v1.8.0

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 #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

v1.2.0

This is a minor release with a few fixes and improvements. See here for details.

What's Changed

• Fix errant files being created during tests by @IAlibay in #945
• bump apptainer version by @mikemhenry in #949
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #950
• move slow import inside function call by @atravitz in #955
• Edits to cli guide by @atravitz in #966
• 'raw' gather report should output all PU repeats by @frannerin in #884
• Add bespokefit cookbook to the docs by @jthorton in #976
• remove index column from -raw output by @atravitz in #977
• use current ofe sphinx theme by @atravitz in #994
• Fix tests for issue 1004 by @IAlibay in #1005

New Contributors

• @atravitz made their first contribution in #955
• @frannerin made their first contribution in #884

Full Changelog: v1.1.0...v1.2.0

v1.1.0 Release

This is a minor release of OpenFE which brings a few fixes and one new feature.

Supported Python versions: 3.10+
Supported OpenMM versions: 8.0, 8.1.1 and 8.1.2
Supported OpenFF toolkit versions: >=0.16 (0.16.x is recommended)

New Features

• Protocols now allow for solvation with dodecahedral and octahedral boxes. By default the box solvation type remains cubic. #673

API changes

• The RelativeHybridTopologyProtocol no longer stores all the structural analysis data in its results object. Instead the data is written to an NPZ format file and the file handle is provided under the structural_analysis results key.
• The PersesAtomMapper now accepts inputs using openff units rather than openmm units.

Other Fixes and Updates

• Added install instructions for conda-lock by @mikemhenry in #867
• Fixed 2D RMSD plotting for < 5 states and cases where states - 1 is not divisible by 4 #896
• Added missing authors to Zenodo CFF file.
• Added duecredit entries for PyMBAR #753
• The minimum Python version was increase to to 3.10 in #922

New Contributors

• @jthorton made their first contribution in #930

Full Changelog: v1.0.1...v1.1.0