mpath_graph 0.0.1
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- checksums.yaml +15 -0
- data/.gitignore +17 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +1 -0
- data/lib/mpath_graph/version.rb +3 -0
- data/lib/mpath_graph.rb +194 -0
- data/mpath_graph.gemspec +24 -0
- metadata +94 -0
checksums.yaml
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data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2014 Israel Buitron
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# MpathGraph
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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gem 'mpath_graph'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install mpath_graph
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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require "bundler/gem_tasks"
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data/lib/mpath_graph.rb
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require "mpath_graph/version"
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require 'ruby-progressbar'
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require 'csv'
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require 'json'
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module MPathGraph
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# Given a set of edges, checks if there is an edged that relates
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# two vertices of a graph.
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#
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# @param i [Integer] Vertex i in a graph.
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# @param j [Integer] Vertex j in a graph.
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# @param edges [Array<Array<Integer>>] Set of edges of a graph.
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#
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# @return [Boolean]
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def self.is_edge?(i, j, edges)
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edges.include?([i,j]) || edges.include?([j,i])
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end
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# Given a cycle checks if it has induced cycles.
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#
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# @param worm [Array<Integer>] Sequence of vertices.
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# @param edges [Array<Array<Integer>>] Set of edges.
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#
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# @return [Boolean]
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def self.has_cycles?(worm, edges, options = {})
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if is_edge? worm[0], worm[-1], edges
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# Check edges
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(0..worm.length-2).each do |i|
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(i+2..worm.length-1).each do |j|
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unless i==0 && j==worm.length-1 # Avoid check endpoints
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if is_edge? worm[i], worm[j], edges
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if options[:verbose] # Verbose cycle
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puts "Cycle\t#{worm[i]},#{worm[j]}"
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end
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return true
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end
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end
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end
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end
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end
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false
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end
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def self.find_cycles(worm, edges)
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if is_edge? worm[0], worm[-1], edges
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# Check edges
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(0..worm.length-2).each do |i|
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(i+2..worm.length-1).each do |j|
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unless i==0 && j==worm.length-1 # Avoid check endpoints
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return [worm[i],worm[j]] if is_edge? worm[i], worm[j], edges
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end
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end
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end
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end
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nil
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end
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def self.random_walk(edges, options = {})
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worm = []
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neighbors = nil
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steps_walked = 0
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initial = options[:initial_vertex] || 0
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worm_size = options[:worm_size] || 5
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walk_limit = options[:walk_limit] || -1
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pause = options[:pause] || false
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induced_cycles_limit = options[:induced_cycles_limit] || -1
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# Initialize worm with initial vertex
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worm << initial
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# Initialize pseudo-random number generator
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prng = Random.new
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# Flush csv row headers to STDIN
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puts ["k-path","Induced cycle","Steps walked"].to_csv
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# Fill worm
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while worm.size < worm_size
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# Find neighbors of last vertex
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neighbors = find_neighbors(worm.last, edges) unless neighbors
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rnd_idx = prng.rand(neighbors.size) # Compute random index
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# Avoid cycles in worm
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if worm.include?(neighbors[rnd_idx])
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# Delete non-valid neighbors for current last vertex
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neighbors.delete(neighbors[rnd_idx])
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# Useless last vertex in worm, drop it!
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if neighbors.empty?
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worm.pop # Drop last vertex
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neighbors = nil # Clean neighbors
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end
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else
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worm << neighbors[rnd_idx] # Append vertex
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neighbors = nil # Clean neighbors
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if worm.size == worm_size # When worm is full
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steps_walked += 1 # Increment worm steps walked
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# Output well-formed worm
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# puts "Checking\t#{worm.inspect}"
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csv_row = [worm]
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# if has_cycles?(worm, edges, verbose: options[:verbose])
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if (cycle = find_cycles(worm, edges))
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csv_row << cycle
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csv_row << steps_walked
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# if options[:verbose] # Verbose worm with cycle
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# puts "Worm\t#{worm.inspect}"
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# puts "Steps walked\t#{steps_walked}"
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# end
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# Pause when verbose
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# if pause
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# STDERR.puts "Press a key to continue..."
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# STDIN.getc
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# end
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# Check induced cycles counter limit
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return if induced_cycles_limit==0
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induced_cycles_limit-=1
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else
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csv_row << nil
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csv_row << steps_walked
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end
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# Flush csv row data to STDIN
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puts csv_row.to_csv
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worm.shift # Drop first vertex in worm (as queue)
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break if steps_walked > walk_limit && walk_limit > 0 # Stop walking
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end
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end
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end
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end
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def self.find_neighbors(vertex, edges)
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neighbors = []
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edges.each do |e|
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if vertex == e[0]
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neighbors << e[1]
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elsif vertex == e[1]
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neighbors << e[0]
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end
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end
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neighbors
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end
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# Given a set of paths it computes a graphs of paths.
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# For each path in set, it compares with all other paths in set
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# and if both share inner then there is an edge that
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# links these vertices.
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#
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# This method is recommended for big _paths_ arrays because it
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# flush to outputstream instead of keep them in memory which is
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# very space-expensive.
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#
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# @param paths [Array<Array<Integer>>] Set of paths.
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# @param output_stream Outputstream.
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# @param options [Hash] Options map.
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def self.compute_paths_graph(paths, output_stream, options = {})
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len = paths.size - 1
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(0..len).each do |i|
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(i+1..len).each do |j|
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unless (paths[i][1...-1] & paths[j]).empty?
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output_stream << [i,j]
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next
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end
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end
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options[:progress_bar].increment unless options[:progress_bar].nil?
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end
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end
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def self.from_csv(file)
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pbar = ProgressBar.create(
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title: "Reading paths graph",
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starting_at: 1,
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total: nil)
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paths = []
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CSV.foreach(file) do |row|
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paths << JSON.parse(row[0])
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pbar.increment
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end
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paths
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end
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end
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data/mpath_graph.gemspec
ADDED
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'mpath_graph/version'
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Gem::Specification.new do |spec|
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spec.name = "mpath_graph"
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spec.version = MPathGraph::VERSION
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spec.authors = ["Israel Buitron"]
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spec.email = ["ibuitron@computacion.cs.cinvestav.mx"]
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spec.description = %q{m-Path graphs library}
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spec.summary = %q{m-Path graphs library}
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spec.homepage = ""
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spec.license = "MIT"
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spec.files = `git ls-files`.split($/)
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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spec.add_development_dependency "bundler", "~> 1.3"
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spec.add_development_dependency "rake"
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spec.add_development_dependency "rspec"
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end
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metadata
ADDED
@@ -0,0 +1,94 @@
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1
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--- !ruby/object:Gem::Specification
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name: mpath_graph
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version: !ruby/object:Gem::Version
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version: 0.0.1
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platform: ruby
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authors:
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- Israel Buitron
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-07-03 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
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- - ~>
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- !ruby/object:Gem::Version
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version: '1.3'
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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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requirements:
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- - ~>
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- !ruby/object:Gem::Version
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version: '1.3'
|
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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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requirements:
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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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requirements:
|
38
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- - ! '>='
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- !ruby/object:Gem::Version
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version: '0'
|
41
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: !ruby/object:Gem::Requirement
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requirements:
|
45
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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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requirements:
|
52
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- - ! '>='
|
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- !ruby/object:Gem::Version
|
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version: '0'
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description: m-Path graphs library
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email:
|
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- ibuitron@computacion.cs.cinvestav.mx
|
58
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executables: []
|
59
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extensions: []
|
60
|
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extra_rdoc_files: []
|
61
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files:
|
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- .gitignore
|
63
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- Gemfile
|
64
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+
- LICENSE.txt
|
65
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- README.md
|
66
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+
- Rakefile
|
67
|
+
- lib/mpath_graph.rb
|
68
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+
- lib/mpath_graph/version.rb
|
69
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- mpath_graph.gemspec
|
70
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homepage: ''
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71
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licenses:
|
72
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- MIT
|
73
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+
metadata: {}
|
74
|
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post_install_message:
|
75
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rdoc_options: []
|
76
|
+
require_paths:
|
77
|
+
- lib
|
78
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ! '>='
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '0'
|
83
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
84
|
+
requirements:
|
85
|
+
- - ! '>='
|
86
|
+
- !ruby/object:Gem::Version
|
87
|
+
version: '0'
|
88
|
+
requirements: []
|
89
|
+
rubyforge_project:
|
90
|
+
rubygems_version: 2.3.0
|
91
|
+
signing_key:
|
92
|
+
specification_version: 4
|
93
|
+
summary: m-Path graphs library
|
94
|
+
test_files: []
|