Pensa

Two bugfixes:

- final frame selected in MDA distance reader
- close figure of discrete states after it is saved

New:
- Function to align trajectories at a selection
- Contribution guidelines

Future releases are to be developed in the "develop" branch.

Now includes subpackages in setup.

New functionality:

- Distances reader based on MDAnalysis
- GPCR feature reader as an example for system-specific additions
- Tutorials for SSI and atom features

New functionality:
- State-specific information
- Water features
- Atom features
- TICA
- Doc pages
- Tutorial using MOR traj. from GPCRmd

Major changes to existing functionality:
- The former modules are now sub-packages.
- The function `get_features()` was renamed to `get_structure_features()` to account for the fact that there are several feature types now.
- Torsion features are by default loaded in radians now. Cosine and sine can be obtained using the option `cossin=True`

Notes:
- Functionality and UI might still change in minor releases to streamline workflows!
- Documentation and tutorials do not cover all of the new functionality yet. We will update this step by step.

Changelog:
Version 0.1.2 ...
- now provides feature names as a list of strings. No more .describe() is necessary.
- corrects the behavior of option bin_width in relative_entropy_analysis(). So far, this option falsely did not have any effect. To retain the old behavior, use bin_width=None, bin_num=10, which are also the new default options.
- removes the obsolete bin_width option in Kolmogorov-Smirnov analysis (this was just a copy-paste artifact)
- fixes the previously undefined variables in reporting of relative_entropy_analysis().
- adds the first tests for pytest (only a dummy for now) and test data.
- adds axis labels for PC comparison and feature correlations.
- adds a tutorial that uses GPCRmd simulations of a mu-opioid receptor.