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genome-interface.rst

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Genome Interface

.. index:: ! genome

.. index:: DefaultGenome


.. py:currentmodule:: genome

This is an outline of the minimal interface that is expected to be present on genome objects; example genome objects can be seen in :py:class:`DefaultGenome` and :py:class:`iznn.IZGenome`.

Class Methods

:py:meth:`parse_config(cls, param_dict) <DefaultGenome.parse_config>`

Takes a dictionary of configuration items, returns an object that will later be passed to the write_config method. This configuration object is considered to be opaque by the rest of the library.

:py:meth:`write_config(cls, f, config) <DefaultGenome.write_config>`

Takes a file-like object and the configuration object created by parse_config. This method should write the configuration item definitions to the given file.

Initialization/Reproduction

:py:class:`__init__(self, key) <DefaultGenome>`

Takes a unique genome instance identifier. The initializer should create the following members:

  • key
  • connections - (gene_key, gene) pairs for the connection gene set.
  • nodes - (gene_key, gene) pairs for the node gene set.
  • fitness

:py:meth:`configure_new(self, config) <DefaultGenome.configure_new>`

Configure the genome as a new random genome based on the given configuration from the top-level Config object.

Crossover/Mutation

:py:meth:`configure_crossover(self, genome1, genome2, config) <DefaultGenome.configure_crossover>`

Configure the genome as a child of the given parent genomes.

:py:meth:`mutate(self, config) <DefaultGenome.mutate>`

Apply mutation operations to the genome, using the given configuration.

.. index:: ! genomic distance

Speciation/Misc

:py:meth:`distance(self, other, config) <DefaultGenome.distance>`

Returns the genomic distance between this genome and the other. This distance value is used to compute genome compatibility for speciation.

:py:meth:`size(self) <DefaultGenome.size>`

Returns a measure of genome complexity. This object is currently only given to reporters at the end of a generation to indicate the complexity of the highest-fitness genome. In the DefaultGenome class, this method currently returns (number of nodes, number of enabled connections).