The Open Free Energy library

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-8-0

All PRs included in this release:

• Ci/add ruff format to openfe protocols by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1604
• Test conda-forge package build on demand by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1612
• Update docker image to use python 3.12 and rdkit==2025.09.1 by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1611
• update example notebooks branch for v1.7.0 docs changes by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1615
• remove colab button, point to updated example notebooks, reorg landing page by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1618
• drop scipy intersphinx link by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1621
• fix docs links for cli and api on landing page by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1620
• ruff formatting part 2 - everything but the tests by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1610
• Ci/add ruff format part3 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1622
• Ci/add ruff format part4 - the final format! by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1623
• add git-blame-ignore-revs for large formatting PRs by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1609
• Only run itergration tests on AWS GPU and CPU runners by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1538
• add yaml syntax check precommit hooks by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1567
• pin openmm to <8.3 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1633
• store 6CZJ.pdb in git repo by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1634
• Switch to using skip_if_missing by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1640
• Fix import error from pr# 1640 by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1642
• add workflow_dispatch event trigger for cleaning up cache by branch by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1644
• allow ci to run on all branches, not just main by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1649
• Create Pooch Cache by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1647
• GZIP the 6CZJ PDB by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1659
• expose the septop and abfe analysis tutorials by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1664
• Update conda pkg test + test to see if it catches missing files by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1630
• Test example notebooks on demand by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1613
• add ruff isort linting rule by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1665
• ruff linting: f-strings and whitespace by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1667
• ruff: address pycodestyle changes by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1668
• add ruff formatting commits to git-blame-ignore-revs by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1669
• Add logging control by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1585
• Refactor/gather use pandas by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1690
• Feat/improve names gathering by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1691
• Add docstring to explain the rounding in gather by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/1687
• add links to ecosystem on docs landing page by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1619
• add manual tests to PR template by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1624
• fix pandas applymap deprecation warning by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1701
• Add CMAPTorsionForce support by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1695
• pull names directly from ligandmapping by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1702
• updating install recommendations to prioritize miniconda and conda-lock by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1692
• Check user charges are not changed by espaloma by @jthorton in https://github.com/OpenFreeEnergy/openfe/pull/1707
• make sure all names are returned as strings by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1711
• Disable JAX acceleration by default by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1694
• Comment out uploading files from feedstock package test by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1714
• remove unused command fetch rbfe-showcase by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1732
• xfail for test_openmm_run_engine if openeye and nagl are both present by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1733
• feat: experimental openfe gather-septop & openfe gather-abfe support by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1710
• docs: handle common case where ExampleNotebooks already exists and is on a tag by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1735
• switch pymbar warning to info and only raise if already set by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1736
• bump ExampleNotebooks version by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1738
• Add AbsoluteFactory options to AlchemicalSettings by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1742
• add docs for gathering septop and abfe by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1737
• release/1.8.0 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1734
• update install instructions by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1744
• update manifest to include all .gz files by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1746

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.7.0...v1.8.0