Make Ontologies object serializable

[diekhans]

Attempting to pickle a pronto.ontology.Ontology

Results in the error:

TypeError: cannot serialize '_io.BufferedReader' object```

Being able to serialize these objects would help with the fact that 
owl is  slow to parse.

[diekhans]

note, setting handle field to None after parse allows pickling

[althonos]

Good idea! I actually don't think I need the handle anymore after parsing (except for __repr__ maybe).

Note that if OWL is slow to parse you can also save if as an OBO file (using Ontology.dump), and then parse it again from OBO. Than wouldn't support imports, but I plan on adding a method to "pack" an ontology with all it's dependencies within a new Ontology object.

You can also potentially speed parsing up by running python in optimized mode (python -O) to disable type checking.

[althonos]

Fixed in eae3420.

[althonos]

Serializing an Ontology will now keep everything but the Ontology.handle attribute: it will be None after you deserialize.

[diekhans]

thanks @althonos !!