coderunner 0.12.5 → 0.12.6

data/VERSION

@@ -1 +1 @@
-0.12.5
+0.12.6

data/coderunner.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.12.5"
+  s.version = "0.12.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2013-06-07"
+  s.date = "2013-06-17"
   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"]

data/lib/coderunner.rb

@@ -118,19 +118,17 @@ CodeRunner::GLOBAL_BINDING = binding
 
 Log.log_file = nil
 
-# $sys = 'macosx' if $sys == 'home'
-# puts $sys; gets
 
 
+
+class CodeRunner
+	
 ####################################
 # Commmand line processing         #
 ####################################
 
 
 # Here are all the methods that map the command line invocation into the correct class method call
-
-class CodeRunner
-
 		COMMAND_LINE_FLAGS_WITH_HELP = [
 	["--recalc-all", "-A", GetoptLong::NO_ARGUMENT, %[Causes each directory to be reprocessed, rather than reading the cache of data. Its exact effect depends on the code module being used. By convention it implies that ALL data analysis will be redone.]],
 	["--reprocess-all", "-a", GetoptLong::NO_ARGUMENT, %[Causes each directory to be reprocessed, rather than reading the cache of data. Its exact effect depends on the code module being used. By convention it implies that VERY LITTLE data analysis will be redone.]],
@@ -202,7 +200,7 @@ EOF
 		["continue_in_new_folder", "cnf", 1, 'Make a new folder in the parent directory and copy all coderunner configuration files to that folder. If options j or f are specified, copy all matching runs to that new folder.', ['folder'], [:j, :f, :U, :N]],
 		["code_runner_execute", "crex",  1, 'Run (within the CodeRunner class) the fragment of Ruby code given.', ['Ruby fragment'], []],	
 		["delete", "del", 0, 'Permanently erase all filtered runs.', [], [:j, :F, :U, :N]],
-		["differences_between", "diff", 1, 'Print a table of all the differences between the input parameters of the given ids.', ['ids'], [:j, :F, :U, :N]],
+		["differences_between", "diff", 0, 'Print a table of all the differences between the input parameters of the filtered ids.', [], [:j, :F, :U, :N]],
 		["directory", "dir", 1, 'Print out the directory for the given run.', ['id'], []],
 		['dumb_film', "dfm", 0, 'Create a film of the specified graphkits using gnuplot "dumb" ASCII terminal.', [], [:F, :G, :g, :U, :N, :j, :f]],
 		["execute", "ex",  1, 'Run (at the top level) the fragment of Ruby code given.', ['Ruby fragment'], []],	

data/lib/coderunner/class_methods.rb

@@ -76,7 +76,7 @@ class CodeRunner
 		runner = fetch_runner(copts)
 		runner.destroy
 	end
-	def self.differences_between(ids, copts = {})
+	def self.differences_between(copts = {})
 		runner = fetch_runner(copts)
 		runs = runner.filtered_ids.map{|id| runner.run_list[id]}
 		vars = runner.run_class.rcp.variables.dup + runner.run_class.rcp.run_info.dup
@@ -684,9 +684,9 @@ EOF
 				else
 					runner = @runners[copts[:Y]]
 				end
-# 				p 'reading defaults', @r.conditions, DEFAULT_RUNNER_OPTIONS
+ 				#p 'reading defaults', runner.recalc_all, DEFAULT_RUNNER_OPTIONS
 				runner.read_defaults
-# 				p 'read defaults', @r.conditions
+ 				#p 'read defaults', runner.recalc_all
 				
 			end #Dir.chdir
 		end

data/lib/coderunner/fortran_namelist.rb

@@ -85,7 +85,7 @@ class Run
 		@deleted_variables = eval(File.read(folder + '/deleted_variables.rb'), binding, folder + '/deleted_variables.rb')
 	rescue Errno::ENOENT
 		@deleted_variables = {}
-		save_deleted_variables
+		#save_deleted_variables
 	end
 
 	@deleted_variables.keys.each{|var| attr_accessor var}
@@ -295,7 +295,9 @@ def self.add_code_variable_to_namelist(namelist, var, value)
 	namelist_file = 'namelists.rb'
 # 	end
 	raise "This namelist: #{namelist} should have an enumerator and does not have one" if enum and not @namelists[namelist][:enumerator]
-	return unless Feedback.get_boolean("An unknown variable has been found in this input file: \n\n\t Namelist: #{namelist}, Name: #{code_name}, Sample Value: #{value.inspect}.\n\nDo you wish to add it to the CodeRunner module? (Recommended: answer yes as long as the variable is not a typo)")
+  unless ENV['CR_NON_INTERACTIVE']
+  	return unless Feedback.get_boolean("An unknown variable has been found in this input file: \n\n\t Namelist: #{namelist}, Name: #{code_name}, Sample Value: #{value.inspect}.\n\nDo you wish to add it to the CodeRunner module? (Recommended: answer yes as long as the variable is not a typo)")
+  end
 
 	while nms = variable_exists?(namelist, var)
 		puts "This variable: #{var} already exists in these namelists: #{nms}. Please give an alternative name for CodeRunner (this will not affect the name that appears in the input file). If you know that the variable has the same meaning in these other namelists, or if you know that none of these namelists will appear at the same time, enter '0' to leave it unchanged."
@@ -355,7 +357,7 @@ def self.add_code_variable_to_namelist(namelist, var, value)
 		attr_accessor var
 	end
   save_namelists
-	edit_variable_help(namelist, var)
+	edit_variable_help(namelist, var) unless ENV['CR_NON_INTERACTIVE']
 # 	folder = File.dirname(__FILE__)
 # 	File.open(folder + '/' + namelist_file, 'w'){|f| f.puts namelists.pretty_inspect}
 end	
@@ -988,10 +990,10 @@ def self.update_defaults_from_source_code(source_code_folder = ARGV[-1])
 	end
 	
 # 	string.gsub!(/^.+?:/, '') # Get rid of file names from grep
- File.open('found1','w'){|f| f.puts string}
+ #File.open('found1','w'){|f| f.puts string}
 #  exit
 	defs = scan_text_for_variables(string) 
-	File.open('found2','w'){|f| f.puts defs.pretty_inspect}
+	#File.open('found2','w'){|f| f.puts defs.pretty_inspect}
 # 	exit
 	namelists.each do |namelist, hash|
 		hash[:variables].each do |var, varhash|
@@ -1043,7 +1045,7 @@ def self.synchronise_variables(source_code_folder = ARGV[2])
 	all_variables_in_source = {}
 	namelist_declarations = {}
 	#source.scan(/^\s*namelist\s*\/(?<namelist>\w+)\/(?<variables>(?:(?:&\s*[\n\r]+)|[^!\n\r])*)/) do 
-	source.scan(Regexp.new("#{/^\s*namelist\s*\/(?<namelist>\w+)\//}(?<variables>#{FORTRAN_SINGLE_LINE})")) do 
+	source.scan(Regexp.new("#{/^\s*namelist\s*\/\s*(?<namelist>\w+)\s*\//}(?<variables>#{FORTRAN_SINGLE_LINE})")) do 
 		namelist = $~[:namelist].to_s.downcase.to_sym
 		variables = $~[:variables].gsub(/!.*/, '')
 		eputs namelist, variables
@@ -1095,6 +1097,7 @@ def self.synchronise_variables(source_code_folder = ARGV[2])
 	eputs nms.keys.zip(nms.values.map{|vs| vs.size})
 	eputs "Namelists to be added to. (Press Enter)"; STDIN.gets
 	n = 0
+  ep nms
 # 	ep nms.values.sum
 	nms.values.sum.each do |var|
 		eputs var if variable_exists? var

data/lib/coderunner/instance_methods.rb

@@ -59,6 +59,9 @@ class CodeRunner
 			super(mess)
 		end
 	end
+	# The defaults that are saved in the root folder
+	
+	FOLDER_DEFAULTS = [:code, :modlet, :executable, :defaults_file, :project]  
 	
 	# Parameters important to the submission of a run, which can be set by command line flags. The runner values provide the default values for the submit function, but can be overidden in that function. All the runner does with them is set them as properties of the run to be submitted. It is the run itself for which the options are relevant.
 	
@@ -66,7 +69,7 @@ class CodeRunner
 	
 	# A hash containing the defaults for most runner options. They are overridden by any options provided during initialisation. They are mostly set at the command line (in practice, the command line flags are read into the command options, which set these defaults in the function CodeRunner.process_command_options which calls CodeRunner.set_runner_defaults). However, if Code Runner is being scripted, these defaults must be set manually or else the options they specify must be provided when initialising a runner.
 	
-	DEFAULT_RUNNER_OPTIONS = ([:conditions, :code, :executable, :sort, :debug, :script_folder, :recalc_all, :multiple_processes, :heuristic_analysis, :test_submission, :reprocess_all, :use_large_cache, :use_large_cache_but_recheck_incomplete, :use_phantom, :no_run, :server, :version, :parameters] + SUBMIT_OPTIONS).inject({}){|hash, option| hash[option] = nil; hash}
+	DEFAULT_RUNNER_OPTIONS = ([:conditions, :sort, :debug, :script_folder, :recalc_all, :multiple_processes, :heuristic_analysis, :test_submission, :reprocess_all, :use_large_cache, :use_large_cache_but_recheck_incomplete, :use_phantom, :no_run, :server, :version, :parameters] + SUBMIT_OPTIONS + FOLDER_DEFAULTS).inject({}){|hash, option| hash[option] = nil; hash}
 	
 	# Options that apply across the CodeRunner class 
 	
@@ -232,9 +235,6 @@ class CodeRunner
 		
 	private :set_max_id
 
-	# The defaults that are saved in the root folder
-	
-	FOLDER_DEFAULTS = [:code, :modlet, :executable, :defaults_file, :project]  
 
 	# Read any default options contained in the file <tt>.code_runner_script_defaults.rb</tt> in the root folder.
 	

data/lib/coderunner/run.rb

@@ -410,7 +410,7 @@ end
 
 def defaults_location
 	if @runner.defaults_file
-		location = [ENV['HOME'] + "/.coderunner/#{@code}crmod/defaults_files", rcp.code_module_folder	+ "/defaults_files"].find{|folder| FileTest.exist? folder and Dir.entries(folder).include? defaults_file_name}
+		location = [rcp.user_defaults_location, rcp.code_module_folder	+ "/defaults_files"].find{|folder| FileTest.exist? folder and Dir.entries(folder).include? defaults_file_name}
 		raise "Defaults file: #{defaults_file_name} not found" unless location
 		return location
 	else
@@ -786,6 +786,7 @@ def self.check_and_update
 		@all = (rcp.variables + rcp.results + rcp.run_info) #.each{|v| ALL.push v}
 # 		ep "GOT HERE"
 		(@all + [:directory, :run_name, :modlet, :relative_directory]).each{|var| send(:attr_accessor, var)}
+    @user_defaults_location = ENV['HOME'] + "/.coderunner/#{@code}crmod/defaults_files"
 		define_method(:output_file) do 
 			return @output_file if @output_file
 			@output_file = super()

data/lib/coderunner/system_modules/generic_linux.rb

@@ -15,6 +15,7 @@ end
 
 def run_command
 	if rcp.uses_mpi
+    raise "Number of processors (nprocs) not specified" unless @nprocs
 		return %[time mpirun -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
 	else
 		return %[#{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.12.5
+  version: 0.12.6
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-07 00:00:00.000000000 Z
+date: 2013-06-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit