanity checks to Estimator classes' constructors.
    Standardised verbose printouts.

Version 0.2.0 (Beta)

    Introducing logsumexp summation scheme fro dTRAM. Interface cleanup (uniform getters, citation,
    naming conventions).

Version 0.2.1 (Beta)
    
    Fix compilation under MS Visual Studio. Refactoring API functions: use _from_matrix instead
    of _me versions.

Version 0.2.2 (Beta)
    
    Fix for sign error in f_K calculations. Partially fixing bad code style.

Version 0.2.3 (Beta)

    Fix iteration variables of iterat_x in constructor of XTRAM

Version 0.2.4 (Beta)

    Fix normalisation in biased thermodynamic states. Extended the test suite. Renaming the dtram
    xtram modules (pytram/dtram -> pytram/_dtram & pytram/xtram -> pytram/_xtram) to prevent a name
    space clash with the pytram.dtram and pytram.xtram API functions (fixes #43).

Version 0.2.5 (Beta)

    Fixes broken __version__ on PyPI (#45). Migration to container-based infrastructure on Travis.
    Covering f_K in unit tests.

Version 0.2.6 (Beta)

    Fixes error in xTRAM (#44)

Version 0.3 (Inactive)

    Fix for #26
    pytram is no longer supported; use PyEMMA instead