coderunner 0.11.2 → 0.11.3

data/Gemfile

@@ -3,6 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
   gem "graphkit", ">= 0.2.0"
+  gem "parallelpipes", ">= 1.0.0"
   gem "rubyhacks", ">= 0.1.0"
   gem "gsl", ">= 1.12.0"
   gem "ruby-netcdf", ">= 0.6.6"

data/VERSION

@@ -1 +1 @@
-0.11.2
+0.11.3

data/coderunner.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.11.2"
+  s.version = "0.11.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
@@ -35,6 +35,7 @@ Gem::Specification.new do |s|
     "lib/code_runner_extension.rb",
     "lib/coderunner.rb",
     "lib/coderunner/class_methods.rb",
+    "lib/coderunner/feedback.rb",
     "lib/coderunner/fortran_namelist.rb",
     "lib/coderunner/graphs_and_films.rb",
     "lib/coderunner/heuristic_run_methods.rb",
@@ -42,6 +43,7 @@ Gem::Specification.new do |s|
     "lib/coderunner/interactive_methods.rb",
     "lib/coderunner/long_regexen.rb",
     "lib/coderunner/merged_code_runner.rb",
+    "lib/coderunner/remote_code_runner.rb",
     "lib/coderunner/run.rb",
     "lib/coderunner/system_modules/franklin.rb",
     "lib/coderunner/system_modules/generic_linux.rb",
@@ -53,6 +55,14 @@ Gem::Specification.new do |s|
     "lib/coderunner/system_modules/moab.rb",
     "lib/coderunner/system_modules/new_hydra.rb",
     "lib/coderunner/system_modules/slurm.rb",
+    "lib/coderunner/test.rb",
+    "lib/coderunner/version.rb",
+    "lib/cubecalccrmod.rb",
+    "lib/cubecalccrmod/cubecalc_defaults.rb",
+    "lib/cubecalccrmod/default_modlets/empty.rb",
+    "lib/cubecalccrmod/default_modlets/empty_defaults.rb",
+    "lib/cubecalccrmod/defaults_files/sleep_defaults.rb",
+    "lib/cubecalccrmod/my_modlets/sleep.rb",
     "test/helper.rb",
     "test/test_coderunner.rb"
   ]
@@ -68,6 +78,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<graphkit>, [">= 0.2.0"])
+      s.add_runtime_dependency(%q<parallelpipes>, [">= 1.0.0"])
       s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.0"])
       s.add_runtime_dependency(%q<gsl>, [">= 1.12.0"])
       s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
@@ -77,6 +88,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<jeweler>, ["~> 1.8.4"])
     else
       s.add_dependency(%q<graphkit>, [">= 0.2.0"])
+      s.add_dependency(%q<parallelpipes>, [">= 1.0.0"])
       s.add_dependency(%q<rubyhacks>, [">= 0.1.0"])
       s.add_dependency(%q<gsl>, [">= 1.12.0"])
       s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
@@ -87,6 +99,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<graphkit>, [">= 0.2.0"])
+    s.add_dependency(%q<parallelpipes>, [">= 1.0.0"])
     s.add_dependency(%q<rubyhacks>, [">= 0.1.0"])
     s.add_dependency(%q<gsl>, [">= 1.12.0"])
     s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])

data/lib/coderunner.rb

@@ -7,10 +7,13 @@ end
 
 # Basic class setup
 
+require 'rubygems'
+require "rubyhacks"
 class CodeRunner
 	
 	COMMAND_FOLDER = Dir.pwd
   SCRIPT_FOLDER = File.dirname(File.expand_path(__FILE__)) + '/coderunner' #i.e. where this script is
+	
 	if ENV['CODE_RUNNER_OPTIONS']
 		GLOBAL_OPTIONS = eval(ENV['CODE_RUNNER_OPTIONS']) # global options are set by the environment but some can be changed.
 	else
@@ -18,7 +21,6 @@ class CodeRunner
 	end
 	SYS = (GLOBAL_OPTIONS[:system] or ENV['CODE_RUNNER_SYSTEM'] or ENV['SYSTEM'] or "generic_linux")
 	require SCRIPT_FOLDER + "/system_modules/#{SYS}.rb"
-	require SCRIPT_FOLDER + "/box_of_tricks.rb"
 	SYSTEM_MODULE = const_get(SYS.variable_to_class_name)
 	include SYSTEM_MODULE
 	class << self
@@ -56,7 +58,7 @@ $stderr.print 'Loading libraries...' unless $has_put_startup_message_for_code_ru
 #read this if you are puzzled by
 # some non-standard use of ruby
 ################################
-require CodeRunner::SCRIPT_FOLDER + "/box_of_tricks.rb"
+#require CodeRunner::SCRIPT_FOLDER + "/box_of_tricks.rb"
 ################################
 
 require "getoptlong"
@@ -64,7 +66,7 @@ require "thread"
 require "fileutils"
 require "drb"
 require "test/unit/assertions"
-require CodeRunner::SCRIPT_FOLDER + '/parallelpipes.rb'
+require 'parallelpipes'
 require 'find'
 
 begin	
@@ -81,10 +83,7 @@ rescue LoadError
 end
 
 #require CodeRunner::SCRIPT_FOLDER + "/gnuplot.rb"
-load CodeRunner::SCRIPT_FOLDER + "/graphkit.rb"
-load CodeRunner::SCRIPT_FOLDER + "/graphkit_gnuplot2.rb"
-load CodeRunner::SCRIPT_FOLDER + "/graphkit_vtk_legacy.rb"
-load CodeRunner::SCRIPT_FOLDER + "/graphkit_mathematica.rb"
+require "graphkit"
 CodeRunner::GraphKit = GraphKit # Backwards compatibility
 
 # load 'gnuplot'
@@ -92,20 +91,20 @@ load CodeRunner::SCRIPT_FOLDER + "/feedback.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
 load CodeRunner::SCRIPT_FOLDER + "/test.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
-load CodeRunner::SCRIPT_FOLDER + "/input_file_generator.rb"
-eprint '.' unless $has_put_startup_message_for_code_runner
+#load CodeRunner::SCRIPT_FOLDER + "/input_file_generator.rb"
+#eprint '.' unless $has_put_startup_message_for_code_runner
 load CodeRunner::SCRIPT_FOLDER + "/long_regexen.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
 load CodeRunner::SCRIPT_FOLDER + "/version.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
 load CodeRunner::SCRIPT_FOLDER + "/heuristic_run_methods.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
-load CodeRunner::SCRIPT_FOLDER + "/code_runner_version.rb"
-eprint '.' unless $has_put_startup_message_for_code_runner
+#load CodeRunner::SCRIPT_FOLDER + "/code_runner_version.rb"
+#eprint '.' unless $has_put_startup_message_for_code_runner
 load CodeRunner::SCRIPT_FOLDER + "/fortran_namelist.rb"
 eprint '.' unless $has_put_startup_message_for_code_runner
 
-
+CodeRunner::CODE_RUNNER_VERSION = Version.new(Gem.loaded_specs['coderunner'].version.to_s)
 
 CodeRunner::GLOBAL_BINDING = binding
 
@@ -166,9 +165,10 @@ class CodeRunner
 		
 	CLF = COMMAND_LINE_FLAGS = COMMAND_LINE_FLAGS_WITH_HELP.map{|arr| arr.slice(0..2)}
 
-	CODE_COMMAND_OPTIONS = (Dir.entries(SCRIPT_FOLDER + "/code_modules/") - [".", "..", ".svn"]).map do |d|
-		["--#{d}-options", "", GetoptLong::REQUIRED_ARGUMENT, %[A hash of options for the #{d} code module]]
-	end
+	CODE_COMMAND_OPTIONS = [] # NEEDS FIXING!!!!
+ 	#(Dir.entries(SCRIPT_FOLDER + "/code_modules/") - [".", "..", ".svn"]).map do |d|
+		#["--#{d}-options", "", GetoptLong::REQUIRED_ARGUMENT, %[A hash of options for the #{d} code module]]
+	#end
 
 	LONG_COMMAND_LINE_OPTIONS = [
 	["--replace-existing", "", GetoptLong::NO_ARGUMENT, %[Use with resubmit: causes each resubmitted run to replace the run being resubmitted.]],

data/lib/coderunner/feedback.rb

@@ -0,0 +1,92 @@
+class Feedback
+
+def gets #No reading from the command line thank you very much!
+	$stdin.gets
+end
+def self.gets
+	$stdin.gets
+end
+
+def Feedback.get_custom(question, regexp)
+	#NB regex is submitted  as a string
+	puts question
+	cont = true
+	while cont
+		puts "---Please enter an answer of the form " + regexp
+		answer = gets.to_s
+		if answer =~ Regexp.new(regexp)
+			cont = false
+		else
+			puts "Incorrect form"
+		end
+	end
+	return answer.chomp
+end
+
+def Feedback.get_boolean(question)
+	puts question
+	cont = true
+	while cont
+		puts "---Please enter y or n"
+		answer = gets
+		if answer =~ /^n$/i
+			cont = false
+			bool = false
+		elsif answer =~ /^y$/i
+			cont = false
+			bool = true
+		else
+			puts "Incorrect selection: #{answer.inspect}"
+		end
+	end
+	return bool
+end
+
+def Feedback.get_float(question)
+	puts question
+	cont = true
+	while cont
+		puts "---Please enter an answer of the form ^-?\\d[.e-\\d]*$"
+		answer = gets
+		if answer =~ /^-?\d[\d\.e-]*$/
+			cont = false
+		else
+			puts "Incorrect selection: #{answer.inspect}"
+		end
+	end
+	return answer.to_f
+end
+
+def Feedback.get_choice(question, choice)
+	case choice
+		when Hash
+			puts question
+			cont = true
+			old_choice = choice; choice = {}
+			old_choice.each do |key,value|
+					choice[key.to_s] = old_choice[key]
+			end
+			while cont
+				puts "Please select your choice (case sensitive)"
+				choice.each do |key,value|
+					puts key.to_s + ":  " + value.to_s
+
+				end
+
+				answer = gets.chomp
+				if choice[answer]
+					cont = false
+					answer = choice[answer]
+				else	
+					puts "Incorrect Selection: #{answer.inspect} - Please try again"
+				end
+			end
+		when Array
+			hash = {}
+			choice.each_with_index{|choice,i| hash[i] = choice}
+			answer = self.get_choice(question, hash)
+	end
+	return answer
+end	
+
+end

data/lib/coderunner/instance_methods.rb

@@ -1733,7 +1733,7 @@ end
 	"/merged_code_runner.rb",
 	'/run.rb', 
 	'/heuristic_run_methods.rb', 
-	'/run_backwards_compatibility.rb'
+	#'/run_backwards_compatibility.rb'
 ].each do |file|
 		file = CodeRunner::SCRIPT_FOLDER + file
 		require file

data/lib/coderunner/long_regexen.rb

@@ -1,5 +1,6 @@
 # $script_folder = File.dirname(File.expand_path(__FILE__))
-require File.dirname(File.expand_path(__FILE__)) + "/box_of_tricks.rb"
+#require File.dirname(File.expand_path(__FILE__)) + "/box_of_tricks.rb"
+require 'rubyhacks'
 
 module LongRegexen 
 
@@ -198,4 +199,4 @@ if $0 == __FILE__
 	puts "t= 0.2000000000E+03 aky=  1.40 akx= -0.02 om= " =~ LongRegexen::FLOAT
 	puts "asd"
 	puts "	-9.81730399614593e+38;  // phi(2,33,43,2)" =~  Regexp.new("^\\s*?#{LongRegexen::FLOAT.verbatim}.*?\\sphi\\(\\d,(?<theta>\\d+),(?<kx>\\d+)")
-end
+end

data/lib/coderunner/remote_code_runner.rb

@@ -0,0 +1,284 @@
+class RemoteCodeRunner < CodeRunner
+	(CodeRunner.instance_methods - (Object.instance_methods + Log.instance_methods)).each do |meth|
+		next if [:sort_runs, :print_out, :filter, :similar_runs, :get_max, :get_min, :generate_combined_ids, :setup_run_class, :get_run_class_name, :readout, :graphkit_from_lists, :graphkit, :graphkit_shorthand, :run_graphkit_shorthand, :axiskit, :filtered_ids,  :filtered_run_list, :make_film_from_lists, :sweep_graphkits, :cache].include? meth
+		next if CodeRunner::DEFAULT_RUNNER_OPTIONS.keys.include? meth
+		next if CodeRunner::DEFAULT_RUNNER_OPTIONS.keys.map{|meth| (meth.to_s + '=').to_sym}.include? meth
+
+		undef_method meth
+	end
+# 	class << self
+# 		undef_method :graphkit_multiple_runners_from_frame_array
+# 			def method_missing(method, *args)
+# 		raise "Not a CodeRunner class method #{method}" unless (CodeRunner.methods + [:puts]).include? method 
+# 		if method.to_s =~ /=$/
+# 			raise NoMethodError.new("unknown set method: #{method}")
+# # 			@attributes[method] = args[0]
+# # 			return
+# 		end
+# 		data = retrieve(method, *args)
+# 		if method.to_s =~ /graphkit/
+# 			return Marshal.load(data)
+# 		else 
+# 			puts data
+# 		end
+# 	end	
+# 	end
+		
+	attr_accessor :combined_ids, :phantom_ids, :ids, :combined_run_list, :phantom_run_list, :run_list, :remote_cache, :libraries
+	
+# 	include Log
+# 	puts instance_methods; exit
+# 	SHOULD_NOT_BE_CALLED = :add_phantom
+	class << self
+		aliold :new
+		def new(host, folder, copts = {})
+			if host.length == 0
+# 				p 'hello'
+# 				copts[:Y] = folder
+# 				copts[:no_print_out] = true
+# 				copts[:no_update] = true
+# 				return go(copts)
+				folder.sub!(/~/, ENV['HOME'])
+# 				Dir.chdir(folder){read_defaults(copts)}
+# 				p copts
+				return CodeRunner.new(folder, copts)
+			end
+			if copts[:cache]
+				if copts[:cache] == :auto and FileTest.exists? cache_file(host, folder)
+					begin
+						runner =  Marshal.load(File.read(cache_file(host, folder)))
+					rescue TypeError, ArgumentError => err
+						eputs err
+						eputs data [0..100] if err.class == TypeError
+						raise err unless err.message =~ /undefined class/
+						repair_marshal_run_class_not_found_error(err)
+						retry
+					end
+					 runner.remote_cache = copts[:cache]
+					 runner.libraries ||= []
+					 return runner
+				else
+					runner =  old_new(host, folder, copts)
+					runner.update
+					runner.remote_cache = copts[:cache]
+					unless FileTest.exist? cache_folder(host, folder) 
+						FileUtils.makedirs cache_folder(host, folder)
+					end
+					File.open(cache_file(host, folder), 'w') do |file|
+						file.puts Marshal.dump(runner)
+					end
+					return runner					
+				end
+			else
+				return old_new(host, folder, copts)
+			end
+
+		end
+		def cache_folder(host, folder)
+			RUNNER_CACHE + "/#{host}/#{folder.gsub(/\//, '_')}"
+		end
+		def cache_file(host, folder)
+			cache_folder(host, folder) + '/runner.msl'
+		end
+	end
+	
+	DISPLAY_REMOTE_INVOCATION = false
+
+	RUNNER_CACHE = ENV['HOME'] + '/.remote_code_runner_cache'
+
+	def initialize(host, folder, copts = {})
+		@folder = folder
+		@host = host
+		#eputs "setting libraries"
+		@libraries = []
+		if host.length == 1
+			unless Object.constants.include? HostManager.to_s.to_sym
+				raise CRFatal.new("Host manager not available")
+			end
+			HostManager.phoenix($default_host_manager_store) do |host_manager|
+# 				@user_name = host_manager.hosts[host].user_name
+# 				@host = host_manager.hosts[host].host
+# 				@port = host_manager.hosts[host].port
+				@ssh_command = host_manager.hosts[host].ssh
+			end
+		else
+# 			@user_name, @host = host.split(/@/)
+			@ssh_command = "ssh " + host
+		end
+# 		@coderunner_location = coderunner_location
+		@attributes = {}
+		process_copts(copts)
+	end
+	def process_copts(copts)
+		@copts = copts.dup
+		@copts[:g] = @copts[:G] = []
+# 		@copts[:f] = nil
+		@copts[:Y] = @copts[:w] = @copts[:r] = @copts[:e]  = nil
+		@copts.delete(:E)
+	end
+	def method_missing(method, *args)
+		raise "Not a CodeRunner method #{method}" unless (CodeRunner.instance_methods + [:puts]).include? method 
+# 		ep method; STDIN.gets
+
+		if method.to_s =~ /=$/
+			raise NoMethodError.new("unknown set method: #{method}")
+# 			@attributes[method] = args[0]
+# 			return
+		end
+		data = retrieve_method(method, *args)
+		if method.to_s =~ /graphkit/
+# 			puts Marshal.load(data).pretty_inspect
+			unless data
+				raise "Error: No data was returned from remote server when calling '#{method}'"
+			end
+			#return Marshal.load(data)
+			return data
+		else 
+			puts data
+		end
+	end	
+	def retrieve_method(method, *args)
+		eputs "Calling Remote Method: #{method}"
+    retrieve("#{method.to_s}(*#{args.inspect})")
+	end
+	def retrieve(string)
