v0.12.0

Highlights

• Adds ability to read FEP+ / Orion NES ligand network files using openfe.setup.ligand_network_planning.load_fepplus_network and openfe.setup.ligand_network_planning.load_orion_network
• Adds openfe.setup.ligand_network_planning.generate_network_from_names and openfe.setup.ligand_network_planning.generate_network_from_indices to create arbitrary networks
• OpenMM RBFE Protocol pdb output now labels A and B state using BFactor column
• network layouts from cli tool now much easier to understand

What's Changed

• Make super slow tests integration tests by @IAlibay in #484
• Added DCO by @mikemhenry in #475
• fix issue with new notebook version by @mikemhenry in #498
• Tell users to install the latest version of openfe by @mikemhenry in #497
• Unpin libnetcdf by @dwhswenson in #500
• add ps to the docker image (interline needed this) by @mikemhenry in #501
• Network planner functions from indices/names by @richardjgowers in #482
• remove version name and upload files by @mikemhenry in #503
• API docs updates by @Yoshanuikabundi in #493
• Update openfecli/tests/data/rbfe_results.tar.gz by @mikemhenry in #496
• Logging improvements in quickrun by @dwhswenson in #504
• see if py311 works okay by @mikemhenry in #508
• Migrate common settings to omm_utils by @IAlibay in #512
• Read network from external files by @IAlibay in #511
• Add system probe by @mikemhenry in #505
• pin pydantic and autodoc_pydantic by @IAlibay in #517
• rfe protocol: Adds bfactor labels to output topology by @richardjgowers in #499
• update network layout to use graphviz by @richardjgowers in #523
• Check the ability to pass user charges by @IAlibay in #524

New Contributors

• @Yoshanuikabundi made their first contribution in #493

Full Changelog: v0.11.1...v0.12.0