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

v1.0.1 Patch Release

This is a patch release of OpenFE which brings a few QOL improvements, including validation scripts
and test adjustments to work with the latest release of Lomap.

API stability: No known changes or deprecations to the API compared to v1.0

Supported Python versions: 3.9+
Supported OpenMM versions: 8.0, and 8.1.1
Supported OpenFF toolkit versions: >=0.13 (0.15.x is recommended)

Changelog for humans: https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-0-1

What's Changed

• fix installer by @mikemhenry in #838
• pin macos runners to macos-12 by @mikemhenry in #841
• Save the Rainforest by @mikemhenry in #839
• debug script for people to test openmm by @mikemhenry in #733
• Add GAFF test (and GAFF skips) to CI by @mikemhenry in #847
• add osx-arm64 py312 test by @mikemhenry in #853
• Test with main on Lomap dev branch by @IAlibay in #855
• Updated CHANGELOG for 1.0.1 by @mikemhenry in #860

Full Commit Changelog: v1.0.0...v1.0.1

v1.0.0 - First stable release

What's Changed

• Fix sing file installer by @mikemhenry in #667
• Protocol to run plain MD simulations by @hannahbaumann in #516
• Set cache to expire after a day by @mikemhenry in #676
• Remove flatten torsions from HTF by @IAlibay in #684
• Expand water virtual site tests by @IAlibay in #680
• Fix barostat frequency passing by @IAlibay in #669
• Properly set the cutoff distance in HTF nonbonded forces by @IAlibay in #675
• Add cookbook entry for user charges by @IAlibay in #687
• Tokenizable atom mappers by @richardjgowers in #690
• Add devtools for json results generation + replace old ones by @IAlibay in #691
• updates to some code & tests following upstream changes by @richardjgowers in #696
• Adding LambdaSettings object for AFE by @hannahbaumann in #681
• Fix typo in README by @mattwthompson in #698
• Renaming and moving some of the protocol settings by @hannahbaumann in #689
• Solvation settings prep by @IAlibay in #695
• Switch settings input to protocol units to creating protocol itself. by @IAlibay in #700
• consequences of gufe #260 change by @richardjgowers in #666
• Fix devtools for #666 changes by @IAlibay in #707
• Add base partial charge setting things by @IAlibay in #706
• Fix checkpointing by @IAlibay in #719
• Add try/except for forward_backward analysis by @hannahbaumann in #721
• fixup scope of try/except around forward/backwards analysis by @richardjgowers in #724
• Add charge backends by @IAlibay in #598
• Doc drive 2 by @richardjgowers in #725
• Changelog automation by @mikemhenry in #728
• Change some MD settings by @hannahbaumann in #729
• Add MD equilibration for AFE calculations by @IAlibay in #720
• Create OutputSettings baseclass by @hannahbaumann in #732
• Change default settings lambda_restraints by @hannahbaumann in #735
• Document cli settings by @richardjgowers in #736
• Codecov and pre-commit ci config by @mikemhenry in #738
• Issue 592 alt radial options by @richardjgowers in #737
• Just don't install espaloma charge by @IAlibay in #763
• Fix Issue 683 by @mikemhenry in #767
• Change changelog title name by @IAlibay in #764
• Fixing API settings things by @IAlibay in #766
• docs: update badge on front page by @richardjgowers in #755
• Add warnings & docs for forward and reverse analysis getters by @IAlibay in #749
• Fix ahfe integration tests - missing restraints lamdas by @IAlibay in #750
• Add NonTransformation to top level __init__.py by @IAlibay in #754
• Checkpoint itnterval by @IAlibay in #773
• Some docstring fixes by @IAlibay in #775
• Docs userguide by @richardjgowers in #760
• Update fetch results by @richardjgowers in #779
• update LomapAtomMapper default settings to established best practices by @richardjgowers in #730
• Add an MD tutorial by @hannahbaumann in #731
• Clean up tutorials by @IAlibay in #782
• docs ligand networks by @RiesBen in #780
• Update CLI help docs by @IAlibay in #797
• docs: working with individual results page by @richardjgowers in #783
• docs setup intro page changes by @hannahbaumann in #812
• Issue 801 execution quickrun by @richardjgowers in #814
• Add alchemical network creation userguide page by @IAlibay in #808
• docs: fix links from top of each notebook by @richardjgowers in #822
• including comments from #793 by @RiesBen in #815
• FIx overlap matrix label issue by @IAlibay in #811
• fix to Protocol keys after off v2.1.1 bump in gufe base settings by @richardjgowers in #823
• Docs protocol cycles results by @richardjgowers in #787
• Add protocol details (hybrid topology, etc) to docs by @hannahbaumann in #776
• docs: chemical system theory by @richardjgowers in #785
• Don't dump all results to std out by @mikemhenry in #824
• added min hardware specs to install doc by @mikemhenry in #821
• added note about the GUFE package by @mikemhenry in #828
• don't test openfecli, it is flaky for some reason by @mikemhenry in #831
• docs: refresh docs landing page by @richardjgowers in #832
• docs: clarify long tests slightly by @richardjgowers in #834
• docs: first pass at working with networks page by @richardjgowers in #830

New Contributors

• @mattwthompson made their first contribution in #698

Full Changelog: v0.15.0...v1.0.0

Release 1.0.0rc1

What's Changed

• Document cli settings by @richardjgowers in #736
• Codecov and pre-commit ci config by @mikemhenry in #738
• Issue 592 alt radial options by @richardjgowers in #737
• Just don't install espaloma charge by @IAlibay in #763
• Fix Issue 683 by @mikemhenry in #767
• Change changelog title name by @IAlibay in #764
• Fixing API settings things by @IAlibay in #766
• docs: update badge on front page by @richardjgowers in #755
• Add warnings & docs for forward and reverse analysis getters by @IAlibay in #749
• Fix ahfe integration tests - missing restraints lamdas by @IAlibay in #750
• Add NonTransformation to top level __init__.py by @IAlibay in #754
• Checkpoint itnterval by @IAlibay in #773
• Some docstring fixes by @IAlibay in #775
• Docs userguide by @richardjgowers in #760
• Update fetch results by @richardjgowers in #779
• update LomapAtomMapper default settings to established best practices by @richardjgowers in #730

Full Changelog: v1.0.0rc0...v1.0.0rc1

v1.0.0rc0

Release candidate for first stable OpenFE release

What's Changed

• Fix sing file installer by @mikemhenry in #667
• Protocol to run plain MD simulations by @hannahbaumann in #516
• Set cache to expire after a day by @mikemhenry in #676
• Remove flatten torsions from HTF by @IAlibay in #684
• Expand water virtual site tests by @IAlibay in #680
• Fix barostat frequency passing by @IAlibay in #669
• Properly set the cutoff distance in HTF nonbonded forces by @IAlibay in #675
• Add cookbook entry for user charges by @IAlibay in #687
• Tokenizable atom mappers by @richardjgowers in #690
• Add devtools for json results generation + replace old ones by @IAlibay in #691
• updates to some code & tests following upstream changes by @richardjgowers in #696
• Adding LambdaSettings object for AFE by @hannahbaumann in #681
• Fix typo in README by @mattwthompson in #698
• Renaming and moving some of the protocol settings by @hannahbaumann in #689
• Solvation settings prep by @IAlibay in #695
• Switch settings input to protocol units to creating protocol itself. by @IAlibay in #700
• consequences of gufe #260 change by @richardjgowers in #666
• Fix devtools for #666 changes by @IAlibay in #707
• Add base partial charge setting things by @IAlibay in #706
• Fix checkpointing by @IAlibay in #719
• Add try/except for forward_backward analysis by @hannahbaumann in #721
• fixup scope of try/except around forward/backwards analysis by @richardjgowers in #724
• Add charge backends by @IAlibay in #598
• Doc drive 2 by @richardjgowers in #725
• Changelog automation by @mikemhenry in #728
• Change some MD settings by @hannahbaumann in #729
• Add MD equilibration for AFE calculations by @IAlibay in #720
• Create OutputSettings baseclass by @hannahbaumann in #732
• Change default settings lambda_restraints by @hannahbaumann in #735

New Contributors

• @mattwthompson made their first contribution in #698

Full Changelog: v0.15.0...v1.0.0rc0

v0.15.0

Highlights

• The ability to do charge correction through alchemical waters has been added to the RBFE protocol.
• Structural analysis (using openfe_analysis) of the RBFE simulations is now provided as part of the results.
• Addition of Kartograf bindings to openfe.

What's Changed

• Fix checkpoint name by @IAlibay in #594
• Create CONTRIBUTING.md by @richardjgowers in #597
• [skip ci] Update README.md by @richardjgowers in #599
• Add duecredit by @IAlibay in #601
• Charge correction via alchemical waters by @IAlibay in #569
• Add neutralize to system_creation's addSolvent by @IAlibay in #613
• use Lomap package's bindings by @richardjgowers in #478
• Remove replica states from results dictionary by @IAlibay in #603
• remove obsolete test data file by @richardjgowers in #621
• cli: gather raw option by @richardjgowers in #620
• Yaml format for CLI input by @richardjgowers in #583
• Kartograf integration by @RiesBen in #249
• Structural analysis by @richardjgowers in #571
• Fix docker image building + CI improvements by @mikemhenry in #641
• Allow Manual Running of Slow Tests by @mikemhenry in #649
• Change get_simsteps function to handle NVT equilibration in plain MD protocol by @hannahbaumann in #647
• emove duecredit.p file by @IAlibay in #655
• Use uuid for unit repeat ids for HFE protocol by @IAlibay in #650
• update to use openfe_analysis 0.2.0+ by @richardjgowers in #656
• Issue 335 float quantity in settings by @richardjgowers in #657

New Contributors

• @hannahbaumann made their first contribution in #647

Full Changelog: v0.14.0...v0.15.0

v0.14.0

Highlights

• Fixes errors caused by conformer generation failing
• Addresses high variance in partial charge generation through Ambertools giving high variance to estimates
• By default the OpenMM_RFE protocol produces energetic analysis of the simulations
• Adds openfe.setup.ligand_network_planning.generate_minimal_redundant_network for more robust ligand networks
• Allows gather CLI command to process partially finished/complete results

What's Changed

• test pydantic v2 by @mikemhenry in #541
• Analysing free energies by @IAlibay in #531
• fix forwards/backwards analysis for very small files by @richardjgowers in #545
• Fix Zenodo by @mikemhenry in #547
• Update CITATION.cff by @richardjgowers in #553
• ci: update to use setup-micromamba by @richardjgowers in #552
• don't include central ligand self edge in radial networks by @richardjgowers in #546
• Log system probe info by @dwhswenson in #513
• Update CITATION.cff by @richardjgowers in #554
• Add Zenodo badge to README by @richardjgowers in #555
• [WIP] Fix RTHP results serialization and test results load by @IAlibay in #550
• Fix energy results out by @richardjgowers in #556
• Added missing nc file by @mikemhenry in #562
• Tests: Test coverage for RFE ProtocolResult by @richardjgowers in #560
• Improve error message if missing one leg for ligand pair by @dwhswenson in #568
• Switch to a unified Sphinx theme by @Yoshanuikabundi in #563
• Fixup mypy matplotlib by @richardjgowers in #575
• add function to create a minimal network with redundancy for all nodes by @JenkeScheen in #559
• Combine installation guides and fix typos by @Yoshanuikabundi in #561
• Get ExampleNotebooks into docs by @Yoshanuikabundi in #538
• clear up language a bit for dg report help text by @mikemhenry in #549
• Absolute solvation free energies + base things for ABFEs by @IAlibay in #573
• rfe protocol: partial charges fix by @richardjgowers in #577
• Explicitly set navigation_keys to False to avoid warning by @IAlibay in #584
• Test AHFE user charges by @IAlibay in #586
• Enforce charges generated by input conformer by @IAlibay in #587
• Add gather --allow-partial, improve related error message by @dwhswenson in #588

