feldtruby 0.2.0

data/.autotest

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+# -*- ruby -*-
+
+require 'autotest/restart'
+
+# Autotest.add_hook :initialize do |at|
+#   at.extra_files << "../some/external/dependency.rb"
+#
+#   at.libs << ":../some/external"
+#
+#   at.add_exception 'vendor'
+#
+#   at.add_mapping(/dependency.rb/) do |f, _|
+#     at.files_matching(/test_.*rb$/)
+#   end
+#
+#   %w(TestA TestB).each do |klass|
+#     at.extra_class_map[klass] = "test/test_misc.rb"
+#   end
+# end
+
+# Autotest.add_hook :run_command do |at|
+#   system "rake build"
+# end

data/History.txt

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+=== 0.2.0 / 2012-12-21
+
+* First public release since we need it in some other projects and local install is messy...
+

data/Manifest.txt

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+.autotest
+History.txt
+Manifest.txt
+README.txt
+README.md
+Rakefile
+TODO
+lib/feldtruby.rb
+lib/feldtruby/array.rb
+lib/feldtruby/array/basic_stats.rb
+lib/feldtruby/array/count_by.rb
+lib/feldtruby/file/file_change_watcher.rb
+lib/feldtruby/file/tempfile.rb
+lib/feldtruby/float.rb
+lib/feldtruby/math/rand.rb
+lib/feldtruby/net/html_doc_getter.rb
+lib/feldtruby/optimize.rb
+lib/feldtruby/optimize/differential_evolution.rb
+lib/feldtruby/optimize/max_steps_termination_criterion.rb
+lib/feldtruby/optimize/objective.rb
+lib/feldtruby/optimize/optimizer.rb
+lib/feldtruby/optimize/random_search.rb
+lib/feldtruby/optimize/search_space.rb
+lib/feldtruby/optimize/stdout_logger.rb
+lib/feldtruby/string/to_iso.rb
+lib/feldtruby/time.rb
+lib/feldtruby/vector.rb
+lib/feldtruby/visualization/circos.rb
+lib/feldtruby/word_counter.rb
+test/helper.rb
+test/test_array.rb
+test/test_array_basic_stats.rb
+test/test_array_count_by.rb
+test/test_float.rb
+test/test_optimize.rb
+test/test_optimize_differential_evolution.rb
+test/test_optimize_objective.rb
+test/test_optimize_populationbasedoptimizer.rb
+test/test_optimize_random_search.rb
+test/test_optimize_search_space.rb
+test/test_time.rb
+test/test_vector.rb
+test/test_html_doc_getter.rb
+test/test_word_counter.rb

data/README.md

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+feldtruby
+=========
+Robert Feldt's Common Ruby Code lib. I will gradually collect the many generally useful Ruby tidbits I have laying around and clean them up into here. Don't want to rewrite these things again and again... So far this collects a number of generally useful additions to the standard Ruby classes/libs and then includes a simple optimization framework (FeldtRuby::Optimize).
+
+email: robert.feldt ((a)) gmail.com
+
+Contents
+--------
+### Time
+	Time.timestamp()    				# Get a timestamp string back with the current time
+
+### Array
+
+Basic calc/statistics: sum, mean, average, stdev, variance, rms, weighted_sum, weighted_mean,
+sum_of_abs, sum_of_abs_deviations
+
+	[1,2,3].swap!(0,2) 					=> [3, 2, 1] # destructive swap of two elements
+	[1,2,5].distance_between_elements 	=> [1, 3]
+    [15, 1, 7, 0].ranks					=> [1, 3, 2, 0]
+    [[2.3, :a], [1.7, :b]].ranks_by {|v| v[0]}	=> [[1, 2.3, :a], [2, 1.7, :b]]
+
+### Float
+	1.456.round_to_decimals(2) 			=> 1.46 (round to given num of decimals)
+
+### FileChangeWatcher
+Watch for file changes in given paths then call hooks with the updated files.
+
+### Kernel
+	rand_int(top)	 					# random integer in range 0...top
+
+### Optimize
+A simple optimization framework with classes:
+
+* Objective				(single or multi-objective optimization critera)
+* SearchSpace			(capture constraints for optimization values/parameters)
+* RandomSearcher 		(random search for optimal values)
+* DifferentialEvolution	(effective numerical optimization with evolutionary algorithm)
+
+but also support for different type of logging etc. Setting up an optimization can
+be quite involved but there is a simple wrapper method, with good defaults, for
+numerical optimization using DE:
+
+	# Optimizing with the Rosenbrock function on [0, 2], see:
+	# 	http://en.wikipedia.org/wiki/Rosenbrock_function
+	require 'feldtruby/optimize'
+	xbest, ybest = FeldtRuby::Optimize.optimize(0, 2) {|x, y|
+		(1 - x)**2 + 100*(y - x*x)**2
+	}
+
+Contributing to feldtruby
+------------------------- 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+Copyright
+------------
+Copyright (c) 2012 Robert Feldt. See LICENSE.txt for
+further details.

