coderunner 0.11.5 → 0.11.6

data/Rakefile

@@ -24,6 +24,7 @@ Jeweler::Tasks.new do |gem|
   gem.authors = ["Edmund Highcock"]
 	gem.extensions = "ext/extconf.rb"
 	gem.files.include('ext/*.c', 'include/*.h', 'ext/*.rb')
+	gem.required_ruby_version = '>= 1.9.1'
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.11.5
+0.11.6

data/coderunner.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.11.5"
+  s.version = "0.11.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2012-10-09"
+  s.date = "2012-10-10"
   s.description = "CodeRunner is a framework for the automated running and analysis of simulations. It automatically generates any necessary input files, organises the output data and analyses it. Because it is a modular system, it can easily be customised to work with any system and any simulation code. One of its greatest strengths is that it is independent of any one simulation code; thus it can easily plot and compare the data from different codes."
   s.email = "edmundhighcock@sourceforge.net"
   s.executables = ["coderunner"]
@@ -71,6 +71,7 @@ Gem::Specification.new do |s|
   s.homepage = "http://coderunner.sourceforge.net"
   s.licenses = ["GPLv3"]
   s.require_paths = ["lib"]
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
   s.rubyforge_project = "coderunner"
   s.rubygems_version = "1.8.24"
   s.summary = "A framework for the automated running and analysis of simulations."

data/lib/coderunner/fortran_namelist.rb

@@ -64,6 +64,12 @@ class Run
 		end
 		arr
 	end
+	
+	@variable_names_from_code_names = @variables_with_hashes.inject({}) do |hash, (var, var_hash)|
+		hash[(var_hash[:code_name] || var)] = var
+	 	hash
+	end
+		
 
 
 	# VARIABLES = VARIABLES_WITH_HELP.keys
@@ -534,9 +540,11 @@ def self.parse_input_file(input_file, strict=true)
 	end
 	namelist_hash = {}
 	regex = Regexp.new("#{rcp.matching_regex.to_s}\\s*(?:\\!(?<comment>.*))?\\n")
+	#ep input_file
 	text.scan(/(?:^\s*\!\s*(?<namelist_comment>[^\n]+))?\n^\&(?<namelist>\S+).*?^\//m) do 
 		namelist = $~[:namelist].to_sym
 		hash = namelist_hash[namelist] = {}
+		#p $~
 		scan_text_for_variables($~.to_s).each do |var, val|
 			add_code_variable_to_namelist(namelist, var, val) if @strict
 			hash[var] =  val
@@ -555,8 +563,8 @@ def self.scan_text_for_variables(text)
 		match = $~
 		var = match[:name].to_sym
 		default = match[:default.to_sym]
-		default = (match[:float] or match[:complex]) ? match[:default].gsub(/(\.)(\D|$)/, '\10\2').gsub(/[dD]/, 'e').gsub(/(\D)(\.)/, '\10\2') : match[:default]
-# 		ep default
+		default = (match[:float] or match[:complex]) ? match[:default].gsub(/(\.)(\D|$)/, '\10\2').gsub(/[dD]/, 'e').gsub(/(\D|^)(\.)/, '\10\2') : match[:default]
+ 		#ep 'default', default
 		default = eval(default) unless match[:word] or match[:complex]
 		default= Complex(*default.scan(LongRegexen::FLOAT).map{|f| f[0].to_f}) if match[:complex]
 		arr.push [var, default]
@@ -787,11 +795,12 @@ def make_info_file(file=ARGV[-1], strict=true)
 		namelist = namelist.to_s.sub(/\_(?<num>\d+)$/, '').to_sym
 		if $~  # I.e if there was a number at the end of the namelist
 # 			ep namelist
-			"This namelist: #{namelist} should have an enumerator and does not have one" if not rcp.namelists[namelist][:enumerator]
+			raise "This namelist: #{namelist} should have an enumerator and does not have one" if not rcp.namelists[namelist][:enumerator]
 			num = $~[:num]
 		end
 		vars.each do |var, value|
-			var = (var.to_s + "_#{num}").to_sym if num
+			#ep 'var', var
+			var = (rcp.variable_names_from_code_names[var.to_sym] + (num ? "_#{num}" : "")).to_sym
 # 				p var, value
 			set(var, value)
 		end

data/lib/coderunner/instance_methods.rb

@@ -206,7 +206,7 @@ class CodeRunner
 	
 	def read_defaults
 		DEFAULT_RUNNER_OPTIONS.each{|key,value| set(key, value)}
-# 				ep DEFAULT_RUNNER_OPTIONS, @multiple_processes
+ 				#ep DEFAULT_RUNNER_OPTIONS, @multiple_processes
 
 		read_folder_defaults
 	end
@@ -343,13 +343,13 @@ class CodeRunner
 			setup_run_class(code.downcase, modlet: modlet)
 	end
 
+	SETUP_RUN_CLASSES =[]
 	
 	# Create, set up and check the validity of the custom class which deals with a particular simulation code. This class will be defined in a custom module in the folder <tt>code_modules/code_name</tt>, where <tt>'code_name'</tt> is the name of the code. The only option is <tt>modlet:</tt>.
 	#
 	# If the custom class has already been set up, this method just returns the class.
 
 
-	SETUP_RUN_CLASSES =[]
 		def self.setup_run_class(code, options={})
 # 		logf(:setup_code)
 # 		log(:code, code)
@@ -387,6 +387,7 @@ class CodeRunner
 
 		
 		code_module_name = SCRIPT_FOLDER+ "/code_modules/#{code}/#{code}.rb"
+		code_module_name = "#{code}crmod"
 		require code_module_name
 # 		ep get_run_class_name(code, nil)
 		run_class = const_get(get_run_class_name(code, nil))
@@ -410,19 +411,22 @@ class CodeRunner
 		#Some codes require an modlet; the flag modlet_required is specified in the code module
 		if run_class.rcp.modlet_required
 			raise CRFatal.new("Modlet necessary and none given") unless modlet
+		end
+		#If a modlet is specified (modlets can also be optional)
+		if modlet
 # 			Log.logi(:modlet, modlet)
-			if (	modlet_location =  "#{SCRIPT_FOLDER}/code_modules/#{code}/default_modlets";
-			        file_name = "#{modlet_location}/#{modlet}.rb"; 
-				FileTest.exist? file_name
-			)
-			elsif (		modlet_location =  "#{SCRIPT_FOLDER}/code_modules/#{code}/my_modlets";
-			        file_name = "#{modlet_location}/#{modlet}.rb"; 
-				FileTest.exist? file_name
-			)
-			else
-				raise CRFatal.new("Could not find modlet file: #{modlet}.rb")
-			end
-			require file_name
+			#if (	modlet_location =  "#{SCRIPT_FOLDER}/code_modules/#{code}/default_modlets";
+			        #file_name = "#{modlet_location}/#{modlet}.rb"; 
+				#FileTest.exist? file_name
+			#)
+			#elsif (		modlet_location =  "#{SCRIPT_FOLDER}/code_modules/#{code}/my_modlets";
+			        #file_name = "#{modlet_location}/#{modlet}.rb"; 
+				#FileTest.exist? file_name
+			#)
+			#else
+				#raise CRFatal.new("Could not find modlet file: #{modlet}.rb")
+			#end
+			#require file_name
 # 			ep run_class.constants
 # 			ep run_class_names
 			
@@ -1391,11 +1395,11 @@ EOF
 	def similar_runs(exclude_variables=[], run=@run) #all runs for which variables are the same as 'run', with the exception of exclude_variables
 		logf(:similar_runs)
 		raise CRFatal.new("generate_combined_ids must be called before this function is called") unless (@combined_run_list.size > 0 and @combined_ids.size > 0) or @ids.size ==0
-		command = (run.class.rcp.variables+run.class.rcp.run_info-exclude_variables  - [:output_file, :error_file]).inject("@combined_ids.find_all{|id| @combined_run_list[id].class == run.class}"){ |s,v|	
-			s + %<.find_all{|id| @combined_run_list[id].#{v}.class == #{run.send(v).inspect}.class and @combined_run_list[id].#{v} == #{run.send(v).inspect}}>} #the second send call retrieves the type conversion
+		command = (run.class.rcp.variables+run.class.rcp.run_info-exclude_variables  - [:output_file, :error_file, :runner, :phantom_runs]).inject("@combined_ids.find_all{|id| @combined_run_list[id].class == run.class}"){ |s,v|	
+			s + %<.find_all{|id| ep '#{v}'; @combined_run_list[id].#{v}.class == #{run.send(v).inspect}.class and @combined_run_list[id].#{v} == #{run.send(v).inspect}}>} #the second send call retrieves the type conversion
 
 #  		log command
-#  		puts command
+  		#puts command
 		begin 
 			similar = instance_eval(command)
 		rescue => err
@@ -1733,7 +1737,7 @@ 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/system_modules/moab.rb

@@ -120,6 +120,8 @@ def get_run_status(job_no, current_status)
 			return :Queueing
 		elsif line =~ /\sR\s/
 			return :Running
+		elsif line =~ /\sH\s/
+			return :Queueing
 		elsif line =~ /\sC\s/
 			return :Unknown
 		else

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.11.5
+  version: 0.11.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-09 00:00:00.000000000 Z
+date: 2012-10-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -262,10 +262,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
-      version: '0'
-      segments:
-      - 0
-      hash: -1092233251972131996
+      version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: