Pyemma

**New features**:

- msm:
- ImpliedTimescales: enable insertion/removal of lag times.
Avoid recomputing existing models. 1030

**Fixes**:

- coordinates:
- If Estimators supporting streaming are used directly, restore previous behaviour. 1034
Note that estimators used directly from the API were not affected.

**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

**New features**:
- coordinates:
- for lag < chunksize improved speed (50%) for TICA. 960
- new config variable "coordinates_check_output" to test for "NaN" and "inf" values in
iterator output for every chunk. The option is disabled by default. It gives insight
during debugging where faulty values are introduced into the pipeline. 967

**Fixes**:
- coordinates:
- save_trajs, frames_from_files: fix input indices checking. 958
- FeatureReader: fix random access iterator unitcell_lengths scaling.
This lead to an error in conjunction with distance calculations, where
frames are collected in a random access pattern. 968
- msm: low-level api removed (use msmtools for now, if you really need it). 550

**New features**:
- plots: network plots can now be plotted using a given Axes object.
- thermo: TRAM supports the new parameter equilibrium which triggers a TRAMMBAR estimation.
- thermo: the model_active_set and msm_active_set attributes in estimated MEMMs is deprecated; every
MSM in models now contains its own active_set.
- thermo: WHAM and MBAR estimations return MultiThermModel objects; return of MEMMs is reserved for
TRAM/TRAMMBAR/DTRAM estimations.

**Fixes**:
- coordinates: MiniBatchKmeans with MD-data is now memory efficient
and successfully converges. It used to only one batch during iteration. 887 890
- coordinates: source and load function accept mdtraj.Trajectory objects to extract topology. 922. Thanks jeiros
- base: fix progress bars for modern joblib versions.
- plots: fix regression in plot_markov_model with newer NumPy versions 907. Thanks ghoti687.
- estimation: for n_jobs=1 no multi-processing is used.
- msm: scale transition path times by time unit of MSM object in order to get
physical time scales. 929

Service release to hot-fix "Permission denied: '/traj_info_usage'" 882