<commit_before>.. _changelog:

Changelog
=========

v3.9 (development)
------------------

API Changes
~~~~~~~~~~~

New Features
~~~~~~~~~~~~
- Added new featurizer ```FeatureSlicer```. ```FeatureSlicer``` can slice
  the ouput of regular featurizer objects to just the required indices
  (gh-1022).
- Added functions to compute error bars for transition probabilities to account
  for finite sampling, and sample transition matrices from these error 
  distributions (i.e. bootstrapping). Located in
  ```msmbuilder.msm.validation.transmat_errorbar``` (gh-1010).
- Added methods for computing the Kullbeck-Leibler, symmetric KL, and 
  Jensen-Shannon divergences of probability distributions, arrays thereof,
  or flattened MSM objects. The array and (flattened) MSM metrics are
  compatible with the custom distance function in ```LandmarkAgglomerative```
  (gh-1035).

Improvements
~~~~~~~~~~~~
- ```FeatureSelector``` is now compatible with Tree-structure Parzen Estimator
  method in Osprey (gh-1018).
- ```sample_dimenstion``` with ```scheme='edge'``` now works properly.


v3.8 (April 26, 2017)
---------------------

We're pleased to annoounce the release of MSMBuilder 3.8. This release
features updates and improvements to contact featurizers, kernel tICA, HMMs,
and preprocessing. There are also some bugfixes and API hygiene improements.
We recommend all users upgrade to MSMBuilder 3.8.

API Changes
~~~~~~~~~~~

New Features
~~~~~~~~~~~~

- ``ContactFeaturizer`` now lets you use a soft_min option for closest
contact distances.

Improvements
~~~~~~~~~~~~

- The ``stride`` parameter in ``KernelTICA`` now works as intended to
automatically generate a set of landmark points (gh-972).
- The ``contacts`` parameter in ``CommonContactFeaturizer`` now performs as the
contacts method in regular ``ContactFeaturizer`` albeit after validating all<commit_msg>fix typo<commit_after>.. _changelog:

Changelog
=========

v3.9 (development)
------------------

API Changes
~~~~~~~~~~~

New Features
~~~~~~~~~~~~
- Added new featurizer ```FeatureSlicer```. ```FeatureSlicer``` can slice
  the ouput of regular featurizer objects to just the required indices
  (gh-1022).
- Added functions to compute error bars for transition probabilities to account
  for finite sampling, and sample transition matrices from these error 
  distributions (i.e. bootstrapping). Located in
  ```msmbuilder.msm.validation.transmat_errorbar``` (gh-1010).
- Added methods for computing the Kullbeck-Leibler, symmetric KL, and 
  Jensen-Shannon divergences of probability distributions, arrays thereof,
  or flattened MSM objects. The array and (flattened) MSM metrics are
  compatible with the custom distance function in ```LandmarkAgglomerative```
  (gh-1035).

Improvements
~~~~~~~~~~~~
- ```FeatureSelector``` is now compatible with Tree-structure Parzen Estimator
  method in Osprey (gh-1018).
- ```msmbuilder.io.sampling.sample_dimension``` with ```scheme='edge'``` now works properly. (#1043)


v3.8 (April 26, 2017)
---------------------

We're pleased to annoounce the release of MSMBuilder 3.8. This release
features updates and improvements to contact featurizers, kernel tICA, HMMs,
and preprocessing. There are also some bugfixes and API hygiene improements.
We recommend all users upgrade to MSMBuilder 3.8.

API Changes
~~~~~~~~~~~

New Features
~~~~~~~~~~~~

- ``ContactFeaturizer`` now lets you use a soft_min option for closest
contact distances.

Improvements
~~~~~~~~~~~~

- The ``stride`` parameter in ``KernelTICA`` now works as intended to
automatically generate a set of landmark points (gh-972).
- The ``contacts`` parameter in ``CommonContactFeaturizer`` now performs as the
contacts method in regular ``ContactFeaturizer`` albeit after validating all
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