MobleyLab/blues: Version 0.2.0

Release from major changes from PR# 117

• BLUES will now support partial configuration from a YAML file
  • Supported settings: Input/output, system parameters, simulation parameters, freezing/restraining atoms, and configuring reporters
• API Changes
  • Addition of SystemFactory class: Provides methods for freezing or restraining atoms in your system
  • Addition of SimulationFactory: Allows addition of a MonteCarloBarostat to your System, enabling NPT simulations
  • Name changes methods in the Simulation class
• Addition of reporters.py module
  • Addition of ReporterConfig class, provides functionality for generating/configuring a some recommended/customized reporters for BLUES simulations:
    • BLUESHDF5Reporter subclass from mdtraj.HDF5Reporter
      • Custom features include:
        • specifying the indices of frames to be recorded,
        • protocolWork/alchemicalLambda from the NCMC simulation
        • simulation parameters
        • exporting your conda environment
    • BLUESStateDataReporter subclass from openmm.app.StateDataReporter
      • Custom features include:
        • title field to set the string prefix that is printed with each report line.
        • enable writing to a file or file-like object for streaming the data (logging.Logger) to the terminal window,
        • specifying the indices of frames to be recorded
        • currentIter/protocolWork/alchemicalLambda from the NCMC simulation
    • NetCDF4Reporter subclass from parmed.openmm.reporters.NetCDFReporter
      • Custom features includes:
        • Add ability to properly flush the data to disc on call to report()
        • specifying the indices of frames to be recorded
        • protocolWork/alchemicalLambda from the NCMC simulation
    • parmed.openmm.reporters.RestartReporter, enabling restarts from the rst7 file