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[WIP] Functions to convert netcdfplus CVs to SimStore CVs#1005

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dwhswenson wants to merge3 commits intoopenpathsampling:master
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This adds a constructor to SimStore-based CVs to create the appropriate SimStore CV from a netcdfplus CV. This is a necessary step toward writing a script that converts netcdfplus files to SimStore files. That will be useful now for users who want to experiment with SimStore, and will be necessary in a pre-2.0 release so that users can upgrade.

Still need to do some custom work on the func_config for MDTraj
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Merging#1005 (2801508) intomaster (8292193) willnot change coverage.
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@@           Coverage Diff           @@##           master    #1005   +/-   ##=======================================  Coverage   81.17%   81.17%           =======================================  Files         139      139             Lines       15143    15143           =======================================  Hits        12292    12292             Misses       2851     2851

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@sroet,@hejung,@gyorgy-hantal (and anyone else who has some old CVs from netcdfplus and is comfortable trying an experimental branch): Could you try this branch out and see if thefrom_netcdfplus_cv methods are working correctly? They work on the things I have tested, but those are based on the way that I create CVs; just checking to see if there are use cases I'm missing.

The following script is a rough template of I hope you can try, especially for any CV that might have an unusual setup:

importopenpathsamplingaspathsfromopenpathsampling.experimental.storage.collective_variablesimportMDTrajFunctionCVstorage=paths.Storage("old_file.nc",mode='r')old=storage.cvs['phi']# was originally defined as a paths.MDTrajFunctionCV# create the new CV using the classmethod `from_netcdfplus_cv`new=MDTrajFunctionCV.from_netcdfplus_cv(old)snap=storage.snapshots[-1]# take an arbitrary snapshot from storageassertold(snap)==new(snap)

So far, the CV types in the following table have been implemented in the new storage. (OnlyFunctionCV changed its name, because SimStore naming changed a little to avoid some domain-specific things in netcdfplus.) If you have a different CV type, let me know and I can prioritize setting up those, as well -- I assume these are the most-used CV types.

openpathsampling.openpathsampling.experimental.storage.collective_variables.
FunctionCVCollectiveVariable
CoordinateFunctionCVCoordinateFunctionCV
MDTrajFunctionCVMDTrajFunctionCV

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