MobleyLab/blues: Version 0.2.3

Published September 4, 2018 | Version 0.2.3

Software Open

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

Files

Name	Size	Download all
MobleyLab/blues-0.2.3.zip md5:bd8330ae78ab206f54e2a972de98d56e	1.4 MB	Preview Download