+		#ep '@host', @host, '@remote_cache', @remote_cache
+    cachename = self.class.cache_folder(@host, @folder) + '/' + string.gsub(/[\/:\\\[\]\(\)]/, '.')
+		if @remote_cache == :auto and 	FileTest.exist?(cachename)
+			return eval(File.read(cachename))
+		end
+		string = @libraries.map{|lib| "require #{lib}"}.join(";") + ";" + string
+
+		eputs "Connecting to server using '#{@ssh_command}'..."
+		eputs "Loading folder #{@folder}..."
+# 		eval = 
+# 		> /dev/null 2> /dev/null > /dev/null 2> /dev/null
+		shell_script = <<EOF
+cd #@folder
+export ROWS=#{Terminal.terminal_size[0]}
+export COLS=#{Terminal.terminal_size[1]} 
+source /etc/bashrc /etc/profile > /dev/null 2> /dev/null
+source ~/.bashrc ~/.bash_login ~/.bash_profile ~/.profile > /dev/null 2> /dev/null
+if [ "$CODE_RUNNER_COMMAND" ]
+	then
+		$CODE_RUNNER_COMMAND runner_eval #{string.inspect} -Z #{@copts.inspect.inspect}	
+	else
+		coderunner runner_eval #{string.inspect} -Z #{@copts.inspect.inspect}
+fi
+
+EOF
+# coderunner runner_eval #{"#{method.to_s}(*#{args.inspect})".inspect} -Z #{@copts.inspect.inspect}
+
+		eputs shell_script if DISPLAY_REMOTE_INVOCATION
+		data = %x[#@ssh_command '#{shell_script}']
+# 		ep data
+		eputs "\nDisconnecting from server..."	
+		eprint "Extracting data..."
+		data_arr = []
+		in_dump = false
+		i = 0
+		loop do
+			
+			if  i>=80 #data.size
+				break
+			
+			else  #if data[i-1] == "E" and data[i-2] == "_" 
+# 				ep data[i...(i + "code_runner_server_dump_start_E".size)], '.....'
+# 			ep data[(-"code_runner_server_dump_end_E\n".size-i+1)..-i] if in_dump
+		
+# 				string = data[0...i]
+	# 			p string
+				if !in_dump and data[i...(i + "code_runner_server_dump_start_E".size)] == "code_runner_server_dump_start_E" #   =~ /.*Begin Output\n\Z/
+# 					ep "IN DUMP"
+					data = data[(i + "code_runner_server_dump_start_E".size)..-1]
+					in_dump = true
+					i = 0
+				elsif in_dump and data[(-"code_runner_server_dump_end_E\n".size-i+1)..-i] == "code_runner_server_dump_end_E\n" #  
+					data_arr.push data[0...(data.size - ("code_runner_server_dump_end_E\n".size+i-1))]
+# 					ep "OUT DUMP"
+	# 				ep data_arr
+# 					data = data[0...-(-"code_runner_server_dump_end_E".size-i)]
+					in_dump = false
+# 					i = 1
+					break
+				end
+			end
+			i+=1
+		end
+		
+		eputs "done"
+# 		ep data_arr; exit
+		
+		
+		begin
+			case data_arr.size
+			when 0
+				output = nil
+			when 1
+				output =  Marshal.load(data_arr[0])
+			else
+				output = data_arr.map{|str| Marshal.load(str)}
+			end
+		rescue TypeError, ArgumentError => err
+			eputs err
+			eputs data[0..100] if err.class == TypeError
+			raise err unless err.message =~ /undefined class/
+			self.class.repair_marshal_run_class_not_found_error(err)
+			#NB this means that all code_names have to contain only lowercase letters:
+# 			code, modlet = err.message.scan(/CodeRunner\:\:([A-Z][a-z0-9]+)([A-Z][\w]+)?Run/)[0]
+# 			ep code, modlet
+# 			modlet.gsub!(/\B([A-Z])/, '_\1') if modlet 
+# 			modlet = modlet.downcase if modlet
+# 			@run_class = CodeRunner.setup_run_class(code.downcase, modlet: modlet)
+			retry
+		end
+
+		if [:refresh, :auto].include? @remote_cache
+			eputs "Writing Cache"
+			File.open(cachename, 'w'){|file| file.puts(output.inspect)}
+		end
+		return output
+
+	end
+	def update
+# 		ep '@server1', @server
+
+		instance_vars = retrieve_method(:marshalled_variables) #.sub(/\A\s*/, '')
+		#begin
+			#instance_vars = Marshal.load(data)
+		#rescue TypeError, ArgumentError => err
+			#eputs err
+			#eputs data [0..100] if err.class == TypeError
+			#raise err unless err.message =~ /undefined class/
+			#self.class.repair_marshal_run_class_not_found_error(err)
+			##NB this means that all code_names have to contain only lowercase letters:
+## 			code, modlet = err.message.scan(/CodeRunner\:\:([A-Z][a-z0-9]+)([A-Z][\w]+)?Run/)[0]
+## 			ep code, modlet
+## 			modlet.gsub!(/\B([A-Z])/, '_\1') if modlet 
+## 			modlet = modlet.downcase if modlet
+## 			@run_class = CodeRunner.setup_run_class(code.downcase, modlet: modlet)
+			#retry
+		#end
+# 		ep @run_class.executable
+		instance_vars[:@run_list].values.each{|run| run.runner=self}
+# 		class_vars.each do |var, val|
+# # 		  		        raise 'found it ' + var.to_s if val.class == CodeRunner
+# 			next if [:@@global_binding, :@@server, :SCRIPT_FOLDER, :@@sys].include? var
+# 			self.class.class_variable_set(var, val)
+# 		end
+		instance_vars.each do |var, val|
+# 		        puts val.class
+# 		        raise 'found it ' + var.to_s if val.class == CodeRunner
+			next if [:@server, :@sys].include? var
+			instance_variable_set(var, val)
+		end
+# 		@run_class.executable = instance_vars[:@executable]
+
+		# 		ep @run_class.executable
+# 		ep '@sort', @sort
+		sort_runs
+# 		ep '@server', @server
+		return self
+	end
+end
+

data/lib/coderunner/run.rb

@@ -231,24 +231,24 @@ def process_directory
 # 	p @directory
 	@readme = nil
 	
-	if @code_runner_version < Version.new('0.5.1')
-		begin
-			update_from_version_0_5_0_and_lower
-		rescue Errno::ENOENT => err # No code runner files were found
-			unless @runner.heuristic_analysis
-				puts err
-				raise CRFatal.new("No code runner files found: suggest using heuristic analysis (flag -H if you are using the code_runner script)")
-			end
-			unless @runner.current_request == :traverse_directories
-				@runner.requests.push :traverse_directories unless @runner.requests.include? :traverse_directories
-				raise CRMild.new("can't begin heuristic analysis until there has been a sweep over all directories") # this will get rescued
-			end
-			@runner.increment_max_id	
-			@id = @runner.max_id
-			@job_no = -1
-			run_heuristic_analysis
-		end
-	end
+	#if @code_runner_version < Version.new('0.5.1')
+		#begin
+			#update_from_version_0_5_0_and_lower
+		#rescue Errno::ENOENT => err # No code runner files were found
+			#unless @runner.heuristic_analysis
+				#puts err
+				#raise CRFatal.new("No code runner files found: suggest using heuristic analysis (flag -H if you are using the code_runner script)")
+			#end
+			#unless @runner.current_request == :traverse_directories
+				#@runner.requests.push :traverse_directories unless @runner.requests.include? :traverse_directories
+				#raise CRMild.new("can't begin heuristic analysis until there has been a sweep over all directories") # this will get rescued
+			#end
+			#@runner.increment_max_id	
+			#@id = @runner.max_id
+			#@job_no = -1
+			#run_heuristic_analysis
+		#end
+	#end
 	
 	
 	read_info
@@ -442,7 +442,7 @@ end
 def update_submission_parameters(parameters, start_from_defaults=true)
 	logf(:update_submission_parameters)
 	if start_from_defaults
-		upgrade_defaults_from_0_5_0 if self.class.constants.include? :DEFAULTS_FILE_NAME_0_5_0
+		#upgrade_defaults_from_0_5_0 if self.class.constants.include? :DEFAULTS_FILE_NAME_0_5_0
 		main_defaults_file = "#{defaults_location}/#{defaults_file_name}"
 		main_defaults_file_text = 		File.read(main_defaults_file)
 		evaluate_defaults_file(main_defaults_file)
@@ -753,11 +753,11 @@ def self.check_and_update
 		@readout_list = (rcp.variables+rcp.results) unless rcp.readout_list
 # 		(variables+results).each{|v| const_get(:READOUT_LIST).push v} unless READOUT_LIST.size > 0
 
-		if rcp.variables_0_5_0
-			rcp.variables_0_5_0.dup.each do |par, info| #for backwards compatibility only
-				rcp.variables_0_5_0[par] = info[0] if info.class == Array
-			end
-		end
+		#if rcp.variables_0_5_0
+			#rcp.variables_0_5_0.dup.each do |par, info| #for backwards compatibility only
+				#rcp.variables_0_5_0[par] = info[0] if info.class == Array
+			#end
+		#end
 
 
 

data/lib/coderunner/test.rb

@@ -0,0 +1,35 @@
+module Tst
+	def self.check(name, obj, test_string, expected_results, error_class)
+		value = obj.instance_eval test_string
+		unless (expected_results.class == Array ? expected_results.include?(value) : value == expected_results)
+			message = "\n==============================\n"
+			message += "=        Test Failed         =\n"
+			message += "==============================\n\n"
+			message += "Object Description: #{name}\n"
+			message += "Object Value: #{obj.inspect}\n"
+			message += "Test: #{test_string.inspect}\n" 
+			message += "Expected Result:  #{expected_results}\n"
+			message += "Actual Result: #{value.inspect}"
+			message += "\n\n==============================="
+			raise error_class.new(message)
+		end
+	end
+
+	class TestProc < Proc
+		alias :test :call
+	end
+	class MakeProc < Proc
+		alias :with_result :call
+	end
+	
+	#MakeProcs - used for making tests
+	KIND_OF = MakeProc.new{|*klasses| TestProc.new{|obj, name=""| check(name, obj, klasses.inject(""){|str, klass| str << " or self.kind_of? #{klass.to_s}"}.sub(/^ or /, '') , true, TypeError)}}
+	VALUE = MakeProc.new{|*values| TestProc.new{|obj, name=""| check(name, obj, "self", values, ArgumentError)}}
+
+	#Some predefined tests
+	FLOAT = KIND_OF.with_result(Float, Integer)
+	FLOAT_STRICT = KIND_OF.with_result(Float)
+	INT= INTEGER = KIND_OF.with_result(Integer)
+	STRING = KIND_OF.with_result(String)
+	FORTRAN_BOOL = VALUE.with_result(*String::FORTRAN_BOOLS)
+end

data/lib/coderunner/version.rb

@@ -0,0 +1,27 @@
+class Version
+  include Comparable
+
+  attr_reader :major, :feature_group, :feature, :bugfix
+
+  def initialize(version="")
+    v = version.split(".")
+    @major = v[0].to_i
+    @feature_group = v[1] ? v[1].to_i : 0
+    @feature = v[2] ? v[2].to_i : 0
+    @bugfix = v[2] ? v[3].to_i : 0
+  end
+  
+  def <=>(other)
+    return @major <=> other.major if ((@major <=> other.major) != 0)
+    return @feature_group <=> other.feature_group if ((@feature_group <=> other.feature_group) != 0)
+    return @feature <=> other.feature if ((@feature <=> other.feature) != 0)
+    return @bugfix <=> other.bugfix
+  end
+  def self.sort
+    self.sort!{|a,b| a <=> b}
+  end
+
+  def to_s
+    @major.to_s + "." + @feature_group.to_s + "." + @feature.to_s + "." + @bugfix.to_s
+  end
+end

data/lib/cubecalccrmod.rb

@@ -0,0 +1,106 @@
+class CodeRunner
+	class Cubecalc < Run
+		
+# @code = 'cubecalc'
+
+@variables = [:calculate_sides, :width, :height, :depth, :area]
+
+@naming_pars = [:width]
+
+@results = [:volume, :sides]
+
+# e.g. number of iterations
+
+@run_info = [:phantom_run_description]
+
+# @@executable_name = 'cubecalc'
+
+@code_long = "Cube Volume Calculator"
+
+@excluded_sub_folders = []
+
+@defaults_file_name = "cubecalc_defaults.rb"
+
+@modlet_required = true
+
+@uses_mpi = false
+
+def process_directory_code_specific
+	if @running
+		@status = :Incomplete
+	else
+		if FileTest.exist? 'results.txt'
+			@status = :Complete
+			@volume = File.readlines('results.txt')[0].scan(LongRegexen::FLOAT)[0][0].to_f
+		else
+			@status = :Failed
+		end
+		@sides = []
+		if FileTest.exist? 'sides.txt'
+			File.read('sides.txt').scan(Regexp.new("is\\s*" + LongRegexen::FLOAT.verbatim + "$")){@sides.push $~[:float].to_f}
+		end
+	end
+end
+
+def print_out_line
+	if @is_phantom
+		if @phantom_run_description == :area
+			return sprintf("%d:%d %30s %10s %f %s", @id, @job_no, @run_name, @status, (@volume or 0.0), @area.to_s)
+		else
+			raise 'there is only one phantom_run_description at the moment'
+		end
+	else
+		return sprintf("%d:%d %30s %10s %f %s", @id, @job_no, @run_name, @status, (@volume or 0.0), @sides.to_s)
+	end
+end
+
+def parameter_string
+	return sprintf("%d %s", @calculate_sides, 'edges.txt')
+end
+
+def generate_input_file
+	File.open('edges.txt', 'w') do |file|
+		file.puts @width
+		file.puts @height
+		file.puts @depth
+	end
+end
+# @run_class.variables.keys[0]
+def parameter_transition(run)
+end
+
+def executable_location
+	@runner.script_folder + '/test_suite'
+end
+	
+
+def generate_phantom_runs
+	return unless @sides
+	@sides.each do |area|
+# 		puts 'creating phantom: ' + @run_name
+		phantom = create_phantom
+		phantom.area = area
+		phantom.phantom_run_description = :area
+	end
+end
+
+def graphkit(name, options)
+	case name
+	when /sides/
+# 		x = AxisKit.autocreate({data: ["'width'", "'depth'", "'height'"], name: 'Properties'})
+		x = GraphKit::AxisKit.autocreate({data: sides, title: "Areas of the Sides:  #@run_name"})
+# 		x.range = [0, x.data.max]
+		kit = GraphKit.autocreate({x: x})
+		kit.style = 'data histograms'
+		kit.file_name = 'inputs'
+# 		kit.with = 'histogram clustered'
+		return kit
+	else
+		raise 'Unknown graph'
+	end
+end
+		
+		
+	end
+end
+

