coderunner 0.17.10 → 0.17.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e64ebfe6d3a4133ee367a12f07e69c668804b7d0
+  metadata.gz: b46beec4f2b3baa9e4bf6933b06a0f7cb8907504
+  data.tar.gz: 1450dbcc231b6ff03b6a484c0defacbccb016845
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+  data.tar.gz: 5f4b357155f3844f46eb46c2c99a9b107ef7149cbb07869a4072880a6a634f39a9b554e22d409d0f06c179e301bff6aec7e7e9e8183e5fa4daa4e45a606f1b33

data/VERSION

@@ -1 +1 @@
-0.17.10
+0.17.11

data/coderunner.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: coderunner 0.17.10 ruby lib
+# stub: coderunner 0.17.11 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.17.10"
+  s.version = "0.17.11"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock"]
-  s.date = "2016-01-21"
+  s.date = "2016-04-01"
   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", "coderunnerrepo"]
@@ -100,7 +100,7 @@ Gem::Specification.new do |s|
   s.licenses = ["GPLv3"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
   s.rubyforge_project = "coderunner"
-  s.rubygems_version = "2.4.8"
+  s.rubygems_version = "2.2.0"
   s.summary = "A framework for the automated running and analysis of simulations."
 
   if s.respond_to? :specification_version then

data/include/code_runner_ext.h

@@ -9,8 +9,8 @@
 #define RFCALL_10_ON(obj, name) (rb_funcall(obj, rb_intern(name), 0))
 #define RFCALL_11(name, arg1) (rb_funcall(self, rb_intern(name), 1, arg1))
 #define RFCALL_11_ON(obj, name, arg1) (rb_funcall(obj, rb_intern(name), 1, arg1))
-#define RFCALL_12(name, arg1, arg2) (rb_funcall(self, rb_intern(name), 1, arg1, arg2))
-#define RFCALL_12_ON(obj, name, arg1, arg2) (rb_funcall(obj, rb_intern(name), 1, arg1, arg2))
+#define RFCALL_12(name, arg1, arg2) (rb_funcall(self, rb_intern(name), 2, arg1, arg2))
+#define RFCALL_12_ON(obj, name, arg1, arg2) (rb_funcall(obj, rb_intern(name), 2, arg1, arg2))
 
 /* Access an element of an array or hash*/
 #define CR_ELEMENT_ACCESS(recvr, key) ( \

data/lib/coderunner/class_methods.rb

@@ -129,24 +129,26 @@ class CodeRunner
 
     concat_string += runner.root_folder + '/' + name
 
-    exec "#{concat_string}"
+    system "#{concat_string}"
   end
 
-  # This section defines the report report writing function in. The latex header is defined in run.rb. It is a run method and can be redefined in a particular CRMOD.
-  # The function is simply called as follows:
+  # This section defines the report report writing function in. The latex
+  # header is defined in run.rb. It is a run method and can be redefined in a
+  # particular CRMOD.  The function is simply called as follows:
   #
-  #   interactively: wr j:<run no.>
-  #   command line: coderunner write_report -j <run no>
+  #   interactively: wr j:<run no.> command line: coderunner write_report -j
+  #   <run no>
   #
   # The requirements to use this function are:
   #
-  #   1. pdflatex version 2014 or higher
-  #   2. gnuplot
-  #   3. ability to write eps graphs
+  #   1. pdflatex version 2014 or higher 2. gnuplot 3. ability to write eps
+  #   graphs
   #
-  # The graphs which are written out to the PDF are read in from a given CRMOD. It should be defined in the main .rb file for the CRMOD, e.g. gs2.rb.
-  # As seen below, this function should be called 'latex_graphs'. To see an example of what this function should look like see GS2CRMOD, but it is simply an array of graphkits
-  # and latex code blocks which describe plots.
+  # The graphs which are written out to the PDF are read in from a given CRMOD.
+  # It should be defined in the main .rb file for the CRMOD, e.g. gs2.rb.  As
+  # seen below, this function should be called 'latex_graphs'. To see an
+  # example of what this function should look like see GS2CRMOD, but it is
+  # simply an array of graphkits and latex code blocks which describe plots.
   def self.write_report(copts={})
     runner = fetch_runner(copts)
     runs = runner.filtered_ids.map{|id| runner.combined_run_list[id]}

data/lib/coderunner/instance_methods.rb

@@ -1096,125 +1096,128 @@ Conditions contain a single = sign: #{conditions}
 		end
 		logf(:submit)
 		Dir.chdir(@root_folder) do
-			@skip=skip
-			mess = false
-			while FileTest.exist?("submitting") 
-				(eputs " Waiting for another process to finish submitting. If you know that no other CodeRunner processes are submitting in this folder (#@root_folder) then delete the file 'submitting' and try again"; mess = true) unless mess
-				sleep rand
-			end
-# 			old_trap = trap(0)
-			#old_trap0 = trap(0){eputs "Aborted Submit (0)!"; File.delete("#@root_folder/submitting"); exit!}
-			old_trap2 = trap(2){eputs "Aborted Submit (2)!"; File.delete("#@root_folder/submitting") if FileTest.exist? "#@root_folder/submitting"; trap(2, "DEFAULT"); trap(0, "DEFAULT"); Process.kill(2, 0)}
-	# 		File.open("submitting", "w"){|file| file.puts ""}
-			FileUtils.touch("submitting")
-			unless options[:no_update_before_submit]
-				@use_large_cache, ulc = false, @use_large_cache; update; @use_large_cache = ulc
-			end
-			generate_combined_ids(:real)
-# 			old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
-			script = "" if options[:job_chain]
-			runs.each_with_index do |run, index|
-				similar = similar_runs([], run)
-				if @skip and similar[0] and not (options[:replace_existing] or options[:rerun])
-					eputs "Found similar run: #{@run_list[similar[0]].run_name}"
-					eputs "Skipping submission..."
-					runs[index] = nil
-					next
-				end
-				unless options[:replace_existing] or options[:rerun]
-					@max_id+=1
-					run.id = @max_id
-				else
-					if options[:replace_existing]
-						FileUtils.rm_r run.directory 
-				  elsif options[:rerun]
-						################# For backwards compatibility
-						SUBMIT_OPTIONS.each do |opt|
-							 run.set(opt, send(opt)) unless run.send(opt)	
-						end
-						###########################################
-						FileUtils.rm "#{run.directory}/code_runner_results.rb"
-						FileUtils.rm "#{run.directory}/.code_runner_run_data"
-					end
-					@run_list.delete(run.id)
-					@ids.delete run.id
-					generate_combined_ids
-				end
-
-				begin
-					
-					unless options[:job_chain]
-						run.prepare_submission unless options[:rerun]
-						next if @test_submission
-						Dir.chdir(run.directory) do 
-							old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
-							######################### The big tomale!
-							run.job_no = run.execute  # Start the simulation and get the job_number
-							#########################
-							run.job_no = get_new_job_no(old_job_nos) unless run.job_no.kind_of? Integer # (if the execute command does not return the job number, look for it manually) 
-# 							eputs 'run.job_no', run.job_no
-							run.output_file = nil # reset the output file
-							run.output_file # Sets the output_file on first call
-							run.error_file = nil # reset the output file
-							run.error_file # Sets the error_file on first call
-							run.write_info
-							eputs "Submitted run: #{run.run_name}"
-						end
-					else
-						run.prepare_submission unless options[:rerun]
-						script << "cd #{run.directory}\n"
-						script << "#{run.run_command}\n"
-						next if @test_submission
-					end
-				rescue => err
-					File.delete("submitting")
-					raise(err)
-				end
-			end # runs.each
-			runs.compact!
-			if options[:job_chain] and not @test_submission and runs.size > 0
-				FileUtils.makedirs('job_chain_files')
-				@id_list = runs.map{|run| run.id}
-				
-				#@executable ||= runs[0].executable
-				@submission_script = script
-				# A hook... default is to do nothing
-				@submission_script = @run_class.modify_job_script(self, runs, @submission_script)
-				# To get out of job_chain_files folder
-				@submission_script = "cd .. \n" + @submission_script
-                @code_run_environment = runs[0].code_run_environment
-				old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
-				################ Submit the run
-				Dir.chdir('job_chain_files'){job_no = execute}
-				################
-				job_no = get_new_job_no(old_job_nos) unless job_no.kind_of? Integer 	# (if the execute command does not return the job number, look for it manually) 
-# 				eputs 'jobchain no', job_no
-				#runs.each{|run| run.job_no = job_no}
-				runs.each do |run| 
-					run.job_no = @job_no = job_no
-					run.output_file = run.relative_directory.split("/").map{|d| ".."}.join("/") + "/job_chain_files/" + output_file
-					run.error_file = run.relative_directory.split("/").map{|d| ".."}.join("/") + "/job_chain_files/" + error_file
-					run.write_info
-					eputs "Submitted run: #{run.run_name}"
-				end
-			end
-			@write_status_dots, wsd = false, @write_status_dots
-			@run_class.update_status(self)
-			runs.each do |run| 
-# 				ep run.id, run_list.keys		
-				Dir.chdir(run.directory){traverse_directories}
-
-			end
-      if is_in_repo? @root_folder and not @test_submission
+      begin
+        @skip=skip
+        mess = false
+        while FileTest.exist?("submitting") 
+          (eputs " Waiting for another process to finish submitting. If you know that no other CodeRunner processes are submitting in this folder (#@root_folder) then delete the file 'submitting' and try again"; mess = true) unless mess
+          sleep rand
+        end
+  # 			old_trap = trap(0)
+        #old_trap0 = trap(0){eputs "Aborted Submit (0)!"; File.delete("#@root_folder/submitting"); exit!}
+        old_trap2 = trap(2){eputs "Aborted Submit (2)!"; File.delete("#@root_folder/submitting") if FileTest.exist? "#@root_folder/submitting"; trap(2, "DEFAULT"); trap(0, "DEFAULT"); Process.kill(2, 0)}
