openpathsampling 1.6.0

This is a long-overdue (and huge) release for OPS. While the only highlight feature is the addition of S-Shooting, this release contains many updates to maintain usability of OPS as its dependencies change, as well as a number of important bug fixes that are recommended for all users.

Deprecations: The FileSetter for external engines (e.g., Gromacs) will be changing from a sequential numeric value to a random string. See #1102 for details.

New features

• S-shooting (#787 @singraber)

Other enhancements

• Clear old ExternalMDSnapshots during iter_generate (#1066)
• New analysis testing utilities (#1068)
• Account for modifier acceptance in engine movers (#1075)
• add no_copy option to NoModifier and Deprecate 'subset_mask' (#1079)
• Take care of coordinate modifcation in selector probability_ratio (#1076)

Experimental (beta) features

• improvements to unpatch after using SimStore (#1065)
• add simstore table access via slice (#1050)

Bugs fixed

• Use MDTraj codecs in SimStore JSON serialization (#1116)
• Prevent double monkey-patching experimental storage (#1109)
• Actually check for CVDefinedVolume.lambda_max == "inf" (#1092)
• SimStore: Fix storable function serialization (#1088)
• SimStore: Fix issue with internalized snapshot box vectors (#1086)
• OpenMMEngine: use masses from mdtraj topolgy directly (#1085 @hejung)
• unbreak API call to selector.probability_ratio (#1082)

Miscellaneous improvements

• Support Python 3.10; Python 3.11 (#1133)
• Fix Dropbox download of precalculated results (#1128)
• revert openmmtools import guard from test notebook (#1106)
• clarify error message on missing units (#1122)
• update copyright to 2022 (#1097)
• Improved implementation of shooting point selector pick (avoid model that might introduce index error in subclasses) (#1110 @hejung)
• Add FutureWarning for default filesetter external engines (#1102 #Deprecations)
• make a missed string into a rawstring (#1096)
• Guard against openmm import warnings (including those from OpenMMTools) (#1091)
• Add CITATIONS.md (#1064)
• Prevent non-string names in StorableNamedObject (#1052)
• Updates in response to changes in dependencies (#1137, #1136, #1134, #1132, #1129, #1114, #1130, #1126, #1093)
• Improvements to continuous integration and testing (#1123, #1100, #1089, #1081, #1078, #1073, #1058)
• Improvements to documentation (#1090, #1087, #1083, #1057 @bdice)

Thanks always to maintainers @sroet and @dwhswenson.