new major

New features:

• coordinates:

  • tica: New option "weights". Can be "empirical", which does the same as before,
    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. #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. #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. #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
  approximation of molecular kinetics from short off-equilibrium simulations. J. Chem. Phys. (submitted),
  https://arxiv.org/abs/1610.06773.
  [2] Nueske, F., Wu, H., Prinz, J.-H., Wehmeyer, C., Clementi, C., and Noe, F. 2017. Markov State Models from
  short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys.
  (submitted).

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