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

v0.11.0 - Cofactor CLI support

What's Changed

• Update installer and container images to python 310 by @mikemhenry in #465
• Pin units - same thing as in gufe by @IAlibay in #466
• Actually actually fix silence_root_logging by @dwhswenson in #467
• CodeCov only on PR by @dwhswenson in #469
• cofactors from CLI by @richardjgowers in #456
• Fix minor typo by @slochower in #471
• Sort while running gather by @dwhswenson in #472
• Reconfigure stdout to be line-buffered in quickrun by @dwhswenson in #468
• Add PDB serialization in RFE protocol by @IAlibay in #450
• Code of Conduct by @mikemhenry in #474
• end to end integration tests for tyk2 tutorial by @richardjgowers in #476
• allow gathering of legacy results by @richardjgowers in #477
• Force no oechem by @richardjgowers in #479
• fixup manifest for new test files by @richardjgowers in #481

New Contributors

• @slochower made their first contribution in #471

Full Changelog: v0.10.1...v0.11.0

v0.10.1 - Hotfix

Fixes some test failures that weren't actually harmful.

What's Changed

• Install GUFE after we restore cache to alwasys get a fresh version by @mikemhenry in #452
• Update to support the newest version of openmmtools by @mikemhenry in #451
• allow single AtomMapper to be passed to network planners by @richardjgowers in #454
• Fix silence_root_logging by @dwhswenson in #453
• explain how to use nvidia-smi to figure out cudatoolkit version by @mikemhenry in #455
• need to update slow tests following execute_DAG update by @richardjgowers in #459
• Run slow tests on push & release by @IAlibay in #460

Full Changelog: v0.10.0...v0.10.1