gemnetic 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA256:
+  metadata.gz: b1837e2240b7ecfbf7b6955a0fb1d98a53d27b74a1d837a10dfa0df9a02cc2b3
+  data.tar.gz: bf81ab58db6e1b1fd4d27a004fb77d93ee1126b1770d9835bd7b82e576c352e2
+SHA512:
+  metadata.gz: e148b2e925f9395b653cabb4a903166958c21733d8a1dfd0297e5d04f8ea8d55e3e5b99bb3f2ed3ea0c4d9f45d2f76aab56bb4ba4d5d466ee48ae92908de2039
+  data.tar.gz: cc6b949879d33e433046cedc581ec948c6aee074338499155353cb0c866135bb4d6329a65f9a8c2471e657200ecfd3e005af33ba88e0940d266debf2210a0e03

data/.gitignore

@@ -0,0 +1,11 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

@@ -0,0 +1,3 @@
+--format documentation
+--color
+--require spec_helper

data/.travis.yml

@@ -0,0 +1,7 @@
+---
+sudo: false
+language: ruby
+cache: bundler
+rvm:
+  - 2.5.1
+before_install: gem install bundler -v 1.16.6

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at canedo@webgoal.com.br. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

@@ -0,0 +1,6 @@
+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in gemnetic.gemspec
+gemspec

data/Gemfile.lock

@@ -0,0 +1,35 @@
+PATH
+  remote: .
+  specs:
+    gemnetic (0.1.0)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    diff-lcs (1.3)
+    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)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  gemnetic!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.17.2

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2018 Canedo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

@@ -0,0 +1,43 @@
+# Gemnetic
+
+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/gemnetic`. 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 'gemnetic'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install gemnetic
+
+## Usage
+
+See the example [here](https://github.com/gknedo/gemnetic/blob/master/example/run.rb).
+
+## 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/gknedo/gemnetic. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+
+## Code of Conduct
+
+Everyone interacting in the Gemnetic project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/gknedo/gemnetic/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

@@ -0,0 +1,6 @@
+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "gemnetic"
+
+# 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

@@ -0,0 +1,8 @@
+#!/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/bin/spec

@@ -0,0 +1,6 @@
+docker-compose run ruby26 rspec
+docker-compose run ruby25 rspec
+docker-compose run ruby24 rspec
+docker-compose run ruby23 rspec
+docker-compose run ruby22 rspec
+docker-compose run ruby21 rspec

data/docker-compose.yml

@@ -0,0 +1,33 @@
+version: '3.7'
+volumes:
+  gems:
+services:
+  gem: &gem
+    image: ruby:latest
+    working_dir: /opt/app
+    volumes:
+      - gems:/usr/local/bundle
+      - .:/opt/app
+  ruby26:
+    <<: *gem
+    image: ruby:2.6-rc
+
+  ruby25:
+    <<: *gem
+    image: ruby:2.5
+
+  ruby24:
+    <<: *gem
+    image: ruby:2.4
+
+  ruby23:
+    <<: *gem
+    image: ruby:2.3
+
+  ruby22:
+    <<: *gem
+    image: ruby:2.2
+
+  ruby21:
+    <<: *gem
+    image: ruby:2.1

data/example/geo.rb

@@ -0,0 +1,37 @@
+class Geo
+  CITIES = [
+    "SP",
+    "RJ",
+    "DF",
+    "BA",
+    "CE",
+    "MG",
+    "AM",
+    "PR",
+    "PE",
+    "RS"
+  ]
+
+  DISTANCES = [
+    [0,   429,  1015, 1962, 3127, 586,  3971, 408,  2660, 1109],
+    [-1,  0,    1148, 1209, 2805, 434,  4374, 852,  2338, 1553],
+    [-1,  -1,   0,    1060, 1687, 716,  1932, 1081, 1657, 1619],
+    [-1,  -1,   -1,   0,    1028, 1372, 5009, 2385, 839,  3090],
+    [-1,  -1,   -1,   -1,   0,    1893, 5763, 2670, 800,  4242],
+    [-1,  -1,   -1,   -1,   -1,   0,    3951, 1004, 2061, 1712],
+    [-1,  -1,   -1,   -1,   -1,   -1,   0,    2734, 5698, 4563],
+    [-1,  -1,   -1,   -1,   -1,   -1,   -1,   0,    3078, 711],
+    [-1,  -1,   -1,   -1,   -1,   -1,   -1,   -1,   0,    2977],
+    [-1,  -1,   -1,   -1,   -1,   -1,   -1,   -1,   -1,   0]
+  ]
+
+  def self.get_distance(index_a, index_b)
+    distance = DISTANCES[index_a][index_b]
+    return get_distance(index_b, index_a) if distance < 0
+    distance
+  end
+
+  def self.get_name(index)
+    return CITIES[index]
+  end
+end

data/example/my_specimen.rb

@@ -0,0 +1,44 @@
+require 'gemnetic'
+require_relative 'geo'
+
+class MySpecimen < Gemnetic::Specimen
+
+  def evaluate
+    (0..9).map do |index|
+      next_index = (index+1) % 10
+      distance = Geo.get_distance(@gens[index], @gens[next_index])
+    end.sum * -1
+  end
+
+  def mutate
+    swap(rand(0..9), rand(0..9))
+    self
+  end
+
+  def randomize
+    (0..9).to_a.sample(10)
+  end
+
+  def crossover specimen
+    new_gens = []
+    self_enumerator = 0
+    specimen_enumerator = 0
+    crossover_probability = rand
+    while new_gens.count < 10
+      from_specimen = rand < crossover_probability
+      gen = from_specimen ? specimen.gens[specimen_enumerator] : @gens[self_enumerator]
+      next unless gen
+      new_gens.push(gen) unless new_gens.include?(gen)
+      self_enumerator = (self_enumerator + 1) % 10 unless from_specimen
+      specimen_enumerator = (specimen_enumerator + 1) % 10 if from_specimen
+    end
+    @gens = new_gens
+    self
+  end
+
+  private
+
+  def swap index_a, index_b
+    @gens[index_a], @gens[index_b] = @gens[index_b], @gens[index_a]
+  end
+end

data/example/run.rb

@@ -0,0 +1,13 @@
+require 'gemnetic'
+require_relative 'my_specimen'
+
+world = Gemnetic::World.new(MySpecimen)
+150.times do
+  p "GEN: #{world.current_generation} "
+  p world.population_to_keep.map{|specimen| specimen.evaluate}
+  world.next_generation
+end
+
+p world.population_to_keep.map{ |specimen| specimen.gens }
+p world.best_specimen
+p world.best_specimen.evaluate

data/gemnetic.gemspec

@@ -0,0 +1,28 @@
+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "gemnetic/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "gemnetic"
+  spec.version       = Gemnetic::VERSION
+  spec.authors       = ["Canedo"]
+  spec.email         = ["canedo@webgoal.com.br"]
+
+  spec.summary       = "A genetic algorithm implementation"
+  spec.homepage      = "https://github.com/gknedo/gemnetic"
+  spec.license       = "MIT"
+
+  # 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('..', __FILE__)) 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", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/lib/gemnetic.rb

@@ -0,0 +1,6 @@
+require "gemnetic/version"
+require "gemnetic/world"
+require "gemnetic/specimen"
+
+module Gemnetic
+end

data/lib/gemnetic/specimen.rb

@@ -0,0 +1,41 @@
+module Gemnetic
+  class Specimen
+    attr_accessor :gens
+
+    def initialize(params = {})
+      @gens = params.fetch(:gens, randomize)
+    end
+
+    def crossover specimen
+      raise NotImplementedError, "You must override the crossover method to crossover two specimens in a new one"
+    end
+
+    def mutate
+      raise NotImplementedError, "You must override the mutate method to generate a new specimen based current specimen"
+    end
+
+    def evaluate
+      raise NotImplementedError, "You must override the evaluate method to calculate the fitness of the specimen"
+    end
+
+    def randomize
+      raise NotImplementedError, "You must override the randomize method to randomize the gens of the specimen"
+    end
+
+    def battle specimen
+      return self unless self.evaluate < specimen.evaluate
+      specimen
+    end
+
+    def dup
+      self.class.new(gens: @gens.dup)
+    end
+
+    def to_s
+      {
+        evaluation: evaluate,
+        gens: @gens
+      }.to_s
+    end
+  end
+end

data/lib/gemnetic/version.rb

@@ -0,0 +1,3 @@
+module Gemnetic
+  VERSION = "0.1.0"
+end

data/lib/gemnetic/world.rb

@@ -0,0 +1,85 @@
+module Gemnetic
+  class World
+    attr_accessor :population_size, :population_keep, :population,
+      :crossover_probability, :mutate_probability, :tournament_probability
+    attr_reader :specimen_class, :current_generation
+
+    def initialize(specimen_class, params = {})
+      @specimen_class = specimen_class
+      @population_size = params.fetch(:population_size, 50)
+      @population_keep = params.fetch(:population_keep, @population_size/10)
+
+      probabilities = [
+        params.fetch(:crossover_probability, 0.4).to_f,
+        params.fetch(:mutate_probability, 0.1).to_f,
+        params.fetch(:tournament_probability, 0.5).to_f
+      ]
+      probabilities_sum = probabilities.sum
+      @crossover_probability = probabilities[0] * probabilities_sum
+      @mutate_probability = probabilities[1] * probabilities_sum
+      @tournament_probability = probabilities[2] * probabilities_sum
+
+      @current_generation = 0
+      @population = []
+
+      validate
+
+      initialize_population if params.fetch(:initialize_population, true)
+    end
+
+    def next_generation
+      new_population = population_to_keep
+      to_create = @population_size - @population_keep
+
+      (to_create*@tournament_probability).to_i.times do
+        new_population.push @population.sample.battle(@population.sample).dup
+      end
+
+      (to_create*@mutate_probability).to_i.times do
+        new_population.push @population.sample.dup.mutate
+      end
+
+      (to_create*@crossover_probability).to_i.times do
+        new_population.push @population.sample.dup.crossover(@population.sample.dup)
+      end
+
+      new_population.uniq! { |specimen| specimen.gens }
+      while new_population.count < @population_size do
+        new_population.push @population.sample.dup.mutate
+        new_population.uniq! { |specimen| specimen.gens }
+      end
+
+      @current_generation += 1
+      @population = new_population
+    end
+
+    def population_to_keep
+      keep = []
+      @population.each do |specimen|
+        next keep.push(specimen) if keep.count < @population_keep
+        keep.sort_by! { |specimen| specimen.evaluate }
+        keep[0] = specimen if specimen.evaluate > keep[0].evaluate
+      end
+
+      keep
+    end
+
+    def best_specimen
+      population_to_keep.last
+    end
+
+    private
+
+    def validate
+      raise ArgumentError.new("Specimen Class can't be nil") unless @specimen_class
+      raise ArgumentError.new("Specimen Class must be a kind of Gemnetic::Specimen") unless @specimen_class.ancestors.include?(Gemnetic::Specimen)
+    end
+
+    def initialize_population
+      @population_size.times do
+        @population.push @specimen_class.new
+      end
+    end
+
+  end
+end

metadata

@@ -0,0 +1,107 @@
+--- !ruby/object:Gem::Specification
+name: gemnetic
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Canedo
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-12-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: 
+email:
+- canedo@webgoal.com.br
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- bin/spec
+- docker-compose.yml
+- example/geo.rb
+- example/my_specimen.rb
+- example/run.rb
+- gemnetic.gemspec
+- lib/gemnetic.rb
+- lib/gemnetic/specimen.rb
+- lib/gemnetic/version.rb
+- lib/gemnetic/world.rb
+homepage: https://github.com/gknedo/gemnetic
+licenses:
+- MIT
+metadata: {}
+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: []
+rubyforge_project: 
+rubygems_version: 2.7.6
+signing_key: 
+specification_version: 4
+summary: A genetic algorithm implementation
+test_files: []