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* Modify quickrun to allow resuming * fix the gather tests * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add check for protocol_dag.json * add basic test * clearer language, hopefully * store protocol dag using transformation key * another tmpdir -> tmp_path fix * add error handling check * fix naming in test * add news item * use assert_click_success * add test for interrupted job * remove checkpoint when a job has completed successfully * add handling for checkpoint error handling without --resume * clean up logic * check for warning * add docs * make a cache dir * use clickexception * update error message * update kwarg * keep everything in the quickrun cache * clearer message * it's ProtocolDAG not protocolDAG * bump CI * bump CI * include output json in caching hash (#1890) * first pass at adding caching with output json * add (hopefully) helpful execution information * add resume command * fix testing path * check that output file isn't created early * clean up tests * line break * fix some comments to say cache instead of checkpoint * fix typo in news item --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alyssa Travitz <alyssa.travitz@omsf.io> Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
openfe - A Python package for executing alchemical free energy calculations.
The openfe package is the flagship project of Open Free Energy,
a pre competitive consortium aiming to provide robust, permissively licensed open source tools for molecular simulation in the drug discovery field.
Using openfe you can easily plan and execute alchemical free energy calculations.
See our website for more information on the project, try for yourself from the comfort of your browser, and we have documentation on using the package.
License
This library is made available under the MIT open source license.
Install
Latest release
The latest release of openfe can be installed via mamba, docker, or a single file installer. See our installation instructions for more details.
Dependencies can be installed via conda through:
Development version
The development version of openfe can be installed directly from the main branch of this repository.
First install the package dependencies using mamba:
mamba env create -f environment.yml
The openfe library can then be installed via:
python -m pip install --no-deps .
Authors
The OpenFE development team.
Acknowledgements
OpenFE is an Open Molecular Software Foundation hosted project.