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MobleyLab/blues: Version 0.2.3

Nathan M. Lim; David L. Mobley; sgill2; khburley; megosato

  • Adds the standard python .gitignore file
  • Adds a .github/ which holds template files for PRs and guidelines for contributing to the code
  • Adds Sphinx docs and ReadTheDocs to the repository
  • Docstrings are now formatted in numpydoc style
  • Code is styled in YAPF style; configured by the setup.cfg file
  • Re-wrote the tests to use pytest
  • Adds CodeCov to the repository
  • Adds Versioneer to the repository
  • Improvements to Travis-CI
    • Builds and deploys conda packages for py3.5/3.6 for both osx/linux platforms
    • Deploys the conda environment yml file onto anaconda cloud
    • Conda packages follow convention, example for version 0.2.3 on python3.5
      • blues-0.2.3-py35g{SHORTHASH}_{#UNRELEASED COMMITS} or blues-0.2.3-py35g6aaba2d_5
  • Minor API changes, renaming some functions in the BLUESSimulation to adhere to conventional python name schemes
    • Move the module (which housed just one single class) into the module
    • Fix in the AlchemicalExternalLangevinIntegrator for issue #115 ref
  • Make package compatible for openmm=7.2.2 and openmmtools=0.15.0
  • Includes changes from #150
    • Removes some code redundancy in syncing the simulation states
    • Correctly resets the velocities before the start of each MD simulation ref
    • Corrects behavior in syncing the simulation states ref
    • Adds some checks in the freezing selection ref

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