networkx 0.1.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 805b70cf94db86eb3c9e144fe644e6f94f4e664a
-  data.tar.gz: 71f71c73039b7b666763268ce87c3780bd9853fb
+SHA256:
+  metadata.gz: 39e75c0ad21604275a008c53a29f282d681f3c50cb7648470cc6e4e2cffa5071
+  data.tar.gz: 93e93f5a2603beb715b38856518ed47e698c0978c5ff02a737a7baff68357e8c
 SHA512:
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+  data.tar.gz: 9b615db49ec2ba5e06bbfecf1710849d079661b301a85493740434eae464bfd74c250c38c31ed2cc5dfb93983cb2c7315fe27452c2f6a243051ac1f80512816b

data/{CONTRIBUTING.md → .github/CONTRIBUTING.md}

@@ -11,10 +11,10 @@ Please proceed with a Pull Request only after you're assigned. It'd be sad if yo
 
 # Developing the gem
 
-1. Clone this repository and install all the required gem dependencies.
+1. Fork this repository and clone it and install all the required gem dependencies.
 
     ```sh
-    git clone https://github.com/athityakumar/networkx.rb.git
+    git clone https://github.com/`your_github_user_id`/networkx.rb.git
     cd networkx.rb
     gem install bundler
     bundle install
@@ -22,13 +22,9 @@ Please proceed with a Pull Request only after you're assigned. It'd be sad if yo
 
 2. Checkout to a different git branch (say, `adds-new-feature`).
 
-3. Add any gem dependencies required, appropriately to the gemspec file or Gemfile.
+3. Add code (, test, and YARD documentation).
 
-4. Add code and YARD documentation.
-
-5. Add tests to `spec/networkx/filename_spec.rb`. Add any files required for testing in the `spec/fixtures/` directory.
-
-6. Run the rspec test-suite.
+4. Run the rspec test-suite.
     ```sh
     # Runs test suite for all files
     bundle exec rspec
@@ -37,7 +33,7 @@ Please proceed with a Pull Request only after you're assigned. It'd be sad if yo
     bundle exec rspec spec/networkx/filename_spec.rb
     ```
 
-7. Run the rubocop for static code quality comments.
+5. Run the rubocop for static code quality comments.
 
     ```sh
     # Runs rubocop test for all files
@@ -47,4 +43,18 @@ Please proceed with a Pull Request only after you're assigned. It'd be sad if yo
     bundle exec rubocop lib/networkx/filename.rb
     ```
 
-8. Send a Pull Request back to this repository. :tada:
+6. Send a Pull Request back to this repository. :tada:
+
+# Note: YARD Document
+
+You can create YARD documentation
+
+1. Create Document for `doc` directory with `yard` command
+2. Create server via `yard server` command
+3. open Browser with `open http://0.0.0.0:8808` e.t.c.
+
+```
+$ yard
+$ yard server
+$ open http://0.0.0.0:8808   
+```

data/{ISSUE_TEMPLATE.md → .github/ISSUE_TEMPLATE.md}

@@ -12,4 +12,4 @@ Thanks for opening this issue. Add a brief description of what this issue is, an
   - Developer mode :
     - [ ] Code quality
     - [ ] Tests
-    - [ ] Documentation
+    - [ ] Documentation

data/{PULL_REQUEST_TEMPLATE.md → .github/PULL_REQUEST_TEMPLATE.md}

@@ -1,12 +1,10 @@
-### 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 Issues : (optional)
 - 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
+  - [ ] Addition or Improvement of documentation

data/.github/workflows/ci.yml

@@ -0,0 +1,17 @@
+name: test
+on: [push, pull_request]
+jobs:
+  build:
+    name: ${{ matrix.os }} Ruby ${{ matrix.ruby }}
+    runs-on: ${{ matrix.os }}-latest
+    strategy:
+      matrix:
+        os:   [ 'ubuntu', 'macos' ]
+        ruby: [ '2.7', '3.0', '3.1' ]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: ${{ matrix.ruby }}
+          bundler-cache: true
+      - run: bundle exec rspec

data/.github/workflows/doc.yml

@@ -0,0 +1,23 @@
+name: doc
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: 3.1
+      - name: Generate document
+        run: gem install -N yard && yard doc
+      - name: Publish Documentation on GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./doc

data/.rspec

@@ -1,2 +1 @@
---color
 --require spec_helper

data/.rubocop.yml

@@ -1,116 +1,102 @@
-require: rubocop-rspec
-
 AllCops:
+  NewCops: enable
+  TargetRubyVersion: 2.7
   Include:
     - 'lib/**/*'
-  Exclude:
-    - 'vendor/**/*'
-    - 'benchmarks/*'
-    - 'profile/*'
+    - 'spec/**/*_spec.rb'
+    - 'Gemfile'
+    - 'Rakefile'
+    - '*.gemspec'
   DisplayCopNames: true
-  TargetRubyVersion: 2.2
 
-# Preferred codebase style ---------------------------------------------
+require:
+  - rubocop-rspec
+  - rubocop-rake
 
 ### Layouts ------------------------------------------------------------
 
-Layout/AlignParameters:
-  EnforcedStyle: with_fixed_indentation
-
-Layout/ExtraSpacing:
-  AllowForAlignment: true
-
-Layout/SpaceAfterComma:
+Lint/AmbiguousOperatorPrecedence:
   Enabled: false
 
-Layout/SpaceAroundEqualsInParameterDefault:
-  EnforcedStyle: no_space
-
-Layout/SpaceAroundOperators:
+Layout/SpaceBeforeBlockBraces:
   Enabled: false
 
 Layout/SpaceInsideBlockBraces:
-  EnforcedStyle: space
+  Enabled: false
 
 Layout/SpaceInsideHashLiteralBraces:
   EnforcedStyle: no_space
 
-### Styles -------------------------------------------------------------
-
-Style/AndOr:
-  EnforcedStyle: conditionals
+### Metrics ------------------------------------------------------------
 
-Style/DoubleNegation:
+Metrics:
   Enabled: false
 
-Style/EmptyCaseCondition:
+### Naming -------------------------------------------------------------
+
+Naming/MethodParameterName:
   Enabled: false
 
-Style/EmptyElse:
-  EnforcedStyle: empty
+Naming/PredicateName:
+  Enabled: false
 
-Style/EmptyMethod:
-  EnforcedStyle: compact
+### Styles -------------------------------------------------------------
 
-Style/FormatString:
-  EnforcedStyle: percent
+Style/CombinableLoops:
+  Enabled: false # there is case that it can't combined loop.
 
-Style/ParallelAssignment:
-  Enabled: false
-
-Style/SingleLineBlockParams:
+Style/Documentation:
   Enabled: false
 
-Style/PerlBackrefs:
+Style/FrozenStringLiteralComment:
   Enabled: false
 
-Style/Documentation:
-  Enabled: false # TODO
-
-### Metrics ------------------------------------------------------------
+Style/NumericPredicate:
+  Enabled: false # it is easier to read `size > 0` than `size.positive?`
 
-Metrics/AbcSize:
-  Enabled: true
+Style/OptionalBooleanParameter:
+  Enabled: false # it is necessary to change distructively.
 
-Metrics/BlockLength:
-  Enabled: true
+Style/ParallelAssignment:
+  Enabled: false # one line style is compact.
 
-Metrics/ClassLength:
-  Max: 200
+Style/PreferredHashMethods:
+  Enabled: false
 
-Metrics/CyclomaticComplexity:
-  Enabled: true
+Style/SymbolArray:
+  Enabled: false # general array literal is easy to read. no problem.
 
-Metrics/PerceivedComplexity:
-  Enabled: true
+Style/ZeroLengthPredicate:
+  Enabled: false # it is so easy to read `a.size > 0` as `!a.empty?`
 
-Metrics/BlockNesting:
-  Enabled: true
+### RSpec --------------------------------------------------------------
 
-Metrics/LineLength:
-  Max: 120
+RSpec/MessageSpies:
+  EnforcedStyle: receive
 
-Metrics/MethodLength:
-  Enabled: true
+RSpec/DescribedClass:
+  Enabled: false
 
-Metrics/ModuleLength:
-  Enabled: true
+RSpec/ExampleLength:
+  Max: 25
 
-Style/MultilineBlockChain:
-  Enabled: true
+RSpec/FilePath:
+  Enabled: false # too many offense
 
-Metrics/ParameterLists:
-  Max: 10
+RSpec/ImplicitSubject:
+  Enabled: false # too many offenses
 
-### Naming -------------------------------------------------------------
+RSpec/MultipleExpectations:
+  Max: 15
 
-Naming/VariableNumber:
-  EnforcedStyle: snake_case
+RSpec/NestedGroups:
+  Max: 5
 
-### RSpec --------------------------------------------------------------
+RSpec/PredicateMatcher:
+  Enabled: false
 
-RSpec/MessageSpies:
-  EnforcedStyle: receive
+RSpec/RepeatedExampleGroupBody:
+  Enabled: false
 
-RSpec/NestedGroups:
-  Max: 5
+RSpec/RepeatedExampleGroupDescription:
+  Enabled: false # too many offenses

data/.yardopts

@@ -1,2 +1 @@
 --markup markdown
---markup-provider redcarpet

data/README.md

@@ -1,57 +1,55 @@
 # NetworkX.rb
 
-[NetworkX](https://networkx.github.io/) is a very popular Python library, that handles various use-cases of the Graph Data Structure. This project intends to provide a working alternative to the Ruby community, by closely mimicing as many features as possible. 
+[![Gem Version](https://badge.fury.io/rb/networkx.svg)](https://badge.fury.io/rb/networkx)
 
-*This project has begun just now, and a v0.1.0 release with basic Graph classes can be expected by January 2018.*
+[NetworkX](https://networkx.github.io/) is a very popular Python library, that handles various use-cases of the Graph Data Structure.  
+This project intends to provide a working alternative to the Ruby community, by closely mimicing as many features as possible. 
 
-### List of contents
+## List of contents
 
 - [Installing](#installing)
-- [Roadmap](#roadmap)
+- [Usage](#Usage)
+- [Document](#document)
 - [Contributing](#contributing)
 - [License](#license)
 
-### Installing
+## Installing
 
-[(Back to top)](#list-of-contents)
+- install it yourself as:
+```console
+$ gem install networkx
+```
 
-- 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`
-- Install networkx gem with `rake install`
-- Start checking out in PRY / IRB console : 
+
+- Or use Bundler & Gemfile
+  1. add this line to your application's Gemfile:
+  ```ruby
+  gem 'networkx'
+  ```
+  2. And then execute:
+  ```console
+  $ bundle install
+  ```
+
+## Usage
 
 ```ruby
 require 'networkx'
-#=> true
 
-# Yet to be implemented
-g = NetworkX::Graph.new()
+g = NetworkX::Graph.new
 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.
-
-- `Edge` : This class should be capable of handling different types of edges. Though a basic undirected Graph doesn't store any metadata in the edges, weighted edges and parametric edges are something that need to be handled.
-
-- `Graph` : The simplest of graphs. This class handles just connections between different `Node`s via `Edge`s.
-
-- `DirectedGraph` : Inherits from `Graph` class. Uses directions between `Edge`s.
-
-### Contributing
+## Document
 
-[(Back to top)](#list-of-contents)
+You can read [Document](https://SciRuby.github.io/networkx.rb/) for this library.
 
-Your contributions are always welcome! Please have a look at the [contribution guidelines](CONTRIBUTING.md) first. :tada:
+## Contributing
 
-### License
+Your contributions are always welcome!  
+Please have a look at the [contribution guidelines](CONTRIBUTING.md) first. :tada:
 
-[(Back to top)](#list-of-contents)
+## License
 
-The MIT License 2017 - [Athitya Kumar](https://github.com/athityakumar). Please have a look at the [LICENSE.md](LICENSE.md) for more details.
+The MIT License 2017 - [Athitya Kumar](https://github.com/athityakumar).   
+Please have a look at the [LICENSE.md](LICENSE.md) for more details.

data/Rakefile

@@ -1,7 +1,6 @@
-require 'bundler/setup'
+require 'bundler/gem_tasks'
 
-require 'rubygems/tasks'
-Gem::Tasks.new
+require 'bundler/setup'
 
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new

data/lib/networkx/auxillary_functions/cliques.rb

@@ -1,6 +1,4 @@
 module NetworkX
-  # TODO: Reduce method complexity and method length
-
   # Returns all cliques in the graph
   #
   # @param graph [Graph, MultiGraph] a graph
@@ -8,6 +6,7 @@ module NetworkX
   # @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] = [] }
@@ -15,13 +14,16 @@ module NetworkX
 
     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 }
+    u = subg.max { |n1, n2| (cand & adj[n1]).length <=> (cand & adj[n2]).length }
     ext_u = cand - adj[u]
     stack = []
     cliques = []
     begin
       loop do
-        if !ext_u.empty?
+        if ext_u.empty?
+          q.pop
+          subg, cand, ext_u = stack.pop
+        else
           q_elem = ext_u.pop
           cand.delete(q_elem)
           q[-1] = q_elem
@@ -36,17 +38,14 @@ module NetworkX
               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 }
+              u = subg.max { |n1, n2| (cand & adj[n1]).length <=> (cand & adj[n2]).length }
               ext_u = cand - adj[u]
             end
           end
-        else
-          q.pop
-          subg, cand, ext_u = stack.pop
         end
       end
     rescue NoMethodError
-      return cliques
+      cliques
     end
   end
 
@@ -58,8 +57,6 @@ module NetworkX
   # @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
+    cliques.count { |c| c.include?(node) }
   end
 end

data/lib/networkx/auxillary_functions/cycles.rb

@@ -1,13 +1,11 @@
 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)
+  def self.cycle_basis(graph, root = nil)
     gnodes = graph.nodes.keys
     cycles = []
     until gnodes.empty?
@@ -19,7 +17,7 @@ module NetworkX
         z = stack.shift
         zused = used[z]
         graph.adj[z].each_key do |u|
-          if !used.key?(u)
+          if !used.has_key?(u)
             pred[u] = z
             stack << u
             used[u] = [z]
@@ -46,8 +44,6 @@ module NetworkX
     cycles
   end
 
-  # TODO: Reduce method complexity and method length
-
   # Returns the cycle containing the given node
   #
   # @param graph [Graph, DiGraph] a graph
@@ -67,6 +63,7 @@ module NetworkX
       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
@@ -76,7 +73,7 @@ module NetworkX
               break
             else
               popped_head = popped_edge[1]
-              active_nodes.delete!(popped_head)
+              active_nodes.delete(popped_head)
             end
 
             unless edges.empty?
@@ -101,4 +98,17 @@ module NetworkX
     end
     raise ArgumentError, 'No cycle found!' if cycle.empty?
   end
+
+  # Returns whether the given undirected cycle has cycle.
+  #
+  # @param undirected_graph [Graph] an undirected graph
+  #
+  # @return [book] true if the given graph has cycle. otherwise, false.
+  def self.cycle?(undirected_graph)
+    uf = NetworkX::UnionFind.new
+    undirected_graph.edges.each do |x, y|
+      uf[x] == uf[y] ? (return [x, y]) : uf.unite(x, y)
+    end
+    false
+  end
 end

data/lib/networkx/auxillary_functions/dag.rb

@@ -7,6 +7,7 @@ module NetworkX
   # @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
@@ -19,12 +20,11 @@ module NetworkX
   # @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
@@ -32,13 +32,17 @@ module NetworkX
   # @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
+    indegree_map = graph.nodes.each_key.map do |u|
+      [u, graph.in_degree(u)] if graph.in_degree(u).positive?
+    end.compact.to_h
+    zero_indegree = graph.nodes.each_key.select { |u| graph.in_degree(u).zero? }
 
     until zero_indegree.empty?
       node = zero_indegree.shift
-      raise ArgumentError, 'Graph changed during iteration!' unless graph.nodes.key?(node)
+      raise ArgumentError, 'Graph changed during iteration!' unless graph.nodes.has_key?(node)
+
       graph.adj[node].each_key do |child|
         indegree_map[child] -= 1
         if indegree_map[child].zero?
@@ -49,6 +53,7 @@ module NetworkX
       nodes << node
     end
     raise ArgumentError, 'Graph contains cycle or graph changed during iteration!' unless indegree_map.empty?
+
     nodes
   end
 end

data/lib/networkx/auxillary_functions/eccentricity.rb

@@ -5,12 +5,13 @@ module NetworkX
   # @param node [Object] node to find the eccentricity of
   #
   # @return [Array<Numeric>, Numeric] eccentricity/eccentricites of all nodes
-  def self.eccentricity(graph, node=nil)
+  def self.eccentricity(graph, node = nil)
     e = {}
     graph.nodes.each do |u, _|
       length = single_source_shortest_path_length(graph, u)
       l = length.length
       raise ArgumentError, 'Found infinite path length!' unless l == graph.nodes.length
+
       e[u] = length.max_by { |a| a[1] }[1]
     end
     node.nil? ? e : e[node]

data/lib/networkx/auxillary_functions/mis.rb

@@ -1,6 +1,4 @@
 module NetworkX
-  # TODO: Reduce method complexity and method length
-
   # Returns the maximal independent set of a graph
   #
   # @param graph [Graph, DiGraph, MultiGraph, MultiDiGraph] a graph
@@ -9,9 +7,11 @@ module NetworkX
   # @return [Numeric] radius of the graph
   def self.maximal_independent_set(graph, nodes)
     raise 'The array containing the nodes should be a subset of the graph!' if (graph.nodes.keys - nodes).empty?
+
     neighbours = []
     nodes.each { |u| graph.adj[u].each { |v, _| neighbours |= [v] } }
     raise 'Nodes is not an independent set of graph!' if (neighbours - nodes).empty?
+
     available_nodes = graph.nodes.keys - (neighbours | nodes)
     until available_nodes.empty?
       node = available_nodes.sample

data/lib/networkx/auxillary_functions/mst.rb

@@ -11,8 +11,6 @@ module NetworkX
     edges
   end
 
-  # TODO: Reduce method complexity and method length
-
   # Returns the minimum spanning tree of a graph
   #
   # @param graph [Graph, DiGraph] a graph
@@ -27,7 +25,7 @@ module NetworkX
       edge = edges.shift
       unless union_find.connected?(edge[0][0], edge[0][1])
         union_find.union(edge[0][0], edge[0][1])
-        mst.add_edge(edge[0][0], edge[0][1], graph.adj[edge[0][0]][edge[0][1]])
+        mst.add_edge(edge[0][0], edge[0][1], **graph.adj[edge[0][0]][edge[0][1]])
       end
     end
     mst