data/lib/cubecalccrmod/cubecalc_defaults.rb

@@ -0,0 +1,6 @@
+@calculate_sides = 0
+
+@width = 1.0
+@depth = 1.0
+@height = 1.0
+

data/lib/cubecalccrmod/default_modlets/empty.rb

@@ -0,0 +1,8 @@
+class CodeRunner
+	class Cubecalc
+		class Empty < Cubecalc
+
+			@defaults_file_name = "empty_defaults.rb"
+		end
+	end
+end

data/lib/cubecalccrmod/default_modlets/empty_defaults.rb

@@ -0,0 +1,6 @@
+@calculate_sides = 1
+
+@width = 1.0
+@depth = 1.0
+@height = 1.0
+

data/lib/cubecalccrmod/defaults_files/sleep_defaults.rb

@@ -0,0 +1,6 @@
+@calculate_sides = 0
+@sleep_time = 3.0
+@width = 1.0
+@depth = 1.0
+@height = 1.0
+

data/lib/cubecalccrmod/my_modlets/sleep.rb

@@ -0,0 +1,14 @@
+class CodeRunner
+	class Cubecalc
+		class Sleep < Cubecalc
+
+@variables = [:calculate_sides, :width, :height, :depth, :sleep_time]
+
+def parameter_string
+	return sprintf("%d %s %d", @calculate_sides, 'edges.txt', @sleep_time)
+end
+
+		end
+	end
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.11.2
+  version: 0.11.3
   prerelease: 
 platform: ruby
 authors:
@@ -27,6 +27,22 @@ dependencies:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: parallelpipes
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: rubyhacks
   requirement: !ruby/object:Gem::Requirement
@@ -170,6 +186,7 @@ files:
 - lib/code_runner_extension.rb
 - lib/coderunner.rb
 - lib/coderunner/class_methods.rb
+- lib/coderunner/feedback.rb
 - lib/coderunner/fortran_namelist.rb
 - lib/coderunner/graphs_and_films.rb
 - lib/coderunner/heuristic_run_methods.rb
@@ -177,6 +194,7 @@ files:
 - lib/coderunner/interactive_methods.rb
 - lib/coderunner/long_regexen.rb
 - lib/coderunner/merged_code_runner.rb
+- lib/coderunner/remote_code_runner.rb
 - lib/coderunner/run.rb
 - lib/coderunner/system_modules/franklin.rb
 - lib/coderunner/system_modules/generic_linux.rb
@@ -188,6 +206,14 @@ files:
 - lib/coderunner/system_modules/moab.rb
 - lib/coderunner/system_modules/new_hydra.rb
 - lib/coderunner/system_modules/slurm.rb
+- lib/coderunner/test.rb
+- lib/coderunner/version.rb
+- lib/cubecalccrmod.rb
+- lib/cubecalccrmod/cubecalc_defaults.rb
+- lib/cubecalccrmod/default_modlets/empty.rb
+- lib/cubecalccrmod/default_modlets/empty_defaults.rb
+- lib/cubecalccrmod/defaults_files/sleep_defaults.rb
+- lib/cubecalccrmod/my_modlets/sleep.rb
 - test/helper.rb
 - test/test_coderunner.rb
 homepage: http://coderunner.sourceforge.net
@@ -205,7 +231,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -3340194866062964858
+      hash: -4238312090004986134
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: