evolvable 0.1.0

checksums.yaml

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+---
+SHA256:
+  metadata.gz: 0d88efd1d44ed47b0c02c2c9f2c309f3affa23606d229aabe54171f3c275e2f0
+  data.tar.gz: 5317b0c6191375de0d27e7dc00ad587b566fd2bf42142395f39d6ee938d32908
+SHA512:
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+  data.tar.gz: 3106710898d9456ae596b1b3812bd49a02509b3c6865d3ac56c973d22455cf2089f3b9e0b6125891bf72706ede2321ae965e0144bf30d95d632aa3dbf5ff1b82

data/.gitignore

@@ -0,0 +1,13 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+
+.byebug_history

data/.rubocop.yml

@@ -0,0 +1,20 @@
+AllCops:
+  TargetRubyVersion: 2.6.1
+
+Style/Documentation:
+  Enabled: false
+
+Style/SymbolArray:
+  Enabled: false
+
+Style/FrozenStringLiteralComment:
+  Enabled: false
+
+Style/ClassAndModuleChildren:
+  Enabled: false
+
+Naming/VariableNumber:
+  EnforcedStyle: 'snake_case'
+
+Metrics/LineLength:
+  Max: 90

data/Gemfile

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+# frozen_string_literal: true
+
+source 'https://rubygems.org'
+
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    evolvable (0.1.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ast (2.4.0)
+    byebug (11.0.0)
+    diff-lcs (1.3)
+    jaro_winkler (1.5.2)
+    parallel (1.13.0)
+    parser (2.6.0.0)
+      ast (~> 2.4.0)
+    powerpack (0.1.2)
+    rainbow (3.0.0)
+    rake (10.5.0)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.2)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
+    rubocop (0.64.0)
+      jaro_winkler (~> 1.5.1)
+      parallel (~> 1.10)
+      parser (>= 2.5, != 2.5.1.1)
+      powerpack (~> 0.1)
+      rainbow (>= 2.2.2, < 4.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (~> 1.4.0)
+    ruby-progressbar (1.10.0)
+    unicode-display_width (1.4.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 2.0)
+  byebug (~> 11.0)
+  evolvable!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+  rubocop (~> 0.64.0)
+
+BUNDLED WITH
+   2.0.1

data/README.md

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+# Evolvable
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/evolvable`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'evolvable'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install evolvable
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/evolvable.

data/bin/console

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+#!/usr/bin/env ruby
+
+require 'bundler/setup'
+require 'evolvable'
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require 'irb'
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/evolvable.gemspec

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+lib = File.expand_path('lib', __dir__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'evolvable/version'
+
+Gem::Specification.new do |spec|
+  spec.name = 'evolvable'
+  spec.version = Evolvable::VERSION
+  spec.authors = ['Matt Ruzicka']
+
+  spec.summary = 'A framework for writing genetic algorithms'
+  spec.summary = 'Make your Ruby objects evolvable with genetic algorithms'
+  spec.homepage = 'https://github.com/mattruzicka/evolvable'
+  spec.license = 'MIT'
+
+  spec.metadata['homepage_uri'] = spec.homepage
+  spec.metadata['source_code_uri'] = 'https://github.com/mattruzicka/evolvable'
+  spec.metadata['changelog_uri'] = 'https://github.com/mattruzicka/evolvable' \
+                                   '/blob/master/CHANGELOG.md'
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir = 'exe'
+  spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_development_dependency 'bundler', '~> 2.0'
+  spec.add_development_dependency 'byebug', '~> 11.0'
+  spec.add_development_dependency 'rubocop', '~> 0.64.0'
+end
+

data/lib/evolvable/callbacks.rb

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+module Evolvable
+  module Callbacks
+    def evolvable_before_evolution(population); end
+
+    def evolvable_after_select(population); end
+
+    def evolvable_after_evolution(population); end
+  end
+end

data/lib/evolvable/crossover.rb

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+class Crossover
+  def call(parent_genes, offspring_count)
+    parent_gene_couples = parent_genes.combination(2).cycle
+    Array.new(offspring_count) do
+      p1_genes, p2_genes = parent_gene_couples.next
+      p1_genes.merge(p2_genes) { |_k, p1_val, p2_val| [p1_val, p2_val].sample }
+      offspring_genes = merge_parent_genes(p1_genes, p2_genes)
+      trim_offspring_genes!(offspring_genes, p1_genes.count)
+      offspring_genes
+    end
+  end
+
+  def inspect
+    "#<#{self.class.name} #{as_json.map { |a| a.join(': ') }.join(', ')} >"
+  end
+
+  def as_json
+    { type: self.class.name }
+  end
+
+  private
+
+  def merge_parent_genes(p1_genes, p2_genes)
+    p1_genes.merge(p2_genes) { |_k, p1_val, p2_val| [p1_val, p2_val].sample }
+  end
+
+  def trim_offspring_genes!(offspring_genes, parent_genes_count)
+    trim_genes_count = offspring_genes.count - parent_genes_count
+    return if trim_genes_count.zero?
+
+    offspring_genes.keys.sample(trim_genes_count).each do |name|
+      offspring_genes.delete(name)
+    end
+  end
+end

data/lib/evolvable/errors/not_implemented.rb

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+module Evolvable
+  module Errors
+    class NotImplemented < StandardError; end
+  end
+end

data/lib/evolvable/helper_methods.rb

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+module Evolvable
+  module HelperMethods
+    def combine_dimensions(dimensions)
+      dimension_lengths = dimensions.map(&:length)
+      genes_count = dimension_lengths.inject(1) { |product, c| product * c }
+
+      genes = Array.new(genes_count) { [] }
+      element_repeat_counts = compute_element_repeat_counts(dimension_lengths)
+      sequence_counts = compute_sequence_counts(dimension_lengths)
+
+      dimensions.each_with_index do |dimension, dim_index|
+        element_count = element_repeat_counts[dim_index]
+        sequence = dimension.flat_map { |e| [e] * element_count }
+        dimension_sequence = sequence * sequence_counts[dim_index]
+        dimension_sequence.each_with_index do |element, gene_index|
+          genes[gene_index][dim_index] = element
+        end
+      end
+
+      genes
+    end
+
+    private
+
+    def compute_element_repeat_counts(dimension_lengths)
+      repeat_counts = Array.new(dimension_lengths.count - 1) do |n|
+        right_side_counts = dimension_lengths[(n + 1)..-1]
+        right_side_counts.inject(1) { |product, a| product * a }
+      end
+      repeat_counts << 1
+      repeat_counts
+    end
+
+    def compute_sequence_counts(dimension_lengths)
+      Array.new(dimension_lengths.count) do |n|
+        if n.zero?
+          1
+        else
+          right_side_counts = dimension_lengths[0...n]
+          right_side_counts.inject(1) { |product, a| product * a }
+        end
+      end
+    end
+  end
+end

data/lib/evolvable/mutation.rb

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+module Evolvable
+  class Mutation
+    extend Forwardable
+
+    def initialize(rate: 0.03)
+      @rate = rate
+    end
+
+    def_delegators :@evolvable_class,
+                   :evolvable_genes_count,
+                   :evolvable_gene_pool_size,
+                   :evolvable_random_genes
+
+    def call!(individuals)
+      @evolvable_class = individuals.first.class
+      mutations_count = find_mutations_count(individuals)
+      return if mutations_count.zero?
+
+      mutant_genes = generate_mutant_genes(mutations_count)
+      individual_mutations_count = mutations_count / individuals.count
+      individual_mutations_count = 1 if individual_mutations_count.zero?
+
+      mutant_genes.each_slice(individual_mutations_count).with_index do |m_genes, index|
+        individual = individuals[index] || individuals.sample
+        genes = individual.genes
+        genes.merge!(m_genes.to_h)
+        rm_genes_count = genes.count - evolvable_genes_count
+        genes.keys.sample(rm_genes_count).each { |key| genes.delete(key) }
+      end
+    end
+
+    def inspect
+      "#<#{self.class.name} #{as_json.map { |a| a.join(': ') }.join(', ')} >"
+    end
+
+    def as_json
+      { type: self.class.name,
+        rate: @rate }
+    end
+
+    private
+
+    def find_mutations_count(individuals)
+      return 0 if @rate.zero?
+
+      count = (individuals.count * evolvable_genes_count * @rate)
+      return count.to_i if count >= 1
+
+      rand <= count ? 1 : 0
+    end
+
+    def generate_mutant_genes(mutations_count)
+      gene_pool_size = evolvable_gene_pool_size
+      mutant_genes = []
+      while mutant_genes.count < mutations_count
+        genes_count = [gene_pool_size, mutations_count - mutant_genes.count].min
+        mutant_genes.concat evolvable_random_genes(genes_count).to_a
+      end
+      mutant_genes
+    end
+  end
+end

data/lib/evolvable/population.rb

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+# frozen_string_literal: true
+
+module Evolvable
+  class Population
+    extend Forwardable
+
+    def initialize(evolvable_class:,
+                   size: 20,
+                   selection_count: 2,
+                   crossover: Crossover.new,
+                   mutation: Mutation.new,
+                   generation_count: 0,
+                   log_progress: false,
+                   individuals: [])
+      @evolvable_class = evolvable_class
+      @size = size
+      @selection_count = selection_count
+      @crossover = crossover
+      @mutation = mutation
+      @generation_count = generation_count
+      @log_progress = log_progress
+      assign_individuals(individuals)
+    end
+
+    attr_reader :evolvable_class,
+                :size,
+                :selection_count,
+                :crossover,
+                :mutation,
+                :generation_count,
+                :individuals
+
+    def_delegators :@evolvable_class,
+                   :evolvable_evaluate!,
+                   :evolvable_initialize,
+                   :evolvable_random_genes,
+                   :evolvable_before_evolution,
+                   :evolvable_after_select,
+                   :evolvable_after_evolution
+
+    def evolve!(generations_count: 1, fitness_goal: nil)
+      @fitness_goal = fitness_goal
+      generations_count.times do
+        @generation_count += 1
+        evolvable_before_evolution(self)
+        evaluate_individuals!
+        log_progress if @log_progress
+        break if fitness_goal_met?
+
+        select_individuals!
+        evolvable_after_select(self)
+        reproduce_individuals!
+        mutate_individuals!
+        evolvable_after_evolution(self)
+      end
+    end
+
+    def evaluate_individuals!
+      evolvable_evaluate!(@individuals)
+      if @fitness_goal
+        @individuals.sort_by! { |i| -(i.fitness - @fitness_goal).abs }
+      else
+        @individuals.sort_by!(&:fitness)
+      end
+    end
+
+    def log_progress
+      @individuals.last.evolvable_progress
+    end
+
+    def fitness_goal_met?
+      @fitness_goal && @individuals.last.fitness >= @fitness_goal
+    end
+
+    def select_individuals!
+      @individuals.slice!(0..-1 - @selection_count)
+    end
+
+    def reproduce_individuals!
+      parent_genes = @individuals.map(&:genes)
+      offspring_genes = @crossover.call(parent_genes, @size)
+      @individuals = offspring_genes.map.with_index do |genes, i|
+        evolvable_initialize(genes, self, i)
+      end
+    end
+
+    def mutate_individuals!
+      @mutation.call!(@individuals)
+    end
+
+    def inspect
+      "#<#{self.class.name} #{as_json} >"
+    end
+
+    def as_json
+      { evolvable_class: @evolvable_class.name,
+        size: @size,
+        selection_count: @selection_count,
+        crossover: @crossover.as_json,
+        mutation: @mutation.as_json,
+        generation_count: @generation_count }
+    end
+
+    private
+
+    def assign_individuals(individuals)
+      @individuals = individuals || []
+      (@size - individuals.count).times do |n|
+        genes = evolvable_random_genes
+        @individuals << evolvable_initialize(genes, self, n)
+      end
+    end
+  end
+end

data/lib/evolvable/version.rb

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+# frozen_string_literal: true
+
+module Evolvable
+  VERSION = '0.1.0'
+end

data/lib/evolvable.rb

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+# frozen_string_literal: true
+
+require 'forwardable'
+require 'logger'
+
+require 'evolvable/version'
+require 'evolvable/population'
+require 'evolvable/crossover'
+require 'evolvable/mutation'
+require 'evolvable/helper_methods'
+require 'evolvable/callbacks'
+require 'evolvable/errors/not_implemented'
+
+module Evolvable
+  extend HelperMethods
+
+  def self.included(base)
+    base.extend Callbacks
+
+    def base.evolvable_gene_pool
+      raise Errors::NotImplemented, __method__
+    end
+
+    def base.evolvable_genes_count
+      evolvable_gene_pool_size
+    end
+
+    def base.evolvable_evaluate!(_individuals); end
+
+    def base.evolvable_initialize(genes, population, _individual_index)
+      evolvable = new
+      evolvable.genes = genes
+      evolvable.population = population
+      evolvable
+    end
+
+    def base.evolvable_population_attrs
+      {}
+    end
+
+    def base.evolvable_population(args = {})
+      clear_evolvable_gene_pool_caches
+      args = evolvable_population_attrs.merge!(args)
+      args[:evolvable_class] = self
+      Population.new(args)
+    end
+
+    def base.evolvable_gene_pool_cache
+      @evolvable_gene_pool_cache ||= evolvable_gene_pool
+    end
+
+    def base.evolvable_gene_pool_size
+      @evolvable_gene_pool_size ||= evolvable_gene_pool_cache.size
+    end
+
+    def base.clear_evolvable_gene_pool_caches
+      @evolvable_gene_pool_cache = nil
+      @evolvable_gene_pool_size = nil
+    end
+
+    def base.evolvable_random_genes(count = nil)
+      gene_pool = evolvable_gene_pool_cache
+      count ||= evolvable_genes_count
+      gene_pool = gene_pool.sample(count) if count < gene_pool.size
+      genes = {}
+      gene_pool.each { |name, potentials| genes[name] = potentials.sample }
+      genes
+    end
+  end
+
+  def self.logger
+    @logger ||= Logger.new(STDOUT)
+  end
+
+  attr_accessor :genes,
+                :population
+
+  def fitness
+    raise Errors::NotImplemented, __method__
+  end
+
+  def evolvable_progress(info = nil)
+    info ||= "Generation: #{population.generation_count} | Fitness: #{fitness}"
+    Evolvable.logger.info(info)
+  end
+end

metadata

@@ -0,0 +1,104 @@
+--- !ruby/object:Gem::Specification
+name: evolvable
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Matt Ruzicka
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2019-03-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '11.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '11.0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.64.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.64.0
+description: 
+email: 
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rubocop.yml"
+- CHANGELOG.md
+- Gemfile
+- Gemfile.lock
+- README.md
+- bin/console
+- bin/setup
+- evolvable.gemspec
+- lib/evolvable.rb
+- lib/evolvable/callbacks.rb
+- lib/evolvable/crossover.rb
+- lib/evolvable/errors/not_implemented.rb
+- lib/evolvable/helper_methods.rb
+- lib/evolvable/mutation.rb
+- lib/evolvable/population.rb
+- lib/evolvable/version.rb
+homepage: https://github.com/mattruzicka/evolvable
+licenses:
+- MIT
+metadata:
+  homepage_uri: https://github.com/mattruzicka/evolvable
+  source_code_uri: https://github.com/mattruzicka/evolvable
+  changelog_uri: https://github.com/mattruzicka/evolvable/blob/master/CHANGELOG.md
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.0.3
+signing_key: 
+specification_version: 4
+summary: Make your Ruby objects evolvable with genetic algorithms
+test_files: []