distribution 0.7.1 → 0.7.2

checksums.yaml

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data/.travis.yml

@@ -1,12 +1,15 @@
 language: ruby
 rvm:
-  - "1.8.7"
-  - "1.9.2"
-  - "1.9.3"
-  - jruby-18mode # JRuby in 1.8 mode
-  - jruby-19mode # JRuby in 1.9 mode
-  - rbx-18mode
-  - rbx-19mode
-# uncomment this line if your project needs to run something other than `rake`:
-# script: bundle exec rspec spec
+  - 1.9.3
+  - 2.0
+  - 2.1
+  - 2.2
+#  - jruby-19mode # JRuby in 1.9 mode -> Problems with bigint
+#  - rbx-19mode
 
+script:
+  bundle exec rake
+
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -y libgsl0-dev

data/Gemfile

@@ -1,5 +1,3 @@
-# A sample Gemfile
 source "https://rubygems.org"
-gem "rspec"
-gem "rb-gsl"
+gem "rb-gsl", :platforms=>[:ruby,:mswin]
 gemspec

data/History.txt

@@ -1,12 +1,15 @@
-=== 0.7.0 / 2011-11-30
+=== 0.7.2 / 2015-04-03
+  * Formatting files according to the community's best practices.
+  * Other minor improvements in gemspec, Rakefile, etc.
 
+=== 0.7.0 / 2011-11-30
 + Basic log-normal distribution support, with pdf and cdf for ruby [dennyabraham and clbustos]
-* Matthew Peterson add Java support for Poisson and Normal distributions. 
+* Matthew Peterson add Java support for Poisson and Normal distributions.
 * Updated Logistic, Normal spec. Added LogNormal spec [clbustos]
 * Updated template for new distributions
 
 === 0.6.0 / 2011-09-23
-* Incomplete Beta functions on math renamed to Regularized beta, because MathExtension::IncompleteBeta calculates regularized beta function, not Incomplete Beta. 
+* Incomplete Beta functions on math renamed to Regularized beta, because MathExtension::IncompleteBeta calculates regularized beta function, not Incomplete Beta.
 * Corrected documention on F distribution and added comments on gamma and beta[Claudio Bustos]
 * Moved ported methods from GSL to lib/math_extension. Updated spec for gamma and beta distributions[Claudio Bustos]
 * Added beta distribution functions. p_value does not seem to work yet.[John Woods]
@@ -20,15 +23,15 @@
 === 0.5.0 / 2011-05-03
 
 * Exception raises on calculation of T's cdf with ruby engine. For now, stick to gsl implementation
-* Added logistic distribution. 
-* Raises an error on binomial if k>n. 
+* Added logistic distribution.
+* Raises an error on binomial if k>n.
 * New rng for exponential distribution, based on F^-1 [clbustos]
 * Added power benchmark
 
 === 0.4.0 / 2011-02-01
 
 * Poisson and exponential distributions implemented. Implementation of inverse cdf for poisson is not perfect, yet.
-* +distribution+ executable can create template files for new distributions. 
+* +distribution+ executable can create template files for new distributions.
 * MathExtension should work fine with Ruby 1.8. Fixed shadowed variable on MathExtension.naive_factorial
 * Added factorial lookup table for n<20.
 * Added exact cdf for Binomial
@@ -39,19 +42,19 @@
 
 * Included support for binomial distribution. p_value is not accurate
 * Included alias for ruby exact methods on discrete distributions, when they are available
-* Works on Jruby and Ruby 1.8.7 
+* Works on Jruby and Ruby 1.8.7
 * Binomial coefficient optimized. Falling factorial method with Swing Prime on factorial provides a 10x improvement over naive version.
 * Working on binomial coefficient using gamma. The same problem as using Sterling: faster than exact version, but when it requires BigDecimal, is 2-3x slower
 * Deleted Fixnum extension on Hypergeometric
 
 === 0.2.0 / 2011-01-27
-* Shorthands for F and T are 'fdist' and 'tdist' now, to avoid confussions 
+* Shorthands for F and T are 'fdist' and 'tdist' now, to avoid confussions
 * Added Hypergeometric distribution with pdf, cdf, p_value. The Ruby version uses a very slow factorial process, but also has pdf_with_stirling if you don't care about accuracy at all. This latter method needs to be improved, actually, in terms of which choose function it calls for the numerator and denominator. Once that's done, it can replace the slower pdf function. [John Woods]
-* Spec for cdf and p_value of Hypergeometric 
+* Spec for cdf and p_value of Hypergeometric
 * New cdf and p_value on Hypergeometric[clbustos]
 * Hypergeometric#pdf returns 0 on max(0,n+m-t)<=k<=min(m,n)
 * Improved factorial calculation, using Luschny algorithms
 
 === 0.1.0 / 2011-01-26
 
-* Basic set (pdf, cdf, p_value) for Normal, Chi Square, F and T distributions 
+* Basic set (pdf, cdf, p_value) for Normal, Chi Square, F and T distributions

data/README.md

@@ -1,10 +1,21 @@
-# [Distribution](https://github.com/clbustos/distribution) Quick Start
+# [Distribution](https://github.com/sciruby/distribution)
+
+[![Build Status](https://travis-ci.org/SciRuby/distribution.svg?branch=master)](https://travis-ci.org/SciRuby/distribution)
+[![Code Climate](https://codeclimate.com/github/SciRuby/distribution/badges/gpa.svg)](https://codeclimate.com/github/SciRuby/distribution)
+
+## Installation
 
 ```
-git clone https://github.com/sciruby/distribution
+$ gem install distribution
 ```
 
-## Description:
+If you have GSL installed and want to speed things up, install `rb-gsl`:
+
+```bash
+$ gem install rb-gsl
+```
+
+## Description
 
 Statistical Distributions library. Includes Normal univariate and bivariate, T, F, Chi Square, Binomial, Hypergeometric, Exponential, Poisson, Beta, LogNormal and Gamma.
 
@@ -12,47 +23,41 @@ Uses Ruby by default and C (statistics2/GSL) or Java extensions where available.
 
 Includes code from statistics2 on Normal, T, F and Chi Square ruby code [http://blade.nagaokaut.ac.jp/~sinara/ruby/math/statistics2]
 
-## Synopsis:
-  * Returns Gaussian PDF for x
-  pdf=Distribution::Normal.pdf(x)
-  * Returns Gaussian CDF for x
-  cdf=Distribution::Normal.cdf(x)
-  * Returns inverse CDF (or p-value) for x
-  pv=Distribution::Normal.p_value(x)
+## Synopsis
 
-## System Requirements:
+* Returns Gaussian PDF for x
 
-To increase (notably!) the speed, please install
+```
+pdf=Distribution::Normal.pdf(x)
+```
 
-* Ruby 1.8-1.9: gsl (prefered) or statistics2
-* Java: Not yet implemented
+* Returns Gaussian CDF for x
 
-## User Installation:
 ```
-  gem install distribution
+cdf=Distribution::Normal.cdf(x)
 ```
-To speep up
+
+* Returns inverse CDF (or p-value) for x
+
 ```
-  gem install gsl
-  gem install statistics
+pv=Distribution::Normal.p_value(x)
 ```
 
-## Developers:
+## Developers
 
-After checking out the source, run:
 ```
-  $ rake newb
+$ git clone https://github.com/SciRuby/distribution.git
 ```
-This task will install any missing dependencies, run the tests/specs,
-and generate the RDoc.
 
-If you want to provide a new distribution, /lib/distribution run
+If you want to provide a new distribution, run `lib/distribution`:
+
 ```
-  $ distribution --new your_distribution
+$ distribution --new your_distribution
 ```
-This should create the main distribution file, the directory with ruby and gsl engines and the rspec on /spec directory.
 
-### API Structure
+This should create the main distribution file, the directory with Ruby and GSL engines and specs on the spec/ directory.
+
+## API Structure
 
   Distribution::<name>.(cdf|pdf|p_value|rng)
 
@@ -88,7 +93,9 @@ Shortnames for distributions:
 ```
   Distribution::T.cdf
 ```
+
 could be called after including Distribution::Shorthand
+
 ```
   tdist_cdf
 ```
@@ -100,6 +107,6 @@ could be called after including Distribution::Shorthand
 
 ## Issues
 
-* On Jruby and Rubinius, BivariateNormal returns incorrect pdf
+* On JRuby and Rubinius, BivariateNormal returns incorrect pdf
 
-For current issues see the [issue tracker pages](https://github.com/clbustos/distribution/issues)
+For current issues see the [issue tracker pages](https://github.com/sciruby/distribution/issues).

data/Rakefile

@@ -1,28 +1,22 @@
-# -*- ruby -*-
-$:.unshift(File.expand_path(File.dirname(__FILE__)+"/lib/"))
-require 'rubygems'
-#require 'hoe'
-require 'distribution'
-# Hoe.plugin :compiler
-# Hoe.plugin :gem_prelude_sucks
-# Hoe.plugin :git
-# Hoe.plugin :inline
-# Hoe.plugin :racc
-# Hoe.plugin :rubyforge
+require 'bundler'
+require 'bundler/gem_tasks'
+require 'rake'
+require 'rspec/core/rake_task'
 
-#Hoe.spec 'distribution' do
-#  self.developer('Claudio Bustos', 'clbustos_at_gmail.com')
-#  self.version=Distribution::VERSION
-#  self.extra_dev_deps << ["rspec",">=2.0"] << ["rubyforge",">=0"]
+# Setup the necessary gems, specified in the gemspec.
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
 
-#end
-# git log --pretty=format:"*%s[%cn]" v0.5.0..HEAD >> History.txt
 desc "Open an irb session preloaded with distribution"
 task :console do
   sh "irb -rubygems -I lib -r distribution.rb"
 end
 
-require 'bundler'
-Bundler::GemHelper.install_tasks
+RSpec::Core::RakeTask.new(:spec)
 
-# vim: syntax=ruby
+task :default => :spec

data/distribution.gemspec

@@ -1,20 +1,26 @@
-# -*- encoding: utf-8 -*-
-require File.expand_path("../lib/distribution/version", __FILE__)
+$LOAD_PATH.unshift File.expand_path('../lib', __FILE__)
+
+require 'date'
+require 'distribution/version'
 
 Gem::Specification.new do |s|
   s.name = "distribution"
   s.version = Distribution::VERSION
-  s.platform = Gem::Platform::RUBY
+  s.date = Date.today.to_s
+  s.homepage = "https://github.com/sciruby/distribution"
+
   s.authors = ['Claudio Bustos']
-  s.email = []
-  s.homepage = "http://rubygems.org/gems/foodie"
+  s.email = ['clbustos@gmail.com']
+
+  s.platform = Gem::Platform::RUBY
   s.summary = "Distribution"
   s.description = "Distribution"
 
-  s.required_rubygems_version = ">= 1.3.6"
-  s.add_development_dependency "bundler", ">= 1.0.0"
-  s.add_development_dependency "rspec"
   s.files = `git ls-files`.split("\n")
   s.executables = `git ls-files`.split("\n").map{|f| f =~ /^bin\/(.*)/ ? $1 : nil}.compact
   s.require_path = 'lib'
+
+  s.add_development_dependency 'bundler'
+  s.add_development_dependency 'rake'
+  s.add_development_dependency "rspec", '~> 3.2'
 end

data/lib/distribution.rb

@@ -1,6 +1,6 @@
-# = distribution.rb - 
+# = distribution.rb -
 # Distribution - Statistical Distributions package for Ruby
-# 
+#
 # Copyright (C) 2011-2014  Claudio Bustos
 #
 # This program is free software; you can redistribute it and/or
@@ -18,62 +18,54 @@
 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 #
 # == Other Sources
-# 
-# * Code of several Ruby engines came from statistics2.rb, 
+#
+# * Code of several Ruby engines came from statistics2.rb,
 #   created by Shin-ichiro HARA(sinara@blade.nagaokaut.ac.jp).
 #   Retrieve from http://blade.nagaokaut.ac.jp/~sinara/ruby/math/statistics2/
 # * Code of Beta and Gamma distribution came from GSL project.
 #   Ported by John O. Woods
 # Specific notices will be placed where there are appropiate
-# 
-if !respond_to? :define_singleton_method
-  class Module
-    public :define_method
-  end
-  
-  class Object
-    def define_singleton_method(name,&block)
-      sc=class <<self;self;end
-      sc.define_method(name,&block)
-    end
-  end
-end
-require 'distribution/math_extension'
+#
 
+require 'distribution/math_extension'
+require 'distribution/version'
 
 # Several distributions modules to calculate pdf, cdf, inverse cdf and generate
 # pseudo-random numbers for several statistical distributions
-# 
+#
 # == Usage:
 #    Distribution::Normal.cdf(1.96)
 #    => 0.97500210485178
 #    Distribution::Normal.p_value(0.95)
 #    => 1.64485364660836
 module Distribution
+
+  SQ2PI = Math.sqrt(2 * Math::PI)
+
   module Shorthand
-    EQUIVALENCES={:p_value=>:p, :cdf=>:cdf, :pdf=>:pdf, :rng=>:r, :exact_pdf=>:epdf, :exact_cdf=>:ecdf, :exact_p_value=>:ep}
-    def self.add_shortcut(sh,m, &block)
-      if EQUIVALENCES.include? m.to_sym 
-        sh_name=sh+"_#{m}"
-        define_method(sh_name,&block)
-        sh_name=sh+"_#{EQUIVALENCES[m.to_sym]}"
-        define_method(sh_name,&block)
-        
+    EQUIVALENCES = { p_value: :p, cdf: :cdf, pdf: :pdf, rng: :r,
+                     exact_pdf: :epdf, exact_cdf: :ecdf, exact_p_value: :ep }
+
+    def self.add_shortcut(shortcut, method, &block)
+      if EQUIVALENCES.include? method.to_sym
+        name = shortcut + "_#{method}"
+        define_method(name, &block)
+
+        name = shortcut + "_#{EQUIVALENCES[method.to_sym]}"
+        define_method(name, &block)
+
       end
     end
   end
-  
-  
-  SQ2PI = Math.sqrt(2 * Math::PI)
 
   # Create a method 'has_<library>' on Module
   # which require a library and return true or false
-  # according to success of failure 
+  # according to success of failure
   def self.create_has_library(library) #:nodoc:
     define_singleton_method("has_#{library}?") do
-      cv="@@#{library}"
-      if !class_variable_defined? cv
-        begin 
+      cv = "@@#{library}"
+      unless class_variable_defined? cv
+        begin
           require library.to_s
           class_variable_set(cv, true)
         rescue LoadError
@@ -83,24 +75,26 @@ module Distribution
       class_variable_get(cv)
     end
   end
-  # Retrieves the libraries used to calculate 
+
+  # Retrieves the libraries used to calculate
   # distributions
   def self.libraries_order
-    order=[:Ruby_]
+    order = [:Ruby_]
     order.unshift(:Statistics2_) if has_statistics2?
     order.unshift(:GSL_) if has_gsl?
     order.unshift(:Java_) if has_java?
     order
   end
+
   create_has_library :gsl
   create_has_library :statistics2
   create_has_library :java
-  
+
   # Magic module
   module Distributable #:nodoc:
-    # Create methods for each module and add methods to 
-    # Distribution::Shorthand. 
-    # 
+    # Create methods for each module and add methods to
+    # Distribution::Shorthand.
+    #
     # Traverse Distribution.libraries_order adding
     # methods availables for each engine module on
     # the current library
@@ -108,41 +102,40 @@ module Distribution
     # Kids: Metaprogramming trickery! Don't do at work.
     # This section was created between a very long reunion
     # and a 456 Km. travel
-    def create_distribution_methods()
+    def create_distribution_methods
       Distribution.libraries_order.each do |l_name|
-      if const_defined? l_name
-        l =const_get(l_name)
-        # Add methods from engine to base base, if not yet included
-        l.singleton_methods.each do |m|
-          if !singleton_methods.include? m
-            define_method(m) do |*args|
-              l.send(m,*args)
-            end
-            # Add method to Distribution::Shorthand
-            sh=const_get(:SHORTHAND)
-            Distribution::Shorthand.add_shortcut(sh,m) do |*args|
-              l.send(m,*args)
+        if const_defined? l_name
+          l = const_get(l_name)
+          # Add methods from engine to base base, if not yet included
+          l.singleton_methods.each do |m|
+            unless singleton_methods.include? m
+              define_method(m) do |*args|
+                l.send(m, *args)
+              end
+              # Add method to Distribution::Shorthand
+              sh = const_get(:SHORTHAND)
+              Distribution::Shorthand.add_shortcut(sh, m) do |*args|
+                l.send(m, *args)
+              end
+
+              module_function m
             end
-            
-            module_function m
           end
-        end 
+        end
       end
-            
-    end
-    # create alias for common methods
-    alias_method :inverse_cdf, :p_value if singleton_methods.include? :p_value
+      # create alias for common methods
+      alias_method :inverse_cdf, :p_value if singleton_methods.include? :p_value
     end
-
   end
-  def self.init_java()
-    $:.unshift(File.dirname(__FILE__)+"/../vendor/java")
+
+  def self.init_java
+    $LOAD_PATH.unshift File.expand_path('../../vendor/java', __FILE__)
     require 'commons-math-2.2.jar'
     java_import 'org.apache.commons.math.distribution.NormalDistributionImpl'
     java_import 'org.apache.commons.math.distribution.PoissonDistributionImpl'
-
   end
-  require 'distribution/normal'  
+
+  require 'distribution/normal'
   require 'distribution/chisquare'
   require 'distribution/gamma'
   require 'distribution/beta'
@@ -156,11 +149,8 @@ module Distribution
   require 'distribution/logistic'
   require 'distribution/lognormal'
   require 'distribution/weibull'
-  
+
   if has_java?
-    init_java()
+    init_java
   end
 end
-
-
-