sciruby 0.2.3 → 0.2.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -1,2 +1,6 @@
 *.gem
-Gemfile.lock
+Gemfile.lock
+*.ipynb
+.ipynb_checkpoints
+gems.html
+pages

data/.travis.yml

@@ -0,0 +1,24 @@
+language: ruby
+
+rvm:
+  - ruby-head
+  - 2.2.2
+  - 2.1.6
+
+matrix:
+  allow_failures:
+    - rvm: ruby-head
+
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq gnuplot-nox libgsl0-dev libsqlite3-dev libatlas-base-dev
+  - sudo ln -s /usr/lib/libtoolize /usr/lib/libtool
+
+env:
+  global:
+    - secure: "Wr93642ujssq2+lTxWiAR0u3Y50MkNfq0jcEjPn9g2A9QQw8UitXZvtGjWa7VK8Cw2iJM7NQdY0G/eE+SBqGQ2d/NyDRwBdLUrQHBILWHeJFHoQnHcfgcGWoXVg2ztxkL6mmo8B5XpKm+ZEh4uYlZYiwp41VegmpmcuxWE0R1N0="
+
+script: bundle exec rake test && bundle exec rake deploy
+
+notifications:
+  irc: "chat.freenode.net#sciruby"

data/CHANGES

@@ -1,3 +1,7 @@
+0.2.4 (2015-06-10)
+
+  * Tests added
+
 0.2.3 (2015-06-09)
 
   * Simpler SciRuby.gems api

data/Gemfile

@@ -1,2 +1,13 @@
+load File.expand_path(File.join(__FILE__, '..', 'scripts', 'helper.rb'))
+
 source 'https://rubygems.org'
-gemspec name: 'sciruby-full'
+
+Helper.sciruby_gems(true).each do |g|
+  gem(g[:name], *g[:version])
+end
+
+# development dependencies
+gem 'minitest'
+gem 'rake'
+gem 'bundler'
+gem 'slim'

data/README.md

@@ -0,0 +1,46 @@
+# SciRuby meta gem
+
+Tools for Scientific Computing in Ruby
+
+* [Website](http://sciruby.com)
+* [NMatrix](http://github.com/SciRuby/nmatrix)
+* [List of gems](https://minad.github.io/sciruby-gems)
+* [Travis-CI](https://travis-ci.org/SciRuby/sciruby)
+
+## Description
+
+This gem acts as a meta gem which provides collects multiple scientific gems, including numeric and visualization libraries.
+
+## Getting started
+
+Installation:
+
+    gem install sciruby
+    gem install sciruby-full
+
+If you want to have a full-blown installation, install `sciruby-full`.
+
+Start a notebook server:
+
+    iruby notebook
+
+Enter commands:
+
+    require 'sciruby'
+    # Scientific gems are auto loaded, you can use them directly!
+    plot = Nyaplot::Plot.new
+    sc = plot.add(:scatter, [0,1,2,3,4], [-1,2,-3,4,-5])
+
+Take a look at [gems.yml](gems.yml) or the [list of gems](https://minad.github.io/sciruby-gems) for interesting gems which are included in `sciruby-full`.
+
+## License
+
+Copyright (c) 2010 onward, The Ruby Science Foundation.
+
+All rights reserved.
+
+SciRuby is licensed under the BSD 3-clause license. See [LICENSE](LICENSE) for details.
+
+## Donations
+
+Support a SciRuby Fellow via [![Pledgie](http://pledgie.com/campaigns/15783.png?skin_name=chrome)](http://www.pledgie.com/campaigns/15783).

data/Rakefile

@@ -0,0 +1,13 @@
+task 'gems.html' do
+  sh 'slimrb --trace scripts/gems.slim > gems.html'
+end
+
+task :test do
+  sh 'scripts/test'
+end
+
+task deploy: 'gems.html' do
+  sh 'scripts/deploy'
+end
+
+task default: %w(test gems.html)

data/gems.yml

@@ -1,157 +1,282 @@
-# Specify all gems which are installed by the `sciruby-full` gem or recommended by the `sciruby` gem.
-
-nmatrix:
-  description: Numerics matrix library
-  module: [N, NMatrix, NVector]
-  category: numerics
-
-gsl-nmatrix:
-  description: Bindings for the GNU scientific library
-  require: gsl
-  module: GSL
-  category: numerics
-
-rubyvis:
-  description: Plotting library
+---
+ai4r:
+  category: artificial intelligence
+  description: Artificial intelligence
+  module: Ai4r
+  version: "~> 1.13"
+algorithms:
+  category: utilities
+  description: Algorithms and data structures
+  module:
+  - Algorithms
+  - Containers
+  version: "~> 0.6"
+awesome_print:
+  category: utilities
+  description: Pretty object printing
+  version: "~> 1.6"
+bio:
+  category: biology
+  description: Bioinformatics suite
+  module: Bio
+  version: "~> 1.4"
+cassowary:
+  category: optimization
+  description: Incremental constraint solver
+  exclude: Native dependencies
+  module: Cassowary
+classifier:
+  category: artificial intelligence
+  description: Machine learning
+  module: Classifier
+  version: "~> 1.3"
+cmath:
+  category: algebra
+  description: Stdlib cmath module
+  maintainer: stdlib
+daru:
+  category: data
+  description: Dataframe library
+  module: Daru
+  version: "~> 0.0"
+darwinning:
+  category: optimization
+  description: Generic algorithms
+  module: Darwinning
+  version: "~> 0.0"
+decisiontree:
+  category: artificial intelligence
+  description: Machine learning
+  module: DecisionTree
+  version: "~> 0.5"
+distribution:
+  category: statistics
+  description: Statistical distributions
+  maintainer: sciruby
+  module: Distribution
+  version: "~> 0.7"
+extendmatrix:
+  category: algebra
+  description: Helper methods for Matrix
+  version: "~> 0.4"
+gga4r:
+  category: optimization
+  description: Generic algorithms
+  module: GeneticAlgorithm
+  version: "~> 0.9"
+gimuby:
+  category: optimization
+  description: Genetic algorithms
+  module: Gimuby
+  version: "~> 0.7"
+gnuplot:
   category: plotting
-
-nyaplot:
   description: Plotting library
+  module: Gnuplot
+  version: "~> 2.6"
+integration:
+  category: numerics
+  description: Numerical integration
+  maintainer: sciruby
+  module: Integration
+  version: "~> 0.1"
+irtruby:
+  category: artificial intelligence
+  description: Machine learning
+  exclude: Not available as a gem
+  module: IRT
+iruby:
+  category: user interface
+  description: Ruby kernel for Jupyter
+  maintainer: sciruby
+  module: IRuby
+  version: "~> 0.2"
+lpsolve:
+  category: optimization
+  description: Linear solver
+  exclude: Outdated native dependencies
+  module: LPSolve
+mathgl:
   category: plotting
-
-plotrb:
   description: Plotting library
+  exclude: Native dependencies
+  module: MathGL
+matrix:
+  category: algebra
+  description: Stdlib matrix module
+  maintainer: stdlib
+  module: Matrix
+minimization:
+  category: numerics
+  description: Numerical minimization
+  maintainer: sciruby
+  module: Minimization
+  version: "~> 0.2"
+modshogun:
+  category: artificial intelligence
+  description: Machine learning
+  exclude: Not available as a gem
+  module: Modshogun
+narray:
+  category: numerics
+  description: Numerics matrix library
+  exclude: Conflicts with nmatrix
+  module: NArray
+nmatrix:
+  category: numerics
+  description: Numerics matrix library
+  maintainer: sciruby
+  module:
+  - N
+  - NMatrix
+  - NVector
+  version: "~> 0.1"
+nyaplot:
   category: plotting
-
-gnuplot:
   description: Plotting library
+  module: Nyaplot
+  version: "~> 0.1"
+ode:
+  category: numerics
+  description: Ordinary differential equations
+  exclude: Fortran dependencies
+  module: Ode
+plotrb:
   category: plotting
-
-iruby:
-  module: IRuby
-  description: Ruby kernel for Jupyter
-  category: user interface
-
+  description: Plotting library
+  module: Plotrb
+  version: "~> 0.0"
+prime:
+  category: algebra
+  description: Stdlib prime module
+  maintainer: stdlib
+  module: Prime
 pry:
-  module: Pry
-  description: Ruby repl
   category: user interface
-
-awesome_print:
-  module: ~
-  description: Pretty object printing
-  category: utilities
-
-daru:
-  description: Dataframe library
-  category: database
-
-integration:
-  description: Numerical integration
+  description: Ruby repl
+  module: Pry
+  version: "~> 0.10"
+publisci:
+  category: publishing
+  description: Publishing toolkit
+  module: PubliSci
+  version: "~> 0.1"
+rb-gsl:
   category: numerics
-
-minimization:
-  description: Numerical minimization
+  description: Bindings for the GNU scientific library
+  exclude: Requires narray
+  module: GSL
+  require: gsl
+rb-libsvm:
+  category: artificial intelligence
+  description: Support vector machines (machine learning)
+  module: Libsvm
+  require: libsvm
+  version: "~> 1.3"
+rinruby:
+  category: statistics
+  description: R interpreter
+  module:
+  - R
+  - RinRuby
+  version: "~> 2.0"
+rserve-client:
+  category: statistics
+  description: R interpreter
+  module: Rserve
+  require: rserve
+  version: "~> 0.3"
+rsruby:
+  category: statistics
+  description: R interpreter
+  exclude: Native dependencies
+  module: RSRuby
+ruby-band:
+  category: artificial intelligence
+  description: Data mining
+  exclude: Requires JRuby
+ruby-dcl:
+  category: plotting
+  description: Plotting
+  exclude: Requires narray
+ruby-fann:
+  category: artificial intelligence
+  description: Neural networks
+  module: RubyFann
+  version: "~> 1.2"
+ruby-fftw3:
   category: numerics
-
-distribution:
-  description: Statistical distributions
+  description: Fast Fourier transformation
+  exclude: Requires narray
+  module: FFTW3
+ruby-minisat:
+  category: algebra
+  description: SAT solver
+  module: MiniSat
+  require: minisat
+  version: "~> 2.2"
+ruby-netcdf:
+  category: data
+  description: Data file
+  exclude: Requires narray
+ruby-opencv:
+  category: artificial intelligence
+  description: Computer vision
+  exclude: Native dependencies
+  module: OpenCV
+ruby-pgplot:
+  category: plotting
+  description: Plotting
+  exclude: Requires narray
+  module: Pgplot
+  require: pgplot
+rubyvis:
+  category: plotting
+  description: Plotting library
+  module: Rubyvis
+  version: "~> 0.5"
+sciruby:
+  category: meta
+  description: SciRuby meta gem
+  maintainer: sciruby
+sciruby-full:
+  category: meta
+  description: SciRuby meta gem (Full installation)
+  maintainer: sciruby
+sicom:
   category: statistics
-
+  description: R interpreter
+  exclude: Requires JRuby
 statsample:
+  category: statistics
   description: Statistics
+  maintainer: sciruby
+  module: Statsample
+  version: "~> 1.4"
+statsample-bivariate-extension:
   category: statistics
-
-statsample-glm:
   description: Statistics
-  module: ~
+  version: "~> 1.1"
+statsample-glm:
   category: statistics
-
-statsample-bivariate-extension:
   description: Statistics
-  module: ~
+  maintainer: sciruby
+  version: "~> 0.1"
+statsample-optimization:
   category: statistics
-
-statsample-timeseries:
-  exclude: because of activesupport conflict
   description: Statistics
-  module: ~
+  exclude: GSL conflict
+statsample-timeseries:
   category: statistics
-
-extendmatrix:
-  description: Helper methods for Matrix
-  module: ~
-  category: numerics
-
-publisci:
-  description: Publishing toolkit
-  module: PubliSci
-  category: publishing
-
-ai4r:
-  description: Artificial intelligence
-  category: machine learning
-
-bio:
-  description: Bioinformatics suite
-  category: biology
-
-ruby-fftw3:
-  module: FFTW3
-  exclude: because it works only with narray
-  description: Fast Fourier transformation
-  category: numerics
-
-ruby-band:
-  exclude: because of dependencies
-  description: Data mining
-  category: machine learning
-  module: ~
-
-classifier:
-  description: Machine learning
-  category: machine learning
-
+  description: Statistics
+  exclude: activesupport version conflict
 stuff-classifier:
+  category: artificial intelligence
   description: Machine learning
-  category: machine learning
   module: StuffClassifier
-
-decisiontree:
-  description: Machine learning
-  category: machine learning
-  module: DecisionTree
-
-irtruby:
-  exclude: because of dependencies
-  description: Machine learning
-  category: machine learning
-  module: IRT
-
-ruby-opencv:
-  description: Computer vision
-  exclude: because of dependencies
-  category: computer vision
-  module: OpenCV
-
-ruby-fann:
-  description: Neural networks
-  category: machine learning
-  module: RubyFann
-
-rb-libsvm:
-  description: Support vector machines (machine learning)
-  category: machine learning
-  module: Libsvm
-
-sciruby:
-  description: SciRuby meta gem
-  category: meta
-  exclude: to avoid circular dependencies
-  module: ~
-
-sciruby-full:
-  description: SciRuby meta gem (Full installation)
-  category: meta
-  exclude: to avoid circular dependencies
-  module: ~
+  version: "~> 0.5"
+unit:
+  category: physics
+  description: Calculation with units
+  module: Unit
+  version: "~> 0.5"

data/lib/sciruby/autoload.rb

@@ -2,7 +2,7 @@ class Module
   alias :const_missing_without_sciruby :const_missing
 
   def const_missing(name)
-    paths = SciRuby.autoload_modules.delete(name)
+    paths = SciRuby.autoload_modules.delete(name.to_sym)
     if paths
       paths.each {|path| require path }
       const_get(name)

data/lib/sciruby/gems.rb

@@ -13,11 +13,7 @@ module SciRuby
 
   # Return map of all installed SciRuby gems
   def installed_gems
-    @installed_gems ||=
-      begin
-        require 'rubygems'
-        Hash[gems.each_value.map(&method(:installed_gem)).compact]
-      end
+    @installed_gems ||= Hash[gems.each_value.map(&method(:installed_gem)).compact]
   end
 
   # Return list of all known SciRuby modules
@@ -37,7 +33,6 @@ module SciRuby
       gem = Hash[gem.map {|k,v| [k.to_sym, v] }]
       gem[:name] = name
       gem[:require] = [*(gem[:require] || name)]
-      gem[:module] = name.capitalize unless gem.include?(:module)
       gem[:module] = [*gem[:module]].map(&:to_sym)
       gem[:module].each {|mod| autoload_modules[mod] = gem[:require] }
       gems[name] = gem
@@ -45,10 +40,12 @@ module SciRuby
   end
 
   def installed_gem(gem)
-    [gem[:name], gem.merge(gem_version: Gem::Specification.find_by_name(gem[:name]).version.to_s)]
+    require 'rubygems' unless defined?(Gem::Specification)
+    [gem[:name], gem.merge(installed_version: Gem::Specification.find_by_name(gem[:name]).version.to_s)]
   rescue Exception
     nil
   end
 
-  load_gems File.expand_path(File.join(__FILE__, '..', '..', '..', 'gems.yml'))
+  GEMS_YML = File.expand_path(File.join(__FILE__, '..', '..', '..', 'gems.yml'))
+  load_gems GEMS_YML
 end

data/lib/sciruby/version.rb

@@ -2,5 +2,5 @@
 module SciRuby
   # SciRuby version string
   # @api public
-  VERSION = '0.2.3'
+  VERSION = '0.2.4'
 end

data/sciruby.gemspec

@@ -1,7 +1,4 @@
-# coding: utf-8
-$: << File.join(File.dirname(__FILE__), 'lib')
-require 'sciruby'
-require 'date'
+require File.expand_path(File.join(__FILE__, '..', 'scripts', 'helper.rb'))
 
 SCIRUBY_FULL = false unless defined?(SCIRUBY_FULL)
 
@@ -16,20 +13,17 @@ Gem::Specification.new do |s|
   s.summary     =
   s.description = "Scientific gems for Ruby#{SCIRUBY_FULL ? ' (Full installation)' : ''}"
 
-  s.require_paths = %w(lib)
-  s.files = `git ls-files`.split($/)
-
   if SCIRUBY_FULL
-    s.files.delete 'sciruby.gemspec'
-    s.files.reject! {|f| f =~ /\Alib/ }
+    s.files = %w(CHANGES CONTRIBUTING.md README.md LICENSE sciruby-full.gemspec)
 
     s.add_runtime_dependency 'sciruby', "= #{SciRuby::VERSION}"
-    SciRuby.gems.each_value.reject {|gem| gem[:exclude] }.each {|gem| s.add_runtime_dependency gem[:name], *gem[:version] }
+    Helper.sciruby_gems(true).each {|gem| s.add_runtime_dependency gem[:name], *gem[:version] }
   else
+    s.files = `git ls-files`.split($/)
     s.files.delete 'sciruby-full.gemspec'
 
     m = "Please consider installing 'sciruby-full' or the following gems:\n"
-    SciRuby.gems.each_value.sort_by {|gem| gem[:name] }.each {|gem| m << "  * #{gem[:name]} - #{gem[:description]}\n" }
+    Helper.sciruby_gems(false).each {|gem| m << "  * #{gem[:name]} - #{gem[:description]}\n" }
     s.post_install_message = m << "\n"
   end
 end

data/scripts/deploy

@@ -0,0 +1,18 @@
+#!/bin/sh
+
+mkdir -p pages
+
+cd pages
+
+git init
+git config user.name "Daniel Mendler"
+git config user.email "mail@daniel-mendler.de"
+
+git remote add origin "https://$GH_TOKEN@github.com/minad/sciruby-gems.git"
+git fetch && git reset origin/gh-pages
+
+cp ../gems.html index.html
+
+git add -A .
+git commit -m "rebuild pages"
+git push -q origin HEAD:gh-pages

data/scripts/gems.slim

@@ -0,0 +1,57 @@
+- require File.expand_path(File.join(__FILE__, '..', 'helper.rb'))
+doctype html
+html
+  head
+    title SciRuby gems
+    link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"
+    link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-table/1.8.1/bootstrap-table.min.css"
+    script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.js"
+    script src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-table/1.8.1/bootstrap-table.min.js"
+  body: .container: .row
+    h1 SciRuby gems
+    ul
+      li
+        | Last updated at #{Time.now.utc}
+        - if ENV['TRAVIS']
+          |  by <a href="https://travis-ci.org/SciRuby/sciruby/jobs/#{ENV['TRAVIS_JOB_ID']}">Travis-CI</a> from commit
+             <a href="https://github.com/SciRuby/sciruby/commit/#{ENV['TRAVIS_COMMIT']}">#{ENV['TRAVIS_COMMIT']}</a>.
+      li #{SciRuby.gems.size} gems listed
+    table.table data={ toggle:            'table',
+                       search:            'true',
+                       sortable:          'true',
+                       show_toggle:       'true',
+                       show_columns:      'true',
+                       mobile_responsive: 'true',
+                       striped:           'true' }
+      thead: tr
+        th data-sortable="true" Maintainer
+        th data-sortable="true" Category
+        th data-sortable="true" Name
+        th data-sortable="true" Version
+        th data-sortable="true" Latest version
+        th data-sortable="true" Description
+        th data-sortable="true" Autoloaded modules
+        th data-sortable="true" Status
+      tbody
+        - Helper.sorted_gems.each do |gem|
+          - spec = Helper.fetch_spec(gem)
+          tr
+            td
+              - if gem[:maintainer]
+                - maintainer_tag = { 'stdlib' => 'info', 'sciruby' => 'success' }
+                span.label class="label-#{maintainer_tag[gem[:maintainer]] || 'warning'}" = gem[:maintainer]
+            td = gem[:category]
+            - if spec
+              td
+                a href=spec.homepage = gem[:name]
+            - else
+              td = gem[:name]
+            td = gem[:version]
+            td
+              - if spec
+                a href="https://rubygems.org/gems/#{gem[:name]}" #{spec.version} (#{spec.date.strftime '%Y-%m-%d'})
+            td = gem[:description]
+            td = gem[:module].join(', ')
+            td
+              - Helper.gem_status(gem).each do |tag, msg|
+                  span.label<> class="label-#{tag}" = msg

data/scripts/helper.rb

@@ -0,0 +1,83 @@
+begin
+  require 'bundler/setup'
+rescue Exception
+end
+
+$: << File.join(File.dirname(__FILE__), '..', 'lib')
+
+require 'sciruby'
+require 'date'
+require 'rubygems'
+
+module Enumerable
+  def stable_sort_by
+    sort_by.with_index {|e, i| [yield(e), i] }
+  end
+end
+
+module Helper
+  extend self
+
+  def sort_hash(object)
+    if Hash === object
+      res = {}
+      object.each {|k, v| res[k] = sort_hash(v) }
+      Hash[res.sort_by {|a| a[0].to_s }]
+    elsif Array === object
+      array = []
+      object.each_with_index {|v, i| array[i] = sort_hash(v) }
+      array
+    else
+      object
+    end
+  end
+
+  def check_gem(name, gem)
+    gem[:name].must_equal name
+    gem.must_be_instance_of Hash
+    gem.each_key {|k| k.must_be_instance_of Symbol }
+    gem[:category].must_be_instance_of String
+    gem[:description].must_be_instance_of String
+    gem[:exclude].must_be_instance_of String if gem[:exclude] != nil
+    gem[:module].must_be_instance_of Array
+    gem[:require].must_be_instance_of Array
+    gem[:require].empty?.must_equal false
+
+    if gem[:exclude] || gem[:maintainer] == 'stdlib' || %w(sciruby sciruby-full).include?(gem[:name])
+      gem[:version].must_be_nil
+    else
+      gem[:version].must_be_instance_of String
+    end
+  end
+
+  def fetch_spec(gem)
+    #STDERR.puts "Fetching #{gem[:name]}..."
+    gem[:maintainer] != 'stdlib' && Gem::SpecFetcher.fetcher.spec_for_dependency(Gem::Dependency.new(gem[:name])).flatten.first
+  end
+
+  def gem_status(gem)
+    status = []
+    status << [:default, "Excluded: #{gem[:exclude]}"] if gem[:exclude]
+    if spec = fetch_spec(gem)
+      status << [:warning, "Last update #{spec.date.strftime '%Y-%m-%d'}"] if Time.now - spec.date > 2*365*24*3600
+      status[:danger] << 'Outdated version constraint' unless Gem::Dependency.new(gem[:name], *gem[:version]).matches_spec?(spec)
+    else
+      status << [:danger, 'Gem not found'] unless gem[:exclude]
+    end unless gem[:exclude] || gem[:maintainer] == 'stdlib'
+    status << [:success, 'OK'] if status.empty?
+    status.sort_by(&:first)
+  end
+
+  def sorted_gems
+    SciRuby.gems.each_value.
+      stable_sort_by {|gem| gem[:name] }.
+      stable_sort_by {|gem| gem[:category] }.
+      stable_sort_by {|gem| gem[:maintainer] == 'sciruby' ? 0 : (gem[:maintainer] ? 1 : 2) }
+  end
+
+  def sciruby_gems(exclude)
+    SciRuby.gems.each_value.sort_by {|gem| gem[:name] }.reject do |gem|
+      gem[:maintainer] == 'stdlib' || %w(sciruby sciruby-full).include?(gem[:name])
+    end.reject {|gem| gem[:exclude] && exclude }
+  end
+end

data/scripts/test

@@ -0,0 +1,77 @@
+#!/usr/bin/env ruby
+
+require File.expand_path(File.join(__FILE__, '..', 'helper.rb'))
+require 'minitest/spec'
+require 'minitest/autorun'
+
+class MiniTest::Spec
+  include Helper
+end
+
+describe 'gems.yml' do
+  it 'is sorted' do
+    sorted = YAML.dump(sort_hash(YAML.load_file(SciRuby::GEMS_YML)))
+    if File.read(SciRuby::GEMS_YML) != sorted
+      puts 'gems.yml has been sorted'
+      File.write(SciRuby::GEMS_YML, sorted)
+      fail
+    end
+  end
+
+  it 'contains no gratuitous keys' do
+    YAML.load_file(SciRuby::GEMS_YML).each do |name, gem|
+      gem.each_key {|k| %w(category maintainer description exclude version module require).include?(k).must_equal true }
+      gem['require'].wont_equal name if gem['require']
+    end
+  end
+end
+
+describe SciRuby do
+  it 'provides Hash of gems' do
+    SciRuby.gems.must_be_instance_of Hash
+    SciRuby.gems.each_key {|k| k.must_be_instance_of String }
+    SciRuby.gems.each do |name, gem|
+      check_gem(name, gem)
+    end
+  end
+
+  it 'provides Hash of installed gems' do
+    SciRuby.installed_gems.must_be_instance_of Hash
+    SciRuby.installed_gems.each_key {|k| k.must_be_instance_of String }
+    SciRuby.installed_gems.each do |name, gem|
+      check_gem(name, gem)
+      gem[:installed_version].must_be_instance_of String
+    end
+  end
+
+  it 'provides list of modules' do
+    SciRuby.modules.must_be_instance_of Array
+    SciRuby.modules.each {|m| m.must_be_instance_of Symbol }
+  end
+
+  it 'provides list of installed modules' do
+    SciRuby.installed_modules.must_be_instance_of Array
+    SciRuby.installed_modules.each {|m| m.must_be_instance_of Symbol }
+  end
+
+  it 'provides list of autoloadable modules' do
+    SciRuby.autoload_modules.must_be_instance_of Hash
+    SciRuby.autoload_modules.each_key {|k| k.must_be_instance_of Symbol }
+    SciRuby.autoload_modules.each_value {|v| v.must_be_instance_of Array }
+  end
+
+  it 'autoloads modules' do
+    SciRuby.autoload_modules.must_include :Prime
+
+    Object.const_defined?(:Prime).must_equal false
+    Prime.must_be_instance_of Class
+    Object.const_defined?(:Prime).must_equal true
+
+    SciRuby.autoload_modules.wont_include :Prime
+
+    SciRuby.installed_gems.each_value.map {|gem| gem[:module] }.flatten.each do |mod|
+      next if mod == :R || mod == :RinRuby # FIXME, don't test RinRuby for now since it requires an installaion of R
+      Object.const_get(mod).wont_equal nil
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sciruby
 version: !ruby/object:Gem::Version
-  version: 0.2.3
+  version: 0.2.4
 platform: ruby
 authors:
 - SciRuby Development Team
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-09 00:00:00.000000000 Z
+date: 2015-06-10 00:00:00.000000000 Z
 dependencies: []
 description: Scientific gems for Ruby
 email:
@@ -18,18 +18,23 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".travis.yml"
 - CHANGES
 - CONTRIBUTING.md
 - Gemfile
-- LICENSE.txt
-- README.rdoc
-- gems.slim
+- LICENSE
+- README.md
+- Rakefile
 - gems.yml
 - lib/sciruby.rb
 - lib/sciruby/autoload.rb
 - lib/sciruby/gems.rb
 - lib/sciruby/version.rb
 - sciruby.gemspec
+- scripts/deploy
+- scripts/gems.slim
+- scripts/helper.rb
+- scripts/test
 homepage: http://sciruby.com
 licenses:
 - BSD
@@ -37,37 +42,55 @@ metadata: {}
 post_install_message: |+
   Please consider installing 'sciruby-full' or the following gems:
     * ai4r - Artificial intelligence
+    * algorithms - Algorithms and data structures
     * awesome_print - Pretty object printing
     * bio - Bioinformatics suite
+    * cassowary - Incremental constraint solver
     * classifier - Machine learning
     * daru - Dataframe library
+    * darwinning - Generic algorithms
     * decisiontree - Machine learning
     * distribution - Statistical distributions
     * extendmatrix - Helper methods for Matrix
+    * gga4r - Generic algorithms
+    * gimuby - Genetic algorithms
     * gnuplot - Plotting library
-    * gsl-nmatrix - Bindings for the GNU scientific library
     * integration - Numerical integration
     * irtruby - Machine learning
     * iruby - Ruby kernel for Jupyter
+    * lpsolve - Linear solver
+    * mathgl - Plotting library
     * minimization - Numerical minimization
+    * modshogun - Machine learning
+    * narray - Numerics matrix library
     * nmatrix - Numerics matrix library
     * nyaplot - Plotting library
+    * ode - Ordinary differential equations
     * plotrb - Plotting library
     * pry - Ruby repl
     * publisci - Publishing toolkit
+    * rb-gsl - Bindings for the GNU scientific library
     * rb-libsvm - Support vector machines (machine learning)
+    * rinruby - R interpreter
+    * rserve-client - R interpreter
+    * rsruby - R interpreter
     * ruby-band - Data mining
+    * ruby-dcl - Plotting
     * ruby-fann - Neural networks
     * ruby-fftw3 - Fast Fourier transformation
+    * ruby-minisat - SAT solver
+    * ruby-netcdf - Data file
     * ruby-opencv - Computer vision
+    * ruby-pgplot - Plotting
     * rubyvis - Plotting library
-    * sciruby - SciRuby meta gem
-    * sciruby-full - SciRuby meta gem (Full installation)
+    * sicom - R interpreter
     * statsample - Statistics
     * statsample-bivariate-extension - Statistics
     * statsample-glm - Statistics
+    * statsample-optimization - Statistics
     * statsample-timeseries - Statistics
     * stuff-classifier - Machine learning
+    * unit - Calculation with units
 
 rdoc_options: []
 require_paths:
@@ -89,4 +112,3 @@ signing_key:
 specification_version: 4
 summary: Scientific gems for Ruby
 test_files: []
-has_rdoc: 

data/README.rdoc

@@ -1,34 +0,0 @@
-= SciRuby meta gem
-
-Tools for Scientific Computing in Ruby
-
-* {Website}[http://sciruby.com]
-* {Google+}[https://plus.google.com/109304769076178160953/posts]
-* {NMatrix}[http://github.com/SciRuby/nmatrix]
-
-== Description
-
-Ruby has for some time had no equivalent to the beautifully constructed numpy, scipy, and matplotlib libraries for Python. We believe that the time for a Ruby science and visualization package has come and gone. Sometimes when a solution of sugar and water becomes super-saturated, from it precipitates a pure, delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap of a finger. So it is, we believe, with the need for numeric and visualization libraries in Ruby.
-
-We are not the first with this idea, but we are trying to bring it to life.
-
-== Installation
-
-    gem install sciruby
-    gem install sciruby-full
-
-See also the {guide in the wiki}[https://github.com/SciRuby/sciruby/wiki/Installation].
-
-== License
-
-Copyright (c) 2010 onward, The Ruby Science Foundation.
-
-All rights reserved.
-
-SciRuby is licensed under the BSD 3-clause license. See {LICENSE.txt}[https://github.com/SciRuby/sciruby/wiki/License] for details.
-
-== Donations
-
-Support a SciRuby Fellow:
-
-{<img src=http://pledgie.com/campaigns/15783.png?skin_name=chrome>}[http://www.pledgie.com/campaigns/15783]

data/gems.slim

@@ -1,24 +0,0 @@
-ruby:
-  require 'sciruby'
-doctype html
-html
-  head
-    title SciRuby gems
-    link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/css/bootstrap.min.css"
-  body
-    h1 SciRuby gems
-    table.table.table-striped
-      thead
-        tr
-          th Name
-          th Category
-          th Description
-          th Autoloaded modules
-      tbody
-        - SciRuby.gems.each_value.sort_by {|gem| gem[:category] }.chunk {|gem| gem[:category] }.each do |cat, gems|
-          - gems.sort_by {|gem| gem [:name] }.each do |gem|
-            tr
-              td = gem[:name]
-              td = gem[:category]
-              td = gem[:description]
-              td = gem[:module].join(', ')