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rinikerlab / PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.
https://rinikerlab.github.io/PyGromosTools/
MIT License
16 stars 14 forks source link

replica exchange simulation submission + minor reeds tweaks #288

Open candidechamp opened 2 years ago

candidechamp commented 2 years ago

I reimplemented (and re-tested) the changes in #222 (as I didn't want to have trouble with merge conflicts, although they all seemed super minor and would have been easily fixed).

The code in here is essentially the same as in #222 with the exception of some imd related functions, where I simplified a call to str2bool (previously was put in an if, else block based on input given to function, which already happens in the function).

To do

Status

PS: Please don't delete the pygromos3_for_reeds branch after merge. I would like to keep this branch in parallel at all times (and probably also have a "release" for it so that there is an easily accessible version for RE-EDS users once I have implemented all I need to).

codecov[bot] commented 2 years ago

Codecov Report

Merging #288 (efa11f8) into main (53767f5) will decrease coverage by 0.01%. The diff coverage is 15.51%.

@@            Coverage Diff             @@
##             main     #288      +/-   ##
==========================================
- Coverage   54.14%   54.12%   -0.02%     
==========================================
  Files          93       93              
  Lines       14285    14279       -6     
==========================================
- Hits         7734     7728       -6     
  Misses       6551     6551
Flag Coverage Δ
unittests 54.12% <15.51%> (-0.02%) :arrow_down:

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Impacted Files Coverage Δ
pygromos/files/simulation_parameters/imd.py 64.80% <ø> (-0.05%) :arrow_down:
...orkers/simulation_workers/simulation_run_worker.py 9.81% <0.00%> (-2.89%) :arrow_down:
pygromos/files/blocks/imd_blocks.py 78.89% <58.33%> (+2.59%) :arrow_up:
pygromos/utils/utils.py 76.03% <100.00%> (+3.76%) :arrow_up:

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candidechamp commented 2 years ago

@MTLehner I think you can merge the code now (you probably want to checkout and submit a quick calculation just to make sure everything is fine on your end).