Changes for 0.2.3 release

[nathanmlim]

After numerous attempts of reverting/reseting the last botched PR that got merge committed without review, I just copied over the files again, which seems to now let me bring in the changes properly.

This PR does a number of things I've been working on lately, which includes:

• 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 engine.py module (which housed just one single class) into the moves.py 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

[codecov[bot]]

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@726d017). Click here to learn what that means. The diff coverage is 62.63%.

@@            Coverage Diff            @@
##             master     #154   +/-   ##
=========================================
  Coverage          ?   59.58%           
=========================================
  Files             ?        7           
  Lines             ?     1477           
  Branches          ?      266           
=========================================
  Hits              ?      880           
  Misses            ?      497           
  Partials          ?      100

Impacted Files	Coverage Δ
blues/__init__.py	100% <100%> (ø)
blues/integrators.py	91.01% <100%> (ø)
blues/utils.py	49.07% <42.3%> (ø)
blues/settings.py	56.12% <46.42%> (ø)
blues/moves.py	58.18% <58.87%> (ø)
blues/reporters.py	39.23% <62.74%> (ø)
blues/simulation.py	75.32% <68.7%> (ø)

[nathanmlim]

@sukanyasasmal @davidlmobley Need an approving review before I can merge. The edits @sukanyasasmal aren't YAPF style convention, so I'll keep it as is.