New Contributors

• @JenkeScheen made their first contribution in #559

Full Changelog: v0.13.0...v0.14.0

v0.13.0

Highlights

• Scores are now in line with other community efforts, 1.0 representing full agreement, 0.0 representing complete disagreement.
• the gather command now performs a MLE to yield absolute binding free energies, there are also options for other breakdowns
• includes many documentation improvements

What's Changed

• fixes implementation of transmuting_methyl_into_ring_score by @richardjgowers in #526
• Assert hybrid PDB contents by @IAlibay in #530
• Add optional path to sys probe by @mikemhenry in #519
• Remove softcore electrostatics entry by @IAlibay in #521
• Adds MLE estimates on gather command by @richardjgowers in #495
• Allow extra attributes in AlchemicalSettings by @richardjgowers in #535
• ci: print duration of 10 slowest tests by @richardjgowers in #534
• Use 1.0 for good AtomMapping scores, 0.0 for bad AtomMapping scores by @richardjgowers in #529
• annotate dry run many molecules test as slow by @richardjgowers in #533
• add flaky marker to test_dry_run_user_charges by @richardjgowers in #537
• Cookbook flowchart by @Yoshanuikabundi in #520
• remove LigandNetwork by @richardjgowers in #536
• rework handle_trajectories to use replicas by @richardjgowers in #539
• support pydantic v1 and v2 by @mikemhenry in #540
• Rejuvenate API refs by @Yoshanuikabundi in #527
• network_from_indices raises warning on disconnected network by @richardjgowers in #514
• docs: fixup typo in tutorial links by @richardjgowers in #542

Full Changelog: v0.12.0...v0.12.1

v0.12.0

Highlights

• Adds ability to read FEP+ / Orion NES ligand network files using openfe.setup.ligand_network_planning.load_fepplus_network and openfe.setup.ligand_network_planning.load_orion_network
• Adds openfe.setup.ligand_network_planning.generate_network_from_names and openfe.setup.ligand_network_planning.generate_network_from_indices to create arbitrary networks
• OpenMM RBFE Protocol pdb output now labels A and B state using BFactor column
• network layouts from cli tool now much easier to understand

What's Changed

• Make super slow tests integration tests by @IAlibay in #484
• Added DCO by @mikemhenry in #475
• fix issue with new notebook version by @mikemhenry in #498
• Tell users to install the latest version of openfe by @mikemhenry in #497
• Unpin libnetcdf by @dwhswenson in #500
• add ps to the docker image (interline needed this) by @mikemhenry in #501
• Network planner functions from indices/names by @richardjgowers in #482
• remove version name and upload files by @mikemhenry in #503
• API docs updates by @Yoshanuikabundi in #493
• Update openfecli/tests/data/rbfe_results.tar.gz by @mikemhenry in #496
• Logging improvements in quickrun by @dwhswenson in #504
• see if py311 works okay by @mikemhenry in #508
• Migrate common settings to omm_utils by @IAlibay in #512
• Read network from external files by @IAlibay in #511
• Add system probe by @mikemhenry in #505
• pin pydantic and autodoc_pydantic by @IAlibay in #517
• rfe protocol: Adds bfactor labels to output topology by @richardjgowers in #499
• update network layout to use graphviz by @richardjgowers in #523
• Check the ability to pass user charges by @IAlibay in #524

New Contributors

• @Yoshanuikabundi made their first contribution in #493

Full Changelog: v0.11.1...v0.12.0

v0.11.1 - Lomap performance patch

What's Changed

• Use common core option when using the Lomap Atom Mapper by @richardjgowers in #485

Full Changelog: v0.11.0...v0.11.1