search

choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
http://openmmtools.readthedocs.io
MIT License
253 stars 81 forks source link

Create alchemy subpackage #721

Closed ijpulidos closed 1 year ago

ijpulidos commented 1 year ago

Description

The idea of this PR is to create the alchemy subpackage in a way that doesn't break the current API.

This is to give room to extend the alchemy capabilities of openmmtools with the tools that would be coming from perses and openfe (for example check roadmap in https://github.com/orgs/choderalab/projects/5)

In the future, I expect that these objects will be moved around to different modules or that the current alchemy.py module changes its name for something more descriptive of what it has. So far, this is just thought as a starting point.

Todos

This shouldn't be changing any of the behavior, this should be reflected in the tests in test_sampling.py and test_alchemy.py passing, which are the ones that call the objects in the alchemy module.

Status

mikemhenry commented 1 year ago

Thanks for kicking this off!

ijpulidos commented 1 year ago

There are some imports in the tests to be fixed, they were relying on the alchemy.py module to import things like openmm and copy, and I think that shouldn't happen. Will fix this.

codecov[bot] commented 1 year ago

Codecov Report

Merging #721 (bfe43f9) into main (0b4d42a) will decrease coverage by 0.73%. The diff coverage is 100.00%.

Additional details and impacted files