remove genetic_material from configuration

README.md

@@ -25,7 +25,7 @@ The high-level steps of an evolutionary algorithm are:
 
 Petri Dish is built around a few key classes: `Configuration`, `Member`, `Metadata`, and `World`. 
 
-- `Configuration`: This class provides a way to configure the behavior of the evolutionary algorithm. It exposes various parameters like `population_size`, `mutation_rate`, `genetic_material`, and several callback functions that can be used to customize the evolution process. 
+- `Configuration`: This class provides a way to configure the behavior of the evolutionary algorithm. It exposes various parameters like `population_size`, `mutation_rate`, and several callback functions that can be used to customize the evolution process. 
 
 - `Member`: This class represents an individual in the population. It has a set of genes and a fitness value, which is computed by a fitness function provided in the configuration.
 

examples/lazy_dog/lazy_dog_example.rb

@@ -31,11 +31,11 @@ def random_midpoint_crossover_function(configuration)
   end
 end
 
-def random_mutation_function(configuration)
+def random_mutation_function(configuration, genetic_material)
   ->(member) do
     mutated_genes = member.genes.map do |gene|
       if rand < configuration.mutation_rate
-        configuration.genetic_material.sample
+        genetic_material.sample
       else
         gene
       end
@@ -49,11 +49,10 @@ def random_mutation_function(configuration)
   config.max_generations = 5000
   config.population_size = 250
   config.mutation_rate = 0.005
-  config.genetic_material = genetic_material
   config.parents_selection_function = twenty_percent_tournament_function(config)
   config.fitness_function = exponential_fitness_function(target_genes)
   config.crossover_function = random_midpoint_crossover_function(config)
-  config.mutation_function = random_mutation_function(config)
+  config.mutation_function = random_mutation_function(config, genetic_material)
   config.end_condition_function = genes_match_target_end_condition_function(target_genes)
   config.highest_fitness_callback = ->(member) { puts "Highest fitness: #{member.fitness} (#{member})" }
 end

examples/traveling_salesperson/salesperson_example.rb

@@ -117,7 +117,6 @@ def hash
   config.max_generations = 100
   config.population_size = 100
   config.mutation_rate = 0.01
-  config.genetic_material = GENETIC_MATERIAL
   config.mutation_function = swap_mutation_function(config)
   config.fitness_function = fitness_function
   config.parents_selection_function = twenty_percent_tournament(config)

lib/petri_dish/configuration.rb

@@ -3,7 +3,6 @@ class Configuration
     attr_accessor :logger,
       :population_size,
       :mutation_rate,
-      :genetic_material,
       :elitism_rate,
       :max_generations,
       :parents_selection_function,
@@ -28,7 +27,6 @@ def initialize
       @population_size = default_population_size
       @mutation_rate = default_mutation_rate
       @elitism_rate = default_elitism_rate
-      @genetic_material = default_genetic_material
       @fitness_function = default_fitness_function
       @parents_selection_function = default_parents_selection_function
       @crossover_function = default_crossover_function
@@ -46,7 +44,6 @@ def validate!
       raise ArgumentError, "population_size must be greater than 0" unless population_size > 0
       raise ArgumentError, "mutation_rate must be between 0 and 1" unless mutation_rate >= 0 && mutation_rate <= 1
       raise ArgumentError, "elitism_rate must be between 0 and 1" unless elitism_rate >= 0 && elitism_rate <= 1
-      raise ArgumentError, "genetic_material must be an Array" unless genetic_material.is_a?(Array)
       raise ArgumentError, "fitness_function must respond to :call" unless fitness_function.respond_to?(:call)
       raise ArgumentError, "parents_selection_function must respond to :call" unless parents_selection_function.respond_to?(:call)
       raise ArgumentError, "crossover_function must respond to :call" unless crossover_function.respond_to?(:call)
@@ -64,7 +61,6 @@ def reset!
       @population_size = default_population_size
       @mutation_rate = default_mutation_rate
       @elitism_rate = default_elitism_rate
-      @genetic_material = default_genetic_material
       @fitness_function = default_fitness_function
       @parents_selection_function = default_parents_selection_function
       @crossover_function = default_crossover_function
@@ -92,8 +88,6 @@ def default_mutation_rate = 0.005
 
     def default_elitism_rate = 0.00
 
-    def default_genetic_material = []
-
     def default_fitness_function = ->(_member) { raise ArgumentError, "fitness_function must be set" }
 
     def default_parents_selection_function = ->(_members) { raise ArgumentError, "parents_selection_function must be set" }

spec/world_spec.rb

@@ -15,7 +15,6 @@
     allow(configuration).to receive(:population_size).and_return(1)
     allow(configuration).to receive(:mutation_rate).and_return(0.005)
     allow(configuration).to receive(:elitism_rate).and_return(0.00)
-    allow(configuration).to receive(:genetic_material).and_return([])
     allow(configuration).to receive(:parents_selection_function).and_return(->(_members) { double(PetriDish::Member, fitness: 0.1) })
     allow(configuration).to receive(:crossover_function).and_return(->(_members) { double(PetriDish::Member, fitness: 0.1) })
     allow(configuration).to receive(:mutation_function).and_return(->(_member) { double(PetriDish::Member, fitness: 0.1) })