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[changelog] added github references
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marscher committed Jan 6, 2017
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Changelog
=========

2.3 (tba)
---------
2.3 (6-1-2017)
--------------

**New features**:

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or "koopman", which uses the re-weighting procedure from [1] to compute equi-
librium covariance matrices. The user can also supply his own re-weighting me-
thod. This must be an object that possesses a function weights(X), that assigns
a weight to every time-step in a trajectory X.
a weight to every time-step in a trajectory X. #1007
- covariance_lagged: This new method can be used to compute covariance matrices
and time-lagged covariance matrices between time-series. It is also possible
to use the re-weighting method from [1] to compute covariance matrices in equi-
librium. This can be triggered by the option "weights", which has the same spe-
cifications as in tica.
cifications as in tica. #1007

- msm:
- estimate_markov_model: New option "weights". Can be empirical, which does the
same as before, or "oom", which triggers a transition matrix estimator based
on OOM theory to compute an equilibrium transition matrix from possibly non-
equilibrium data. See Ref. [2] for details.
- timescales_msm: The same change as in estimate_markov_model.
equilibrium data. See Ref. [2] for details. #1012, #1016
- timescales_msm: The same change as in estimate_markov_model. #1012, #1016
- TPT: if user provided sets A and B do not overlap (no need to split), preserve order of user states. #1005

- general: Added an automatic check for new releases upon import. #986

- References:
[1] Wu, H., Nueske, F., Paul, F., Klus, S., Koltai, P., and Noe, F. 2017. Bias reduced variational
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(submitted).


- msm:
- ...
- TPT: if user provided sets A and B do not overlap (no need to split), preserve order of user states. #1005

- general: Added an automatic check for new releases upon import. #986

**Fixes**:

- coordinates:
- ...
- kmeans: fixed a rare bug, which led to a segfault, if NaN is contained in input data. #1010
- Featurizer: fix reshaping of AnglesFeature. #1018. Thanks @RobertArbon

- plots:
- Fix drawing into existing figures for network plots. #1020
- plots: Fix drawing into existing figures for network plots. #1020


2.2.7 (10-21-16)
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