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