Serialization

[iskandr]

We previously had implementations of __getstate__ and __setstate__ which (1) didn't work for non-human genomes and (2) used fragile positional arguments. This PR:

• Creates a Serializable base class for Genome, EnsemblRelease, Gene, Transcript, and Exon, Species. This allows us to share serialization/flattening code between these objects with copy/paste madness.
• Adds to_json/from_json and to_dict/from_dict methods to all serializable objects.
• Moves normalize_chromosome and normalize_strand to a separate module (no changes to actual code)
• Moved global state from species.py onto the Species class

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This change is

[tavinathanson]

What happened to repr?

[iskandr]

All of our implementations just call str so I made that the default in Serializable. Maybe that object needs to be renamed to something like SaneDefaultsForClassesWhichImplementToDict.

[coveralls]

Coverage increased (+0.7%) to 80.679% when pulling dc38ec7 on json_serialization into 3108c6e on master.

[coveralls]

Coverage increased (+0.6%) to 80.607% when pulling 90bdfc1 on json_serialization into 3108c6e on master.

[tavinathanson]

I could see a use-case for not wanting to rely on sorting, but rather on some instrinsic ordering (e.g. ID first, name second, etc.). Any interest in using OrderedDicts instead?

[iskandr]

You mean just use the order of items() but have to_dict() return an OrderedDict?

[coveralls]

Coverage increased (+0.6%) to 80.607% when pulling 90bdfc1 on json_serialization into 3108c6e on master.

[tavinathanson]

I'm getting confused between the tuple here and the one above. Maybe rename _class_to_tuple to _class_to_full_name_tuple and _tuple_to_class to _full_name_tuple_to_class?

[tavinathanson]

LGTM % comments 👍

[coveralls]

Coverage increased (+1.3%) to 81.356% when pulling 3649597 on json_serialization into 3108c6e on master.

[coveralls]

Coverage increased (+1.3%) to 81.356% when pulling 3649597 on json_serialization into 3108c6e on master.

[coveralls]

Coverage increased (+0.5%) to 80.544% when pulling 8d7bf72 on json_serialization into 3108c6e on master.

[coveralls]

Coverage increased (+0.5%) to 80.568% when pulling 8d7bf72 on json_serialization into 3108c6e on master.

[coveralls]

Coverage increased (+1.1%) to 81.503% when pulling b341b14 on json_serialization into f2e4eea on master.

[coveralls]

Coverage increased (+1.1%) to 81.503% when pulling b341b14 on json_serialization into f2e4eea on master.

[coveralls]

Coverage increased (+1.06%) to 81.419% when pulling 421498d on json_serialization into f2e4eea on master.