Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1.6.0

All PRs included in this release:

relaxing pydantic pin by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1387
min pin kartograf by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1393
remove openmm exclusion from docs by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1407
Restraints API by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1043
Let mypy find unused ignores by @mattwthompson in https://github.com/OpenFreeEnergy/openfe/pull/1423
pin micromamba version to latest by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1348
bumping python versions to 3.11-13 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1373
fix conda cron CI build by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1432
clean up single file installer ci by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1434
CI: update mypy ci by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1433
Fix up collinearity tests [Issue #1419] by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1436
updating daily CI runners by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1435
DSSP selection fixes (issue #1420) by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1438
Fix protein chain selection (Issue #1421) by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1437
Add slow markers on >60s restraint tests by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1441
add news item for openmm 8.3 support by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1446
release prep 1.6.0 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1447
add a blurb for the 1.6.0 changelog by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1448

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

- Python
Published by atravitz 11 months ago

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html#v1-5-0

All PRs included in this release:

adding rich as a dependency by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1256
Fix docs version by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1262
Update cli docs by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1264
move openmm test data from figshare to zenodo by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1270
Pin click to <8.2.0 until we fix tests by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1271
Add Alyssa to citations file. by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1274
update notebook names by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1279
updating nb name for openfe fetch by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1281
Remove duplicate line in environment.yml by @CurtisColwell in https://github.com/OpenFreeEnergy/openfe/pull/1280
add retries for flaky notebooks by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1278
Add box vector fix to AFE base by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1275
News for AFE box fix by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1286
Feat/add lock file by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1290
Small FF assignment refactor of the AFE base unit class by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1289
Exit with return value from pytest.main by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1297
fix syntax with conda-lock by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1292
updating syntax for click 8.2 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1276
cleaning up and formatting network planning tests by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1304
Protocols test migration & MD Protocol simulation tests by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1294
Import vendored openff.models from gufe by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1260
make network planning tests more thorough by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1307
[Issue 1310] Switch type hint for lambdas to list[float] by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1341
Update docker build docs by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1344
Update CLI help messages by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1265
clean up CI workflow files by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1346
bump to setup-micromamba v2 and checkout v4 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1347
Don't run package tests on PR commits by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1364
set openmmtools >= 0.25.0 as min openmmtools version by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1360
Decouple checkpoint_interval from online_analysis_interval by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1362
test larger cpu runner by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1170
Pin OpenMM 8.2 as min version for CI testing by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/1366
make tutorial data use parallel repeats instead of serial repeats by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1365
comment out TODO that was getting rendered by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1375
Konnektor integration by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/927
bump to cinnabar 0.5.0 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1378
move to minimum of pydantic v2 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1379
update docs to show default as element_change=True by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1380
improve ligand network description by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1172
Update userguide's ligand network wording for how scores are used. by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/1382
bump openff-units and pint pins by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1374
updating environment yaml by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1385
Release prep v1.5.0 by @atravitz in https://github.com/OpenFreeEnergy/openfe/pull/1390

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.4.0...v1.5.0

- Python
Published by atravitz 12 months ago

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

New Contributors

@CurtisColwell made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/1235

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.3.1...v1.4.0

- Python
Published by atravitz about 1 year ago

Changelog for humans

https://docs.openfree.energy/en/stable/CHANGELOG.html

All PRs included in this release:

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

New Contributors

@ethanholz made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/1201

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.3.0...v1.3.1

- Python
Published by atravitz about 1 year ago

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

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

- Python
Published by atravitz over 1 year ago

What's Changed

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

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

- Python
Published by atravitz over 1 year ago

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

New Contributors

@atravitz made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/955
@frannerin made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/884

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

- Python
Published by atravitz over 1 year ago

openfe - 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. https://github.com/OpenFreeEnergy/openfe/pull/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 https://github.com/OpenFreeEnergy/openfe/pull/867
Fixed 2D RMSD plotting for < 5 states and cases where states - 1 is not divisible by 4 https://github.com/OpenFreeEnergy/openfe/pull/896
Added missing authors to Zenodo CFF file.
Added duecredit entries for PyMBAR https://github.com/OpenFreeEnergy/openfe/pull/753
The minimum Python version was increase to to 3.10 in https://github.com/OpenFreeEnergy/openfe/pull/922

New Contributors

@jthorton made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/930

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.0.1...v1.1.0

- Python
Published by IAlibay over 1 year ago

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 https://github.com/OpenFreeEnergy/openfe/pull/838
pin macos runners to macos-12 by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/841
Save the Rainforest by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/839
debug script for people to test openmm by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/733
Add GAFF test (and GAFF skips) to CI by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/847
add osx-arm64 py312 test by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/853
Test with main on Lomap dev branch by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/855
Updated CHANGELOG for 1.0.1 by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/860

Full Commit Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.0.0...v1.0.1

- Python
Published by mikemhenry about 2 years ago

openfe - v1.0.0 - First stable release

What's Changed

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

New Contributors

@mattwthompson made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/698

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.15.0...v1.0.0

- Python
Published by richardjgowers about 2 years ago

What's Changed

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

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v1.0.0rc0...v1.0.0rc1

- Python
Published by mikemhenry about 2 years ago

openfe - v1.0.0rc0

Release candidate for first stable OpenFE release

What's Changed

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

New Contributors

@mattwthompson made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/698

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.15.0...v1.0.0rc0

- Python
Published by richardjgowers over 2 years ago

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

New Contributors

@hannahbaumann made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/647

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.14.0...v0.15.0

- Python
Published by IAlibay over 2 years ago

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

New Contributors

@JenkeScheen made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/559

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.13.0...v0.14.0

- Python
Published by richardjgowers over 2 years ago

openfe - v0.14.0 - Energetics analysis

What's Changed

test pydantic v2 by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/541
Analysing free energies by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/531
fix forwards/backwards analysis for very small files by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/545
Fix Zenodo by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/547
Update CITATION.cff by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/553
ci: update to use setup-micromamba by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/552

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.13.0...v0.14.0

- Python
Published by richardjgowers almost 3 years ago

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

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.12.0...v0.12.1

- Python
Published by richardjgowers almost 3 years ago

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

New Contributors

@Yoshanuikabundi made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/493

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.11.1...v0.12.0

- Python
Published by richardjgowers almost 3 years ago

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

New Contributors

@Yoshanuikabundi made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/493

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.11.1...v0.11.2

- Python
Published by richardjgowers almost 3 years ago

openfe - v0.11.1 - Lomap performance patch

What's Changed

Use common core option when using the Lomap Atom Mapper by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/485

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.11.0...v0.11.1

- Python
Published by richardjgowers almost 3 years ago

openfe - v0.11.0 - Cofactor CLI support

What's Changed

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

New Contributors

@slochower made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/471

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.10.1...v0.11.0

- Python
Published by richardjgowers almost 3 years ago

openfe - 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 https://github.com/OpenFreeEnergy/openfe/pull/452
Update to support the newest version of openmmtools by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/451
allow single AtomMapper to be passed to network planners by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/454
Fix silencerootlogging by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/453
explain how to use nvidia-smi to figure out cudatoolkit version by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/455
need to update slow tests following execute_DAG update by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/459
Run slow tests on push & release by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/460

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.10.0...v0.10.1

- Python
Published by richardjgowers about 3 years ago

What's Changed

Cautiously allow core element changes by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/438
Fix handling of ThreeParticleAverageSite virtual sites by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/395
Pin PyMBAR to sub v4 by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/444
Add toopenff() intermediary for toopeneye() calls by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/446
rename water molecules so addSolvent doesn't replace with ion by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/441
quickrun command now retries simulations by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/447
add fetchables for showcase notebook inputs by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/437
remove rateofconvergence by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/433
Update gather.py - protocol failure robustness by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/381

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.9.1...v0.10.0

- Python
Published by richardjgowers about 3 years ago

By default, now not water is the selection used to write out particle coordinates instead of all. This setting is controlled by the output_indices setting in SimulationSettings for the RFE Settings object.

What's Changed

Don't build docker image on tags by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/435
all to not water for writing by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/431

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

- Python
Published by mikemhenry about 3 years ago

openfe - v0.9.0

Improvements to the OpenMM RBFE Protocol. see #387

What's Changed

Switch rbfe tutorial fetch to point to main; not master by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/430
[RFE protocol] Allow multiple small molecules + allow running with non-OpenFF force fields by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/387

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.8.1...v0.9.0

- Python
Published by richardjgowers about 3 years ago

openfe - v0.8.1

Lots of fixes around CLI docs and documentation styling

What's Changed

Speed up first output from plan-*-network by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/412
Fix problem with ligand loading order in testplan*_network by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/416
Regroup CLI Sections by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/414
Add comment to docs that first import is slow by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/417
adding style to the docs by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/419
Fix links in docs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/423
Progress bar for maximal network by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/411
Update custom.css by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/426
Update equilrfesettings.py by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/424
Update links to docs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/425
update readme install instructions by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/428
CLI Updates by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/429

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.8.0...v0.8.1

- Python
Published by richardjgowers about 3 years ago

openfe - v0.8.0 - OMSF Symposium release

Highlights:

Big overhaul to documentation.
Lots of new CLI features

What's Changed

update package versions by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/371
CLI: Remove openfe import required for help by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/374
Semi "wet" test by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/378
test CLI command by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/373
Switching to micromamba for install and add cluster docs by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/376
CLI: mol_dir => molecules by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/383
CLI: ligand network viewer by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/384
CLI: Network Planners: Flatten output directories by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/382
update offmodels and offtk pins by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/377
Install docs: Use Mambaforge by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/389
Don't trigger docker build on non-main branch pushes by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/391
autodoc pydantic for openmm_rfe settings by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/385
CLI fetch command by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/380
Improving our landing page by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/396
Enable online-analysis by default by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/388
Fix nesting of shared directory for checkpoint by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/397
Silence openmmtools.multistate API warnings by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/398
Add ligand network output to CLI network planners by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/399
Add tutorial fetchables by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/404
Pull execute dag by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/405
Update gather.py - output file refactor by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/393
DOCS: Cleanup guide intro by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/341
Make docs reasonable to be user facing by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/401
add missing settings docs by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/407
Rbfe fetch assets by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/409
receptor => complex by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/410
Remove mapper from plan-*-network command by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/402

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.7.4...v0.8.0

- Python
Published by richardjgowers about 3 years ago

openfe - v0.7.4

What's Changed

Fix analyzer cleaning up scope issues by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/361
Remove test skipping by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/359
lomap mapper updates for 2.3.0 by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/364
Push Apptainer Image to GHCR + Build Installer & Docker Image using Conda-Forge Package by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/353
Update hash for hmass change upstream by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/367
Swap LangevinSplittingDynamicMove to LangevinDynamicsMove by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/332
Issue 368 init docs by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/369
cookbook docs by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/318

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.7.3...v0.7.4

- Python
Published by richardjgowers about 3 years ago

openfe - v0.7.3 - multi-DAG result and memory fixes

What's Changed

Use pip instead of conda for sphinx-toolbox by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/351
only build installer on demand by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/352
openmmrfe: make repeatids non 0 assuming by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/356
Fix test incompatibility by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/358
Cleanup contexts upon calculation completion, failure by @dotsdl in https://github.com/OpenFreeEnergy/openfe/pull/354

New Contributors

@dotsdl made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/354

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.7.2...v0.7.3

- Python
Published by IAlibay about 3 years ago

openfe - v0.7.2 - docs and alchemiscale hotfix

What's Changed

Don't exclude py3.10 macos runners by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/319
Start adding API docs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/325
fix issue where we would get a key error if OFE_SLOW_TESTS was unset by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/339
Issue 292 rfe context usage by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/345
Add image building by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/321
Fix single file installer by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/308
Add Docs for Containers and Single File Installer by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/347
DOCS: Core models and CLI usage by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/340

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.7.1...v0.7.2

- Python
Published by richardjgowers about 3 years ago

openfe - v0.7.1 easy_campaign hotfix 1

Fixes a small issue in Protocol round tripping against json files. See #336

What's Changed

pull AlchemicalNetwork into top namespace by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/327
Explanation docs (initial work and structure) by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/317
Delete cache from closed PRs by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/330
autodoc_pydantic is on cf as autodoc-pydantic by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/331
fixes #324 by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/328
fix packaging by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/323
Add pytest slow test filter by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/333
Update package-tests.yaml by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/337
Use JSON_HANDLER classes in ResultClient storage by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/334
Fix protocol roundtrip by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/336

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.7.0...v0.7.1

- Python
Published by richardjgowers about 3 years ago

openfe - v0.7.0 - easy_campaign release

What's Changed

Silence root logging (on perses imports) by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/265
Storage migration: Add to openfe by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/266
Openfecli dummyprotocol tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/269
Add function to visualization3D.py - showComponentCoords by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/262
Gufe update by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/270
Fix serialization of protocol by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/219
Get plugcli from conda-forge by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/271
Pin libnetcdf to avoid current failures by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/273
Maximal network planner by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/245
Gufe fixup by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/286
Let's try to not import with eyes open by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/287
Temporarily fix docs building by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/288
Easy alchemical network planners by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/254
fix execute_DAG usage following gufe update by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/304
Fix Version Info + Switch to pyproject.toml by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/282
add fetch-depth to CI version check by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/307
Quickrun updates by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/293
using gufe Settings in RBFE Protocol by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/267
Fix typo in CI file - don't allow codecov to run on schedule by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/309
Add periodicity setting tests by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/281
Remove tolerance checks by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/274
Add platform warning for non CUDA selection by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/311
rbfe -> rfe rename by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/310
Switch to pydata theme + add readme docs badge by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/316
Speed up doc building by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/326
simple duration printout by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/294

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.6.1...v0.7.0

- Python
Published by richardjgowers about 3 years ago

openfe - v0.6.1

What's Changed

convert output of getestimate and getuncertainty to openff-units.Qu… by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/264

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.6.0...v0.6.1

- Python
Published by richardjgowers over 3 years ago

openfe - v0.2

Initial release of relative free energy protocols

- Python
Published by richardjgowers over 3 years ago

openfe - v0.6.0

What's Changed

temporarily pin numpy because of numba issues by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/238
update mapping visualization of bond changes by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/241
Remove LigandAtomMapping by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/252
fixup following gufe API change by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/256
Api cleanout by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/255
Update environment.yml by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/257
adding 3D structure Mapping Vis to LigandMapping by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/248
Sort nodes/edges on creation of NetworkX graph by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/247
Remove unused RTD config by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/258

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.5...v0.6.0

- Python
Published by richardjgowers over 3 years ago

openfe - v0.5

Mainly bug fixes concerning constraint mapping in the RBFE Protocol

What's Changed

TST: fix stray directories being made during testing by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/220
Dry run now returns sampler via debug dictionary entry by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/217
MAINT: Fixed up implicit none errors from mypy by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/226
Bug hunt fixes by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/225
Add --log option to CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/218
Xml regression tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/231
MAINT: remove old offtk from test matrix by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/236
bump pin on gufe by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/235

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.4...v0.5

- Python
Published by richardjgowers over 3 years ago

openfe - v0.4

What's Changed

Fix the number of production steps being used by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/141
change Lomap atom mapper to default to threed=True by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/143
Mapping distance by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/145
added check for element changes in openmm rbfe protocol by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/146
Visualization align mapped mols to eachother by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/148
WIP: Perses atom mappers by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/147
Add lower pin for lomap2 in environment yaml file by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/157
Fixes the openmm rbfe protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/159
Fix rms tolerance check by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/161
154 add test for persesmapper not finding a mapping by @RiesBen in https://github.com/OpenFreeEnergy/openfe/pull/158
Add vacuum support for relative ligand transform by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/160
Fix tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/163
remove py 3.8 from CI by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/162
Remove universal bdist_wheel in setup.cfg by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/165
Fix to json by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/168
Add sams and independent samplers to equil RBFE protocol by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/125
Using gufe protocols by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/142
Make dry run return true, add basepath by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/186
Fix results_cls attribute name by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/188
Fix result_cls again by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/189
fix gathering of protocol results by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/191
Make unit close reporter at end of simulation by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/190
some mock based tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/193
quickrun CLI command by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/171
pin dependencies for release by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/194
Optional codecov failures by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/196
Atom mapping tests by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/198
add logo badge by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/197
Expose loaders in CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/200
[DOCS] Add quickrun command docs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/202
Are we there yet? The py310 edition by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/185
squashed a bug in mapping repr by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/207
[DOCS] Fixing RTD by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/204
fix gufe API usage in _create; move setup/methods -> protocols/ by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/211
[DOCS] Add dumping_transformation by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/210
[Docs] Installation info by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/212
[WIP] quickrun should error if a unit errors by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/209
Finish quickrun error handling by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/215
Pin to 0.4 gufe series for release by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/216

New Contributors

@RiesBen made their first contribution in https://github.com/OpenFreeEnergy/openfe/pull/148

Full Changelog: https://github.com/OpenFreeEnergy/openfe/compare/v0.3...v0.4

- Python
Published by richardjgowers over 3 years ago

openfe - v0.2.1

Install Instructions

Online Installer

To play with the latest notebook, use this command to install the latest version of our packages:

conda env create openfe/openfe-notebooks Then run:

conda activate openfe-notebooks git clone https://github.com/OpenFreeEnergy/ExampleNotebooks.git openfe-example-notebooks cd openfe-example-notebooks git checkout april-2022 jupyter notebook openmm-rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb

Offline Installer

Download the relevant installer for your operating system and preferred python version. We have attached the version of the example notebook that works with the latest release of openfe.

If you used our single file installer from the last release, download new-deps.tar.gz. Then activate the old environment before extracting and installing the packages with pip:

```

Be sure the old environment is activated!

mkdir new-deps && tar xzvf new-deps.tar.gz -C new-deps pip install new-deps/* ```

Bug Fixes

Hotfix of results

- Python
Published by richardjgowers about 4 years ago

openfe - Alpha Release

What's Changed

Initial skeleton by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/21
Add some changes requested in PR #21 by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/22
Fix setup.cfg to include packages by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/25
Add base Scorer by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/26
atommapping implementation by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/28
Prevent CodeCov from running on forks, cron jobs by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/27
Convert to normal package; add utils; move errors to utils/errors by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/32
AtomMapper base classes by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/30
Remove Scorers by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/33
Molecule class by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/39
[WIP] Network container class by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/40
Add a simple coveragerc to ignore tests in reporting by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/44
Tests for Network object by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/43
Add Versioneer by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/45
WIP: Lomap atommapper by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/31
suggested Network & Molecule changes by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/46
update AtomMapping type annotations by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/48
Set up basic mypy CI by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/50
omit _version.py from coverage by @IAlibay in https://github.com/OpenFreeEnergy/openfe/pull/53
Proposed API change on AtomMapper by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/56
CLI Skeleton by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/49
network planning functions started by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/41
CLI for AtomMapping by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/57
added stubs for Molecule conversions by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/58
Molecule serialization/deserialization by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/63
Network Serialization by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/64
Docsdocsdocs by @richardjgowers in https://github.com/OpenFreeEnergy/openfe/pull/66
Skip running OE license check on PR by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/71
Add serialization test data script by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/69
Add support to get molecule name from _Name prop by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/68
Add support for CLI --mol to load SDF by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/67
Add visualization to AtomMapping by @mikemhenry in https://github.com/OpenFreeEnergy/openfe/pull/60
[WIP] Combine visualization with CLI by @dwhswenson in https://github.com/OpenFreeEnergy/openfe/pull/72

Full Changelog: https://github.com/OpenFreeEnergy/openfe/commits/v0.1

- Python
Published by mikemhenry about 4 years ago

Recent Releases of openfe

openfe - v1.6.0

Changelog for humans

All PRs included in this release:

openfe - v1.5.0

Changelog for humans

All PRs included in this release:

openfe - v1.4.0

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All PRs included in this release:

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openfe - v1.3.0

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openfe - v1.1.0 Release

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openfe - v0.12.0

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openfe - v0.10.1 - Hotfix

What's Changed

openfe - v0.10.0

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openfe - v0.9.1

What's Changed

openfe - v0.9.0

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openfe - v0.8.1

What's Changed

openfe - v0.8.0 - OMSF Symposium release

Highlights:

What's Changed

openfe - v0.7.4

What's Changed