networkx 0.2.0 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rubocop.yml

@@ -1,12 +1,12 @@
 AllCops:
   NewCops: enable
-  TargetRubyVersion: 3.0
+  TargetRubyVersion: 2.7
   Include:
     - 'lib/**/*'
     - 'spec/**/*_spec.rb'
     - 'Gemfile'
     - 'Rakefile'
-    - '*.gemspace'
+    - '*.gemspec'
   DisplayCopNames: true
 
 require:

data/README.md

@@ -1,23 +1,37 @@
 # NetworkX.rb
 
+[![Gem Version](https://badge.fury.io/rb/networkx.svg)](https://badge.fury.io/rb/networkx)
+
 [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
 
 - [Installing](#installing)
+- [Usage](#Usage)
 - [Document](#document)
-- [Roadmap](#roadmap)
 - [Contributing](#contributing)
 - [License](#license)
 
 ## Installing
 
-- 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 it yourself as:
+```console
+$ gem install networkx
+```
+
+
+- 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'
@@ -30,22 +44,6 @@ g.add_edge('start', 'stop')
 
 You can read [Document](https://SciRuby.github.io/networkx.rb/) for this library.
 
-## 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 :
-
-- `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
 
 Your contributions are always welcome!  

data/lib/networkx/link_analysis/pagerank.rb

@@ -2,61 +2,16 @@ module NetworkX
   # Computes pagerank values for the graph
   #
   # @param graph [Graph] a graph
-  # @param init [Array<Numeric>] initial pagerank values for the nodes
   # @param alpha [Numeric] the alpha value to compute the pagerank
   # @param eps [Numeric] tolerence to check for convergence
   # @param max_iter [Integer] max iterations for the pagerank algorithm to run
   #
-  # @return [Array<Numeric>] pagerank values of the graph
-  def self.pagerank(graph, init = nil, alpha = 0.85, eps = 1e-4, max_iter = 100)
-    dim = graph.nodes.length
-    if init.nil?
-      init = graph.nodes(data: false).to_h{ |i| [i, 1.0 / dim] }
-    else
-      s = init.values.sum.to_f
-      init = init.transform_values { |v| v / s }
-    end
-    raise ArgumentError, 'Init array needs to have same length as number of graph nodes!' \
-                          unless dim == init.length
-
-    matrix = []
-    elem_ind = {}
-    p = []
-    curr = init.values
-    init.keys.each_with_index { |n, i| elem_ind[n] = i }
-    graph.adj.each do |_u, u_edges|
-      adj_arr = Array.new(dim, 0)
-      u_edges.each do |v, _|
-        adj_arr[elem_ind[v]] = 1
-      end
-      matrix << adj_arr
-    end
-    (0..(dim - 1)).each do |i|
-      p[i] = []
-      (0..(dim - 1)).each { |j| p[i][j] = matrix[i][j] / (matrix[i].sum * 1.0) }
-    end
-
-    max_iter.times do |_|
-      prev = curr.clone
-      dim.times do |i|
-        ip = 0
-        dim.times { |j| ip += p.transpose[i][j] * prev[j] }
-        curr[i] = (alpha * ip) + ((1 - alpha) / (dim * 1.0))
-      end
-      err = 0
-      dim.times { |i| err += (prev[i] - curr[i]).abs }
-      return curr if err < eps
-    end
-    raise ArgumentError, 'PageRank failed to converge!'
-  end
-
-  def self.pagerank2(graph, alpha: 0.85, personalization: nil, eps: 1e-6, max_iter: 100)
+  # @return [Hash of Object => Float] pagerank values of the graph
+  def self.pagerank(graph, alpha: 0.85, personalization: nil, eps: 1e-6, max_iter: 100)
     n = graph.number_of_nodes
 
     matrix, index_to_node = NetworkX.to_matrix(graph, 0)
 
-    # index_to_node = {0=>0, 1=>1, 2=>2, 3=>3}
-
     index_from_node = index_to_node.invert
 
     probabilities = Array.new(n) do |i|
@@ -84,6 +39,7 @@ module NetworkX
       err = (0...n).map{|i| (prev[i] - curr[i]).abs }.sum
       return (0...n).map{|i| [index_to_node[i], curr[i]] }.sort.to_h if err < eps
     end
+    warn "pagerank() failed within #{max_iter} iterations. Please inclease max_iter: or loosen eps:"
     (0...n).map{|i| [index_to_node[i], curr[i]] }.sort.to_h
   end
 end

data/lib/networkx/version.rb

@@ -1,3 +1,3 @@
 module NetworkX
-  VERSION = '0.2.0'.freeze
+  VERSION = '0.3.0'.freeze
 end

data/networkx.gemspec

@@ -13,13 +13,15 @@ Gem::Specification.new do |spec|
   spec.email         = ['athityakumar@gmail.com']
   spec.summary       = 'A Ruby implemenation of the well-known graph library called networkx.'
   spec.description   = NetworkX::DESCRIPTION
-  spec.homepage      = 'https://github.com/athityakumar/networkx.rb'
+  spec.homepage      = 'https://github.com/SciRuby/networkx.rb'
   spec.license       = 'MIT'
   spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
   spec.bindir        = 'bin'
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
+  spec.required_ruby_version = '>= 2.7'
+
   spec.add_development_dependency 'bundler', '~> 2.0'
   spec.add_development_dependency 'rake', '~> 13.0'
   spec.add_development_dependency 'rspec', '~> 3.0'
@@ -34,4 +36,6 @@ Gem::Specification.new do |spec|
 
   spec.add_runtime_dependency 'matrix', '~> 0.4'
   spec.add_runtime_dependency 'rb_heap', '~> 1.0'
+
+  spec.metadata['rubygems_mfa_required'] = 'true'
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: networkx
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Athitya Kumar
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-11-25 00:00:00.000000000 Z
+date: 2022-11-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -207,7 +207,6 @@ files:
 - ".github/PULL_REQUEST_TEMPLATE.md"
 - ".github/workflows/ci.yml"
 - ".github/workflows/doc.yml"
-- ".github/workflows/gem-push.yml"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
@@ -259,10 +258,11 @@ files:
 - lib/networkx/traversals/edge_dfs.rb
 - lib/networkx/version.rb
 - networkx.gemspec
-homepage: https://github.com/athityakumar/networkx.rb
+homepage: https://github.com/SciRuby/networkx.rb
 licenses:
 - MIT
-metadata: {}
+metadata:
+  rubygems_mfa_required: 'true'
 post_install_message:
 rdoc_options: []
 require_paths:
@@ -271,7 +271,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.7'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="

data/.github/workflows/gem-push.yml

@@ -1,45 +0,0 @@
-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}}"