wallace 0.0.0

data/lib/species/bit_string_species.rb

@@ -0,0 +1,18 @@
+# Bit-strings are implemented as a specialised form of array species that are
+# confined to only containing 0 and 1 integers.
+class Wallace::Species::BitStringSpecies < Wallace::Species::ArraySpecies
+
+  name = :bit_string
+
+  # Constructs a new bit-string based species.
+  #
+  # *Parameters:*
+  # * opts, hash of keyword options used by this method.
+  #   -> id, the unique identifier for this species.
+  #   -> length, the length constraints imposed on individuals of this species.
+  def initialize(opts = {})
+    opts[:length] = [0, 1]
+    super(opts)
+  end
+
+end

data/lib/species/init.rb

@@ -0,0 +1,4 @@
+require_relative 'array_species.rb'
+require_relative 'string_species.rb'
+require_relative 'bit_string_species.rb'
+require_relative 'permutation_species.rb'

data/lib/species/permutation_species.rb

@@ -0,0 +1,22 @@
+class Wallace::Species::PermutationSpecies < Wallace::Species
+
+  # Constructs a new permutation species.
+  #
+  # *Parameters:*
+  # * opts, hash of keyword options used by this method.
+  #   -> id, the unique identifier for this species.
+  #   -> values, the list of values to be permuted.
+  def initialize(opts = {})
+    super(opts)
+    @values = opts[:values]
+  end
+
+  # Spawns a new permutation of this species list of values.
+  #
+  # *Parameters:*
+  # * rng, random number generation to use during process.
+  def spawn(rng)
+    Wallace::Individual.new(self, @values.shuffle(random: rng))
+  end
+
+end

data/lib/species/string_species.rb

@@ -0,0 +1,29 @@
+# String-based species represent their members as strings. Species may impose
+# constraints on the length and alphabet of these strings. If more constraints
+# are desired then the species can be easily extended or sub-classed to
+# implement those constraints.
+class Wallace::Species::StringSpecies < Wallace::Species::ArraySpecies
+
+  name = :string
+
+  # Constructs a new string-based species.
+  #
+  # *Parameters:*
+  # * opts, hash of keyword options used by this method.
+  #   -> id, the unique identifier for this species.
+  #   -> length, the length constraints imposed on individuals of this species.
+  #   -> alphabet, the alphabet used to generate strings.
+  def initialize(opts = {})
+    opts[:values] = opts.delete(:alphabet)
+    super(opts)
+  end
+
+  # Creates a new string-based individual using the alphabet and length
+  # constraints of this species.
+  def spawn(rng)
+    ind = super(rng)
+    ind.data = ind.data.join
+    return ind
+  end
+
+end

data/lib/utility/init.rb

@@ -0,0 +1,4 @@
+module Wallace::Utility; end
+
+require_relative "scaled_array"
+require_relative "sorted_array"

data/lib/utility/scaled_array.rb

@@ -0,0 +1,88 @@
+class Wallace::Utility::ScaledArray
+
+  def initialize(items, probabilities)
+    @items = items
+    @cprob = []
+    
+    # Convert the probabilities into cumulative probabilities.
+    sum = 0.0
+    for p in probabilities
+      @cprob << sum
+      sum += p
+    end
+    
+  end
+  
+  def sample
+    point = Random.rand
+    return self.select(point)
+  end
+  
+  def select(point)
+    
+    # Initialise the lower and upper bounds of the binary search
+    # at either end of the distribution.
+    lb = 0
+    ub = @items.length - 1
+    
+    # Keep searching until the upper and lower bound converge.
+    until lb == ub
+    
+      # Select the point in between the lower and upper bound
+      # as the pivot.
+      pivot = lb + ((ub - lb) / 2)
+      
+      # If the point is less than the start of the area for
+      # the pivot, move the upper bound back one.
+      if point < @cprob[pivot]
+        ub = pivot - 1
+        
+      # Check if the point lies within the bounds of the pivot.
+      elsif pivot == ub or point < @cprob[pivot+1]
+        lb = ub = pivot
+        
+      # If it doesn't, then move the lower bound forward.
+      else
+        lb = pivot + 1
+      end
+      
+    
+    end
+    
+    return @items[lb]
+    
+  end
+  
+  
+  def select_old(point)
+  
+    # If there is only a single item in the distribution,
+    # then return that item.
+    return @items[0] if @items.length == 1
+    
+    # Initialise the lower and upper bounds of the binary search
+    # at either end of the distribution.
+    lb = 0
+    ub = @items.length - 1
+    
+    # Keep searching until the upper and lower bound converge.
+    until lb == ub
+    
+      # Select the point in between the lower and upper bound
+      # as the pivot.
+      pivot = lb + ((ub - lb) / 2)
+    
+      if point <= @cprob[pivot]
+        ub = pivot
+      else
+        lb = pivot + 1
+      end
+      
+    
+    end
+    
+    return @items[pivot]
+    
+  end
+
+end

