sciruby 0.2.4 → 0.2.5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 8307708e990dc2da9b0f255e57ccebb9d2e112d8
+  metadata.gz: 6213f46112349dd0ee6c1aec4ab40a5764238506
+  data.tar.gz: 56d7ff8a77d1f4857703f9981121a7cc8c6d3805
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-  data.tar.gz: ea961303d3cca616ed48bf08212c3561fe350e69e3e5e059a4365c599ed84eb72265d0282d3dbec0428e9c54d093e0641ba133ea106299c505625381651f0464
+  metadata.gz: c42d783ed409a3ea39c174204b6896792558d7019d00094d465812ac8f2d5306b78bd3f7fc1236984c2b063b50bb0a88e60c7dfeeeb24bfed5e799b3e3af8d53
+  data.tar.gz: a6492cf1b2d5d6a323b4aba5c1b4ea83793ee4049c64466cc1a23171d9b3eb4f99f5729e94d4a0506d3a6350ae00e3942249aefaaf85194322064aca22904aee

data/.travis.yml

@@ -11,12 +11,14 @@ matrix:
 
 before_install:
   - sudo apt-get update -qq
-  - sudo apt-get install -qq gnuplot-nox libgsl0-dev libsqlite3-dev libatlas-base-dev
+  - sudo apt-get install -qq gnuplot-nox libgsl0-dev libsqlite3-dev libatlas-base-dev libmagickcore-dev
   - sudo ln -s /usr/lib/libtoolize /usr/lib/libtool
 
 env:
   global:
     - secure: "Wr93642ujssq2+lTxWiAR0u3Y50MkNfq0jcEjPn9g2A9QQw8UitXZvtGjWa7VK8Cw2iJM7NQdY0G/eE+SBqGQ2d/NyDRwBdLUrQHBILWHeJFHoQnHcfgcGWoXVg2ztxkL6mmo8B5XpKm+ZEh4uYlZYiwp41VegmpmcuxWE0R1N0="
+    - secure: "JXusYvgkICUl5+cMsB73dyi8n+Eo4XX+XGPydGa3ut8Znf6BG41u58afFfzQQBwWREQMT8ch0DKbytNJahR1ljFgW6T9iKLw7LRxisT0D/nv5GHnJS0GxNb+zoOlhkAKVIsqVXg482AThahaGB7El7MX4GtGuDXbNRQmpp778Sw="
+    - secure: "JGBNlzoawWbbwliHj4HfH38y6MDygEO68v2tYIuSrMavpjiKzOqU7IsQEtr8kxTrUDFQ2i9ptvCo7ApCihZazYfRCYIj9G2FYYYNOQQQcTBvkhh/4W1xcnOkoLcTkXNzXyiGcG3/nZVVcug7lJ2GicWpqMO/0mFIsEHX9cFAVd8="
 
 script: bundle exec rake test && bundle exec rake deploy
 

data/CHANGES

@@ -1,3 +1,8 @@
+0.2.5 (2015-06-13)
+
+  * More gems added
+  * Support for autoloading qualified modules A::B
+
 0.2.4 (2015-06-10)
 
   * Tests added

data/CONTRIBUTING.md

@@ -6,13 +6,14 @@ This guide covers way in which you can contribute.
 
 There are various ways in which you can improve SciRuby. Coding and documentation are the two primary possibilities and participate in the [mailing list][mailing-list] -- suggesting ideas and changes is very important!
 
-Apart from adding features and functionality, you can also create tests (we use RSpec), guides on how to do something using SciRuby, document the libraries and help find and fix bugs.
+Apart from adding features and functionality, you can also create tests, guides on how to do something using SciRuby, document the libraries and help find and fix bugs.
 
-Start by visiting our [issue tracker](https://github.com/SciRuby/sciruby/issues?state=open) if you want to start contributing, there's probably something with which you can help.
+Start by visiting our [issue tracker](https://github.com/SciRuby/sciruby/issues?state=open) and the
+[status list of the various gems](http://gems.sciruby.com). If you want to start contributing, there's probably something with which you can help.
 
 ## Projects
 
-SciRuby is an umbrella for many other projects in Ruby. There's not much hierarchy or anything, but we believe that the most important one at the time is [NMatrix][nmatrix], as it's very hard to create some scientific library that doesn't need a good numerical linear algebra library to deal with vectors and matrices.
+SciRuby is an umbrella for many other projects in Ruby. The most important one at the time is [NMatrix][nmatrix], as it's very hard to create some scientific library that doesn't need a good numerical linear algebra library to deal with vectors and matrices.
 
 So, the SciRuby subprojects are, in no particular order:
 
@@ -21,6 +22,7 @@ So, the SciRuby subprojects are, in no particular order:
 - [Distribution][distribution]: Diverse statistical distributions. Uses C (statistics2/GSL) or Java extensions when available.
 - [Integration][integration]: Integration methods.
 - [Minimization][minimization]: Various minimization algorithms in pure Ruby.
+- [IRuby][iruby]: Ruby kernel for the IPython/Jupyter notebook
 
 ## Documentation
 
@@ -43,4 +45,5 @@ Before commiting any code, you *MUST* read our [Contributor Agreement](http://gi
 [distribution]: https://github.com/SciRuby/distribution
 [integration]: https://github.com/SciRuby/integration
 [minimization]: https://github.com/SciRuby/minimization
+[iruby]: https://github.com/SciRuby/iruby
 [rdoc]: http://rdoc.rubyforge.org/

data/README.md

@@ -4,34 +4,40 @@ 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)
+* [List of scientific gems](http://gems.sciruby.com)
+* [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.
+This gem acts as a meta gem which provides collects multiple [scientific gems](http://gems.sciruby.com), including numeric and visualization libraries.
 
 ## Getting started
 
 Installation:
 
-    gem install sciruby
-    gem install sciruby-full
+~~~
+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
+~~~
+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])
+~~~ ruby
+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`.
+Take a look at [gems.yml](gems.yml) or the [list of gems](http://gems.sciruby.com) for interesting gems which are included in `sciruby-full`.
 
 ## License
 

data/Rakefile

@@ -1,5 +1,5 @@
 task 'gems.html' do
-  sh 'slimrb --trace scripts/gems.slim > gems.html'
+  sh 'slimrb --trace scripts/gems.slim > /tmp/gems.html && mv /tmp/gems.html .'
 end
 
 task :test do

data/gems.yml

@@ -1,6 +1,6 @@
 ---
 ai4r:
-  category: artificial intelligence
+  category: ai
   description: Artificial intelligence
   module: Ai4r
   version: "~> 1.13"
@@ -15,6 +15,17 @@ awesome_print:
   category: utilities
   description: Pretty object printing
   version: "~> 1.6"
+bibsync:
+  category: publishing
+  description: Bibliography synchronization
+  module: BibSync
+  version: "~> 0.0"
+bibtex-ruby:
+  category: publishing
+  description: BibTeX parser
+  module: BibTeX
+  require: bibtex
+  version: "~> 4.0"
 bio:
   category: biology
   description: Bioinformatics suite
@@ -26,14 +37,15 @@ cassowary:
   exclude: Native dependencies
   module: Cassowary
 classifier:
-  category: artificial intelligence
+  category: ai
   description: Machine learning
   module: Classifier
   version: "~> 1.3"
 cmath:
   category: algebra
   description: Stdlib cmath module
-  maintainer: stdlib
+  module: CMath
+  owner: stdlib
 daru:
   category: data
   description: Dataframe library
@@ -45,19 +57,20 @@ darwinning:
   module: Darwinning
   version: "~> 0.0"
 decisiontree:
-  category: artificial intelligence
+  category: ai
   description: Machine learning
   module: DecisionTree
   version: "~> 0.5"
 distribution:
   category: statistics
   description: Statistical distributions
-  maintainer: sciruby
   module: Distribution
+  owner: sciruby
   version: "~> 0.7"
 extendmatrix:
   category: algebra
   description: Helper methods for Matrix
+  owner: sciruby
   version: "~> 0.4"
 gga4r:
   category: optimization
@@ -74,23 +87,39 @@ gnuplot:
   description: Plotting library
   module: Gnuplot
   version: "~> 2.6"
+gruff:
+  category: plotting
+  description: Plotting library
+  module: Gruff
+  version: "~> 0.6"
+histogram:
+  category: statistics
+  description: Histogram method
+  module: Histogram
+  version: "~> 0.2"
 integration:
   category: numerics
   description: Numerical integration
-  maintainer: sciruby
   module: Integration
+  owner: sciruby
   version: "~> 0.1"
 irtruby:
-  category: artificial intelligence
+  category: ai
   description: Machine learning
   exclude: Not available as a gem
   module: IRT
 iruby:
-  category: user interface
+  category: ui
   description: Ruby kernel for Jupyter
-  maintainer: sciruby
   module: IRuby
+  owner: sciruby
   version: "~> 0.2"
+liblinear-ruby:
+  category: ai
+  description: Linear classifier
+  module: Liblinear
+  require: liblinear
+  version: "~> 0.0"
 lpsolve:
   category: optimization
   description: Linear solver
@@ -104,32 +133,49 @@ mathgl:
 matrix:
   category: algebra
   description: Stdlib matrix module
-  maintainer: stdlib
-  module: Matrix
+  module:
+  - Matrix
+  - Vector
+  owner: stdlib
+mdarray:
+  category: numerics
+  description: Numerical matrix library
+  exclude: Requires JRuby
+  module: MDArray
+measurable:
+  category: ai
+  description: Distance measures for machine learning
+  module: Measurable
+  version: "~> 0.0"
+mikon:
+  category: data
+  description: Dataframe library
+  module: Mikon
+  version: "~> 0.0"
 minimization:
   category: numerics
   description: Numerical minimization
-  maintainer: sciruby
   module: Minimization
+  owner: sciruby
   version: "~> 0.2"
 modshogun:
-  category: artificial intelligence
+  category: ai
   description: Machine learning
   exclude: Not available as a gem
   module: Modshogun
 narray:
   category: numerics
-  description: Numerics matrix library
+  description: Numerical matrix library
   exclude: Conflicts with nmatrix
   module: NArray
 nmatrix:
   category: numerics
-  description: Numerics matrix library
-  maintainer: sciruby
+  description: Numerical matrix library
   module:
   - N
   - NMatrix
   - NVector
+  owner: sciruby
   version: "~> 0.1"
 nyaplot:
   category: plotting
@@ -141,6 +187,24 @@ ode:
   description: Ordinary differential equations
   exclude: Fortran dependencies
   module: Ode
+omoikane:
+  category: ai
+  description: Machine learning
+  module: Omoikane
+  version: "~> 0.0"
+parallel:
+  category: utilties
+  description: Parallel processing
+  module: Parallel
+  version: "~> 1.6"
+phys-units:
+  category: physics
+  description: Calculation with units
+  module:
+  - Phys::Unit
+  - Phys::Quantity
+  require: phys/units
+  version: "~> 0.9"
 plotrb:
   category: plotting
   description: Plotting library
@@ -149,11 +213,11 @@ plotrb:
 prime:
   category: algebra
   description: Stdlib prime module
-  maintainer: stdlib
   module: Prime
+  owner: stdlib
 pry:
-  category: user interface
-  description: Ruby repl
+  category: ui
+  description: Ruby shell
   module: Pry
   version: "~> 0.10"
 publisci:
@@ -168,11 +232,16 @@ rb-gsl:
   module: GSL
   require: gsl
 rb-libsvm:
-  category: artificial intelligence
+  category: ai
   description: Support vector machines (machine learning)
   module: Libsvm
   require: libsvm
   version: "~> 1.3"
+rbmetis:
+  category: graph
+  description: Graph partitioning
+  exclude: Native dependencies
+  module: RbMetis
 rinruby:
   category: statistics
   description: R interpreter
@@ -192,15 +261,16 @@ rsruby:
   exclude: Native dependencies
   module: RSRuby
 ruby-band:
-  category: artificial intelligence
+  category: ai
   description: Data mining
   exclude: Requires JRuby
 ruby-dcl:
   category: plotting
   description: Plotting
   exclude: Requires narray
+  module: NumRu::DCL
 ruby-fann:
-  category: artificial intelligence
+  category: ai
   description: Neural networks
   module: RubyFann
   version: "~> 1.2"
@@ -219,8 +289,9 @@ ruby-netcdf:
   category: data
   description: Data file
   exclude: Requires narray
+  module: NumRu::NetCDF
 ruby-opencv:
-  category: artificial intelligence
+  category: ai
   description: Computer vision
   exclude: Native dependencies
   module: OpenCV
@@ -238,43 +309,51 @@ rubyvis:
 sciruby:
   category: meta
   description: SciRuby meta gem
-  maintainer: sciruby
+  owner: sciruby
 sciruby-full:
   category: meta
   description: SciRuby meta gem (Full installation)
-  maintainer: sciruby
-sicom:
-  category: statistics
-  description: R interpreter
-  exclude: Requires JRuby
+  owner: sciruby
 statsample:
   category: statistics
   description: Statistics
-  maintainer: sciruby
   module: Statsample
+  owner: sciruby
   version: "~> 1.4"
 statsample-bivariate-extension:
   category: statistics
-  description: Statistics
+  description: Statsample extension (Autoloaded)
   version: "~> 1.1"
 statsample-glm:
   category: statistics
   description: Statistics
-  maintainer: sciruby
+  module: Statsample::GLM
+  owner: sciruby
   version: "~> 0.1"
 statsample-optimization:
   category: statistics
-  description: Statistics
+  description: Statsample extension (Autoloaded)
   exclude: GSL conflict
+statsample-sem:
+  category: statistics
+  description: Statistics
+  exclude: Outdated dependencies
+  module: Statsample::SEM
 statsample-timeseries:
   category: statistics
   description: Statistics
   exclude: activesupport version conflict
+  module: Statsample::Timeseries
 stuff-classifier:
-  category: artificial intelligence
+  category: ai
   description: Machine learning
   module: StuffClassifier
   version: "~> 0.5"
+treat:
+  category: linguistics
+  description: Natural language processing
+  exclude: birch doesn't compile with 2.2
+  module: Treat
 unit:
   category: physics
   description: Calculation with units

data/lib/sciruby/autoload.rb

@@ -2,12 +2,16 @@ class Module
   alias :const_missing_without_sciruby :const_missing
 
   def const_missing(name)
-    paths = SciRuby.autoload_modules.delete(name.to_sym)
-    if paths
-      paths.each {|path| require path }
-      const_get(name)
-    else
+    (Object != self && sciruby_autoload("#{self.name}::#{name}")) ||
+      sciruby_autoload(name) ||
       const_missing_without_sciruby(name)
-    end
+  end
+
+  private
+
+  def sciruby_autoload(name)
+    return unless paths = SciRuby.autoload_modules.delete(name.to_s)
+    paths.each {|path| require path }
+    const_get(name)
   end
 end

data/lib/sciruby/gems.rb

@@ -33,8 +33,14 @@ module SciRuby
       gem = Hash[gem.map {|k,v| [k.to_sym, v] }]
       gem[:name] = name
       gem[:require] = [*(gem[:require] || name)]
-      gem[:module] = [*gem[:module]].map(&:to_sym)
-      gem[:module].each {|mod| autoload_modules[mod] = gem[:require] }
+      gem[:module] = [*gem[:module]]
+      gem[:module].each do |mod|
+        parts = mod.split('::')
+        parts.size.times do |i|
+          m = parts[0..i].join('::')
+          autoload_modules[m] = (i < parts.size - 1 && autoload_modules[m]) || gem[:require]
+        end
+      end
       gems[name] = gem
     end
   end

data/lib/sciruby/version.rb

@@ -2,5 +2,5 @@
 module SciRuby
   # SciRuby version string
   # @api public
-  VERSION = '0.2.4'
+  VERSION = '0.2.5'
 end

data/sciruby.gemspec

@@ -1,9 +1,7 @@
 require File.expand_path(File.join(__FILE__, '..', 'scripts', 'helper.rb'))
 
-SCIRUBY_FULL = false unless defined?(SCIRUBY_FULL)
-
 Gem::Specification.new do |s|
-  s.name        = SCIRUBY_FULL ? 'sciruby-full' : 'sciruby'
+  s.name        = __FILE__.sub('.gemspec', '')
   s.date        = Date.today.to_s
   s.version     = SciRuby::VERSION
   s.authors     = ['SciRuby Development Team']
@@ -11,9 +9,9 @@ Gem::Specification.new do |s|
   s.license     = 'BSD'
   s.homepage    = 'http://sciruby.com'
   s.summary     =
-  s.description = "Scientific gems for Ruby#{SCIRUBY_FULL ? ' (Full installation)' : ''}"
+  s.description = "Scientific gems for Ruby#{__FILE__ =~ /full/ ? ' (Full installation)' : ''}"
 
-  if SCIRUBY_FULL
+  if __FILE__ =~ /full/
     s.files = %w(CHANGES CONTRIBUTING.md README.md LICENSE sciruby-full.gemspec)
 
     s.add_runtime_dependency 'sciruby', "= #{SciRuby::VERSION}"

data/scripts/deploy

@@ -13,6 +13,6 @@ git fetch && git reset origin/gh-pages
 
 cp ../gems.html index.html
 
-git add -A .
+git add index.html
 git commit -m "rebuild pages"
 git push -q origin HEAD:gh-pages

data/scripts/gems.slim

@@ -5,53 +5,104 @@ html
     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"
+    link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.3.0/css/font-awesome.min.css"
     script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.js"
+    script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.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
+    css:
+      td, th { white-space: nowrap; font-size: small; }
+      td .fa-diamond, .fa-close { color: #8B0000 }
+      td .fa-github { color: #000000 }
+      td .fa-book { color: #191970 }
+      td .fa-home, .fa-check { color: #006400 }
+      td .fa-warning { color: #FF8C00 }
+      h1 { margin-bottom: -1em; }
+      a { color: #8B0000 }
+      a:hover { color: #F00 }
+      tr.exclude { background: #F88 !important }
+      tr.warnings { background: #FF8 !important }
+  body: .container: .row: .col-md-12
+    h1
+      img width="50" src="http://upload.wikimedia.org/wikipedia/commons/7/73/Ruby_logo.svg"
+      a< href="http://sciruby.com" SciRuby gems
     table.table data={ toggle:            'table',
                        search:            'true',
                        sortable:          'true',
                        show_toggle:       'true',
                        show_columns:      'true',
                        mobile_responsive: 'true',
-                       striped:           'true' }
+                       striped:           'true',
+                       height:            550 }
       thead: tr
-        th data-sortable="true" Maintainer
-        th data-sortable="true" Category
+        th data-sortable="true": span title="Status" S
+        th data-sortable="true": span.fa.fa-umbrella title="Owner"
+        th data-sortable="true": span.fa.fa-folder-open-o title="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
+        th: span.fa.fa-external-link title="Links"
+        th data-sortable="true": span title="Version constraint" C
+        th data-sortable="true": span title="Version" V
+        th data-sortable="true": span.fa.fa-calendar title="Release date"
+        th data-sortable="true" Autoload modules
+        th data-sortable="true": span.fa.fa-exclamation-circle title="Issues"
+        th data-sortable="true": span.fa.fa-star title="Stars"
+        th data-sortable="true": span.fa.fa-eye title="Watchers"
+        th data-sortable="true": span.fa.fa-code-fork title="Forks"
+        th data-sortable="true"
+          span.fa.fa-warning>
+          | Warnings
       tbody
-        - Helper.sorted_gems.each do |gem|
-          - spec = Helper.fetch_spec(gem)
-          tr
+        - Helper.table_gems.each do |gem|
+          tr class=gem[:status]
             td
-              - if gem[:maintainer]
-                - maintainer_tag = { 'stdlib' => 'info', 'sciruby' => 'success' }
-                span.label class="label-#{maintainer_tag[gem[:maintainer]] || 'warning'}" = gem[:maintainer]
+              - if gem[:status] == 'exclude'
+                span.fa.fa-close title="Excluded from sciruby-full"
+              - elsif gem[:status] == 'ok'
+                span.fa.fa-check title="Ok, included in sciruby-full"
+              - else
+                span.fa.fa-warning title="#{gem[:warnings].size} warnings, included in sciruby-full"
+            td = gem[:owner]
             td = gem[:category]
-            - if spec
-              td
-                a href=spec.homepage = gem[:name]
+            - if gem[:homepage]
+              td: a href=gem[:homepage] = gem[:name]
             - else
               td = gem[:name]
+            td = gem[:description]
+            td
+              - if gem[:homepage]
+                a<> href=gem[:homepage] : span.fa.fa-home
+              - if gem[:docs]
+                a<> href=gem[:docs] : span.fa.fa-book
+              - if gem[:spec]
+                a<> href="https://rubygems.org/gems/#{gem[:name]}": span.fa.fa-diamond
+              - if gem[:github]
+                a<> href="https://github.com/#{gem[:github]}": span.fa.fa-github
             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(', ')
+              - if gem[:spec]
+                a href="https://rubygems.org/gems/#{gem[:name]}" = gem[:spec].version
             td
-              - Helper.gem_status(gem).each do |tag, msg|
-                  span.label<> class="label-#{tag}" = msg
+              - if gem[:spec]
+                = gem[:date]
+            td == gem[:module].join(', ')
+            - if gem[:github]
+              td: a href="https://github.com/#{gem[:github]}/issues" = gem[:issues]
+              td: a href="https://github.com/#{gem[:github]}/stargazers" = gem[:stars]
+              td: a href="https://github.com/#{gem[:github]}/watchers" = gem[:watchers]
+              td: a href="https://github.com/#{gem[:github]}/network" = gem[:forks]
+            - else
+              td
+              td
+              td
+              td
+            td == gem[:warnings].join(', ')
+    .footer
+      ' 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'].to_s[0,8]}</a>.
+      - else
+        ' by #{`hostname -f`.chomp}.
+      | #{SciRuby.gems.size} gems registered in <a href="https://github.com/SciRuby/sciruby/blob/master/gems.yml">sciruby/gems.yml</a>,
+        #{SciRuby.gems.each_value.count {|gem| !gem[:exclude] }} included in <a href="https://rubygems.org/gems/sciruby-full">sciruby-full</a>,
+        #{SciRuby.gems.each_value.count {|gem| gem[:exclude] }} excluded.

data/scripts/helper.rb

@@ -43,7 +43,7 @@ module Helper
     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])
+    if gem[:exclude] || gem[:owner] == 'stdlib' || %w(sciruby sciruby-full).include?(gem[:name])
       gem[:version].must_be_nil
     else
       gem[:version].must_be_instance_of String
@@ -52,32 +52,101 @@ module Helper
 
   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
+    dep = Gem::Dependency.new(gem[:name])
+    spec = Gem::SpecFetcher.fetcher.spec_for_dependency(dep, false).flatten[-2]
+    return spec if spec
+    dep.prerelease = true
+    Gem::SpecFetcher.fetcher.spec_for_dependency(dep, false).flatten[-2]
   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)
+  def gem_warnings(gem)
+    warnings = []
+    warnings << "Excluded: #{gem[:exclude]}" if gem[:exclude]
+    if gem[:spec]
+      warnings << "Last update #{gem[:date]}" if Time.now - gem[:spec].date > 2*365*24*3600
+      warnings << 'Outdated version constraint' if gem[:version] && !Gem::Dependency.new(gem[:name], *gem[:version]).matches_spec?(gem[:spec])
+      warnings << 'Github repository unknown' unless gem[:github]
     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)
+      warnings << 'Gem not found' unless gem[:exclude] || gem[:owner] == 'stdlib'
+    end
+    warnings << %{<a href="https://versioneye.com/ruby/#{gem[:name]}">Outdated dependencies</a>} if versioneye(gem[:name])
+    warnings
   end
 
-  def sorted_gems
-    SciRuby.gems.each_value.
-      stable_sort_by {|gem| gem[:name] }.
+  def table_gems
+    require 'parallel'
+    require 'net/http'
+    require 'json'
+
+    owner_order = {
+      'sciruby' => 0,
+      'stdlib'  => 1
+    }
+    owner_order.default = 2
+
+    status_order = {
+      'ok'       => 0,
+      'warnings' => 1,
+      'exclude'  => 2
+    }
+
+    Parallel.map(SciRuby.gems.values, in_processes: 8) do |gem|
+      gem = gem.dup
+
+      if gem[:owner] == 'stdlib'
+        gem[:homepage] = gem[:docs] = "http://ruby-doc.org/stdlib/libdoc/#{gem[:name]}/rdoc/"
+        gem[:github] = "ruby/ruby/blob/trunk/lib/#{gem[:name]}.rb"
+        gem[:module] = gem[:module].map {|mod| %{<a href="#{gem[:docs]}#{mod.gsub('::', '/')}.html">#{mod}</a>} }
+      elsif spec = fetch_spec(gem)
+        gem[:spec] = spec
+        gem[:date] = spec.date.strftime('%Y-%m-%d')
+        gem[:homepage] = spec.homepage
+        gem[:docs] = "http://www.rubydoc.info/gems/#{gem[:name]}/#{spec.version}"
+        gem[:module] = gem[:module].map {|mod| %{<a href="#{gem[:docs]}/#{mod.gsub('::', '/')}">#{mod}</a>} }
+        github_infos(gem)
+      end
+      gem[:warnings] = gem_warnings(gem)
+
+      if gem[:exclude]
+        gem[:status] = 'exclude'
+      elsif gem[:warnings].empty?
+        gem[:status] = 'ok'
+      else
+        gem[:status] = 'warnings'
+      end
+
+      gem
+    end.stable_sort_by {|gem| gem[:name] }.
       stable_sort_by {|gem| gem[:category] }.
-      stable_sort_by {|gem| gem[:maintainer] == 'sciruby' ? 0 : (gem[:maintainer] ? 1 : 2) }
+      stable_sort_by {|gem| owner_order[gem[:owner]] }.
+      stable_sort_by {|gem| status_order[gem[:status]] }
+  end
+
+  def github_infos(gem)
+    if gem[:github] = github_name(gem)
+      data = JSON.parse(Net::HTTP.get(URI("https://api.github.com/repos/#{gem[:github]}?client_id=#{ENV['CLIENT_ID']}&client_secret=#{ENV['CLIENT_SECRET']}")))
+      gem[:issues] = data['open_issues_count']
+      gem[:forks] = data['forks_count']
+      gem[:stars] = data['stargazers_count']
+      gem[:watchers] = data['subscribers_count']
+    end
+  end
+
+  def github_name(gem)
+    return $1 if gem[:spec].homepage =~ %r{github.com/([^/]+/[^/]+)}
+    JSON.parse(Net::HTTP.get(URI("https://rubygems.org/api/v1/gems/#{gem[:name]}.json"))).each do |k,v|
+      return $1 if k =~ /_uri/ && v =~ %r{github.com/([^/]+/[^/]+)}
+    end
+    nil
+  end
+
+  def versioneye(name)
+    Net::HTTP.get(URI("https://www.versioneye.com/ruby/#{name}/badge")) =~ /out of date/
   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])
+      gem[:owner] == 'stdlib' || %w(sciruby sciruby-full).include?(gem[:name])
     end.reject {|gem| gem[:exclude] && exclude }
   end
 end

data/scripts/test

@@ -20,7 +20,7 @@ describe 'gems.yml' do
 
   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.each_key {|k| %w(category owner description exclude version module require).include?(k).must_equal true }
       gem['require'].wont_equal name if gem['require']
     end
   end
@@ -46,32 +46,37 @@ describe SciRuby do
 
   it 'provides list of modules' do
     SciRuby.modules.must_be_instance_of Array
-    SciRuby.modules.each {|m| m.must_be_instance_of Symbol }
+    SciRuby.modules.each {|m| m.must_be_instance_of String }
   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 }
+    SciRuby.installed_modules.each {|m| m.must_be_instance_of String }
   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_key {|k| k.must_be_instance_of String }
     SciRuby.autoload_modules.each_value {|v| v.must_be_instance_of Array }
   end
 
+  it 'has unique modules' do
+    mods = SciRuby.gems.each_value.map {|gem| gem[:module] }.flatten
+    mods.uniq.must_equal mods
+  end
+
   it 'autoloads modules' do
-    SciRuby.autoload_modules.must_include :Prime
+    SciRuby.autoload_modules.must_include 'Prime'
 
-    Object.const_defined?(:Prime).must_equal false
+    Object.const_defined?('Prime').must_equal false
     Prime.must_be_instance_of Class
-    Object.const_defined?(:Prime).must_equal true
+    Object.const_defined?('Prime').must_equal true
 
-    SciRuby.autoload_modules.wont_include :Prime
+    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
+      next if mod == 'R' || mod == 'RinRuby' # FIXME, don't test RinRuby for now since it requires an installaion of R
+      eval(mod).wont_equal nil
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sciruby
 version: !ruby/object:Gem::Version
-  version: 0.2.4
+  version: 0.2.5
 platform: ruby
 authors:
 - SciRuby Development Team
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-10 00:00:00.000000000 Z
+date: 2015-06-13 00:00:00.000000000 Z
 dependencies: []
 description: Scientific gems for Ruby
 email:
@@ -44,6 +44,8 @@ post_install_message: |+
     * ai4r - Artificial intelligence
     * algorithms - Algorithms and data structures
     * awesome_print - Pretty object printing
+    * bibsync - Bibliography synchronization
+    * bibtex-ruby - BibTeX parser
     * bio - Bioinformatics suite
     * cassowary - Incremental constraint solver
     * classifier - Machine learning
@@ -55,22 +57,32 @@ post_install_message: |+
     * gga4r - Generic algorithms
     * gimuby - Genetic algorithms
     * gnuplot - Plotting library
+    * gruff - Plotting library
+    * histogram - Histogram method
     * integration - Numerical integration
     * irtruby - Machine learning
     * iruby - Ruby kernel for Jupyter
+    * liblinear-ruby - Linear classifier
     * lpsolve - Linear solver
     * mathgl - Plotting library
+    * mdarray - Numerical matrix library
+    * measurable - Distance measures for machine learning
+    * mikon - Dataframe library
     * minimization - Numerical minimization
     * modshogun - Machine learning
-    * narray - Numerics matrix library
-    * nmatrix - Numerics matrix library
+    * narray - Numerical matrix library
+    * nmatrix - Numerical matrix library
     * nyaplot - Plotting library
     * ode - Ordinary differential equations
+    * omoikane - Machine learning
+    * parallel - Parallel processing
+    * phys-units - Calculation with units
     * plotrb - Plotting library
-    * pry - Ruby repl
+    * pry - Ruby shell
     * publisci - Publishing toolkit
     * rb-gsl - Bindings for the GNU scientific library
     * rb-libsvm - Support vector machines (machine learning)
+    * rbmetis - Graph partitioning
     * rinruby - R interpreter
     * rserve-client - R interpreter
     * rsruby - R interpreter
@@ -83,13 +95,14 @@ post_install_message: |+
     * ruby-opencv - Computer vision
     * ruby-pgplot - Plotting
     * rubyvis - Plotting library
-    * sicom - R interpreter
     * statsample - Statistics
-    * statsample-bivariate-extension - Statistics
+    * statsample-bivariate-extension - Statsample extension (Autoloaded)
     * statsample-glm - Statistics
-    * statsample-optimization - Statistics
+    * statsample-optimization - Statsample extension (Autoloaded)
+    * statsample-sem - Statistics
     * statsample-timeseries - Statistics
     * stuff-classifier - Machine learning
+    * treat - Natural language processing
     * unit - Calculation with units
 
 rdoc_options: []