networkx 0.1.0 → 0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 0275c9f6161b6bcf973af9f18a989969ce757bd0
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+  data.tar.gz: 71f71c73039b7b666763268ce87c3780bd9853fb
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data/.rubocop.yml

@@ -8,7 +8,7 @@ AllCops:
     - 'benchmarks/*'
     - 'profile/*'
   DisplayCopNames: true
-  TargetRubyVersion: 2.1
+  TargetRubyVersion: 2.2
 
 # Preferred codebase style ---------------------------------------------
 
@@ -52,9 +52,6 @@ Style/EmptyElse:
 Style/EmptyMethod:
   EnforcedStyle: compact
 
-Style/FileName:
-  Enabled: false
-
 Style/FormatString:
   EnforcedStyle: percent
 
@@ -73,33 +70,43 @@ Style/Documentation:
 ### Metrics ------------------------------------------------------------
 
 Metrics/AbcSize:
-  Max: 20
+  Enabled: true
 
 Metrics/BlockLength:
-  Exclude:
-    - 'spec/**/*'
+  Enabled: true
 
 Metrics/ClassLength:
   Max: 200
 
 Metrics/CyclomaticComplexity:
-  Max: 7
+  Enabled: true
+
+Metrics/PerceivedComplexity:
+  Enabled: true
+
+Metrics/BlockNesting:
+  Enabled: true
 
 Metrics/LineLength:
   Max: 120
 
 Metrics/MethodLength:
-  Max: 15
+  Enabled: true
 
 Metrics/ModuleLength:
-  Max: 200
+  Enabled: true
 
 Style/MultilineBlockChain:
-  Enabled: false
+  Enabled: true
 
 Metrics/ParameterLists:
   Max: 10
 
+### Naming -------------------------------------------------------------
+
+Naming/VariableNumber:
+  EnforcedStyle: snake_case
+
 ### RSpec --------------------------------------------------------------
 
 RSpec/MessageSpies:

data/CONTRIBUTING.md

@@ -14,8 +14,8 @@ Please proceed with a Pull Request only after you're assigned. It'd be sad if yo
 1. Clone this repository and install all the required gem dependencies.
 
     ```sh
-    git clone https://github.com/athityakumar/daru-io.git
-    cd daru-io
+    git clone https://github.com/athityakumar/networkx.rb.git
+    cd networkx.rb
     gem install bundler
     bundle install
     ```

data/Guardfile

@@ -1,7 +1,7 @@
 guard :rspec, cmd: 'rspec' do
   watch(%r{^spec/.+_spec\.rb$})
   watch(%r{^lib/networkx/(.+)\.rb$}) { |m| "spec/#{m[1]}_spec.rb" }
-  watch('spec/spec_helper.rb')   { 'spec' }
+  watch('spec/spec_helper.rb')       { 'spec' }
 end
 
 # TODO: Run Rubocop in the background

data/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+### Description
+
+Thanks for opening this issue. Add a brief description of what this issue is, and how to recreate it. Do tag the relevant issue(s) and PR(s) below. If required, add the stack trace of the error.
+
+- Relevant Issues : (optional)
+- Relevant PRs : (optional)
+- Type of issue :
+  - User mode :
+    - [ ] Installation
+    - [ ] Feature request
+    - [ ] Bug in existing feature
+  - Developer mode :
+    - [ ] Code quality
+    - [ ] Tests
+    - [ ] Documentation

data/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,12 @@
+### Description
+
+Thanks for contributing this Pull Request. Add a brief description of what this Pull Request does. Do tag the relevant issue(s) and PR(s) below. If required, add some screenshot(s) to support your changes.
+
+- Relevant Issues : (required)
+- Relevant PRs : (optional)
+- Type of change :
+  - [ ] New feature
+  - [ ] Bug fix for existing feature
+  - [ ] Code quality improvement
+  - [ ] Addition or Improvement of tests
+  - [ ] Addition or Improvement of documentation

data/README.md

@@ -13,6 +13,8 @@
 
 ### Installing
 
+[(Back to top)](#list-of-contents)
+
 - Clone the repository with `git clone git@github.com:athityakumar/networkx.rb.git`
 - Navigate to networkx with `cd networkx.rb`
 - Install dependencies with `gem install bundler && bundle install`
@@ -30,6 +32,8 @@ g.add_edge('start', 'stop')
 
