Releases: OpenFreeEnergy/openfe
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
andopenfe.setup.ligand_network_planning.load_orion_network
- Adds
openfe.setup.ligand_network_planning.generate_network_from_names
andopenfe.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