wallace 0.0.0
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- data/Gemfile +14 -0
- data/README.md +12 -0
- data/Rakefile +52 -0
- data/VERSION +1 -0
- data/bin/.gitkeep +0 -0
- data/lib/analysers/fitness_distribution_analyser.rb +28 -0
- data/lib/analysers/init.rb +1 -0
- data/lib/core/analyser.rb +63 -0
- data/lib/core/breeder.rb +68 -0
- data/lib/core/breeding_graph.rb +59 -0
- data/lib/core/breeding_graph/init.rb +3 -0
- data/lib/core/breeding_graph/input_node.rb +55 -0
- data/lib/core/breeding_graph/node.rb +68 -0
- data/lib/core/breeding_graph/node_input.rb +6 -0
- data/lib/core/evaluator.rb +52 -0
- data/lib/core/evolver.rb +47 -0
- data/lib/core/exceptions.rb +6 -0
- data/lib/core/experiment.rb +22 -0
- data/lib/core/fitness.rb +8 -0
- data/lib/core/fraction.rb +7 -0
- data/lib/core/individual.rb +65 -0
- data/lib/core/logger.rb +5 -0
- data/lib/core/migrator.rb +6 -0
- data/lib/core/operator.rb +54 -0
- data/lib/core/population.rb +56 -0
- data/lib/core/selector.rb +43 -0
- data/lib/core/species.rb +52 -0
- data/lib/core/state.rb +29 -0
- data/lib/core/subpopulation.rb +53 -0
- data/lib/core/termination.rb +39 -0
- data/lib/distributions/gaussian_distribution.rb +60 -0
- data/lib/distributions/init.rb +3 -0
- data/lib/fitness/init.rb +1 -0
- data/lib/fitness/raw_fitness.rb +30 -0
- data/lib/loggers/csv_logger.rb +20 -0
- data/lib/loggers/init.rb +1 -0
- data/lib/loggers/mongo_logger.rb +5 -0
- data/lib/loggers/sqlite_logger.rb +5 -0
- data/lib/modules/ge/backus_naur_form.rb +125 -0
- data/lib/modules/ge/grammar_derivation.rb +30 -0
- data/lib/modules/ge/grammar_species.rb +29 -0
- data/lib/modules/ge/init.rb +5 -0
- data/lib/modules/init.rb +2 -0
- data/lib/modules/koza/builder.rb +48 -0
- data/lib/modules/koza/builder/full_builder.rb +92 -0
- data/lib/modules/koza/builder/grow_builder.rb +103 -0
- data/lib/modules/koza/builder/half_builder.rb +70 -0
- data/lib/modules/koza/builder/init.rb +3 -0
- data/lib/modules/koza/ephemeral.rb +33 -0
- data/lib/modules/koza/init.rb +12 -0
- data/lib/modules/koza/koza_node.rb +108 -0
- data/lib/modules/koza/koza_node_value.rb +72 -0
- data/lib/modules/koza/koza_node_value_set.rb +51 -0
- data/lib/modules/koza/koza_species.rb +48 -0
- data/lib/modules/koza/koza_tree.rb +159 -0
- data/lib/modules/koza/operators/init.rb +4 -0
- data/lib/modules/koza/operators/subtree_crossover_operation.rb +43 -0
- data/lib/modules/koza/operators/subtree_mutation_operation.rb +32 -0
- data/lib/operators/bit_flip_mutation_operation.rb +29 -0
- data/lib/operators/boundary_mutation_operation.rb +28 -0
- data/lib/operators/cycle_crossover_operation.rb +77 -0
- data/lib/operators/gaussian_mutation_operation.rb +39 -0
- data/lib/operators/half_uniform_crossover_operation.rb +24 -0
- data/lib/operators/init.rb +26 -0
- data/lib/operators/merging_crossover_operation.rb +27 -0
- data/lib/operators/one_point_crossover_operation.rb +29 -0
- data/lib/operators/order_crossover_operation.rb +38 -0
- data/lib/operators/partially_mapped_crossover_operation.rb +44 -0
- data/lib/operators/point_mutation_operation.rb +31 -0
- data/lib/operators/position_crossover_operation.rb +50 -0
- data/lib/operators/reverse_sequence_mutation_operation.rb +13 -0
- data/lib/operators/shuffle_mutation_operation.rb +17 -0
- data/lib/operators/splice_crossover_operation.rb +42 -0
- data/lib/operators/subtour_exchange_crossover_operation.rb +54 -0
- data/lib/operators/swap_mutation_operation.rb +29 -0
- data/lib/operators/three_parent_crossover_operation.rb +16 -0
- data/lib/operators/two_point_crossover_operation.rb +31 -0
- data/lib/operators/twors_mutation_operation.rb +18 -0
- data/lib/operators/uniform_crossover_operation.rb +30 -0
- data/lib/operators/uniform_mutation_operation.rb +31 -0
- data/lib/operators/variable_one_point_crossover_operation.rb +80 -0
- data/lib/patches/enumerable.rb +85 -0
- data/lib/patches/init.rb +5 -0
- data/lib/patches/range.rb +13 -0
- data/lib/selectors/init.rb +5 -0
- data/lib/selectors/random_selector.rb +14 -0
- data/lib/selectors/roulette_selector.rb +23 -0
- data/lib/selectors/tournament_selector.rb +36 -0
- data/lib/species/array_species.rb +40 -0
- data/lib/species/bit_string_species.rb +18 -0
- data/lib/species/init.rb +4 -0
- data/lib/species/permutation_species.rb +22 -0
- data/lib/species/string_species.rb +29 -0
- data/lib/utility/init.rb +4 -0
- data/lib/utility/scaled_array.rb +88 -0
- data/lib/utility/sorted_array.rb +39 -0
- data/lib/wallace.rb +40 -0
- data/test/.gitkeep +0 -0
- metadata +248 -0
@@ -0,0 +1,18 @@
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# Bit-strings are implemented as a specialised form of array species that are
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# confined to only containing 0 and 1 integers.
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class Wallace::Species::BitStringSpecies < Wallace::Species::ArraySpecies
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name = :bit_string
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# Constructs a new bit-string based species.
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#
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# *Parameters:*
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# * opts, hash of keyword options used by this method.
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# -> id, the unique identifier for this species.
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# -> length, the length constraints imposed on individuals of this species.
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def initialize(opts = {})
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opts[:length] = [0, 1]
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super(opts)
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end
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end
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data/lib/species/init.rb
ADDED
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class Wallace::Species::PermutationSpecies < Wallace::Species
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# Constructs a new permutation species.
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#
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# *Parameters:*
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# * opts, hash of keyword options used by this method.
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# -> id, the unique identifier for this species.
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# -> values, the list of values to be permuted.
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def initialize(opts = {})
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super(opts)
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@values = opts[:values]
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end
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# Spawns a new permutation of this species list of values.
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#
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# *Parameters:*
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# * rng, random number generation to use during process.
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def spawn(rng)
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Wallace::Individual.new(self, @values.shuffle(random: rng))
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end
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end
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# String-based species represent their members as strings. Species may impose
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# constraints on the length and alphabet of these strings. If more constraints
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# are desired then the species can be easily extended or sub-classed to
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# implement those constraints.
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class Wallace::Species::StringSpecies < Wallace::Species::ArraySpecies
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name = :string
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# Constructs a new string-based species.
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#
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# *Parameters:*
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# * opts, hash of keyword options used by this method.
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# -> id, the unique identifier for this species.
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# -> length, the length constraints imposed on individuals of this species.
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# -> alphabet, the alphabet used to generate strings.
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def initialize(opts = {})
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opts[:values] = opts.delete(:alphabet)
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super(opts)
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end
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# Creates a new string-based individual using the alphabet and length
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# constraints of this species.
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def spawn(rng)
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ind = super(rng)
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ind.data = ind.data.join
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return ind
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end
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end
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data/lib/utility/init.rb
ADDED
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class Wallace::Utility::ScaledArray
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def initialize(items, probabilities)
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@items = items
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@cprob = []
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# Convert the probabilities into cumulative probabilities.
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sum = 0.0
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for p in probabilities
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@cprob << sum
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sum += p
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end
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end
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def sample
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point = Random.rand
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return self.select(point)
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end
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def select(point)
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# Initialise the lower and upper bounds of the binary search
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# at either end of the distribution.
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lb = 0
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ub = @items.length - 1
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# Keep searching until the upper and lower bound converge.
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until lb == ub
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# Select the point in between the lower and upper bound
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# as the pivot.
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pivot = lb + ((ub - lb) / 2)
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# If the point is less than the start of the area for
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# the pivot, move the upper bound back one.
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if point < @cprob[pivot]
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ub = pivot - 1
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# Check if the point lies within the bounds of the pivot.
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elsif pivot == ub or point < @cprob[pivot+1]
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lb = ub = pivot
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# If it doesn't, then move the lower bound forward.
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else
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lb = pivot + 1
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end
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end
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return @items[lb]
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end
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def select_old(point)
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# If there is only a single item in the distribution,
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# then return that item.
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return @items[0] if @items.length == 1
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# Initialise the lower and upper bounds of the binary search
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# at either end of the distribution.
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lb = 0
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ub = @items.length - 1
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# Keep searching until the upper and lower bound converge.
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until lb == ub
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# Select the point in between the lower and upper bound
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# as the pivot.
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pivot = lb + ((ub - lb) / 2)
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if point <= @cprob[pivot]
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ub = pivot
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else
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lb = pivot + 1
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end
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end
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return @items[pivot]
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end
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end
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class Wallace::Utility::SortedArray < Array
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def initialize(array = nil)
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super(array.sort) if array != nil
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end
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def set(values)
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end
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# Inserts a value into the array at its correct sorted position.
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def <<(value)
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insert(calculate_index(value), value)
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end
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def push(*values)
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values.each{|v| self << v}
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return self
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end
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# Calculates the correct index to insert the value into the
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# array at.
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#
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# \*TODO:*
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# * This is a rubbish O(n) implementation.
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# | A RB-binary tree or a better insertion sort method should
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# | be implemented.
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def calculate_index(value)
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i = 0
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self.each { |v|
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if v > value
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break
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end
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i += 1
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}
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return i
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end
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end
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data/lib/wallace.rb
ADDED
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module Wallace; end
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# Load Peach if we're using JRuby.
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require 'peach' if defined?(RUBY_VERSION) and RUBY_ENGINE == 'jruby'
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# Load all monkey patches.
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require_relative 'patches/init.rb'
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# Load core files.
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require_relative 'core/state.rb'
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require_relative 'core/analyser.rb'
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require_relative 'core/operator.rb'
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require_relative 'core/selector.rb'
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require_relative 'core/fitness.rb'
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require_relative 'core/evaluator.rb'
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require_relative 'core/species.rb'
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require_relative 'core/breeder.rb'
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require_relative 'core/migrator.rb'
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require_relative 'core/termination.rb'
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require_relative 'core/population.rb'
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require_relative 'core/subpopulation.rb'
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require_relative 'core/evolver.rb'
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require_relative 'core/individual.rb'
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require_relative 'core/fraction.rb'
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require_relative 'core/exceptions.rb'
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require_relative 'core/breeding_graph.rb'
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require_relative 'core/breeding_graph/init.rb'
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# Load all default selectors, species, etc.
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require_relative 'distributions/init.rb'
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require_relative 'selectors/init.rb'
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require_relative 'species/init.rb'
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require_relative 'operators/init.rb'
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require_relative 'fitness/init.rb'
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# Load all modules.
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require_relative 'modules/init.rb'
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# Load utilities.
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require_relative 'utility/init.rb'
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data/test/.gitkeep
ADDED
File without changes
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metadata
ADDED
@@ -0,0 +1,248 @@
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--- !ruby/object:Gem::Specification
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name: wallace
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version: !ruby/object:Gem::Version
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version: 0.0.0
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prerelease:
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platform: ruby
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authors:
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- Chris Timperley
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2013-12-12 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: peach
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.8.7
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.8.7
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
51
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- - ! '>='
|
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- !ruby/object:Gem::Version
|
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version: '0'
|
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
|
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none: false
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requirements:
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: rdoc
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requirement: !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
|
70
|
+
type: :development
|
71
|
+
prerelease: false
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
73
|
+
none: false
|
74
|
+
requirements:
|
75
|
+
- - ! '>='
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: '0'
|
78
|
+
- !ruby/object:Gem::Dependency
|
79
|
+
name: bundler
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
81
|
+
none: false
|
82
|
+
requirements:
|
83
|
+
- - ! '>='
|
84
|
+
- !ruby/object:Gem::Version
|
85
|
+
version: '0'
|
86
|
+
type: :development
|
87
|
+
prerelease: false
|
88
|
+
version_requirements: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
90
|
+
requirements:
|
91
|
+
- - ! '>='
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: '0'
|
94
|
+
- !ruby/object:Gem::Dependency
|
95
|
+
name: peach
|
96
|
+
requirement: !ruby/object:Gem::Requirement
|
97
|
+
none: false
|
98
|
+
requirements:
|
99
|
+
- - ~>
|
100
|
+
- !ruby/object:Gem::Version
|
101
|
+
version: 0.5.1
|
102
|
+
type: :runtime
|
103
|
+
prerelease: false
|
104
|
+
version_requirements: !ruby/object:Gem::Requirement
|
105
|
+
none: false
|
106
|
+
requirements:
|
107
|
+
- - ~>
|
108
|
+
- !ruby/object:Gem::Version
|
109
|
+
version: 0.5.1
|
110
|
+
description: ! " Wallace is a powerful, flexible and modular toolkit for running
|
111
|
+
Evolutionary Algorithms in Ruby.\n Out of the box it provides support for steady-state
|
112
|
+
EAs, genetic algorithms, genetic programming,\n grammatical evolution and other
|
113
|
+
types of EAs.\n"
|
114
|
+
email: christimperley@gmail.com
|
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|
+
executables:
|
116
|
+
- .gitkeep
|
117
|
+
extensions: []
|
118
|
+
extra_rdoc_files:
|
119
|
+
- README.md
|
120
|
+
files:
|
121
|
+
- Gemfile
|
122
|
+
- README.md
|
123
|
+
- Rakefile
|
124
|
+
- VERSION
|
125
|
+
- bin/.gitkeep
|
126
|
+
- lib/analysers/fitness_distribution_analyser.rb
|
127
|
+
- lib/analysers/init.rb
|
128
|
+
- lib/core/analyser.rb
|
129
|
+
- lib/core/breeder.rb
|
130
|
+
- lib/core/breeding_graph.rb
|
131
|
+
- lib/core/breeding_graph/init.rb
|
132
|
+
- lib/core/breeding_graph/input_node.rb
|
133
|
+
- lib/core/breeding_graph/node.rb
|
134
|
+
- lib/core/breeding_graph/node_input.rb
|
135
|
+
- lib/core/evaluator.rb
|
136
|
+
- lib/core/evolver.rb
|
137
|
+
- lib/core/exceptions.rb
|
138
|
+
- lib/core/experiment.rb
|
139
|
+
- lib/core/fitness.rb
|
140
|
+
- lib/core/fraction.rb
|
141
|
+
- lib/core/individual.rb
|
142
|
+
- lib/core/logger.rb
|
143
|
+
- lib/core/migrator.rb
|
144
|
+
- lib/core/operator.rb
|
145
|
+
- lib/core/population.rb
|
146
|
+
- lib/core/selector.rb
|
147
|
+
- lib/core/species.rb
|
148
|
+
- lib/core/state.rb
|
149
|
+
- lib/core/subpopulation.rb
|
150
|
+
- lib/core/termination.rb
|
151
|
+
- lib/distributions/gaussian_distribution.rb
|
152
|
+
- lib/distributions/init.rb
|
153
|
+
- lib/fitness/init.rb
|
154
|
+
- lib/fitness/raw_fitness.rb
|
155
|
+
- lib/loggers/csv_logger.rb
|
156
|
+
- lib/loggers/init.rb
|
157
|
+
- lib/loggers/mongo_logger.rb
|
158
|
+
- lib/loggers/sqlite_logger.rb
|
159
|
+
- lib/modules/ge/backus_naur_form.rb
|
160
|
+
- lib/modules/ge/grammar_derivation.rb
|
161
|
+
- lib/modules/ge/grammar_species.rb
|
162
|
+
- lib/modules/ge/init.rb
|
163
|
+
- lib/modules/init.rb
|
164
|
+
- lib/modules/koza/builder.rb
|
165
|
+
- lib/modules/koza/builder/full_builder.rb
|
166
|
+
- lib/modules/koza/builder/grow_builder.rb
|
167
|
+
- lib/modules/koza/builder/half_builder.rb
|
168
|
+
- lib/modules/koza/builder/init.rb
|
169
|
+
- lib/modules/koza/ephemeral.rb
|
170
|
+
- lib/modules/koza/init.rb
|
171
|
+
- lib/modules/koza/koza_node.rb
|
172
|
+
- lib/modules/koza/koza_node_value.rb
|
173
|
+
- lib/modules/koza/koza_node_value_set.rb
|
174
|
+
- lib/modules/koza/koza_species.rb
|
175
|
+
- lib/modules/koza/koza_tree.rb
|
176
|
+
- lib/modules/koza/operators/init.rb
|
177
|
+
- lib/modules/koza/operators/subtree_crossover_operation.rb
|
178
|
+
- lib/modules/koza/operators/subtree_mutation_operation.rb
|
179
|
+
- lib/operators/bit_flip_mutation_operation.rb
|
180
|
+
- lib/operators/boundary_mutation_operation.rb
|
181
|
+
- lib/operators/cycle_crossover_operation.rb
|
182
|
+
- lib/operators/gaussian_mutation_operation.rb
|
183
|
+
- lib/operators/half_uniform_crossover_operation.rb
|
184
|
+
- lib/operators/init.rb
|
185
|
+
- lib/operators/merging_crossover_operation.rb
|
186
|
+
- lib/operators/one_point_crossover_operation.rb
|
187
|
+
- lib/operators/order_crossover_operation.rb
|
188
|
+
- lib/operators/partially_mapped_crossover_operation.rb
|
189
|
+
- lib/operators/point_mutation_operation.rb
|
190
|
+
- lib/operators/position_crossover_operation.rb
|
191
|
+
- lib/operators/reverse_sequence_mutation_operation.rb
|
192
|
+
- lib/operators/shuffle_mutation_operation.rb
|
193
|
+
- lib/operators/splice_crossover_operation.rb
|
194
|
+
- lib/operators/subtour_exchange_crossover_operation.rb
|
195
|
+
- lib/operators/swap_mutation_operation.rb
|
196
|
+
- lib/operators/three_parent_crossover_operation.rb
|
197
|
+
- lib/operators/two_point_crossover_operation.rb
|
198
|
+
- lib/operators/twors_mutation_operation.rb
|
199
|
+
- lib/operators/uniform_crossover_operation.rb
|
200
|
+
- lib/operators/uniform_mutation_operation.rb
|
201
|
+
- lib/operators/variable_one_point_crossover_operation.rb
|
202
|
+
- lib/patches/enumerable.rb
|
203
|
+
- lib/patches/init.rb
|
204
|
+
- lib/patches/range.rb
|
205
|
+
- lib/selectors/init.rb
|
206
|
+
- lib/selectors/random_selector.rb
|
207
|
+
- lib/selectors/roulette_selector.rb
|
208
|
+
- lib/selectors/tournament_selector.rb
|
209
|
+
- lib/species/array_species.rb
|
210
|
+
- lib/species/bit_string_species.rb
|
211
|
+
- lib/species/init.rb
|
212
|
+
- lib/species/permutation_species.rb
|
213
|
+
- lib/species/string_species.rb
|
214
|
+
- lib/utility/init.rb
|
215
|
+
- lib/utility/scaled_array.rb
|
216
|
+
- lib/utility/sorted_array.rb
|
217
|
+
- lib/wallace.rb
|
218
|
+
- test/.gitkeep
|
219
|
+
homepage: http://github.com/ChrisTimperley/Wallace.rb
|
220
|
+
licenses:
|
221
|
+
- MIT
|
222
|
+
post_install_message:
|
223
|
+
rdoc_options: []
|
224
|
+
require_paths:
|
225
|
+
- lib
|
226
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
227
|
+
none: false
|
228
|
+
requirements:
|
229
|
+
- - ! '>='
|
230
|
+
- !ruby/object:Gem::Version
|
231
|
+
version: '0'
|
232
|
+
segments:
|
233
|
+
- 0
|
234
|
+
hash: -521889391
|
235
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
236
|
+
none: false
|
237
|
+
requirements:
|
238
|
+
- - ! '>='
|
239
|
+
- !ruby/object:Gem::Version
|
240
|
+
version: '0'
|
241
|
+
requirements: []
|
242
|
+
rubyforge_project:
|
243
|
+
rubygems_version: 1.8.28
|
244
|
+
signing_key:
|
245
|
+
specification_version: 3
|
246
|
+
summary: A powerful, flexible and modular toolkit for running Evolutionary Algorithms
|
247
|
+
in Ruby
|
248
|
+
test_files: []
|