mpath_graph 0.0.1

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data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in mpath_graph.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 Israel Buitron
+
+MIT License
+
+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

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+# MpathGraph
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'mpath_graph'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install mpath_graph
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/mpath_graph/version.rb

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+module MPathGraph
+  VERSION = "0.0.1"
+end

data/lib/mpath_graph.rb

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+require "mpath_graph/version"
+require 'ruby-progressbar'
+require 'csv'
+require 'json'
+
+module MPathGraph
+  # Given a set of edges, checks if there is an edged that relates
+  # two vertices of a graph.
+  # 
+  # @param i [Integer] Vertex i in a graph.
+  # @param j [Integer] Vertex j in a graph.
+  # @param edges [Array<Array<Integer>>] Set of edges of a graph.
+  # 
+  # @return [Boolean]
+  def self.is_edge?(i, j, edges)
+    edges.include?([i,j]) || edges.include?([j,i])
+  end
+
+  # Given a cycle checks if it has induced cycles.
+  # 
+  # @param worm [Array<Integer>] Sequence of vertices.
+  # @param edges [Array<Array<Integer>>] Set of edges.
+  # 
+  # @return [Boolean]
+  def self.has_cycles?(worm, edges, options = {})
+    if is_edge? worm[0], worm[-1], edges
+      # Check edges
+      (0..worm.length-2).each do |i|
+        (i+2..worm.length-1).each do |j|
+          unless i==0 && j==worm.length-1 # Avoid check endpoints
+            if is_edge? worm[i], worm[j], edges
+              if options[:verbose] # Verbose cycle
+                puts "Cycle\t#{worm[i]},#{worm[j]}"
+              end
+
+              return true 
+            end
+          end
+        end
+      end
+    end
+    false
+  end
+
+  def self.find_cycles(worm, edges)
+    if is_edge? worm[0], worm[-1], edges
+      # Check edges
+      (0..worm.length-2).each do |i|
+        (i+2..worm.length-1).each do |j|
+          unless i==0 && j==worm.length-1 # Avoid check endpoints
+            return [worm[i],worm[j]] if is_edge? worm[i], worm[j], edges
+          end
+        end
+      end
+    end
+    nil
+  end
+
+  def self.random_walk(edges, options = {})
+    worm         = []
+    neighbors    = nil
+    steps_walked = 0
+    initial      = options[:initial_vertex] || 0
+    worm_size    = options[:worm_size]      || 5
+    walk_limit   = options[:walk_limit]     || -1
+    pause        = options[:pause]          || false
+    induced_cycles_limit = options[:induced_cycles_limit]     || -1
+
+    # Initialize worm with initial vertex
+    worm << initial
+
+    # Initialize pseudo-random number generator
+    prng = Random.new
+
+    # Flush csv row headers to STDIN 
+    puts ["k-path","Induced cycle","Steps walked"].to_csv
+
+    # Fill worm
+    while worm.size < worm_size
+      # Find neighbors of last vertex
+      neighbors = find_neighbors(worm.last, edges) unless neighbors
+
+      rnd_idx = prng.rand(neighbors.size) # Compute random index
+
+      # Avoid cycles in worm
+      if worm.include?(neighbors[rnd_idx])
+        # Delete non-valid neighbors for current last vertex
+        neighbors.delete(neighbors[rnd_idx])
+
+        # Useless last vertex in worm, drop it!
+        if neighbors.empty?
+          worm.pop          # Drop last vertex
+          neighbors = nil   # Clean neighbors
+        end
+      else
+        worm << neighbors[rnd_idx]  # Append vertex
+        neighbors = nil             # Clean neighbors
+
+        if worm.size == worm_size # When worm is full
+          steps_walked += 1       # Increment worm steps walked
+
+          # Output well-formed worm
+          # puts "Checking\t#{worm.inspect}"
+          csv_row = [worm]
+
+          # if has_cycles?(worm, edges, verbose: options[:verbose])
+          if (cycle = find_cycles(worm, edges))
+            csv_row << cycle
+            csv_row << steps_walked
+
+            # if options[:verbose]           # Verbose worm with cycle
+            #   puts "Worm\t#{worm.inspect}"
+            #   puts "Steps walked\t#{steps_walked}"
+            # end
+
+            # Pause when verbose
+            # if pause
+            #   STDERR.puts "Press a key to continue..."
+            #   STDIN.getc
+            # end
+
+            # Check induced cycles counter limit
+            return if induced_cycles_limit==0
+            induced_cycles_limit-=1
+          else
+            csv_row << nil
+            csv_row << steps_walked
+          end
+
+          # Flush csv row data to STDIN 
+          puts csv_row.to_csv
+
+          worm.shift              # Drop first vertex in worm (as queue)
+          break if steps_walked > walk_limit && walk_limit > 0 # Stop walking
+        end
+      end
+    end
+  end
+
+  def self.find_neighbors(vertex, edges)
+    neighbors = []
+
+    edges.each do |e|
+      if vertex == e[0]
+        neighbors << e[1]
+      elsif vertex == e[1]
+        neighbors << e[0]
+      end
+    end
+
+    neighbors
+  end
+
+  # Given a set of paths it computes a graphs of paths.
+  # For each path in set, it compares with all other paths in set
+  # and if both share inner then there is an edge that
+  # links these vertices.
+  # 
+  # This method is recommended for big _paths_ arrays because it
+  # flush to outputstream instead of keep them in memory which is
+  # very space-expensive.
+  # 
+  # @param paths [Array<Array<Integer>>] Set of paths.
+  # @param output_stream Outputstream.
+  # @param options [Hash] Options map.
+  def self.compute_paths_graph(paths, output_stream, options = {})
+    len = paths.size - 1
+
+    (0..len).each do |i|
+      (i+1..len).each do |j|
+        unless (paths[i][1...-1] & paths[j]).empty?
+          output_stream << [i,j]
+          next
+        end
+      end
+      options[:progress_bar].increment unless options[:progress_bar].nil?
+    end
+  end
+
+  def self.from_csv(file)
+    pbar = ProgressBar.create(
+      title: "Reading paths graph",
+      starting_at: 1,
+      total: nil)
+
+    paths = []
+    CSV.foreach(file) do |row|
+      paths << JSON.parse(row[0])
+      pbar.increment
+    end
+    
+    paths
+  end
+end

data/mpath_graph.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'mpath_graph/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "mpath_graph"
+  spec.version       = MPathGraph::VERSION
+  spec.authors       = ["Israel Buitron"]
+  spec.email         = ["ibuitron@computacion.cs.cinvestav.mx"]
+  spec.description   = %q{m-Path graphs library}
+  spec.summary       = %q{m-Path graphs library}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: mpath_graph
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Israel Buitron
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-07-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: m-Path graphs library
+email:
+- ibuitron@computacion.cs.cinvestav.mx
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/mpath_graph.rb
+- lib/mpath_graph/version.rb
+- mpath_graph.gemspec
+homepage: ''
+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: 2.3.0
+signing_key: 
+specification_version: 4
+summary: m-Path graphs library
+test_files: []