v1.4.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-4-0

All PRs included in this release:

What's Changed

• fix docker build workflow by @atravitz in #1220
• moving under the hood to the user guide by @atravitz in #1221
• cli gather should allow lists of filepaths by @atravitz in #1212
• pin numpy to <2.0 by @atravitz in #1230
• fix cli settings help message formatting by @atravitz in #1225
• Switch to setuptools_scm by @mikemhenry in #1237
• Alphabetize environment.yaml by @CurtisColwell in #1235
• Pass through failed simulations to output by @atravitz in #1227
• fixing a test's --allow-partial call by @atravitz in #1247
• use pandas by @atravitz in #1244
• print message to stderr when no valid results files are found by @atravitz in #1245
• Single repeat error handling by @atravitz in #1243
• add news entry for 1245 by @atravitz in #1248
• Clean up tutorial index by @atravitz in #1233
• making a news entry more clear by @atravitz in #1249
• pin to ofe-sphinx-theme v0.2.0 by @atravitz in #1250
• pretty print tables with rich by @atravitz in #1246
• require -o option for CLI charge generation by @atravitz in #1255
• immediate print planning cli output by @atravitz in #1254

New Contributors

• @CurtisColwell made their first contribution in #1235

Full Changelog: v1.3.1...v1.4.0

v1.3.1

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-3-1

All PRs included in this release:

• update docs build by @atravitz in #1142
• Fix/pin sphinx le73 by @mikemhenry in #1147
• bump to artifact v4 by @atravitz in #1146
• reordering tutorials by @atravitz in #1141
• fixing docker cron by @atravitz in #1139
• Make sure default shell doesn't hide errors by @mikemhenry in #1150
• installation docs: reordering entries for clarity, plus typo fixes by @atravitz in #1140
• adding unzipped cdk8 data by @atravitz in #1151
• see what happens if we remove the flaky mark by @mikemhenry in #1152
• move test data to zenodo by @atravitz in #1148
• Remove note about openmmforcefeild version requirement by @mikemhenry in #1162
• Set all FloatQuantity default settings to float values by @IAlibay in #1165
• remove macos x86_64 from single file installer list by @atravitz in #1154
• block interchange 0.4.2 in env setup by @atravitz in #1167
• add cpu aws runner by @mikemhenry in #1169
• make conda-lock a subheader of mamba install by @atravitz in #1171
• bump single file installers to python 3.11 by @atravitz in #1166
• Fix breaking tests from gufe updates by @atravitz in #1107
• Remove handle_trajectories by @IAlibay in #1182
• Unpin interchange since we have a new openmmff release by @mikemhenry in #1183
• Temporary solution for #1173 by @IAlibay in #1174
• Make get gpu info more robust by @mikemhenry in #1186
• make gufe lowercase in docs by @atravitz in #1190
• remove deps in pyproject.toml by @mikemhenry in #1191
• fix rbfe parallel results dataset by @atravitz in #1196
• 1104 gather check json files by @atravitz in #1112
• ci: update to the new start and stop actions by @ethanholz in #1201
• adding changelog entry for 1112 by @atravitz in #1207
• switch kcal/mol to kilocalorie_per_mole for roundtrip consistency by @atravitz in #1210
• migrate json loading to new gufe syntax by @atravitz in #1177
• pooch - add triplicate retries by @atravitz in #1213
• 1002: improve missing data error handling by @atravitz in #1199
• bump disk space for gpu runner by @mikemhenry in #1209
• only show --allow-partial suggestion if user hasn't used it by @atravitz in #1208
• Updated CHANGELOG for 1.3.1 by @atravitz in #1216
• add PR 1210 to changelog for 1.3.1 by @atravitz in #1218

New Contributors

• @ethanholz made their first contribution in #1201

Full Changelog: v1.3.0...v1.3.1

v1.3.0

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-3-0

All PRs in this release:

• Move CLI README so that it's easier to find by @atravitz in #1009
• Add release checklist by @atravitz in #1007
• Temporarily pin openmm to < 8.2 by @IAlibay in #1015
• Edits to User Guide documentation by @atravitz in #995
• More user guide edits by @atravitz in #1018
• add example notebooks bump to task list by @atravitz in #1022
• detect if API breaks on PR by @mikemhenry in #727
• Remove macos12 ahead of brownout by @atravitz in #1025
• Compute selection: deviceIndex & enforce 1 thread in vacuum by @IAlibay in #752
• include gufe main and latest in ci matrix by @atravitz in #1036
• 986 input validation for directory names by @atravitz in #1024
• create test data for quickrun submitted in parallel by @atravitz in #1040
• Add gather docstrings by @atravitz in #1041
• Make MST network test deterministic by @jthorton in #1046
• Fix TYK2 example network tests by @jthorton in #1047
• switch ci matrix to test against gufe main again by @atravitz in #1050
• add warning for unsupported settings yaml parameters by @atravitz in #1051
• fix issue #1042 and also test openfecli for API breaks by @mikemhenry in #1054
• Fix CI- GUFE imports by @jthorton in #1060
• Make MD output settings optional by @hannahbaumann in #1058
• CLI adaptive settings for charge change transformations by @jthorton in #1053
• Simplify settings help message by @atravitz in #1052
• Add gather support for parallel dir structure by @atravitz in #1044
• Test cofactor networks generated with the CLI by @jthorton in #1048
• move import to speed up cli by @atravitz in #1066
• Support outdir created at runtime by @atravitz in #1072
• Write tests for position and velocity writing frequency by @hannahbaumann in #1086
• 1089 fix tests for missing gather data by @atravitz in #1090
• Update docs for parallel repeat file structure by @jthorton in #1092
• add support for one repeat per json by @atravitz in #1076
• Use MBAR bootstrap error by @jthorton in #1077
• gather - show all failed edges in error message by @atravitz in #1095
• Testing out what partial charges could look over the CLI by @IAlibay in #1068
• Add perses back in for testing, pin gufe, and fix bootstrap tests by @mikemhenry in #1108
• Add lomap network generator by @atravitz in #1082
• Fixes multistate structural analysis time storing & reading by @IAlibay in #1114
• Add support for variable position/velocity trajectory writing by @IAlibay in #1083
• updating news entry for clarity by @atravitz in #1118
• remove "easy_" prefix from cli output by @atravitz in #1121
• Add a note on charge generation during CLI workflows by @jthorton in #1117
• Add supported software versions by @atravitz in #1119
• Release prep v1.3.0 by @atravitz in #1124
• updating lomap and openfe analysis pins by @atravitz in #1125
• Fix issue 1128 & 1129 by @mikemhenry in #1135
• adding user message for --n-protocol-repeats transparency by @atravitz in #1137

Full Changelog: v1.2.0...v1.3.0

v1.2.0

This is a minor release with a few fixes and improvements. See here for details.

What's Changed

• Fix errant files being created during tests by @IAlibay in #945
• bump apptainer version by @mikemhenry in #949
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #950
• move slow import inside function call by @atravitz in #955
• Edits to cli guide by @atravitz in #966
• 'raw' gather report should output all PU repeats by @frannerin in #884
• Add bespokefit cookbook to the docs by @jthorton in #976
• remove index column from -raw output by @atravitz in #977
• use current ofe sphinx theme by @atravitz in #994
• Fix tests for issue 1004 by @IAlibay in #1005

New Contributors

• @atravitz made their first contribution in #955
• @frannerin made their first contribution in #884

Full Changelog: v1.1.0...v1.2.0

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