data/lib/utility/sorted_array.rb

@@ -0,0 +1,39 @@
+class Wallace::Utility::SortedArray < Array
+
+  def initialize(array = nil)
+    super(array.sort) if array != nil
+  end
+  
+  def set(values)
+    
+  end
+
+  # Inserts a value into the array at its correct sorted position.
+  def <<(value)
+    insert(calculate_index(value), value)
+  end
+  
+  def push(*values)
+    values.each{|v| self << v}
+    return self
+  end
+
+  # Calculates the correct index to insert the value into the
+  # array at.
+  #
+  # \*TODO:*
+  # * This is a rubbish O(n) implementation.
+  # | A RB-binary tree or a better insertion sort method should
+  # | be implemented.
+  def calculate_index(value)
+    i = 0
+    self.each { |v|
+      if v > value
+        break
+      end
+      i += 1
+    }
+    return i
+  end
+
+end

data/lib/wallace.rb

@@ -0,0 +1,40 @@
+module Wallace; end
+
+# Load Peach if we're using JRuby.
+require 'peach' if defined?(RUBY_VERSION) and RUBY_ENGINE == 'jruby'
+
+# Load all monkey patches.
+require_relative 'patches/init.rb'
+
+# Load core files.
+require_relative 'core/state.rb'
+require_relative 'core/analyser.rb'
+require_relative 'core/operator.rb'
+require_relative 'core/selector.rb'
+require_relative 'core/fitness.rb'
+require_relative 'core/evaluator.rb'
+require_relative 'core/species.rb'
+require_relative 'core/breeder.rb'
+require_relative 'core/migrator.rb'
+require_relative 'core/termination.rb'
+require_relative 'core/population.rb'
+require_relative 'core/subpopulation.rb'
+require_relative 'core/evolver.rb'
+require_relative 'core/individual.rb'
+require_relative 'core/fraction.rb'
+require_relative 'core/exceptions.rb'
+require_relative 'core/breeding_graph.rb'
+require_relative 'core/breeding_graph/init.rb'
+
+# Load all default selectors, species, etc.
+require_relative 'distributions/init.rb'
+require_relative 'selectors/init.rb'
+require_relative 'species/init.rb'
+require_relative 'operators/init.rb'
+require_relative 'fitness/init.rb'
+
+# Load all modules.
+require_relative 'modules/init.rb'
+
+# Load utilities.
+require_relative 'utility/init.rb'

