Bugfix/write to hdf5

[yaoyic]

PR Checklist

• Bug fix
• [] Feature addition/change
• [] Documentation addition/change
• [] Test addition/change
• Black formatting

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Describe your changes here:

Aldo reported the issue that an Ensemble could not be saved to HDF5 again after features fraction_native_contacts and rmsd are computed and attached to the ensemble. This is a tentative fix. Aldo could you check whether this is working and maybe add some test cases?

[sayeg84]

This is working but it still fails for other features such as rg. I realized this because I tried to make a test using the RG and the code broke. I could also wait for a general fix for being able to serialize a model that contains any of the features obtainable through a Featurizer.

Should we move this PR only for two features or maybe wait for one that fixes for all?

[yaoyic]

@sayeg84 do you have a general test that test for all features. I am afraid there is no general fix to this, since a feature's metadata cannot be a dictionary with every possible type without any consequence. With that I mean sure we can try to pickle stuff up, but 1. metadata of a h5 dataset has limited space requirement and 2. pickling may depend on the python version and corresponding package version compatibility. It would be great if I had made a clearer definition for the interface regarding which metadata is valid or so, but for now we have to deal with them case by case.
For the time being, would you be able to contribute and push a few tests that covers all features, and then I will try to fix the bugs accordingly?