v2.5

As of this version the usage of Python 2.7 is officially deprecated. Please upgrade
your Python installation to at least version 3.5.

New features:

• base: most Estimators and Models in msm, thermo and coordinates packages can be saved to disk now.
  Multiple models/estimators can be stored in the same file, which uses HDF5 as backend. #849, 867, #1155, #1200, #1205
• coordinates: Added Variational Approach for Markov Processes (VAMP) estimator and scoring method, see [2]. #1237
• coodinates: selection based features allow alignment to a reference structure. #1184
• coordinates: two new center of mass features: ResidueCOMFeature() and GroupCOMFeature()
• coordinates: new configuration variable 'default_chunksize' can be set to limit the size of a fragmented
  extracted per iteration from a data source. This is invariant to the dimension of data sets. #1190
• msm: Added Augmented Markov Models. A way to include averaged experimental
  data into estimation of Markov models from molecular simulations. The method is described in [1]. #1111
• msm: Added mincount_connectivity argument to MSM estimators. This option enables to omit counts below
  a given threshold. #1106
• datasets: added Prinz potential (quadwell). #1226

References:
[1] Olsson S, Wu H, Paul F, Clementi C, Noe F: Combining experimental and simulation data of molecular
processes via augmented Markov models. PNAS 114, 8265-8270 (2017).
[2] Wu H, Noé F: Variational approach for learning Markov processes from time series data.
arXiv:1707.04659 (2017).

Fixes:

• datasets: fixed get_multi_temperature_data and get_umbrella_sampling_data for Python 3. #1102
• coordinates: fixed StreamingTransformers (TICA, Kmeans, etc.) not respecting the in_memory flag. #1112
• coordinates: made TrajectoryInfoCache more fail-safe in case of concurrent processes. #1122
• msm: fix setting of dt_model for BayesianMSM. This bug led to wrongly scaled time units for mean first passage times,
  correlation and relaxation times as well for timescales for this estimator. #1116
• coordinates: Added the covariance property of time-lagged to CovarianceLagged. #1125
• coordinates: clustering code modernized in C++ with pybind11 interface. #1142
• variational: covartools code modernized in C++ with pybind11 interface. #1147
• estimators: n_jobs setting does not look for OMP_NUM_THREADS, but for PYEMMA_NJOBS and SLURM_CPUS_ON_NODE to avoid
  multiplying OpenMP threads with PyEMMA processes. On SLURM the number of allocated cores is used.
  If nothing is set, the physical cpu count is considered.
• msm: calling score_cv does not modify the object anymore. #1178
• base:estimator: fixed signature of fit function for compatability with scikit-learn. #1193
• coordinates: assign_to_centers now handles stride argument again. #1190