Release 1.3 - #930

The highlights of OpenPathSampling 1.3 are the PLUMED wrapper for OPS CVs (previously an external repository), and the optional progress indicators for analysis. In addition, OPS 1.3 brings several bugfixes, and adds support for newer versions of dependencies.

New features and enhancements

• PLUMED Collective Variables in OPS (PLUMED Collective Variables in OPS #910 @apdealbao)
• Gromacs engine and example updates (Gromacs engine/example updates #909)
• Progress indicators for analysis (Progress indicators for TIS analysis #895, Progress indicators for path density; move summary #902, Progress indicator for shooting point analysis #906)
• storage.filename is now an absolute path and a read-only property (storage.filename is now an absolute path and a read-only property #903 @hejung)

Bugs fixed

• Pin ujson<2 (bug in later versions can break reloading) (Pin ujson<2; nbconvert<6 #926)
• use uuid instead of 'is' for selecting ensembles in rate calculation (use uuid instead of 'is' for selecting ensembles in rate calculation #919 @sroet)
• Fix missing names in ExternalMDSnapshot (Fix missing names in ExternalMDSnapshot #908)
• DirectSimulation should use engine.start/.stop (DirectSimulation should use engine.start/.stop #905)

Miscellaneous improvements

• Support for ujson 3 ((Set reject_bytes=False for ujson >= 3 #917 @sroet, support ujson v3 (part 2) #921 @hejung)
• Improvements and maintenance of devtools (Fix miniconda install #912, Pin ujson<2; nbconvert<6 #926, Clean up devtools #927)
• Support for pandas 1.0 (Fix pandas Deprecaction and Future Warnings #898 @sroet, Fix toy_mstis_3 for change in pandas #925)
• Improvements to documentation (Add GromacsEngine to docs #901, Gromacs engine/example updates #909)
• make tqdm optional for tests (make tqdm optional for tests #916 @sroet)
• Fix missing newline in the VisitAllStatesEnsemble (Fix missing newline in the VisitAllStatesEnsemble #900)