+    # 		File.open("submitting", "w"){|file| file.puts ""}
+        FileUtils.touch("submitting")
+        unless options[:no_update_before_submit]
+          @use_large_cache, ulc = false, @use_large_cache; update; @use_large_cache = ulc
+        end
+        generate_combined_ids(:real)
+  # 			old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
+        script = "" if options[:job_chain]
+        runs.each_with_index do |run, index|
+          similar = similar_runs([], run)
+          if @skip and similar[0] and not (options[:replace_existing] or options[:rerun])
+            eputs "Found similar run: #{@run_list[similar[0]].run_name}"
+            eputs "Skipping submission..."
+            runs[index] = nil
+            next
+          end
+          unless options[:replace_existing] or options[:rerun]
+            @max_id+=1
+            run.id = @max_id
+          else
+            if options[:replace_existing]
+              FileUtils.rm_r run.directory 
+            elsif options[:rerun]
+              ################# For backwards compatibility
+              SUBMIT_OPTIONS.each do |opt|
+                 run.set(opt, send(opt)) unless run.send(opt)	
+              end
+              ###########################################
+              FileUtils.rm "#{run.directory}/code_runner_results.rb"
+              FileUtils.rm "#{run.directory}/.code_runner_run_data"
+            end
+            @run_list.delete(run.id)
+            @ids.delete run.id
+            generate_combined_ids
+          end
+
+          begin
+            
+            unless options[:job_chain]
+              run.prepare_submission unless options[:rerun]
+              next if @test_submission
+              Dir.chdir(run.directory) do 
+                old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
+                ######################### The big tomale!
+                run.job_no = run.execute  # Start the simulation and get the job_number
+                #########################
+                run.job_no = get_new_job_no(old_job_nos) unless run.job_no.kind_of? Integer # (if the execute command does not return the job number, look for it manually) 
+  # 							eputs 'run.job_no', run.job_no
+                run.output_file = nil # reset the output file
+                run.output_file # Sets the output_file on first call
+                run.error_file = nil # reset the output file
+                run.error_file # Sets the error_file on first call
+                run.write_info
+                eputs "Submitted run: #{run.run_name}"
+              end
+            else
+              run.prepare_submission unless options[:rerun]
+              script << "cd #{run.directory}\n"
+              script << "#{run.run_command}\n"
+              next if @test_submission
+            end
+          rescue => err
+            File.delete("submitting")
+            raise(err)
+          end
+        end # runs.each
+        runs.compact!
+        if options[:job_chain] and not @test_submission and runs.size > 0
+          FileUtils.makedirs('job_chain_files')
+          @id_list = runs.map{|run| run.id}
+          
+          #@executable ||= runs[0].executable
+          @submission_script = script
+          # A hook... default is to do nothing
+          @submission_script = @run_class.modify_job_script(self, runs, @submission_script)
+          # To get out of job_chain_files folder
+          @submission_script = "cd .. \n" + @submission_script
+                  @code_run_environment = runs[0].code_run_environment
+          old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
+          ################ Submit the run
+          Dir.chdir('job_chain_files'){job_no = execute}
+          ################
+          job_no = get_new_job_no(old_job_nos) unless job_no.kind_of? Integer 	# (if the execute command does not return the job number, look for it manually) 
+  # 				eputs 'jobchain no', job_no
+          #runs.each{|run| run.job_no = job_no}
+          runs.each do |run| 
+            run.job_no = @job_no = job_no
+            run.output_file = run.relative_directory.split("/").map{|d| ".."}.join("/") + "/job_chain_files/" + output_file
+            run.error_file = run.relative_directory.split("/").map{|d| ".."}.join("/") + "/job_chain_files/" + error_file
+            run.write_info
+            eputs "Submitted run: #{run.run_name}"
+          end
+        end
+        @write_status_dots, wsd = false, @write_status_dots
+        @run_class.update_status(self)
         runs.each do |run| 
-          Dir.chdir(run.directory){run.add_to_repo}
+  # 				ep run.id, run_list.keys		
+          Dir.chdir(run.directory){traverse_directories}
+
         end
-      end
-			@write_status_dots = wsd	
-			save_large_cache
-			File.delete("submitting")
+        if is_in_repo? @root_folder and not @test_submission
+          runs.each do |run| 
+            Dir.chdir(run.directory){run.add_to_repo}
+          end
+        end
+        @write_status_dots = wsd	
+        save_large_cache
+        File.delete("submitting")
+      ensure
 			#trap(0, old_trap0)
-			trap(2, old_trap2)
+        trap(2, old_trap2)
+      end
 	
 			
 		end # Dir.chdir(@root_folder)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.17.10
+  version: 0.17.11
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-21 00:00:00.000000000 Z
+date: 2016-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -287,7 +287,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: coderunner
-rubygems_version: 2.4.8
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: A framework for the automated running and analysis of simulations.