Auto Alchemical Path, Split Langevin Integrators, and More

Features added by this release

• Automatic Alchemical Path Determination (#726)
• Langevin Splitting Integrator which allows custom sub-division of a timestep for more accurate simulations (#747)
• Online Free Energy Analysis with simulation stop criteria of target error in free energy difference (#712)
• Jupyter Notebooks can now be pre-rendered as static HTML or PDF files, PDF requires LaTeX (#740)
• Experiments can be parallelized by splitting MPI communicator (#726)

Improvements added by this release

• Centroids for restraints now selectable through DSL string instead of whole molecule
• Ionic Strength ability added to setup pipeline
• Website fully documented, all pages filled in
• API fully documented on website and auto-generated from docstrings
• YAML pages on website should be much easier to read

Notable Bugs Fixed

• Removed Ligand rotation/displacement attempts with Boresch restraints to improve replica exchange
• Analyze module fully tested, related bugs found and corrected

Notable Refactoring and Dependency changes

• YAMLBuilder class and yamlbuilder.py file refactored ExperimentBuilder and experiment.py respectively
• Anisotropic Dispersion correction options reduced to a single setting
• Added MDTraj, Jupyer, and Matplotlib as dependencies
• Updated OpenMMTools dependency minimum version to 0.13.0