Revise IOTypes

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IOTypes have evolved since 1.4 was published. Before 1.5 is published, we need to review and revise IOTypes for this sim.

The sim-specific IOTypes are:

Reference type serialization:

• [x] AlleleIO
• [x] GeneIO

Data type serialization:

• [x] BunnyCountsIO
• [x] ProportionsCountsIO

Dynamic element serialization involving a PhetioGroup:

• [x] BunnyIO (Bunny is created by BunnyGroup)
• [x] WolfIO (Wolf is created by WolfGroup)

Dynamic element serialization with no PhetioGroup (does that even make sense?):

• [x] GenePairIO (GenePair is created by Genotype)
• [x] GenotypeIO (Genotype is created by Bunny)
• [x] PhenotypeIO (Phenotype is created by Bunny)

Questions:

• [x] Can I use the default toStateObject for BunnyCountsIO and ProportionsCountsIO?

• [x] Are GenePairIO, GenotypeIO, and PhenotypeIO really "dynamic element serialization"? They do not involved a PhetioGroup. They are values related to a Bunny instance, so should they be "data type serialization"?

• [x] Why do GenePairIO, GenotypeIO, and PhenotypeIO use applyState instead of fromStateObject? Is it because their tandems also need to be restored? Is this a general pattern for 'Dynamic element serialization' that doesn't involve a PhetioGroup? Is the default fromStateObject getting called, and what is it doing?

• [x] Is required still necessary with TypeScript, like in Phenotype.ts?

  private applyState( stateObject: PhenotypeStateObject ): void {
    this._furAllele = required( Allele.AlleleIO.fromStateObject( stateObject.furAllele ) );
    this._earsAllele = required( Allele.AlleleIO.fromStateObject( stateObject.earsAllele ) );
    this._teethAllele = required( Allele.AlleleIO.fromStateObject( stateObject.teethAllele ) );
  }

• [ ] Should I create OrganismIO, so that the IOType hierarchy matches the core class hierarchy? I.e. Bunny extends Organism and Wolf extends Organism.

• [ ] BunnyIO problems in #327

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Natural Selection is not currently a publication priority, so unassigning.

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I reviewed these IOTypes and my questions with @zepumph on 7/25/2023, resulting in the above commits. Tested in the State wrapper, no errors, and manual inspection looks correct.

Closing.