Release 1.6.0#1138
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- Class SShootingSimulation added. - Class SShootingAnalysis added. - Class NonCanonicalSequentialMover added. - Class NonCanonicalSequentialMoveChange added. - Class DoubleWell added. - Class OverdampedLangevinIntegrator added. - Example IPython notebook sshooting-example.ipynb added. - Nosetests for all classes added.
Co-authored-by: David W.H. Swenson <dwhs@hyperblazer.net>
Co-authored-by: David W.H. Swenson <dwhs@hyperblazer.net>
Bump version to 1.5.3.dev0
Fix documentation issues
add simstore table access via slice
Prevent non-string names in StorableNamedObject
Remove engine binary after tests
Get tests working again
Looks like this should get us through the unit tests. * For Python 3.11, this changes to using the SimStore CalalbleCodec in netcdfplus. It is too much of a pain to maintain the opcode translation. This means that dill will be a hard requirement of OPS (at least, if you're in Python 3.11 or greater, but we'll include it everywhere) * The CallableCodec had previously benefitted from the bytes codec our JSON system has. To get this to work for ujson, I changed CallableCodec to directly output base64-encoded strings. We'll retain the ability to load old files, but new files will write different bytes for CVs. To-dos brought up by these changes: * Add FutureWarning for old SimStore storages * Add test that we can still load old SimStore storages * Move Python 3.11 netcdfplus warning to storage initialization
… into support-py310-py311
Support Python 3.10; Python 3.11
Update pins
Pin nbval != 0.10.0
In OpenMM 8.1, it seems that we must pass `None` for engine properties. The empty dict is no longer treated the same.
Fix engine props for OpenMM 8.1
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@sroet: Interesting -- GitHub now automatically lists "contributors" on a release (see https://github.com/openpathsampling/openpathsampling/releases/tag/v1.6.0), but it is only for those who are @-mentioned in the release notes. I added a line at the bottom to acknowledge us; I'll have to update my release notes writer for that! |
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That is interesting indeed. I see you had a good push on this during my holidays 😉 |
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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
FileSetterfor external engines (e.g., Gromacs) will be changing from a sequential numeric value to a random string. See #1102 for details.New features
Other enhancements
iter_generate(#1066)Experimental (beta) features
Bugs fixed
Miscellaneous improvements