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OpenFreeEnergy / openfe Public

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changelog updates for 1.8.1#1832

Merged

atravitz merged 48 commits intomainOpenFreeEnergy/openfe:mainfrom

sync-1.8.1OpenFreeEnergy/openfe:sync-1.8.1Copy head branch name to clipboard

Feb 5, 2026

Conversation Commits48 (48)Checks Files changed

Merged

changelog updates for 1.8.1#1832
atravitz merged 48 commits intomainfrom
sync-1.8.1

Commits

Commits on Feb 4, 2026

update install instructions (#1744)
atravitz
committed
update manifest to include all .gz files (#1746)
atravitz
committed
bump cuda version to 11.8 (#1749)

mikemhenry
authored and
atravitz
committed
fix deprecation warning on view_components_3d (#1750)
atravitz
committed
expose KartografAtomMapper alongside other AtomMappers (#1751)
atravitz
committed
fix psutils import (#1779)
atravitz
committed
[pre-commit.ci] pre-commit autoupdate (#1778)

pre-commit-ci[bot]
authored and
atravitz
committed
Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762)

committed
rename openfecli fixture to avoid duplication with openfe fixture (#1755)

atravitz
and
IAlibay
committed
openfe gather: add progress bar for loading JSONs (#1786)
atravitz
committed
add dill mock to fix openfe docs build (#1792)
atravitz
committed
Fix issue 1795 (#1796)

IAlibay
authored and
atravitz
committed
manually add absolute settings news item to changelog (#1821)
atravitz
committed
Fixes docstring to clarify argument does not have a default (#1819)

IAlibay
authored and
atravitz
committed
fix ligand network cropping bug (#1822)
atravitz
committed
fix pydantic deprecation of copy method
atravitz
committed

Commits on Feb 5, 2026

fix pydantic deprecation of dict method - septop (#1831)
atravitz
committed
Updated CHANGELOG for 1.8.1
atravitz
committed
fix changelog links
atravitz
committed
add openeye w/ python 3.13 test to CI (#1745)
atravitz
committed
bump python version for conda cron (#1748)
atravitz
committed
remove mypy rdkit pin (#1753)
atravitz
committed
Make the multistate hybrid topology samplers not require the HybridTopologyFactory (#1768)

IAlibay
authored and
atravitz
committed
Migrate validation to Protocol._validate in HybridTopologyProtocol (#1740)

authored and
atravitz
committed
Move rfe protocol (#1769)

IAlibay
authored and
atravitz
committed
HybridTop Unit methods (#1770)

authored and
atravitz
committed
Have two separate system generators for state A & B in hybrid protocol (#1772)

IAlibay
authored and
atravitz
committed
HybridTop structural analysis via API rather than CLI (#1771)

IAlibay
authored and
atravitz
committed
making some language clearer on github-facing things (#1758)
atravitz
committed
Moving AFE Protocols around a bit (#1775)

IAlibay
authored and
atravitz
committed
Create setup, run, and analysis units for HybridTop Protocol (#1773)

IAlibay
and
atravitz
committed
update docs for multiple protocol units (#1793)
atravitz
committed
Update docstring for hybridtop classes (#1794)

authored and
atravitz
committed
Small improvement in RelativeHybridTopologyProtocol docstring (#1797)

IAlibay
authored and
atravitz
committed
turn off zenodo retry (#1802)
atravitz
committed
only run CI on macos python 3.12 (#1803)
atravitz
committed
Turn AFE protocols into multiple units (#1776)

IAlibay
authored and
atravitz
committed
move to src layout (#1805)
atravitz
committed
Temporarily build pooch from main w/ hotfix (#1806)
atravitz
committed
make CLI starting guide easier to find from the landing page (#1787)
atravitz
committed
Update pyproject.toml (#1813)

IAlibay
authored and
atravitz
committed
refactor: clean up test data handling (#1815)
atravitz
committed
min pin pooch to fix data fetching (#1820)
atravitz
committed
fix ligand network cropping bug (#1822)
atravitz
committed
fix api break check path (#1825)
atravitz
committed
fix pydantic deprecation of copy method (#1829)
atravitz
committed
fix scope mismatch with zenodo data (#1828)
atravitz
committed
Merge branch 'main' of github.com:OpenFreeEnergy/openfe into sync-1.8.1
atravitz
committed

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