data/README.txt

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+= feldtruby
+
+* https://github.com/robertfeldt/feldtruby
+
+== DESCRIPTION:
+
+Robert Feldt's Common Ruby Code lib. I will gradually collect the many generally useful Ruby tidbits I have laying around and clean them up into here. Don't want to rewrite these things again and again... So far this collects a number of generally useful additions to the standard Ruby classes/libs and then includes a simple optimization framework (FeldtRuby::Optimize).
+
+email: robert.feldt ((a)) gmail.com
+
+== FEATURES/PROBLEMS:
+
+* FIX (list of features or problems)
+
+== SYNOPSIS:
+
+  FIX (code sample of usage)
+
+== REQUIREMENTS:
+
+* FIX (list of requirements)
+
+== INSTALL:
+
+* FIX (sudo gem install, anything else)
+
+== DEVELOPERS:
+
+After checking out the source, run:
+
+  $ rake newb
+
+This task will install any missing dependencies, run the tests/specs,
+and generate the RDoc.
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2012 FIX
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+'Software'), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

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+# -*- ruby -*-
+
+require 'rubygems'
+require 'hoe'
+
+# Hoe.plugin :compiler
+# Hoe.plugin :gem_prelude_sucks
+# Hoe.plugin :inline
+# Hoe.plugin :racc
+# Hoe.plugin :rcov
+# Hoe.plugin :rubyforge
+
+Hoe.plugin :gemcutter
+
+Hoe.spec 'feldtruby' do
+  developer 'Robert Feldt', 'robert.feldt@gmail.com'
+
+  license 'MIT' # this should match the license in the README
+end

data/TODO

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+* Add Pareto front calculations and saving by the stats logger and/or in collab with the Objective!? 
+  - In one way it is easier for the Objective to keep track of these things since it already saves the global mins and maxs.
+  - OTOH it may be more logical that the optimizer or the stats object keeps track of this.
+
+* Consider if the quality of the candidate vectors should be be attached to them instead of being handled separately. 
+  - We can add instance vars to any Ruby object with "special tricks"... ;)

data/lib/feldtruby/array/basic_stats.rb

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+module BasicStatistics
+	def sum
+		self.inject(0) {|s, e| s+e}
+	end
+
+	def mean
+		return 0 if self.length == 0
+		self.sum / self.length.to_f
+	end
+
+	def average; mean(); end
+
+	def median
+		sorted = self.sort
+		if self.length % 2 == 0
+			mid = self.length / 2
+			(sorted[mid-1] + sorted[mid])/2.0
+		else
+			sorted[self.length/2.0]
+		end
+	end
+
+	def variance
+		return 0 if self.length == 0
+		avg = self.mean
+		self.map {|e| (e-avg)**2}.sum / self.length.to_f
+	end
+
+	def stdev
+		Math.sqrt( self.variance )
+	end
+
+	def root_mean_square
+		Math.sqrt( self.map {|v| v**2}.mean )
+	end
+
+	def rms; self.root_mean_square(); end
+
+	def rms_from_scalar(scalar)
+		Math.sqrt( self.map {|v| (v-scalar)**2}.mean )		
+	end
+
+	# Weighted sum of elements
+	def weighted_sum(weights = nil)
+		if weights
+			raise "Not same num of weights (#{weights.length}) as num of elements (#{self.length})" if self.length != weights.length
+			self.zip(weights).map {|e,w| e*w}.sum
+		else
+			self.sum
+		end
+	end
+
+	# Weighted mean of elements
+	def weighted_mean(weights = nil)
+		if weights
+			self.weighted_sum(weights) / weights.sum.to_f
+		else
+			self.mean
+		end
+	end
+
+	def sum_of_abs_deviations(fromValue = 0.0)
+		sum = 0.0
+		self.each {|v| sum += (v-fromValue).abs}
+		sum
+	end
+
+	def sum_of_abs
+		sum = 0.0
+		self.each {|v| sum += v.abs}
+		sum
+	end
+
+	def sum_squared_error(b)
+		sum = 0.0
+		self.each_with_index {|e,i| d = e-b[i]; sum += d*d}
+		sum
+	end
+
+	# Return summary stats for an array of numbers.
+	def summary_stats
+ 		"%.3f (min = %.1f, max = %.1f, median = %.1f, stdev = %.2f)" % [mean, self.min, self.max, median, stdev]
+ 	end
+end
+
+class Array
+	include BasicStatistics
+end

data/lib/feldtruby/array/count_by.rb

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+class Array
+  def count_by(&proc)
+    counts = Hash.new(0)
+    self.each {|e| counts[proc.call(e)] += 1}
+    counts
+  end
+end

data/lib/feldtruby/array.rb

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+require 'feldtruby/array/basic_stats'
+
+class Array
+	# Calculate the distance between the elements.
+	def distance_between_elements
+		return nil if self.length == 0
+		self[0...-1].zip(self[1..-1]).map {|x,y| y-x}
+	end
+
+	# Swap two elements given their indices. Assumes both indices are in range.
+	def swap!(index1, index2)
+		self[index1], self[index2] = self[index2], self[index1]
+	end
+
+	# Rank of values in array from 1..length
+	def ranks
+		ranks = Array.new(length)
+		self.each_with_index.map {|e,i| [i, e]}.sort_by {|v| v.last}.each_with_index.map {|v,i| ranks[v.first]=length-i}
+		ranks
+	end
+
+	# Prepend (or append) ranks after sorting by the value supplied from a block
+	def ranks_by(prependRanks = true, &mapToValueUsedForRanking)
+		res = Array.new(length)
+		sorted_with_indices = self.each_with_index.map {|e,i| [i, e]}.sort_by {|v| mapToValueUsedForRanking.call(v.last)}
+		sorted_with_indices.each_with_index.map do |v,index|
+			orig_index, orig_element = v
+			rank = length - index
+			new_element = prependRanks ? ([rank] + orig_element) : (orig_element + [rank])
+			res[orig_index] = new_element
+		end
+		res
+	end
+end

data/lib/feldtruby/file/file_change_watcher.rb

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+# Watch directories for changes and provide callback hooks for when files change.
+# Partly inspired by and built on code from Autotest/Zentest by Ryan Davis and Eric Hodel.
+#
+require 'find'
+
+class String
+	def starts_with?(str)
+		self[0, str.length] == str
+	end
+end
+
+# Watch for file changes in given paths then call hooks with the updated files.
+class FileChangeWatcher
+	attr_accessor :find_directories, :last_mtime, :sleep_time, :exclusions
+
+	def initialize(specifiedDirectories = ["."], sleepTime = 5*60, excludeFilesRegexps = [], &runWhenFilesUpdated)
+		specified_directories  = specifiedDirectories.reject { |path| path.starts_with?("-") }
+		self.find_directories  = specified_directories.empty? ? ['.'] : specified_directories
+		self.exclusions = excludeFilesRegexps
+		self.sleep_time = sleepTime
+		self.last_mtime = nil # Ensure we run first time when started
+		@hooks = Hash.new { |h,k| h[k] = [] }
+		add_hook :updated, &runWhenFilesUpdated if runWhenFilesUpdated
+	end
+
+	# Find the files to process, ignoring temporary files, source
+	# configuration management files, etc., and return a Hash mapping
+	# filename to modification time.
+	def find_files
+		result = {}
+		targets = self.find_directories
+		targets.each do |target|
+			Find.find target do |f|
+				next if test ?d, f
+				next if f =~ /(swp|~|rej|orig)$/ # temporary/patch files
+				next if f =~ /^\.\/tmp/          # temporary dir, used by isolate
+				next if f =~ /\/\.?#/            # Emacs autosave/cvs merge files
+				filename = f.sub(/^\.\//, '')
+				result[filename] = File.stat(filename).mtime rescue next
+			end
+		end
+		result
+	end
+
+	def exclude_matched_files(files, exclusionRegexps)
+		files.reject {|f| exclusionRegexps.any? {|exre| exre.match(f)}}
+	end
+
+  	# Find files that has changed since last time. 
+  	# Call updated hook if any found.
+	def find_updated_files files = find_files
+		hook :checkingChanges, files
+		updated = self.last_mtime.nil? ? files : files.select { |filename, mtime| self.last_mtime < mtime }
+		updated = exclude_matched_files(updated, self.exclusions)
+
+		unless updated.empty? then
+			self.last_mtime = Time.now
+			hook :updated, updated
+		end
+	end
+
+	# Add the supplied block to the available hooks, with the given
+	# name.
+	def add_hook name, &block
+		# New hooks added in front
+		@hooks[name] = [block] + @hooks[name]
+	end
+
+	# Call the event hook named +name+, passing in optional args
+	# depending on the hook itself.
+	#
+	# Returns false if no hook handled the event.
+	#
+	def hook name, *args
+		@hooks[name].any? { |plugin| plugin[self, *args] }
+	end
+
+	def wait_for_changes
+		hook :waiting
+		Kernel.sleep self.sleep_time until find_updated_files
+	end
+end
+
+if __FILE__ == $0
+	dirs_to_watch = ARGV.length > 0 ? ARGV : ["."]
+	watcher = FileChangeWatcher.new(dirs_to_watch) {|fwc, ufs| puts ufs.inspect}
+	watcher.wait_for_changes
+end