metadata

@@ -0,0 +1,248 @@
+--- !ruby/object:Gem::Specification
+name: wallace
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Chris Timperley
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-12-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: peach
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.7
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: peach
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.5.1
+description: ! "    Wallace is a powerful, flexible and modular toolkit for running
+  Evolutionary Algorithms in Ruby.\n    Out of the box it provides support for steady-state
+  EAs, genetic algorithms, genetic programming,\n    grammatical evolution and other
+  types of EAs.\n"
+email: christimperley@gmail.com
+executables:
+- .gitkeep
+extensions: []
+extra_rdoc_files:
+- README.md
+files:
+- Gemfile
+- README.md
+- Rakefile
+- VERSION
+- bin/.gitkeep
+- lib/analysers/fitness_distribution_analyser.rb
+- lib/analysers/init.rb
+- lib/core/analyser.rb
+- lib/core/breeder.rb
+- lib/core/breeding_graph.rb
+- lib/core/breeding_graph/init.rb
+- lib/core/breeding_graph/input_node.rb
+- lib/core/breeding_graph/node.rb
+- lib/core/breeding_graph/node_input.rb
+- lib/core/evaluator.rb
+- lib/core/evolver.rb
+- lib/core/exceptions.rb
+- lib/core/experiment.rb
+- lib/core/fitness.rb
+- lib/core/fraction.rb
+- lib/core/individual.rb
+- lib/core/logger.rb
+- lib/core/migrator.rb
+- lib/core/operator.rb
+- lib/core/population.rb
+- lib/core/selector.rb
+- lib/core/species.rb
+- lib/core/state.rb
+- lib/core/subpopulation.rb
+- lib/core/termination.rb
+- lib/distributions/gaussian_distribution.rb
+- lib/distributions/init.rb
+- lib/fitness/init.rb
+- lib/fitness/raw_fitness.rb
+- lib/loggers/csv_logger.rb
+- lib/loggers/init.rb
+- lib/loggers/mongo_logger.rb
+- lib/loggers/sqlite_logger.rb
+- lib/modules/ge/backus_naur_form.rb
+- lib/modules/ge/grammar_derivation.rb
+- lib/modules/ge/grammar_species.rb
+- lib/modules/ge/init.rb
+- lib/modules/init.rb
+- lib/modules/koza/builder.rb
+- lib/modules/koza/builder/full_builder.rb
+- lib/modules/koza/builder/grow_builder.rb
+- lib/modules/koza/builder/half_builder.rb
+- lib/modules/koza/builder/init.rb
+- lib/modules/koza/ephemeral.rb
+- lib/modules/koza/init.rb
+- lib/modules/koza/koza_node.rb
+- lib/modules/koza/koza_node_value.rb
+- lib/modules/koza/koza_node_value_set.rb
+- lib/modules/koza/koza_species.rb
+- lib/modules/koza/koza_tree.rb
+- lib/modules/koza/operators/init.rb
+- lib/modules/koza/operators/subtree_crossover_operation.rb
+- lib/modules/koza/operators/subtree_mutation_operation.rb
+- lib/operators/bit_flip_mutation_operation.rb
+- lib/operators/boundary_mutation_operation.rb
+- lib/operators/cycle_crossover_operation.rb
+- lib/operators/gaussian_mutation_operation.rb
+- lib/operators/half_uniform_crossover_operation.rb
+- lib/operators/init.rb
+- lib/operators/merging_crossover_operation.rb
+- lib/operators/one_point_crossover_operation.rb
+- lib/operators/order_crossover_operation.rb
+- lib/operators/partially_mapped_crossover_operation.rb
+- lib/operators/point_mutation_operation.rb
+- lib/operators/position_crossover_operation.rb
+- lib/operators/reverse_sequence_mutation_operation.rb
+- lib/operators/shuffle_mutation_operation.rb
+- lib/operators/splice_crossover_operation.rb
+- lib/operators/subtour_exchange_crossover_operation.rb
+- lib/operators/swap_mutation_operation.rb
+- lib/operators/three_parent_crossover_operation.rb
+- lib/operators/two_point_crossover_operation.rb
+- lib/operators/twors_mutation_operation.rb
+- lib/operators/uniform_crossover_operation.rb
+- lib/operators/uniform_mutation_operation.rb
+- lib/operators/variable_one_point_crossover_operation.rb
+- lib/patches/enumerable.rb
+- lib/patches/init.rb
+- lib/patches/range.rb
+- lib/selectors/init.rb
+- lib/selectors/random_selector.rb
+- lib/selectors/roulette_selector.rb
+- lib/selectors/tournament_selector.rb
+- lib/species/array_species.rb
+- lib/species/bit_string_species.rb
+- lib/species/init.rb
+- lib/species/permutation_species.rb
+- lib/species/string_species.rb
+- lib/utility/init.rb
+- lib/utility/scaled_array.rb
+- lib/utility/sorted_array.rb
+- lib/wallace.rb
+- test/.gitkeep
+homepage: http://github.com/ChrisTimperley/Wallace.rb
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: -521889391
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.28
+signing_key: 
+specification_version: 3
+summary: A powerful, flexible and modular toolkit for running Evolutionary Algorithms
+  in Ruby
+test_files: []