Restore velocities only if found in serialized nc file

[ijpulidos]

Description

Restores velocities only if variable is found in the serialized files. This allows back compatibility with serialized files using openmmtools<0.21.3, since velocities were added in that release.

Resolves #612

Todos

• Implement feature / fix bug
• Add tests
• Update documentation as needed
• Update changelog to summarize changes in behavior, enhancements, and bugfixes implemented in this PR

Status

• Ready to go

Changelog

Bug when restoring serialized files generated by ``openmmtools<0.21.3``. Fixed by catching the ``KeyError`` exception when deserializing.

[ijpulidos]

I had to add .nc data files using an older version of openmmtools (0.21.2) to test that we can resume simulations from them correctly.

I thought about emulating this behavior by removing the velocities variables from the NetCDF Datasets themselves, but NetCDF doesn't have an API for removing variables.

[mikemhenry]

Could you add a note that this fix enables reading of older nc files? Other than that, LGTM

[ijpulidos]

Please note that I had to restructure the tests a bit, you can see the same number of tests are getting run (just in case you are wondering). But I had to make a new base class for avoiding running redundant tests in child classes.

The core reason for this is that the serialized objects in the data .nc files that the new test are using, are meant to be used only with the MultiStateSampler object and not all the others that inherit from it in the tests, due to missing variables/fields in the files.

@mikemhenry @jchodera This should be good to go now, can you please review it? Thanks.

[mikemhenry]

LGTM