Pyemma

**New features**:
- coordinates: SQLite backend for trajectory info data. This enables fast access to this data
on parallel filesystems where multiple processes are writing to the database. This greatly
speeds ups reader construction and enables fast random access for formats which usually do not
support it. 798
- plots: new optional parameter **arrow_label_size** for network plotting functions to use a custom
font size for the arrow labels; the default state and arrow label sizes are now determined by the
matplotlib default. 858
- coordinates: save_trajs takes optional parameter "image_molecules" to correct for broken
molecules across periodic boundary conditions. 841

**Fixes**:
- coordinates: set chunksize correctly. 846
- coordinates: For angle features it was possible to use both cossin=True and deg=True, which
makes not sense. 857
- coordinates: fixed a memory error in kmeans clustering which affected large data sets (>=64GB). 839
- base: fixed a bug in ProgressReporter (_progress_force_finish in stack trace). 869
- docs: fixed a lot of docstrings for inherited classes both in coordinates and msm package.

**Fixes**:
- clustering: fixed serious bug in **minRMSD** distance calculation, which led to
lots of empty clusters. The bug was introduced in version 2.1. If you used
this metric, please re-assign your trajectories. 825
- clustering: fixed KMeans with minRMSD metric. 814
- thermo: made estimate_umbrella_sampling more robust w.r.t. input and fixed doumentation. 812 827
- msm: low-level api usage deprecation warnings only show up when actually used.

**New features**:
- thermo: added TRAM estimation.
- thermo: added plotting feature for implied timescales.
- thermo: added Jupyter notebook examples: :ref:`ref-notebooks`.
- thermo: show convergence progress during estimation.

**Fixes**:
- clustering: fix parallel cluster assignment with minRMSD metric.
- base: during estimation the model was accessed in an inappropriate way,
which led to the crash "AttributeError: object has no attribute '_model'" 764.
- coordinates.io: fixed a bug when trying to pyemma.coordinates.load certain MD formats.
The iterator could have returned None in some cases 790.
- coordiantes.save_traj(s): use new backend introduced in 2.1, speed up for non random
accessible trajectory formats like XTC. Avoids reading trajectory info for files not
being indexed by the input mapping. Fixes 788.

Fixes
- some issues in parallel environments (eg. shared file systems on clusters)
in conjunction with enabled trajectory cache [default]).
- File-logging disabled by default
- No files are written to your home directory until you request it (eg. by setting the
config directory [pyemma.config.cfg_dir = "path" or invoke pyemma.config.save(filename)]

Improvements
- Parallel assignment of cluster centers via threads.