data/lib/feldtruby/file/tempfile.rb

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+# Find a unique temp file name starting with _basename_
+# and having a file suffix _suffix_, then supply it to a block. 
+# After the block has executed make sure there is no tempfile 
+# with that name, if there is delete it.
+def File.with_tempfile(suffix = ".temp", basename = "temp")
+	tempfilename = basename + rand(1e7).to_s + suffix
+	while Dir.exist?(tempfilename)
+		tempfilename = basename + rand(1e7).to_s + suffix
+	end
+	begin
+		yield tempfilename
+	ensure
+		File.delete(tempfilename) if Dir.exist?(tempfilename)
+	end
+end
+
+# Find a unique temp file name in the same way as for with_tempfile
+# but now save a string to that file before supplying the filename
+# to the block. 
+def File.with_tempfile_containing(contents, suffix = ".temp", basename = "temp")
+	File.with_tempfile do |tempfilename|
+		File.open(tempfilename, "w") {|fh| fh.write(contents)}
+		yield tempfilename
+	end
+end

data/lib/feldtruby/float.rb

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+require 'feldtruby'
+
+class Numeric
+	def round_to_decimals(numDecimals = 2)
+		factor = 10**numDecimals
+		(self * factor).round / factor.to_f
+	end
+
+	def protected_division_with(denom)
+		return 0.0 if denom == 0
+		self / denom
+	end
+
+	def ratio_diff_vs(other)
+		(self - other).protected_division_with(other)
+	end
+end

data/lib/feldtruby/math/rand.rb

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+module Kernel
+	def rand_int(top)
+		(top * rand()).floor
+	end
+end

data/lib/feldtruby/net/html_doc_getter.rb

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+require 'feldtruby'
+require 'nokogiri'
+require 'open-uri'
+
+# Fetch html pages from a site but ensure some time between subsequent get operations.
+# To minimize the risk that we "annoy" the site operators.
+class FeldtRuby::HtmlDocGetter
+  def initialize(minTimeBetweenGets = 1.0, maxRandomDelayBetweenGets = 3.0)
+    @min_delay = minTimeBetweenGets
+    @delta_delay = maxRandomDelayBetweenGets - @min_delay
+    @delay_until = Time.now - 1.0 # Ensure no wait the first time
+  end
+  def get(url)
+    wait_until_delay_passed()
+    begin
+      open(url).read
+    ensure
+      set_new_delay
+    end
+  end
+  def get_html_doc(url)
+    Nokogiri::HTML(get(url))
+  end
+  def wait_until_delay_passed
+    now = Time.now
+    sleep(@delay_until - now) if now < @delay_until
+  end
+  def set_new_delay
+    @delay_until = Time.now + (@min_delay + rand() * @delta_delay)
+  end
+end