1409272
doi
10.5281/zenodo.1409272
oai:zenodo.org:1409272
David L. Mobley
University of California, Irvine
sgill2
khburley
megosato
MobleyLab/blues: Version 0.2.3
Nathan M. Lim
@MobleyLab
url:https://github.com/MobleyLab/blues/tree/0.2.3
info:eu-repo/semantics/openAccess
Other (Open)
<ul>
<li>Adds the standard python <code>.gitignore</code> file</li>
<li>Adds a <code>.github/</code> which holds template files for PRs and guidelines for contributing to the code</li>
<li>Adds Sphinx docs and ReadTheDocs to the repository</li>
<li>Docstrings are now formatted in numpydoc style</li>
<li>Code is styled in YAPF style; configured by the <code>setup.cfg</code> file</li>
<li>Re-wrote the tests to use pytest</li>
<li>Adds CodeCov to the repository</li>
<li>Adds Versioneer to the repository</li>
<li>Improvements to Travis-CI<ul>
<li>Builds and deploys conda packages for py3.5/3.6 for both osx/linux platforms</li>
<li>Deploys the conda environment yml file onto anaconda cloud</li>
<li>Conda packages follow convention, example for version 0.2.3 on python3.5<ul>
<li><code>blues-0.2.3-py35g{SHORTHASH}_{#UNRELEASED COMMITS}</code> or <code>blues-0.2.3-py35g6aaba2d_5</code></li>
</ul>
</li>
</ul>
</li>
<li>Minor API changes, renaming some functions in the BLUESSimulation to adhere to conventional python name schemes<ul>
<li>Move the <code>engine.py</code> module (which housed just one single class) into the <code>moves.py</code> module</li>
<li>Fix in the <code>AlchemicalExternalLangevinIntegrator</code> for issue #115 <a href="https://github.com/nathanmlim/blues/blob/8079e40bda8c092da65123722ba3b54376ea5268/blues/integrators.py#L136">ref</a></li>
</ul>
</li>
<li>Make package compatible for openmm=7.2.2 and openmmtools=0.15.0</li>
<li>Includes changes from #150 <ul>
<li>Removes some code redundancy in syncing the simulation states</li>
<li>Correctly resets the velocities before the start of each MD simulation <a href="https://github.com/MobleyLab/blues/blob/fix-0.2.3/blues/simulation.py#L1248">ref</a></li>
<li>Corrects behavior in syncing the simulation states <a href="https://github.com/MobleyLab/blues/blob/9172607d3b1d7941a894e51d130c85a77f1bbbac/blues/simulation.py#L1143">ref</a></li>
<li>Adds some checks in the freezing selection <a href="https://github.com/MobleyLab/blues/blob/9172607d3b1d7941a894e51d130c85a77f1bbbac/blues/simulation.py#L439">ref</a></li>
</ul>
</li>
</ul>
Zenodo
2018-09-04
info:eu-repo/semantics/other
598014
0.2.3
1603393942.151152
1355618
md5:bd8330ae78ab206f54e2a972de98d56e
https://zenodo.org/records/1409272/files/MobleyLab/blues-0.2.3.zip
public
https://github.com/MobleyLab/blues/tree/0.2.3
Is supplement to
url
10.5281/zenodo.598014
isVersionOf
doi