networkx 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: 3f43ce74dd6bd8fbe91d6b5f29f3b7af355881e9
-  data.tar.gz: 0275c9f6161b6bcf973af9f18a989969ce757bd0
+SHA256:
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+  data.tar.gz: 60ef78a9da3df8d7f61e297af48873795b21d9675138e953dd160597d9bfdc09
 SHA512:
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+  data.tar.gz: 46886910fc5f3bb550fb089af740bb5c0e32cd5a1ff3dd2394a13256ddc3f6b4e9f32c48c37d2d827b2bc8edba36cd0894201aec833a2fb4d59318f7fb85b7ae

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

@@ -11,24 +11,20 @@ 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/daru-io.git
-    cd daru-io
+    git clone https://github.com/`your_github_user_id`/networkx.rb.git
+    cd networkx.rb
     gem install bundler
     bundle install
     ```
 
 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/.github/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/.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,10 @@
+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 : (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

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/.github/workflows/gem-push.yml

@@ -0,0 +1,45 @@
+name: Ruby Gem
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    name: Build + Publish
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby 2.6
+      uses: actions/setup-ruby@v1
+      with:
+        ruby-version: 2.6.x
+
+    - name: Publish to GPR
+      run: |
+        mkdir -p $HOME/.gem
+        touch $HOME/.gem/credentials
+        chmod 0600 $HOME/.gem/credentials
+        printf -- "---\n:github: ${GEM_HOST_API_KEY}\n" > $HOME/.gem/credentials
+        gem build *.gemspec
+        gem push --KEY github --host https://rubygems.pkg.github.com/${OWNER} *.gem
+      env:
+        GEM_HOST_API_KEY: "Bearer ${{secrets.GITHUB_TOKEN}}"
+        OWNER: ${{ github.repository_owner }}
+
+    - name: Publish to RubyGems
+      run: |
+        mkdir -p $HOME/.gem
+        touch $HOME/.gem/credentials
+        chmod 0600 $HOME/.gem/credentials
+        printf -- "---\n:rubygems_api_key: ${GEM_HOST_API_KEY}\n" > $HOME/.gem/credentials
+        gem build *.gemspec
+        gem push *.gem
+      env:
+        GEM_HOST_API_KEY: "${{secrets.RUBYGEMS_AUTH_TOKEN}}"

data/.rspec

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

data/.rubocop.yml

@@ -1,109 +1,102 @@
-require: rubocop-rspec
-
 AllCops:
+  NewCops: enable
+  TargetRubyVersion: 3.0
   Include:
     - 'lib/**/*'
-  Exclude:
-    - 'vendor/**/*'
-    - 'benchmarks/*'
-    - 'profile/*'
+    - 'spec/**/*_spec.rb'
+    - 'Gemfile'
+    - 'Rakefile'
+    - '*.gemspace'
   DisplayCopNames: true
-  TargetRubyVersion: 2.1
 
-# 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 -------------------------------------------------------------
+### Metrics ------------------------------------------------------------
 
-Style/AndOr:
-  EnforcedStyle: conditionals
+Metrics:
+  Enabled: false
 
-Style/DoubleNegation:
+### Naming -------------------------------------------------------------
+
+Naming/MethodParameterName:
   Enabled: false
 
-Style/EmptyCaseCondition:
+Naming/PredicateName:
   Enabled: false
 
-Style/EmptyElse:
-  EnforcedStyle: empty
+### Styles -------------------------------------------------------------
+
+Style/CombinableLoops:
+  Enabled: false # there is case that it can't combined loop.
 
-Style/EmptyMethod:
-  EnforcedStyle: compact
+Style/Documentation:
+  Enabled: false
 
-Style/FileName:
+Style/FrozenStringLiteralComment:
   Enabled: false
 
-Style/FormatString:
-  EnforcedStyle: percent
+Style/NumericPredicate:
+  Enabled: false # it is easier to read `size > 0` than `size.positive?`
+
+Style/OptionalBooleanParameter:
+  Enabled: false # it is necessary to change distructively.
 
 Style/ParallelAssignment:
-  Enabled: false
+  Enabled: false # one line style is compact.
 
-Style/SingleLineBlockParams:
+Style/PreferredHashMethods:
   Enabled: false
 
-Style/PerlBackrefs:
-  Enabled: false
+Style/SymbolArray:
+  Enabled: false # general array literal is easy to read. no problem.
 
-Style/Documentation:
-  Enabled: false # TODO
+Style/ZeroLengthPredicate:
+  Enabled: false # it is so easy to read `a.size > 0` as `!a.empty?`
 
-### Metrics ------------------------------------------------------------
+### RSpec --------------------------------------------------------------
 
-Metrics/AbcSize:
-  Max: 20
+RSpec/MessageSpies:
+  EnforcedStyle: receive
 
-Metrics/BlockLength:
-  Exclude:
-    - 'spec/**/*'
+RSpec/DescribedClass:
+  Enabled: false
 
-Metrics/ClassLength:
-  Max: 200
+RSpec/ExampleLength:
+  Max: 25
 
-Metrics/CyclomaticComplexity:
-  Max: 7
+RSpec/FilePath:
+  Enabled: false # too many offense
 
-Metrics/LineLength:
-  Max: 120
+RSpec/ImplicitSubject:
+  Enabled: false # too many offenses
 
-Metrics/MethodLength:
+RSpec/MultipleExpectations:
   Max: 15
 
-Metrics/ModuleLength:
-  Max: 200
+RSpec/NestedGroups:
+  Max: 5
 
-Style/MultilineBlockChain:
+RSpec/PredicateMatcher:
   Enabled: false
 
-Metrics/ParameterLists:
-  Max: 10
-
-### RSpec --------------------------------------------------------------
-
-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 +1,57 @@
 # 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. 
+[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. 
 
-*This project has begun just now, and a v0.1.0 release with basic Graph classes can be expected by January 2018.*
-
-### List of contents
+## List of contents
 
 - [Installing](#installing)
+- [Document](#document)
 - [Roadmap](#roadmap)
 - [Contributing](#contributing)
 - [License](#license)
 
-### Installing
+## Installing
 
-- Clone the repository with `git clone git@github.com:athityakumar/networkx.rb.git`
+- Clone the repository or fork
+  - Clone this repository with `git clone https://github.com/SciRuby/networkx.rb.git`
+  - or You can fork and do clone it.
 - 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 : 
 
 ```ruby
 require 'networkx'
-#=> true
 
-# Yet to be implemented
-g = NetworkX::Graph.new()
+g = NetworkX::Graph.new
 g.add_edge('start', 'stop')
 ``` 
 
-### Roadmap
-
-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 :
+## Document
 
-- `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.
+You can read [Document](https://SciRuby.github.io/networkx.rb/) for this library.
 
-- `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.
+## Roadmap
 
-- `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.
+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 :
 
-[(Back to top)](#list-of-contents)
+- `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.
 
-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.
+- `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.
 
-### Contributing
+- `Graph` : The simplest of graphs.  
+  This class handles just connections between different `Node`s via `Edge`s.
 
-[(Back to top)](#list-of-contents)
+- `DirectedGraph` : Inherits from `Graph` class.  
+  Uses directions between `Edge`s.
 
-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

@@ -0,0 +1,62 @@
+module NetworkX
+  # 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 { |n1, n2| (cand & adj[n1]).length <=> (cand & adj[n2]).length }
+    ext_u = cand - adj[u]
+    stack = []
+    cliques = []
+    begin
+      loop do
+        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
+          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 { |n1, n2| (cand & adj[n1]).length <=> (cand & adj[n2]).length }
+              ext_u = cand - adj[u]
+            end
+          end
+        end
+      end
+    rescue NoMethodError
+      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)
+    cliques.count { |c| c.include?(node) }
+  end
+end

data/lib/networkx/auxillary_functions/cycles.rb

@@ -0,0 +1,114 @@
+module NetworkX
+  # 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.has_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
+
+  # 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
+
+  # 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