v1.9.0

Changelog for humans

https://docs.openfree.energy/en/latest/CHANGELOG.html#v1-9-0

All PRs included in this release:

• add openeye w/ python 3.13 test to CI by @atravitz in #1745

• bump python version for conda cron by @atravitz in #1748

• remove mypy rdkit pin by @atravitz in #1753

• Make the multistate hybrid topology samplers not require the HybridTopologyFactory by @IAlibay in #1768

• Migrate validation to Protocol._validate in HybridTopologyProtocol by @IAlibay in #1740

• Move rfe protocol by @IAlibay in #1769

• Breakdown rfe protocolunit by @IAlibay in #1770

• Have two separate system generators for state A & B in hybrid protocol by @IAlibay in #1772

• HybridTop structural analysis via API rather than CLI by @IAlibay in #1771

• making some language clearer on github-facing things by @atravitz in #1758

• Moving AFE Protocols around a bit by @IAlibay in #1775

• Create setup, run, and analysis units for HybridTop Protocol by @IAlibay in #1773

• update docs for multiple protocol units by @atravitz in #1793

• Update docstring for hybridtop classes by @IAlibay in #1794

• Small improvement in RelativeHybridTopologyProtocol docstring by @IAlibay in #1797

• turn off zenodo retry by @atravitz in #1802

• only run CI on macos python 3.12 by @atravitz in #1803

• Turn AFE protocols into multiple units by @IAlibay in #1776

• move to src layout by @atravitz in #1805

• Temporarily build pooch from main w/ hotfix by @atravitz in #1806

• make CLI starting guide easier to find from the landing page by @atravitz in #1787

• Update pyproject.toml by @IAlibay in #1813

• refactor: clean up test data handling by @atravitz in #1815

• min pin pooch to fix data fetching by @atravitz in #1820

• fix api break check path by @atravitz in #1825

• fix scope mismatch with zenodo data by @atravitz in #1828

• numpy >=2.3.0 support by @atravitz in #1558

• pin smirnoff99frosst by @atravitz in #1837

• add --download-only option to openfe test by @atravitz in #1814

• Release/v1.9.0 by @atravitz in #1835

Full Changelog: v1.8.1...v1.9.0

v1.8.1

Changelog for humans

https://docs.openfree.energy/en/latest/CHANGELOG.html#v1-8-1

All PRs included in this release:

• fix changelog links by @atravitz
• Updated CHANGELOG for 1.8.1 by @atravitz
• fix pydantic deprecation of dict method - septop (#1831) by @atravitz
• fix pydantic deprecation of copy method by @atravitz
• fix ligand network cropping bug (#1822) by @atravitz
• Fixes docstring to clarify argument does not have a default (#1819) by @IAlibay
• manually add absolute settings news item to changelog (#1821) by @atravitz
• Fix issue 1795 (#1796) by @IAlibay
• add dill mock to fix openfe docs build (#1792) by @atravitz
• openfe gather: add progress bar for loading JSONs (#1786) by @atravitz
• rename openfecli fixture to avoid duplication with openfe fixture (#1755) by @atravitz
• Disable NAGL as a partial charge backend when OEToolkit is installed but not chosen as the registry backend. (#1762) by @IAlibay
• [pre-commit.ci] pre-commit autoupdate (#1778) by @pre-commit-ci[bot]
• fix psutils import (#1779) by @atravitz
• expose KartografAtomMapper alongside other AtomMappers (#1751) by @atravitz
• fix deprecation warning on view_components_3d (#1750) by @atravitz
• bump cuda version to 11.8 (#1749) by @mikemhenry
• update manifest to include all .gz files (#1746) by @atravitz
• update install instructions (#1744) by @atravitz

Full Changelog: v1.8.0...v1.8.1

v1.8.0

Changelog for humans

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

All PRs included in this release:

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

Full Changelog: v1.7.0...v1.8.0

v1.7.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-7-0

What's Changed

• Update citation file with new ordering. by @IAlibay in #1452
• use isolated folder for conda cron ci by @atravitz in #1453
• Evaluate host idxs atoms in DSSP filters after distance evaluation [Issue #1418] by @IAlibay in #1440
• Fix minimum distance in host finding [Issue #1422] by @IAlibay in #1442
• Always use atoms in both helices and beta sheets in the DSSP filter by @hannahbaumann in #1462
• Update restraint settings (force constant and min/max distance) by @hannahbaumann in #1463
• Implement single residue boresch host finding by @IAlibay in #1470
• add pyproject toml formatting by @atravitz in #1475
• Change bonded host strategy to use lowest variance restraint by @IAlibay in #1477
• Changes in Boresch restraint default settings by @hannahbaumann in #1486
• don't run CI for rtd changes by @atravitz in #1490
• Bump number of retires when fetching data with pooch by @mikemhenry in #1487
• Move ligand utils to gufe by @atravitz in #1479
• SepTop Protocol by @hannahbaumann in #1057
• temporary pin to pre-pydantic v2 gufe commit by @atravitz in #1533
• SepTop: Addressing issues raised in review by @hannahbaumann in #1532
• Ensure PEP-639 Support by @mikemhenry in #1546
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #1552
• add comment to explain gufe pin in env yamls by @atravitz in #1553
• Add clear error for constraint KeyError by @jthorton in #1529
• Release prep v1.6.1 by @atravitz in #1544
• Change the default atom mapping in the CLI to Kartograf by @jthorton in #1530
• add espaloma tests by @mikemhenry in #1450
• Add SepTop to gen serialized results by @hannahbaumann in #1560
• Disable user supplied host & guest atoms in restraint settings by @IAlibay in #1557
• Fix test to check if we are printing --allow-partial when a user uses --allow-partial by @mikemhenry in #1564
• migrate to pydantic v2 by @atravitz in #1535
• fix nb link by @atravitz in #1574
• General HTF improvments and speed ups! by @jthorton in #1566
• Fix validation in AHFE Protocol by @IAlibay in #1572
• add dark mode to docs by @atravitz in #1565
• Expose geometry objects as the BoreschRestraintGeometry objects by @IAlibay in #1578
• Add RBFE equilibration method details by @jthorton in #1581
• rename gufe.settings.types -> gufe.settings.typing by @atravitz in #1583
• Remove duplicate available_platforms fixture from septop slow tests by @IAlibay in #1586
• Fix inline comment in slow septop test by @IAlibay in #1587
• Add the standard correction to the error estimate in SepTop by @IAlibay in #1588
• Remove thermostat when getting restrained system in SepTop by @IAlibay in #1584
• Update DOI badge link in README.md by @hmacdope in #1593
• Fix sampler setup for dry runs by @hannahbaumann in #1590
• Make CUDA the default compute platform by @IAlibay in #1576
• Fast/ adaptive settings by @jthorton in #1523
• Fix docs and validations for the lambda schedules by @hannahbaumann in #1597
• deprecate openfe utils 3dviz in favor of gufe method by @atravitz in #1592
• Update expected atom count in SepTop solvent slow test by @IAlibay in #1598
• ABFE protocol by @IAlibay in #1045
• Prepare for release v1.7 by @IAlibay in #1601
• add test data to manifest by @atravitz in #1603
• add notes about dropping 3.10 maintenance by @atravitz in #1605
• min python 3.10 by @atravitz in #1606
• add .txt data files to manifest by @atravitz in #1608

New Contributors

• @ijpulidos made their first contribution in #1539
• @hmacdope made their first contribution in #1593

Full Changelog: v1.6.0...v1.7.0

v1.6.1

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-6-1

All PRs included in this release:

• update partial charge tests now that a production NAGL model is available in #1506
• debug slow python 3.13 tests in #1468
• update quickrun execution docs and add MPS link in #1483
• add jq cookbook in #1488
• debug docs build in #1489
• add pip example for jq in #1505
• debug rtd build memory error in #1510
• temp pin numpy in #1542
• Removing unnecessary limit on resids in #1539
• update docs theme in #1545

Full Changelog: v1.6.0...v1.6.1

v1.6.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1.6.0

All PRs included in this release:

• relaxing pydantic pin by @atravitz in #1387
• min pin kartograf by @atravitz in #1393
• remove openmm exclusion from docs by @atravitz in #1407
• Restraints API by @IAlibay in #1043
• Let mypy find unused ignores by @mattwthompson in #1423
• pin micromamba version to latest by @atravitz in #1348
• bumping python versions to 3.11-13 by @atravitz in #1373
• fix conda cron CI build by @atravitz in #1432
• clean up single file installer ci by @atravitz in #1434
• CI: update mypy ci by @atravitz in #1433
• Fix up collinearity tests [Issue #1419] by @IAlibay in #1436
• updating daily CI runners by @atravitz in #1435
• DSSP selection fixes (issue #1420) by @IAlibay in #1438
• Fix protein chain selection (Issue #1421) by @IAlibay in #1437
• Add slow markers on >60s restraint tests by @IAlibay in #1441
• add news item for openmm 8.3 support by @atravitz in #1446
• release prep 1.6.0 by @atravitz in #1447
• add a blurb for the 1.6.0 changelog by @atravitz in #1448

Full Changelog: v1.5.0...v1.6.0

v1.5.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-5-0

All PRs included in this release:

