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

v1.0.0 - First stable release

What's Changed

• Readonly settings by @richardjgowers in #169
• Remove settings remove_com from OpenMMSystemGeneratorFFSettings (added to openfe IntegratorSettings) by @hannahbaumann in #275
• Api docs by @richardjgowers in #277
• Move settings from SystemSettings to ForcefieldSettings by @hannahbaumann in #276
• Test latest openff-toolkit with gufe main by @mikemhenry in #281
• fixes issue #263 by @richardjgowers in #283
• Bump CodeCov action by @mattwthompson in #285
• Issue 170 lam validators by @richardjgowers in #287
• Doc push by @richardjgowers in #289
• Add rever for changelog by @richardjgowers in #290
• Add UUID JSON codec by @hmacdope in #294
• Dep warnings for dict mapping by @richardjgowers in #296
• Update default off version to 2.1.1 by @IAlibay in #304
• Adding CA ions to parsing list - proteincomponent.py by @RiesBen in #265

New Contributors

• @hannahbaumann made their first contribution in #275
• @mattwthompson made their first contribution in #285
• @hmacdope made their first contribution in #294

Full Changelog: v0.10.0...v1.0.0

v1.0.0rc0

What's Changed

• Readonly settings by @richardjgowers in #169
• Remove settings remove_com from OpenMMSystemGeneratorFFSettings (added to openfe IntegratorSettings) by @hannahbaumann in #275
• Api docs by @richardjgowers in #277
• Move settings from SystemSettings to ForcefieldSettings by @hannahbaumann in #276
• Test latest openff-toolkit with gufe main by @mikemhenry in #281
• fixes issue #263 by @richardjgowers in #283
• Bump CodeCov action by @mattwthompson in #285
• Issue 170 lam validators by @richardjgowers in #287
• Doc push by @richardjgowers in #289

New Contributors

• @hannahbaumann made their first contribution in #275
• @mattwthompson made their first contribution in #285

Full Changelog: v0.10.0...v1.0.0rc0

v0.10.0 - Gearing up for v1.0

What's Changed

• Versioning and migration for GufeTokenizables by @dwhswenson in #227
• adding mol name labels from ofe-name to mapping vis by @RiesBen in #241
• Don't run conda_cron on PRs by @dwhswenson in #256
• External resource updates by @dwhswenson in #257
• Support name in SmallMoleculeComponent.copy_with_replacements by @dwhswenson in #273
• makes AtomMappers subclass from GufeTokenizable by @richardjgowers in #266
• change signature of Protocol.create to have a list of ComponentMappings by @richardjgowers in #260

Full Changelog: 0.9.5...v0.10.0

v0.9.5 - Serialization hotfix

What's Changed

• Fix quantity array codec by @richardjgowers in #236
• Switch to OFE theme by @Yoshanuikabundi in #242
• Clarify "DAG dependency order" in docstrings by @Yoshanuikabundi in #244
• Add NPY dtype codec by @IAlibay in #228

Full Changelog: v0.9.4...0.9.5

v0.9.4 - Pydantic v2 support

What's Changed

• support pydantic v1 and v2 by @mikemhenry in #225
• Always raise, don't swallow exception, if exception is KeyboardInterrupt in ProtocolUnit.execute by @dotsdl in #215
• test pydantic v2 by @mikemhenry in #226
• Fixes ProtocolResult.from_dict by @richardjgowers in #230
• ci: update micromamba action by @richardjgowers in #231
• Fix conda-cron by @IAlibay in #232

Full Changelog: v0.9.3...v0.9.4

v0.9.3 - Docs galore

What's Changed

• Transformation docstrings fixes by @Yoshanuikabundi in #210
• Pin autodoc_pydantic by @IAlibay in #213
• FEAT: add LigandNetwork.is_connected() method by @richardjgowers in #214
• Prevent _GufeTozenizableMeta.__call__ from overwriting signature of __init__ by @Yoshanuikabundi in #216
• Issue 217 ligand network no edges by @richardjgowers in #218
• LigandNetwork.to_*_alchemical_network by @dwhswenson in #204
• Add checks for partial charges by @IAlibay in #219
• Improve docstrings as needed for OpenFE by @Yoshanuikabundi in #220
• docs: fixup docs on enlarge graph by @richardjgowers in #224

New Contributors

• @Yoshanuikabundi made their first contribution in #210

Full Changelog: v0.9.2...v0.9.3

Hotfix - Nonstandard protein fix

What's Changed

• proteincomponent: tweak conversions to/from openmm/rdkit by @richardjgowers in #209

Full Changelog: v0.9.1...v0.9.2