 ### Roadmap
 
+[(Back to top)](#list-of-contents)
+
 Quite easily, any networkx user would be able to understand the number of details that have been implemented in the Python library. As a humble start towards the release of v0.1.0, the following could be the goals to achieve :
 
 - `Node` : This class should be capable of handling different types of nodes (not just `String` / `Integer`). A possible complex use-case could be XML nodes.
@@ -40,10 +44,6 @@ Quite easily, any networkx user would be able to understand the number of detail
 
 - `DirectedGraph` : Inherits from `Graph` class. Uses directions between `Edge`s.
 
-[(Back to top)](#list-of-contents)
-
-After months of extensive searching, we realised there was not a single repository that could guide a newbie to machine learning and natural language processing in Ruby. Thus, after a series of naming discussions, `sciruby-examples` was born.
-
 ### Contributing
 
 [(Back to top)](#list-of-contents)

data/RELEASE_POLICY.md

@@ -0,0 +1,20 @@
+# RELEASE POLICY
+
+Applicable from networkx v0.0.0 onwards
+
+### Versioning
+
+NetworkX follows semantic versioning whereby the version number is always in the form MAJOR.MINOR.PATCH
+
+- Patch bump : Bug fixes
+- Minor bump : New features (with backwards compatibility)
+- Major bump : API breaking changes
+
+For Major and Minor bumps release candidates should be released around 2 weeks prior to the bump and are indicated by MAJOR.MINOR.0.rc.
+
+For more information see the full semantic versioning specification at http://semver.org/.
+
+### Release Timing
+
+Patch releases should be done after every fix of a major bug (as tagged in the github issue tracker).
+Major releases should be kept to the minimum.

data/lib/networkx.rb

@@ -1 +1,37 @@
-require 'networkx/version'
+require 'set'
+require 'nmatrix'
+require 'rb_heap'
+require 'securerandom'
+require_relative 'networkx/version'
+require_relative 'networkx/graph'
+require_relative 'networkx/digraph'
+require_relative 'networkx/multigraph'
+require_relative 'networkx/multidigraph'
+require_relative 'networkx/traversals/bfs'
+require_relative 'networkx/traversals/dfs'
+require_relative 'networkx/traversals/edge_dfs'
+require_relative 'networkx/shortest_path/unweighted'
+require_relative 'networkx/to_matrix'
+require_relative 'networkx/shortest_path/dense'
+require_relative 'networkx/shortest_path/weighted'
+require_relative 'networkx/shortest_path/astar'
+require_relative 'networkx/operators/product'
+require_relative 'networkx/operators/binary'
+require_relative 'networkx/operators/unary'
+require_relative 'networkx/operators/all'
+require_relative 'networkx/flow/utils'
+require_relative 'networkx/flow/edmondskarp'
+require_relative 'networkx/flow/shortestaugmentingpath'
+require_relative 'networkx/flow/capacityscaling'
+require_relative 'networkx/flow/preflowpush'
+require_relative 'networkx/auxillary_functions/cliques'
+require_relative 'networkx/auxillary_functions/dag'
+require_relative 'networkx/auxillary_functions/eccentricity'
+require_relative 'networkx/auxillary_functions/mis'
+require_relative 'networkx/auxillary_functions/mst'
+require_relative 'networkx/auxillary_functions/union_find'
+require_relative 'networkx/auxillary_functions/vitality'
+require_relative 'networkx/auxillary_functions/wiener'
+require_relative 'networkx/auxillary_functions/cycles'
+require_relative 'networkx/link_analysis/hits'
+require_relative 'networkx/link_analysis/pagerank'

data/lib/networkx/auxillary_functions/cliques.rb

@@ -0,0 +1,65 @@
+module NetworkX
+  # TODO: Reduce method complexity and method length
+
+  # Returns all cliques in the graph
+  #
+  # @param graph [Graph, MultiGraph] a graph
+  #
+  # @return [Array<Array<Object>>] Arrays of nodes in the cliques
+  def self.find_cliques(graph)
+    return nil if graph.nodes.empty?
+    q = [nil]
+    adj = {}
+    graph.nodes.each_key { |u| adj[u] = [] }
+    graph.adj.each { |u, u_edges| u_edges.each_key { |v| adj[u] << v if u != v } }
+
+    subg = graph.nodes.keys
+    cand = graph.nodes.keys
+    u = subg.max { |n_1, n_2| (cand & adj[n_1]).length <=> (cand & adj[n_2]).length }
+    ext_u = cand - adj[u]
+    stack = []
+    cliques = []
+    begin
+      loop do
+        if !ext_u.empty?
+          q_elem = ext_u.pop
+          cand.delete(q_elem)
+          q[-1] = q_elem
+          adj_q = adj[q_elem]
+          subg_q = subg & adj_q
+          if subg_q.empty?
+            cliques << q[0..(q.length - 1)]
+          else
+            cand_q = cand & adj_q
+            unless cand_q.empty?
+              stack << [subg, cand, ext_u]
+              q << nil
+              subg = subg_q
+              cand = cand_q
+              u = subg.max { |n_1, n_2| (cand & adj[n_1]).length <=> (cand & adj[n_2]).length }
+              ext_u = cand - adj[u]
+            end
+          end
+        else
+          q.pop
+          subg, cand, ext_u = stack.pop
+        end
+      end
+    rescue NoMethodError
+      return cliques
+    end
+  end
+
+  # Returns the number of cliques in a graph containing a node
+  #
+  # @param graph [Graph, MultiGraph] a graph
+  # @param node [Object] a node
+  #
+  # @return [Numeric] Number of cliques containing the given node
+  def self.number_of_cliques(graph, node)
+    cliques = find_cliques(graph)
+    num_cliq_arr = []
+    cliques.each { |c| num_cliq_arr << 1 if c.include?(node) }
+    num_cliq_arr.length
+  end
+end

data/lib/networkx/auxillary_functions/cycles.rb

@@ -0,0 +1,104 @@
+module NetworkX
+  # TODO: Reduce method complexity and method length
+
+  # Returns all basis cycles in graph
+  #
+  # @param graph [Graph] a graph
+  # @param root [Object, Nil] root for the graph cycles
+  #
+  # @return [Array<Array<Object>>] Arrays of nodes in the cycles
+  def self.cycle_basis(graph, root=nil)
+    gnodes = graph.nodes.keys
+    cycles = []
+    until gnodes.empty?
+      root = gnodes.shift if root.nil?
+      stack = [root]
+      pred = {root => root}
+      used = {root => []}
+      until stack.empty?
+        z = stack.shift
+        zused = used[z]
+        graph.adj[z].each_key do |u|
+          if !used.key?(u)
+            pred[u] = z
+            stack << u
+            used[u] = [z]
+          elsif u == z
+            cycles << [z]
+          elsif !zused.include?(u)
+            pn = used[u]
+            cycle = [u, z]
+            p = pred[z]
+            until pn.include?(p)
+              cycle << p
+              p = pred[p]
+            end
+            cycle << p
+            cycles << cycle
+            used[u] << z
+            used[u] = used[u].uniq
+          end
+        end
+      end
+      gnodes -= pred.keys
+      root = nil
+    end
+    cycles
+  end
+
+  # TODO: Reduce method complexity and method length
+
+  # Returns the cycle containing the given node
+  #
+  # @param graph [Graph, DiGraph] a graph
+  # @param node [Object] node to be included in the cycle
+  #
+  # @return [Array<Array<Object>>] Arrays of nodes in the cycle
+  def self.find_cycle(graph, node)
+    explored = Set.new
+    cycle = []
+    final_node = nil
+    unless explored.include?(node)
+      edges = []
+      seen = [node]
+      active_nodes = [node]
+      previous_head = nil
+
+      edge_dfs(graph, node).each do |edge|
+        tail, head = edge
+        next if explored.include?(head)
+        if !previous_head.nil? && tail != previous_head
+          loop do
+            popped_edge = edges.pop
+            if popped_edge.nil?
+              edges = []
+              active_nodes = [tail]
+              break
+            else
+              popped_head = popped_edge[1]
+              active_nodes.delete!(popped_head)
+            end
+
+            unless edges.empty?
+              last_head = edges[-1][1]
+              break if tail == last_head
+            end
+          end
+        end
+        edges << edge
+
+        if active_nodes.include?(head)
+          cycle += edges
+          final_node = head
+          break
+        else
+          seen << head
+          active_nodes << head
+          previous_head = head
+        end
+      end
+      cycle.each_with_index { |edge, i| return cycle[i..(cycle.length - 1)] if final_node == edge[0] }
+    end
+    raise ArgumentError, 'No cycle found!' if cycle.empty?
+  end
+end

data/lib/networkx/auxillary_functions/dag.rb

@@ -0,0 +1,54 @@
+module NetworkX
+  # Returns the descendants of a given node
+  #
+  # @param graph [Graph, DiGraph, MultiGraph, MultiDiGraph] a graph
+  # @param source [Object] node to find descendents of
+  #
+  # @return [Array<Object>] Array of the descendants
+  def self.descendants(graph, source)
+    raise ArgumentError, 'Source is not present in the graph!' unless graph.node?(source)
+    des = single_source_shortest_path_length(graph, source).map { |u, _| u }.uniq
+    des - [source]
+  end
+
+  # Returns the ancestors of a given node
+  #
+  # @param graph [Graph, DiGraph, MultiGraph, MultiDiGraph] a graph
+  # @param source [Object] node to find ancestors of
+  #
+  # @return [Array<Object>] Array of the ancestors
+  def self.ancestors(graph, source)
+    raise ArgumentError, 'Source is not present in the graph!' unless graph.node?(source)
+    anc = single_source_shortest_path_length(graph.reverse, source).map { |u, _| u }.uniq
+    anc - [source]
+  end
+
+  # TODO: Reduce method complexity and method length
+
+  # Returns the nodes arranged in the topologically sorted fashion
+  #
+  # @param graph [DiGraph] a graph
+  #
+  # @return [Array<Object>] Array of the nodes
+  def self.topological_sort(graph)
+    raise ArgumentError, 'Topological Sort not defined on undirected graphs!' unless graph.directed?
+    nodes = []
+    indegree_map = Hash[graph.nodes.each_key.map { |u| [u, graph.in_degree(u)] if graph.in_degree(u) > 0 }.compact]
+    zero_indegree = graph.nodes.each_key.map { |u| u if graph.in_degree(u).zero? }.compact
+
+    until zero_indegree.empty?
+      node = zero_indegree.shift
+      raise ArgumentError, 'Graph changed during iteration!' unless graph.nodes.key?(node)
+      graph.adj[node].each_key do |child|
+        indegree_map[child] -= 1
+        if indegree_map[child].zero?
+          zero_indegree << child
+          indegree_map.delete(child)
+        end
+      end
+      nodes << node
+    end
+    raise ArgumentError, 'Graph contains cycle or graph changed during iteration!' unless indegree_map.empty?
+    nodes
+  end
+end