Releases | Open Source Science

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

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.5.0...v1.6.0

- Python
Published by atravitz 7 months ago

gufe - 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 https://github.com/OpenFreeEnergy/gufe/pull/539
Move data to zenodo by @mikemhenry in https://github.com/OpenFreeEnergy/gufe/pull/553
Release prep 1.5.0 by @atravitz in https://github.com/OpenFreeEnergy/gufe/pull/567

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.4.1...v1.5.0

- Python
Published by atravitz 9 months ago

gufe - 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 https://github.com/OpenFreeEnergy/gufe/pull/545

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.4.0...v1.4.1

- Python
Published by atravitz 10 months ago

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

New Contributors

@ijpulidos made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/512
@Mert-csrg made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/484

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.3.0...v1.4.0

- Python
Published by atravitz 10 months ago

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

New Contributors

@pre-commit-ci made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/451

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.2.0...v1.3.0

- Python
Published by dotsdl 12 months ago

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

New Contributors

@atravitz made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/390

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.1.0...v1.2.0

- Python
Published by dotsdl about 1 year ago

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

New Contributors

@jthorton made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/326
@ianmkenney made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/286
@LilDojd made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/315

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v1.0.0...v1.1.0

- Python
Published by dotsdl over 1 year ago

gufe - v1.0.0 - First stable release

What's Changed

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

New Contributors

@hannahbaumann made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/275
@mattwthompson made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/285
@hmacdope made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/294

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.10.0...v1.0.0

- Python
Published by richardjgowers almost 2 years ago

gufe - v1.0.0rc0

What's Changed

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

New Contributors

@hannahbaumann made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/275
@mattwthompson made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/285

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.10.0...v1.0.0rc0

- Python
Published by richardjgowers about 2 years ago

gufe - v0.10.0 - Gearing up for v1.0

What's Changed

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

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/0.9.5...v0.10.0

- Python
Published by richardjgowers about 2 years ago

gufe - v0.9.5 - Serialization hotfix

What's Changed

Fix quantity array codec by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/236
Switch to OFE theme by @Yoshanuikabundi in https://github.com/OpenFreeEnergy/gufe/pull/242
Clarify "DAG dependency order" in docstrings by @Yoshanuikabundi in https://github.com/OpenFreeEnergy/gufe/pull/244
Add NPY dtype codec by @IAlibay in https://github.com/OpenFreeEnergy/gufe/pull/228

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.9.4...0.9.5

- Python
Published by richardjgowers over 2 years ago

gufe - v0.9.4 - Pydantic v2 support

What's Changed

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

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.9.3...v0.9.4

- Python
Published by richardjgowers over 2 years ago

gufe - v0.9.3 - Docs galore

What's Changed

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

New Contributors

@Yoshanuikabundi made their first contribution in https://github.com/OpenFreeEnergy/gufe/pull/210

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.9.2...v0.9.3

- Python
Published by richardjgowers over 2 years ago

gufe - Hotfix - Nonstandard protein fix

What's Changed

proteincomponent: tweak conversions to/from openmm/rdkit by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/209

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.9.1...v0.9.2

- Python
Published by richardjgowers over 2 years ago

gufe - v0.9.1 - Hotfix

Allows backwards compatibility of ProtocolUnitResults created before v0.9.0

What's Changed

Docs: Overview of gufe by @dwhswenson in https://github.com/OpenFreeEnergy/gufe/pull/200
Pin openff-units, pint to avoid typing issues by @dwhswenson in https://github.com/OpenFreeEnergy/gufe/pull/206
Makes starttime, endtime optional args for ProtocolUnitResult by @dotsdl in https://github.com/OpenFreeEnergy/gufe/pull/208

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.9.0...v0.9.1

- Python
Published by richardjgowers over 2 years ago

gufe - v0.9.0

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What's Changed

Add LigandNetwork class by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/195
Fix packaging issues by @IAlibay in https://github.com/OpenFreeEnergy/gufe/pull/198
remove ProtocolResult.getrateof_convergence by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/196
joblib requirement fixed upstream by @IAlibay in https://github.com/OpenFreeEnergy/gufe/pull/199
Allow older rdkit versions, previously required 2022.9 by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/202
executeDAG nretries keyword by @richardjgowers in https://github.com/OpenFreeEnergy/gufe/pull/203

Full Changelog: https://github.com/OpenFreeEnergy/gufe/compare/v0.8.0...v0.9.0

- Python
Published by richardjgowers over 2 years ago

gufe - v0.8.0

Breaking change: use of pin for openff-model's FloatQuantity. This might affect Settings hashes