• adding rich as a dependency by @atravitz in #1256
• Fix docs version by @atravitz in #1262
• Update cli docs by @atravitz in #1264
• move openmm test data from figshare to zenodo by @atravitz in #1270
• Pin click to <8.2.0 until we fix tests by @mikemhenry in #1271
• Add Alyssa to citations file. by @IAlibay in #1274
• update notebook names by @atravitz in #1279
• updating nb name for openfe fetch by @atravitz in #1281
• Remove duplicate line in environment.yml by @CurtisColwell in #1280
• add retries for flaky notebooks by @atravitz in #1278
• Add box vector fix to AFE base by @IAlibay in #1275
• News for AFE box fix by @IAlibay in #1286
• Feat/add lock file by @mikemhenry in #1290
• Small FF assignment refactor of the AFE base unit class by @IAlibay in #1289
• Exit with return value from pytest.main by @mikemhenry in #1297
• fix syntax with conda-lock by @mikemhenry in #1292
• updating syntax for click 8.2 by @atravitz in #1276
• cleaning up and formatting network planning tests by @atravitz in #1304
• Protocols test migration & MD Protocol simulation tests by @IAlibay in #1294
• Import vendored openff.models from gufe by @mikemhenry in #1260
• make network planning tests more thorough by @atravitz in #1307
• [Issue 1310] Switch type hint for lambdas to list[float] by @IAlibay in #1341
• Update docker build docs by @mikemhenry in #1344
• Update CLI help messages by @atravitz in #1265
• clean up CI workflow files by @atravitz in #1346
• bump to setup-micromamba v2 and checkout v4 by @atravitz in #1347
• Don't run package tests on PR commits by @mikemhenry in #1364
• set openmmtools >= 0.25.0 as min openmmtools version by @mikemhenry in #1360
• Decouple checkpoint_interval from online_analysis_interval by @IAlibay in #1362
• test larger cpu runner by @mikemhenry in #1170
• Pin OpenMM 8.2 as min version for CI testing by @mikemhenry in #1366
• make tutorial data use parallel repeats instead of serial repeats by @atravitz in #1365
• comment out TODO that was getting rendered by @atravitz in #1375
• Konnektor integration by @RiesBen in #927
• bump to cinnabar 0.5.0 by @atravitz in #1378
• move to minimum of pydantic v2 by @atravitz in #1379
• update docs to show default as element_change=True by @atravitz in #1380
• improve ligand network description by @atravitz in #1172
• Update userguide's ligand network wording for how scores are used. by @IAlibay in #1382
• bump openff-units and pint pins by @atravitz in #1374
• updating environment yaml by @atravitz in #1385
• Release prep v1.5.0 by @atravitz in #1390

Full Changelog: v1.4.0...v1.5.0

v1.4.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-4-0

All PRs included in this release:

What's Changed

• fix docker build workflow by @atravitz in #1220
• moving under the hood to the user guide by @atravitz in #1221
• cli gather should allow lists of filepaths by @atravitz in #1212
• pin numpy to <2.0 by @atravitz in #1230
• fix cli settings help message formatting by @atravitz in #1225
• Switch to setuptools_scm by @mikemhenry in #1237
• Alphabetize environment.yaml by @CurtisColwell in #1235
• Pass through failed simulations to output by @atravitz in #1227
• fixing a test's --allow-partial call by @atravitz in #1247
• use pandas by @atravitz in #1244
• print message to stderr when no valid results files are found by @atravitz in #1245
• Single repeat error handling by @atravitz in #1243
• add news entry for 1245 by @atravitz in #1248
• Clean up tutorial index by @atravitz in #1233
• making a news entry more clear by @atravitz in #1249
• pin to ofe-sphinx-theme v0.2.0 by @atravitz in #1250
• pretty print tables with rich by @atravitz in #1246
• require -o option for CLI charge generation by @atravitz in #1255
• immediate print planning cli output by @atravitz in #1254

New Contributors

• @CurtisColwell made their first contribution in #1235

Full Changelog: v1.3.1...v1.4.0

v1.3.1

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-3-1

All PRs included in this release:

• update docs build by @atravitz in #1142
• Fix/pin sphinx le73 by @mikemhenry in #1147
• bump to artifact v4 by @atravitz in #1146
• reordering tutorials by @atravitz in #1141
• fixing docker cron by @atravitz in #1139
• Make sure default shell doesn't hide errors by @mikemhenry in #1150
• installation docs: reordering entries for clarity, plus typo fixes by @atravitz in #1140
• adding unzipped cdk8 data by @atravitz in #1151
• see what happens if we remove the flaky mark by @mikemhenry in #1152
• move test data to zenodo by @atravitz in #1148
• Remove note about openmmforcefeild version requirement by @mikemhenry in #1162
• Set all FloatQuantity default settings to float values by @IAlibay in #1165
• remove macos x86_64 from single file installer list by @atravitz in #1154
• block interchange 0.4.2 in env setup by @atravitz in #1167
• add cpu aws runner by @mikemhenry in #1169
• make conda-lock a subheader of mamba install by @atravitz in #1171
• bump single file installers to python 3.11 by @atravitz in #1166
• Fix breaking tests from gufe updates by @atravitz in #1107
• Remove handle_trajectories by @IAlibay in #1182
• Unpin interchange since we have a new openmmff release by @mikemhenry in #1183
• Temporary solution for #1173 by @IAlibay in #1174
• Make get gpu info more robust by @mikemhenry in #1186
• make gufe lowercase in docs by @atravitz in #1190
• remove deps in pyproject.toml by @mikemhenry in #1191
• fix rbfe parallel results dataset by @atravitz in #1196
• 1104 gather check json files by @atravitz in #1112
• ci: update to the new start and stop actions by @ethanholz in #1201
• adding changelog entry for 1112 by @atravitz in #1207
• switch kcal/mol to kilocalorie_per_mole for roundtrip consistency by @atravitz in #1210
• migrate json loading to new gufe syntax by @atravitz in #1177
• pooch - add triplicate retries by @atravitz in #1213
• 1002: improve missing data error handling by @atravitz in #1199
• bump disk space for gpu runner by @mikemhenry in #1209
• only show --allow-partial suggestion if user hasn't used it by @atravitz in #1208
• Updated CHANGELOG for 1.3.1 by @atravitz in #1216
• add PR 1210 to changelog for 1.3.1 by @atravitz in #1218

New Contributors

• @ethanholz made their first contribution in #1201

Full Changelog: v1.3.0...v1.3.1

v1.3.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-3-0

All PRs in this release:

• Move CLI README so that it's easier to find by @atravitz in #1009
• Add release checklist by @atravitz in #1007
• Temporarily pin openmm to < 8.2 by @IAlibay in #1015
• Edits to User Guide documentation by @atravitz in #995
• More user guide edits by @atravitz in #1018
• add example notebooks bump to task list by @atravitz in #1022
• detect if API breaks on PR by @mikemhenry in #727
• Remove macos12 ahead of brownout by @atravitz in #1025
• Compute selection: deviceIndex & enforce 1 thread in vacuum by @IAlibay in #752
• include gufe main and latest in ci matrix by @atravitz in #1036
• 986 input validation for directory names by @atravitz in #1024
• create test data for quickrun submitted in parallel by @atravitz in #1040
• Add gather docstrings by @atravitz in #1041
• Make MST network test deterministic by @jthorton in #1046
• Fix TYK2 example network tests by @jthorton in #1047
• switch ci matrix to test against gufe main again by @atravitz in #1050
• add warning for unsupported settings yaml parameters by @atravitz in #1051
• fix issue #1042 and also test openfecli for API breaks by @mikemhenry in #1054
• Fix CI- GUFE imports by @jthorton in #1060
• Make MD output settings optional by @hannahbaumann in #1058
• CLI adaptive settings for charge change transformations by @jthorton in #1053
• Simplify settings help message by @atravitz in #1052
• Add gather support for parallel dir structure by @atravitz in #1044
• Test cofactor networks generated with the CLI by @jthorton in #1048
• move import to speed up cli by @atravitz in #1066
• Support outdir created at runtime by @atravitz in #1072
• Write tests for position and velocity writing frequency by @hannahbaumann in #1086
• 1089 fix tests for missing gather data by @atravitz in #1090
• Update docs for parallel repeat file structure by @jthorton in #1092
• add support for one repeat per json by @atravitz in #1076
• Use MBAR bootstrap error by @jthorton in #1077
• gather - show all failed edges in error message by @atravitz in #1095
• Testing out what partial charges could look over the CLI by @IAlibay in #1068
• Add perses back in for testing, pin gufe, and fix bootstrap tests by @mikemhenry in #1108
• Add lomap network generator by @atravitz in #1082
• Fixes multistate structural analysis time storing & reading by @IAlibay in #1114
• Add support for variable position/velocity trajectory writing by @IAlibay in #1083
• updating news entry for clarity by @atravitz in #1118
• remove "easy_" prefix from cli output by @atravitz in #1121
• Add a note on charge generation during CLI workflows by @jthorton in #1117
• Add supported software versions by @atravitz in #1119
• Release prep v1.3.0 by @atravitz in #1124
• updating lomap and openfe analysis pins by @atravitz in #1125
• Fix issue 1128 & 1129 by @mikemhenry in #1135
• adding user message for --n-protocol-repeats transparency by @atravitz in #1137

Full Changelog: v1.2.0...v1.3.0