coderunner 0.13.9 → 0.13.10

data/VERSION

@@ -1 +1 @@
-0.13.9
+0.13.10

data/coderunner.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.13.9"
+  s.version = "0.13.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]

data/lib/coderunner/fortran_namelist.rb

@@ -113,7 +113,7 @@ end
 # in namelist 
 
 def self.known_code_variable?(namelist, var)
-	return true if rcp.namelists[namelist] and rcp.namelists[namelist][:variables].map{|(v,h)| (h[:code_name] or v).to_s.downcase.to_sym}.include? var.to_s.downcase.to_sym
+	return true if rcp.namelists[namelist.to_s.downcase.to_sym] and rcp.namelists[namelist.to_s.downcase.to_sym][:variables].map{|(v,h)| (h[:code_name] or v).to_s.downcase.to_sym}.include? var.to_s.downcase.to_sym
 # 	end
 	return false
 end
@@ -290,7 +290,7 @@ end
 # in the simulation code.
 
 def self.add_code_variable_to_namelist(namelist, var, value)
-	code_name = var
+	code_name = var.to_s.downcase.to_sym
 	var = var.to_s.downcase.to_sym
 	namelist = namelist.to_s.sub(/_(?<num>\d+)$/, '').to_sym
 	enum = $~ ? $~[:num] : nil
@@ -298,7 +298,7 @@ def self.add_code_variable_to_namelist(namelist, var, value)
 	namelists = rcp.namelists
 	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]
+	raise "This namelist: #{namelist} should have an enumerator and does not have one" if enum and (not rcp.namelists[namelist] or not rcp.namelists[namelist][:enumerator])
   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
@@ -548,7 +548,7 @@ def self.parse_input_file(input_file, strict=true)
 	regex = Regexp.new("#{rcp.matching_regex.to_s}\\s*(?:\\!(?<comment>.*))?\\n")
 	#ep input_file
 	text.scan(/(?:(?:^|\A)\s*\!\s*(?<namelist_comment>[^\n]+)\n)?(?:^|\A)\&(?<namelist>\S+).*?^\//m) do 
-		namelist = $~[:namelist].to_sym
+		namelist = $~[:namelist].downcase.to_sym
 		hash = namelist_hash[namelist] = {}
 		#p $~
 		scan_text_for_variables($~.to_s).each do |var, val|
@@ -557,7 +557,7 @@ def self.parse_input_file(input_file, strict=true)
 			hash[var] =  val
 		end
 	end
- 	pp 'inputfile', namelist_hash
+ 	#pp 'inputfile', namelist_hash
 	namelist_hash
 end
 
@@ -568,7 +568,7 @@ def self.scan_text_for_variables(text)
 	arr = []
 	text.scan(regex) do
 		match = $~
-		var = match[:name].to_sym
+		var = match[:name].downcase.to_sym
 		default = match[:default.to_sym]
 		default = (match[:float] or match[:complex]) ? match[:default].gsub(/(\.)(\D|$)/, '\10\2').gsub(/[dD]/, 'e').gsub(/(\D|^)(\.)/, '\10\2') : match[:default]
  		#ep 'default', default
@@ -1112,13 +1112,39 @@ def self.get_sample_value(source, var)
 			return sample_val
 end
 
+# Add variables found in the given namelist file and delete variables not found in it. 
+#
+def self.synchronise_variables_from_input_file(input_file =  ARGV[2])
+	namelists = parse_input_file(input_file)
+	nms = {}
+	all_variables_in_source = {}
+	namelist_declarations = {}
+	namelists.each do |nmlist, vars|
+		all_variables_in_source[nmlist.to_s.sub(/_\d+/, '').to_sym] = []
+		vars.each do |var, value|
+			all_variables_in_source[nmlist.to_s.sub(/_\d+/, '').to_sym].push var
+			p ['nmlist', nmlist, 'var', var]
+			next if known_code_variable?(nmlist, var)
+			add_code_variable_to_namelist(nmlist, var, value)
+		end
+	end
+	delete_old_variables(all_variables_in_source)
+end
+
+
 # Find unknown input variables in the source code and add them to the database of namelists
 # Delete input variables which are no longer present in the source code
                                          
 def self.synchronise_variables(source_code_folder = ARGV[2])
 	source = get_aggregated_source_code_text(source_code_folder)
 	nms, all_variables_in_source, namelist_declarations = get_namelists_and_variables_from_source_code(source)
+	process_synchronisation(nms, all_variables_in_source, namelist_declarations)
+end
 # 	ep source.size
+
+# Delete variables unless they are still present in the source code
+
+def self.delete_old_variables(all_variables_in_source)
 	variables_to_delete = {}	
 	#pp 'namelists', rcp.namelists
 	rcp.namelists.each do |namelist, namelist_hash|
@@ -1146,6 +1172,10 @@ def self.synchronise_variables(source_code_folder = ARGV[2])
 			end
 		end
 	end
+end
+
+def self.process_synchronisation(nms, all_variables_in_source, namelist_declarations)
+	delete_old_variables(all_variables_in_source)
 
 	raise "No namelists found" if nms.size == 0
 	eputs nms.keys.zip(nms.values.map{|vs| vs.size})

data/lib/coderunner/graphs_and_films.rb

@@ -533,7 +533,7 @@ class CodeRunner
 		eputs "making film"
 		frame_rate = (options[:frame_rate] or options[:fr] || 15)
 		film_name = (options[:film_name] or options [:fn] or end_graphkit.file_name + '_film').gsub(/\s/, '_')
-		puts `ffmpeg -y #{options[:bitrate] ? "-b #{options[:bitrate]}" : ""} -r #{frame_rate} -threads #{(@multiple_processes or 1)} -i film_frames/frame_%0#{fd}d#{extension} -sameq #{film_name}.mp4`
+		puts `ffmpeg -y #{options[:bitrate] ? "-b #{options[:bitrate]}" : ""} -r #{frame_rate} -threads #{(@multiple_processes or 1)} -i film_frames/frame_%0#{fd}d#{extension} -qscale 0 #{film_name}.mp4`
 		end
 	end
 	
@@ -737,7 +737,7 @@ class CodeRunner
 		eputs "making film"
 		frame_rate = (options[:frame_rate] or options[:fr] || 15)
 		film_name = (options[:film_name] or options [:fn] or graphkit_frame_array[0][1].file_name + '_film').gsub(/\s/, '_')
-		puts `ffmpeg -y #{options[:bitrate] ? "-b #{options[:bitrate]}" : ""} -r #{frame_rate} -threads #{(@multiple_processes or 1)} -i film_frames/frame_%0#{fd}d#{extension} -sameq #{film_name}.mp4`
+		puts `ffmpeg -y #{options[:bitrate] ? "-b #{options[:bitrate]}" : ""} -r #{frame_rate} -threads #{(@multiple_processes or 1)} -i film_frames/frame_%0#{fd}d#{extension} -qscale 0 #{film_name}.mp4`
 		end
 	end
 

data/lib/coderunner/system_modules/dirac.rb

@@ -14,7 +14,7 @@ class CodeRunner
 		
 		def batch_script
 			ppn_checks
-			hours, minutes, seconds = hours_minutes_seconds
+			hours, mins, secs = hours_minutes_seconds
 	<<EOF
 		#!/bin/bash --login 
 		#PBS -N #{executable_name}.#{job_identifier}

data/lib/coderunner/system_modules/moab.rb

@@ -80,7 +80,7 @@ module Moab
 			raise "Please specify wall mins using the W flag"
 		end
 		eputs "Allotted wall time is " + sprintf("%02d:%02d:%02d", hours, mins, secs)
-		return [hours, minutes, seconds]
+		return [hours, mins, secs]
 	end
 	def ppn_checks
 		eputs "Warning: Underuse of nodes (#{ppn} cores per node instead of #{max_ppn})" if ppn.to_i < max_ppn 
@@ -88,7 +88,7 @@ module Moab
 	end
 	def batch_script
 		ppn_checks
-		hours, minutes, seconds = hours_minutes_seconds
+		hours, mins, secs = hours_minutes_seconds
 <<EOF
 	#!/bin/bash --login 
 	#PBS -N #{executable_name}.#{job_identifier}

data/lib/cubecalccrmod/deleted_variables.rb

@@ -27,4 +27,358 @@
     [{:test=>"kind_of? Numeric",
       :explanation=>
        "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
-   :type=>:Float}}
+   :type=>:Float},
+ :beta=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:beta,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :zeff=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:zeff,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :grid_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:grid_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :aky=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:aky,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :akx=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:akx,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :ntheta=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:ntheta,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :nperiod=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nperiod,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :eps=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:eps,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :epsl=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:epsl,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :shat=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:shat,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :pk=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:pk,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :shift=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:shift,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :equilibrium_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:equilibrium_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :model_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:model_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :ngauss=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:ngauss,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :negrid=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:negrid,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :gridfac=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:gridfac,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :omprimfac=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:omprimfac,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :boundary_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:boundary_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :adiabatic_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:adiabatic_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :g_exb=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:g_exb,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :nonad_zero=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nonad_zero,
+   :must_pass=>
+    [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+      :explanation=>
+       "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+   :type=>:Fortran_Bool},
+ :field_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:field_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :wstar_units=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:wstar_units,
+   :must_pass=>
+    [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+      :explanation=>
+       "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+   :type=>:Fortran_Bool},
+ :fphi=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:fphi,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :fapar=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:fapar,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :faperp=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:faperp,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :delt=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:delt,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :nstep=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nstep,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :delt_adj=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:delt_adj,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :delt_minimum=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:delt_minimum,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :layout=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:layout,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :collision_model=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:collision_model,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :nonlinear_mode=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nonlinear_mode,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :flow_mode=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:flow_mode,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :cfl=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:cfl,
+   :must_pass=>
+    [{:test=>"kind_of? Numeric",
+      :explanation=>
+       "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+   :type=>:Float},
+ :nspec=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nspec,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer}}

data/lib/cubecalccrmod/namelists.rb

@@ -54,4 +54,25 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float,
-       :autoscanned_defaults=>[1.0]}}}}
+       :autoscanned_defaults=>[1.0]}}},
+ :parameters=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :kt_grids_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :kt_grids_single_parameters=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :theta_grid_parameters=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :theta_grid_knobs=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :theta_grid_salpha_knobs=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :le_grids_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :dist_fn_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :fields_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :reinit_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :layouts_knobs=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :collisions_knobs=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :nonlinear_terms_knobs=>
+  {:description=>"", :should_include=>"true", :variables=>{}},
+ :species_knobs=>{:description=>"", :should_include=>"true", :variables=>{}}}

data/test/test_coderunner.rb

@@ -21,7 +21,7 @@ $coderunner_command = "#{$ruby_command}  -I lib/ lib/coderunner.rb"
 	#raise "Couldn't build test program using #{string}" unless system string
 #end
 
-if true
+if false
 class TestSubmission  < Test::Unit::TestCase
 	def setup
 		string = $cpp_command + ' ../cubecalc.cc -o cubecalc'
@@ -363,7 +363,7 @@ end # if false/true
 #end
 #
 #
-ENV['CR_NON_INTERACTIVE'] = 'true'
+#ENV['CR_NON_INTERACTIVE'] = 'true'
 class TestFortranNamelistC < Test::Unit::TestCase
 	def setup
 	end
@@ -372,6 +372,7 @@ class TestFortranNamelistC < Test::Unit::TestCase
 		CodeRunner.setup_run_class('cubecalc', modlet: 'with_namelist')
 		assert_equal(File.read('test/cubecalc_namelist.cc').size+1, CodeRunner::Cubecalc::WithNamelist.get_aggregated_source_code_text('test').size)
 		CodeRunner::Cubecalc::WithNamelist.synchronise_variables('test')
+		CodeRunner::Cubecalc::WithNamelist.synchronise_variables_from_input_file('test/cubecalc.in')
 		CodeRunner::Cubecalc::WithNamelist.update_defaults_from_source_code('test')
 	end
 	def test_mediawiki_write

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.13.9
+  version: 0.13.10
   prerelease: 
 platform: ruby
 authors: