daru 0.1.3.1 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: b1c4cea3ce18551587e30424210f9183fa83c97b
+  metadata.gz: 4dd52552d2407c0d16e3aee91f9307366d3d1a02
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data/.gitignore

@@ -4,3 +4,5 @@ doc/
 .yardoc/
 .bundle
 vendor/
+profile/out/
+coverage/

data/.rspec

@@ -1 +1,2 @@
---color
+--require ./spec/spec_helper.rb
+--color

data/.rspec_formatter.rb

@@ -0,0 +1,33 @@
+RSpec::Support.require_rspec_core 'formatters/base_text_formatter'
+
+class SimpleFormatter < RSpec::Core::Formatters::BaseTextFormatter
+  RSpec::Core::Formatters.register self,
+    :example_passed, :example_pending, :example_failed, :dump_pending, :dump_failures, :dump_summary
+
+  def example_passed(message)
+    # Do nothing
+  end
+
+  def example_pending(message)
+    # Do nothing
+  end
+
+  def example_failed(message)
+    # Do nothing
+  end
+
+  def dump_pending(message)
+    # Do nothing
+  end
+
+  def dump_failures(message)
+  end
+
+  def dump_summary(message)
+    colorizer = ::RSpec::Core::Formatters::ConsoleCodes
+
+    output.puts "\nFinished in #{message.formatted_duration} " \
+       "(files took #{message.formatted_load_time} to load)\n" \
+       "#{message.colorized_totals_line(colorizer)}\n"
+  end
+end

data/.rubocop.yml

@@ -1,14 +1,15 @@
-inherit_from: .rubocop_todo.yml
-
 AllCops:
   Include:
     - 'lib/**/*'
   Exclude:
+    - '**/*.erb'
     - 'spec/*'
     - 'spec/**/*'
     - 'vendor/**/*'
     - 'benchmarks/*'
+    - 'profile/*'
   DisplayCopNames: true
+  TargetRubyVersion: 2.0
 
 # Preferred codebase style ---------------------------------------------
 Style/ExtraSpacing:
@@ -35,6 +36,15 @@ Style/AlignParameters:
 Style/EmptyElse:
   EnforcedStyle: empty
 
+Metrics/LineLength:
+  Max: 120
+
+Metrics/ModuleLength:
+  Max: 200
+
+Metrics/ClassLength:
+  Max: 200
+
 Style/ParallelAssignment:
   Enabled: false
 
@@ -56,10 +66,24 @@ Style/SpaceAroundOperators:
 Style/EmptyCaseCondition:
   Enabled: false
 
+Style/MultilineBlockChain:
+  Enabled: false
+
 # Neither of prefered styles are good enough :(
 Style/BlockDelimiters:
   Enabled: false
 
+# Current preferred metrics --------------------------------------------
+# Better values are encouraged, but not required.
+Metrics/AbcSize:
+  Max: 20
+
+Metrics/MethodLength:
+  Max: 15
+
+Metrics/CyclomaticComplexity:
+  Max: 7
+
 # TODO -----------------------------------------------------------------
 
 Style/Documentation:

data/History.md

@@ -1,3 +1,41 @@
+# 0.1.4 ()
+
+* Major Enhancements
+  - Added new dependency 'backports' to support #to_h in Ruby 2.0. (@lokeshh)
+  - Greatly improve code test coverage. (@zverok)
+  - Greatly refactor code and make some methods faster, smaller and more readable. (@zverok)
+  - Add support for categorical data with different coding schemes and several methods for in built categorical data support. Add a new index 'Daru::CategoricalIndex'. (@lokeshh)
+  - Removed runtime dependencies on 'spreadsheet' and 'reportbuilder'. They are now loaded if the libraries are already present in the system. (@v0dro)
+
+* Minor enhancements
+  - Update SqlDataSource to improve the performance of DataFrame.from_sql. (@dansbits)
+  - Remove default DataFrame name. Now DataFrames will no name by default. (@zverok)
+  - Better looking #inspect for Vector and DataFrame. (@zverok)
+  - Better looking #to_html for Vector and DataFrame. Also better #to_html for MultiIndex. (@zverok)
+  - Remove monkey patching on Array and add those methods to Daru::ArrayHelper. (@zverok)
+  - Add a rake task for running RSpec for every Ruby version with a single command. (@lokeshh)
+  - Add rake tasks for easily setting up and testing test harness. (@lokeshh)
+  - Added `Daru::Vector#to_nmatrix`.
+  - Remove the 'metadata' feature introduced in v0.1.3. (@gnilrets)
+  - Added `DataFrame#to_df` and `Vector#to_df`. (@gnilrets)
+
+* Fixes
+  - DataFrame#clone preserves order and name. (@wlevine)
+  - Vector#where preserves name. (@v0dro)
+  - Fix bug in DataFrame#pivot_table that prevented anything other than Array or Symbol to be specified in the :values option. (@v0dro)
+  - Daru::Index#each returns an Enumerator if block is not specified. (@v0dro)
+  - Fixes bug where joins failed when nils were in join keys. (@gnilrets)
+  - DataFrame#merge now preserves the vector name type when merging. (@lokeshh)
+
+* Deprecations
+  - Remove methods DataFrame#vector and DataFrame#column. (@zverok)
+  - Remove the missing_values feature of daru. The only values that are now treated as 'missing' are `nil` and `Float::NAN`. (@lokeshh)
+
+# 0.1.3.1 (12 May 2016)
+
+* Fixes
+    - Fixed small error with usage of newly introduced #each_with_object (@v0dro).
+
 # 0.1.3 (May 2016)
 
 * Enhancements

data/README.md

@@ -2,6 +2,7 @@
 
 [![Gem Version](https://badge.fury.io/rb/daru.svg)](http://badge.fury.io/rb/daru)
 [![Build Status](https://travis-ci.org/v0dro/daru.svg)](https://travis-ci.org/v0dro/daru)
+[![Gitter](https://badges.gitter.im/v0dro/daru.svg)](https://gitter.im/v0dro/daru?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 ## Introduction
 
@@ -33,20 +34,33 @@ daru makes it easy and intuitive to process data predominantly through 2 data st
 * [Basic Creation of Vectors and DataFrame](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Creation%20of%20Vector%20and%20DataFrame.ipynb)
 * [Detailed Usage of Daru::Vector](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Usage%20of%20Vector.ipynb)
 * [Detailed Usage of Daru::DataFrame](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Usage%20of%20DataFrame.ipynb)
-* [Visualizing Data With Daru::DataFrame](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Visualization/Visualizing%20data%20with%20daru%20DataFrame.ipynb)
 * [Searching and combining data in daru](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Searching%20and%20Combining%20Data.ipynb)
 * [Grouping, Splitting and Pivoting Data](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Grouping%2C%20Splitting%20and%20Pivoting.ipynb)
+* [Usage of Catgorical Data](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Categorical%20Data/Categorical%20Data.ipynb)
+
+#### Visualization
+* [Visualizing Data With Daru::DataFrame](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Visualization/Visualizing%20data%20with%20daru%20DataFrame.ipynb)
+* [Plotting using Nyaplot](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Plotting/Visualization.ipynb)
+* [Plotting using GnuplotRB](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Plotting/Gnuplotrb.ipynb)
+* [Vector plotting with Gruff](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Plotting/Gruff%20Vector.ipynb)
+* [DataFrame plotting with Gruff](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Plotting/Gruff%20DataFrame.ipynb)
 
 #### Notebooks on Time series
 
 * [Basic Time Series](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Basic%20Time%20Series.ipynb)
 * [Time Series Analysis and Plotting](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Time%20Series%20Functions.ipynb)
 
+#### Notebooks on Indexing
+* [Indexing in Vector](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Categorical%20Data/Indexing%20in%20Vector.ipynb)
+* [Indexing in DataFrame](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Categorical%20Data/Indexing%20in%20DataFrame.ipynb)
+
 ### Case Studies
 
 * [Logistic Regression Analysis with daru and statsample-glm](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Logistic%20Regression%20with%20daru%20and%20statsample-glm.ipynb)
 * [Finding and Plotting most heard artists from a Last.fm dataset](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Finding%20and%20plotting%20the%20most%20heard%20artists%20on%20last%20fm.ipynb)
 * [Analyzing baby names with daru](http://nbviewer.ipython.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Analyzing%20baby%20names/Use%20Case%20-%20Daru%20for%20analyzing%20baby%20names%20data.ipynb)
+* [Example usage of Categorical Data](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Categorical%20Data/examples/%5BExample%5D%20Categorical%20Data.ipynb)
+* [Example usage of Categorical Index](http://nbviewer.jupyter.org/github/SciRuby/sciruby-notebooks/blob/master/Data%20Analysis/Categorical%20Data/examples/%5BExample%5D%20Categorical%20Index.ipynb)
 
 ## Blog Posts
 
@@ -59,6 +73,12 @@ daru makes it easy and intuitive to process data predominantly through 2 data st
 * [Analysis of Time Series in daru](http://v0dro.github.io/blog/2015/07/31/analysis-of-time-series-in-daru/)
 * [Date Offsets in Daru](http://v0dro.github.io/blog/2015/07/27/date-offsets-in-daru/)
 
+### Categorical Data
+
+* [Categorical Index](http://lokeshh.github.io/blog/2016/06/14/categorical-index/)
+* [Categorical Data](http://lokeshh.github.io/blog/2016/06/21/categorical-data/)
+* [Visualization with Categorical Data](http://lokeshh.github.io/blog/2016/07/02/visualization/)
+
 ## Basic Usage
 
 daru exposes two major data structures: `DataFrame` and `Vector`. The Vector is a basic 1-D structure corresponding to a labelled Array, while the `DataFrame` - daru's primary data structure - is 2-D spreadsheet-like structure for manipulating and storing data sets.
@@ -168,18 +188,6 @@ In addition to nyaplot, daru also supports plotting out of the box with [gnuplot
 
 Docs can be found [here](https://rubygems.org/gems/daru).
 
-## Roadmap
-
-* Enable creation of DataFrame by only specifying an NMatrix/MDArray in initialize. Vector naming happens automatically (alphabetic) or is specified in an Array.
-* Assignment of a column to a single number should set the entire column to that number.
-* Multiple column assignment with []=
-* Multiple value assignment for vectors with []=.
-* #find\_max function which will evaluate a block and return the row for the value of the block is max.
-* Sort by index.
-* Statistics on DataFrame over rows.
-* Calculate percentage change.
-* Have some sample data sets for users to play around with. Should be able to load these from the code itself.
-
 ## Contributing
 
 Pick a feature from the Roadmap or the issue tracker or think of your own and send me a Pull Request!
@@ -188,6 +196,7 @@ For details see [CONTRIBUTING](https://github.com/v0dro/daru/blob/master/CONTRIB
 
 ## Acknowledgements
 
+* Google and the Ruby Science Foundation for the Google Summer of Code 2016 grant for speed enhancements and implementation of support for categorical data. Special thanks to [@lokeshh](https://github.com/lokeshh), [@zverok](https://github.com/zverok) and [@agisga](https://github.com/agisga) for their efforts. 
 * Google and the Ruby Science Foundation for the Google Summer of Code 2015 grant for further developing daru and integrating it with other ruby gems.
 * Thank you [last.fm](http://www.last.fm/) for making user data accessible to the public.
 

data/Rakefile

@@ -2,7 +2,50 @@ require 'rspec/core/rake_task'
 require 'bundler/gem_tasks'
 
 lib_folder = File.expand_path("../lib", __FILE__)
-RSpec::Core::RakeTask.new(:spec)
+
+RUBIES = ['ruby-2.0.0-p643', 'ruby-2.1.5', 'ruby-2.2.1', 'ruby-2.3.0']
+
+def spec_run_all
+  RUBIES.each do |ruby_v|
+    puts "\n  Using #{ruby_v}\n\n"
+    command = "$rvm_path/wrappers/#{ruby_v}/rake summary"
+    run command
+  end
+end
+
+task :spec do
+  case ARGV[1]
+  when 'setup'
+    spec_setup
+  when 'run'
+    spec_run_all if ARGV[2] == 'all'
+  when nil
+    run 'rspec spec'
+  end
+end
+
+# Stubs
+task :setup
+task :run
+task :all
+
+def spec_setup
+  RUBIES.each do |ruby_v|
+    puts "Installing #{ruby_v}..."
+    run "rvm install #{ruby_v}"
+    path = "$rvm_path/wrappers/#{ruby_v}"
+    run "#{path}/gem install bundler"
+    run "#{path}/bundle install"
+  end
+end
+
+#task all: [:cop, :run_all]
+
+task :summary do
+  run 'rspec spec/ -r ./.rspec_formatter.rb -f SimpleFormatter' rescue nil
+end
+
+#RSpec::Core::RakeTask.new(:spec)
 
 task :default => :spec
 
@@ -11,6 +54,10 @@ task :console do |task|
   run *cmd
 end
 
+task :cop do |task|
+  run 'rubocop' rescue nil
+end
+
 task :pry do |task|
   cmd = [ 'pry', "-r '#{lib_folder}/daru.rb'" ]
   run *cmd
@@ -18,4 +65,5 @@ end
 
 def run *cmd
   sh(cmd.join(" "))
-end
+end
+

data/benchmarks/csv_reading.rb

@@ -0,0 +1,22 @@
+# Date - 28 june 2016. daru version - 0.1.3.1
+# Compare speed of Ruby stdlib CSV and DataFrame.from_csv.
+
+require 'benchmark'
+require 'csv'
+require 'daru'
+
+Benchmark.bm do |x|
+  x.report("Ruby CSV") do
+    CSV.read("TradeoffData.csv")
+  end
+
+  x.report("DataFrame.from_csv") do
+    Daru::DataFrame.from_csv("TradeoffData.csv")
+  end
+end
+
+# FIXME: Improve this. It's 4 times slower than Ruby CSV reading!!
+
+#        user     system      total        real
+# Ruby CSV  0.010000   0.000000   0.010000 (  0.002385)
+# DataFrame.from_csv  0.000000   0.000000   0.000000 (  0.008225)

data/daru.gemspec

@@ -49,15 +49,18 @@ Cheers!
 *************************************************************************
 EOF
 
-  spec.add_runtime_dependency 'reportbuilder', '~> 1.4'
-  spec.add_runtime_dependency 'spreadsheet', '~> 1.1.1'
 
+  spec.add_runtime_dependency 'backports'
+
+  spec.add_development_dependency 'reportbuilder', '~> 1.4'
+  spec.add_development_dependency 'spreadsheet', '~> 1.1.1'
   spec.add_development_dependency 'bundler', '~> 1.10'
   spec.add_development_dependency 'rake', '~>10.5'
   spec.add_development_dependency 'pry', '~> 0.10'
   spec.add_development_dependency 'pry-byebug'
   spec.add_development_dependency 'rserve-client', '~> 0.3'
   spec.add_development_dependency 'rspec', '~> 3.4'
+  spec.add_development_dependency 'rspec-its'
   spec.add_development_dependency 'awesome_print'
   spec.add_development_dependency 'nyaplot', '~> 0.1.5'
   spec.add_development_dependency 'nmatrix', '~> 0.2.1'
@@ -68,4 +71,8 @@ EOF
   spec.add_development_dependency 'activerecord', '~> 4.0'
   spec.add_development_dependency 'sqlite3'
   spec.add_development_dependency 'rubocop', '>= 0.40.0'
+  spec.add_development_dependency 'ruby-prof'
+  spec.add_development_dependency 'simplecov'
+  spec.add_development_dependency 'nokogiri'
+  spec.add_development_dependency 'gruff'
 end

data/lib/daru.rb

@@ -1,6 +1,8 @@
+# :nocov:
 def jruby?
   RUBY_ENGINE == 'jruby'
 end
+# :nocov:
 
 module Daru
   DAYS_OF_WEEK = {
@@ -28,15 +30,20 @@ module Daru
     12 => 31
   }.freeze
 
+  MISSING_VALUES = [nil, Float::NAN].freeze
+
   @lazy_update = false
 
   SPLIT_TOKEN = ','.freeze
 
+  @plotting_library = :nyaplot
+
   class << self
     # A variable which will set whether Vector metadata is updated immediately or lazily.
     # Call the #update method every time a values are set or removed in order to update
     # metadata like positions of missing values.
     attr_accessor :lazy_update
+    attr_reader :plotting_library
 
     def create_has_library(library)
       lib_underscore = library.to_s.tr('-', '_')
@@ -48,31 +55,54 @@ module Daru
             require library.to_s
             class_variable_set(cv, true)
           rescue LoadError
+            # :nocov:
             class_variable_set(cv, false)
+            # :nocov:
           end
         end
         class_variable_get(cv)
       end
     end
+
+    def plotting_library= lib
+      case lib
+      when :gruff, :nyaplot
+        @plotting_library = lib
+      else
+        raise ArgumentError, "Unsupported library #{lib}"
+      end
+    end
   end
 
   create_has_library :gsl
   create_has_library :nmatrix
   create_has_library :nyaplot
+  create_has_library :gruff
 end
 
-autoload :Spreadsheet, 'spreadsheet'
-autoload :CSV, 'csv'
+[['reportbuilder', '~>1.4'], ['spreadsheet', '~>1.1.1']].each do |lib|
+  begin
+    gem lib[0], lib[1]
+    require lib[0]
+  rescue LoadError
+    STDERR.puts "\nInstall the #{lib[0]} gem version #{lib[1]} for using"\
+    " #{lib[0]} functions."
+  end
+end
 
+autoload :CSV, 'csv'
 require 'matrix'
-require 'securerandom'
-require 'reportbuilder'
 
 require 'daru/version.rb'
+
+require 'daru/helpers/array.rb'
 require 'daru/index.rb'
 require 'daru/vector.rb'
 require 'daru/dataframe.rb'
 require 'daru/monkeys.rb'
+require 'daru/formatters/table'
+require 'daru/iruby/helpers'
+require 'daru/exceptions.rb'
 
 require 'daru/core/group_by.rb'
 require 'daru/core/query.rb'
@@ -80,3 +110,5 @@ require 'daru/core/merge.rb'
 
 require 'daru/date_time/offsets.rb'
 require 'daru/date_time/index.rb'
+
+require 'backports'