v1.7.1

Changelog for humans

https://gufe.openfree.energy/en/stable/CHANGELOG.html#v1-7-1

• Replace pprint with model_dump in _ipython_display_ of SettingsBaseModel (#653)
• min pin rdkit (#665)
• fix msgpack pint.errors.OffsetUnitCalculusError when defining in celsius (#666)
• Added Protocol how-to doc (#594)
• expose GufeTokenizableTestsMixin (#669)
• run ci on all branches (#673)

Full Changelog: v1.7.0...v1.7.1

v1.7.0

Changelog for humans

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

What's Changed

• bump codecov by @atravitz in #597
• add tests for settings models by @atravitz in #595
• adding charge difference to ligandmapping by @atravitz in #602
• Increase default force field version to openff-2.2.1 by @IAlibay in #601
• migrate to pydantic v2 by @IAlibay in #584
• Ensure PEP-639 Support by @mikemhenry in #630
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in #632
• Allow ProtocolUnitResults to store stderr and stdout bytes by @ianmkenney in #600
• Add ChemicalSystem.isin method by @jthorton in #608
• pin pydantic to <2.12 by @atravitz in #636
• stderr and stdout should be optional by @atravitz in #638
• define pressure units in bar by @atravitz in #637
• add pyproject.toml pre-commit formatter by @atravitz in #640
• user-facing clarity fixes for custom quantities by @atravitz in #645
• fix pydantic deprecated model_fields call by @atravitz in #647
• Fix formal charge setting for RNA by @IAlibay in #639
• Include all protocol_units in ProtocolDAGResult._unit_result_mapping by @dotsdl in #622
• Change nonbonded_cutoff default value to 0.9 nm by @IAlibay in #648
• add 3d viz to ligandatommapping by @atravitz in #646
• add docs for custom gufe pydantic types by @atravitz in #650
• release/v1.7.0 by @atravitz in #651
• add missed changelog entries for v1.7.0 by @atravitz in #652

Full Changelog: v1.6.1...v1.7.0

v1.6.1

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

All PRs included in this release

• bump docs python version from 3.10 to 3.12 in #598
• Try not needing ambertools in #620
• remove unneeded channel from env build in #623
• Release prep v1.6.1 in #627

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

v1.6.0

Incremental release that adds support for openmm 8.3 and python 3.13.

Changelog for humans

See our CHANGELOG for more details: https://gufe.openfree.energy/en/latest/CHANGELOG.html#v1-6-0

All PRs included in this release:

• Move JSON (de)serialization to the serialization subpackage by @ianmkenney in #532
• Fix conda-cron: add pooch to test dependencies by @IAlibay in #575
• move component properties from AtomMapping up to ComponentMapping by @atravitz in #564
• Fix package build python version by @IAlibay in #578
• Included concepts and extensible points docs by @dotsdl in #530
• adding workaround to support python 3.12 deserialization of pathlib._local objects serialized with python 3.13 by @atravitz in #577
• switch from black and isort to ruff by @atravitz in #587
• updating ci python versions (drop 3.10, add 3.13) by @atravitz in #586
• bump rdkit for mypy ci by @atravitz in #589
• fix conda cron by @atravitz in #593
• prep for 1.6.0 release by @atravitz in #596

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

v1.5.0

Incremental release that adds support for openmm 8.2.

See our CHANGELOG for more details: https://gufe.openfree.energy/en/latest/CHANGELOG.html#v1-5-0

What's Changed

• Minimal changes to support openmm 8.2 and 8.1.2 by @mikemhenry in #539
• Move data to zenodo by @mikemhenry in #553
• Release prep 1.5.0 by @atravitz in #567

Full Changelog: v1.4.1...v1.5.0

v1.4.1

See our CHANGELOG for more details: https://gufe.openfree.energy/en/latest/CHANGELOG.html#v1-4-1

What's Changed

• Fix typo in visualization by @IAlibay in #545

Full Changelog: v1.4.0...v1.4.1

v1.4.0

Incremental release that adds msgpack serialization, expanded ion support, and support for pint v0.24.x. We also removed openff-models from our dependencies.

See our CHANGELOG for more details: https://gufe.openfree.energy/en/latest/CHANGELOG.html#v1-4-0

What's Changed

• remove deps in pyproject.toml by @mikemhenry in #511
• Run pyupgrade on codebase now that we support >=3.10 by @mikemhenry in #505
• temporarily switch docs to furo by @atravitz in #506
• structure docs according to diataxis by @atravitz in #509
• adding content to landing page by @atravitz in #507
• Fix openmm bonds types for order and type in to_openmm_topology by @ijpulidos in #512
• Protocol validation method by @ianmkenney in #502
• Implement msgpack serialization/deserialization by @ianmkenney in #492
• add some docstrings to tokenization.py by @atravitz in #515
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #524
• proteincomponent.py updates by @Mert-csrg in #484
• add core concepts content by @atravitz in #510
• Add keyed_chain roundtrip test to GufeTokenizableTestsMixin by @ianmkenney in #523
• Added CITATION.cff by @dotsdl in #519
• add installation instructions by @atravitz in #526
• Fix/issue 397 by @mikemhenry in #535
• Unpin off units by @IAlibay in #533
• Release 1.4.0 by @atravitz in #536

New Contributors

• @ijpulidos made their first contribution in #512
• @Mert-csrg made their first contribution in #484

Full Changelog: v1.3.0...v1.4.0

v1.3.0 - Incremental minor release

This is an incremental minor release, featuring many smaller bugfixes and guardrails to ensure more predictable behavior for downstream ecosystem packages. Thanks to all the contributors for this release!

See our CHANGELOG for details.

What's Changed

• add ExecutionInterrupt (special exception) by @atravitz in #459
• Add zenodo badge by @IAlibay in #470
• switch user-set partial charges warning to log.info by @atravitz in #468
• Sort ligand network edges by SMC inchikey by @jthorton in #467
• partial charge checking - throw error for negative net charge diff by @atravitz in #477
• Enforce protocol settings at instantiation by @ianmkenney in #461
• exclude rdkit 2024.03.06 by @atravitz in #485
• Update partial charge check by @atravitz in #478
• Use correct default shell by @mikemhenry in #489
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #451
• Added deprecation warning to Transformation.dump/load; removed ExplicitMoleculeComponent.to_json/from_json by @dotsdl in #460
• Add explicit hydrogens kwarg to OpenFF export in SmallMoleculeComponent by @dotsdl in #462
• v1.3.0 release prep by @dotsdl in #504

New Contributors

• @pre-commit-ci made their first contribution in #451

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

v1.2.0 - Incremental minor release

This is an incremental release, featuring serialization improvements, several new features required by ecosystem tools such as stratocaster, and some bugfixes and documentation improvements. Thanks to all the contributors to this release!

See our CHANGELOG for details.

What's Changed

• adding to LigandNetwork docstring by @atravitz in #390
• Fixing the conda cron by @IAlibay in #398
• 383 get connected subgraphs in an alchemicalnetwork by @atravitz in #409
• auto format all the things by @mikemhenry in #421
• Add pre-commit.ci by @mikemhenry in #384
• switch from macos-12 pin to macos-latest by @atravitz in #424
• Add the n_protocol_dag_results property to ProtocolResult by @ianmkenney in #381
• run pre-commit on empty pr by @mikemhenry in #431
• Save atom hybridization by @jthorton in #408
• Add a method for comparing components in ChemicalSystem objects by @ianmkenney in #418
• ignore another big auto format by @mikemhenry in #437
• Make Transformation and NonTransformation subclass TransformationBase by @dotsdl in #311
• Remove PR trigger from conda_cron by @IAlibay in #447
• Added zstandard compression tooling, added to bytes codec for JSON serialization by @dotsdl in #438
• Issue warning when pickling an ExplicitMoleculeComponent that RDKit Mol properties not preserved by @dotsdl in #344
• adds LigandNetwork.reduce_graph by @richardjgowers in #320
• Add AtomMappingError by @jthorton in #440
• Add Protocol Errors by @jthorton in #441
• release v1.2.0 by @dotsdl in #452

New Contributors

• @atravitz made their first contribution in #390

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

v1.1.0 - Incremental minor release

This is an incremental release, featuring some serialization convenience methods and minor bugfixes. Thanks to all the contributors to this release!

See our CHANGELOG for details.

What's Changed

• Pin CI to macos-12 by @IAlibay in #312
• Improve partial charge check by @jthorton in #326
• Bump minimum Python version to 3.10 by @mattwthompson in #340
• Mention 1.0 Release by @mikemhenry in #335
• Fix CI by @IAlibay in #348
• Add KeyedChain GufeTokenizable representation by @ianmkenney in #286
• Added some convenience methods to KeyedChain for symmetry; test simplifications by @dotsdl in #362
• Proposed fix to dag ordering by @LilDojd in #315
• JSON serialization on GufeTokenizable by @jthorton in #368
• Removed all hardcoded gufe keys from GufeTokenizable tests in test suite by @dotsdl in #374
• Save edge annotations in LigandNetwork.to_graphml by @jthorton in #369
• Backfill the news items for v1.1.0 by @IAlibay in #386
• Release : v1.1.0 by @dotsdl in #389

New Contributors

• @jthorton made their first contribution in #326
• @ianmkenney made their first contribution in #286
• @LilDojd made their first contribution in #315

Full Changelog: v1.0.0...v1.1.0