v2.5.12 patch release

What's Changed

• Improved topology LRU cache by @clonker in #1545
• Remove bhmm as dependency by @clonker in #1550
• Remove msmtools by @clonker in #1555
• remove pybind submodule by @clonker in #1556
• Deprecations for coordinates api by @clonker in #1557
• Use spawn() for multiprocessing instead of fork() by @sents in #1565
• Change ipywidgets version check to use version. Fixes #1571. by @clonker in #1573
• Fix tests, use deeptime double well discrete data. by @clonker in #1574

New Contributors

• @sents made their first contribution in #1565

Full Changelog: v2.5.11...v2.5.12

v2.5.11 patch release

What's Changed

• Fix periodic width initialization in umbrella sampling by @sefalkner in #1522
• Only pass copy of trajectory list to mdtraj.load and (CI) update macos image by @clonker in #1526
• solve some syntax warnings by @sroet in #1530
• use mambabuild in CI and fix rmsd computation in clustering by @clonker in #1531
• update deeptime clustering include by @clonker in #1540

New Contributors

• @sefalkner made their first contribution in #1522

Full Changelog: v2.5.10...v2.5.11

Minor patch release

Mainly fixes incompatibility to deeptime.

What's Changed

• [CI] azure pipelines setup by @clonker in #1505
• Use int instead of numpy.int by @sroet in #1504
• Update types.py by @sroet in #1503
• save_trajs support for fragmented data source by @clonker in #1514

New Contributors

• @sroet made their first contribution in #1504

Full Changelog: v2.5.9...v2.5.10

Patch release

v2.5.9

patch release

Minor patch release

v2.5.8

Minor patch release

minor patch release

[doc] amend changelog

[ci skip]

service release

For now all future versions will only support Python 3. #1395

New features:

• msm: for Bayesian MSMs we show an optional progress bar for the counting computation. #1344
• msm: ImpliedTimescales allow to only store timescales and its samples for the purpose of saving memory. #1377
• double_well_discrete: allows the setting of a random seed #1388

Fixes:

• msm: fix connected sets for Bayesian MSMs in case the mincount connectivity (ergodic cutoff) parameter truncated the count matrix. #1343
• plots: fix vmin, vmax keyword arguments for plot_contour(). #1376
• coordinates: forcefully enable checking of coordinates data streaming for invalid (not initialized) data. #1384
• coordinates: for sake of faster strided MD data reading, we now require a version of MDTraj >= 1.9.2 #1391
• coordinates: VAMP: changed default projection vector from right to left, since only the left singular functions induce a kinetic map wrt. the conventional forward propagator, while the right singular functions induce
  a kinetic map wrt. the backward propagator. #1394
• coordinates: VAMP: fixed variance cutoff to really include as many dimensions to meet subspace variance criterion. #1397

Contributors:

• @marscher
• @fabian-paul
• @brookehus
• @thempel

Patch release

New features:

• coordinates: added Nystroem-TICA, which uses sparse sampling to approximate the input space. #1261, #1273
• plots: added multi-dimensional stacked histogram plot function. #1264

Fixes:

• msm: Chapman Kolmogorov validator ensures there are no side effects on the tested model. #1255
• datasets: Fix default values for kT to ensure integrator produces sane values. #1272, #1275
• coordinates: fixed handling of default chunksize. #1284

Patch release

Quick fix release to repair chunking in the coordinates package.

Fixes:

• msm: fix bug in ImpliedTimescales, which happened when an estimation failed for a given lag time. #1248
• coordinates: fixed handling of default chunksize. #1247, #1251, #1252
• base: updated pybind to 2.2.2. #1249

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