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