coderunner 0.17.3 → 0.17.4

data/VERSION

@@ -1 +1 @@
-0.17.3
+0.17.4

data/coderunner.gemspec

@@ -2,17 +2,14 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: coderunner 0.17.3 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.17.3"
+  s.version = "0.17.4"
 
   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 = "2015-09-09"
+  s.date = "2015-09-10"
   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", "coderunnerrepo"]
@@ -97,13 +94,14 @@ 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 = "2.4.8"
+  s.rubygems_version = "1.8.23"
   s.summary = "A framework for the automated running and analysis of simulations."
 
   if s.respond_to? :specification_version then
-    s.specification_version = 4
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<graphkit>, [">= 0.4.2"])

data/lib/coderunner.rb

@@ -201,13 +201,13 @@ EOF
 	COMMANDS_WITH_HELP = [
 		["available_modlets", "av", 0, 'List the available modlets for the code module.', [], [:C]],
 		["available_defaults_files", "avd", 0, 'List the defaults files for the code module.', [], [:C]],
-		["cancel", "can", 1, 'Cancel the specified job.', ['id'], [:U]],
+		["cancel", "can", 0, 'Cancel the specified job.', [], [:j, :f, :U, :N]],
 		["code_command", "cc", 1, 'Call a class method of the run class. Effectively this will call run_class.class_eval(command). See documentation for whichever code module is in use.', ['command'], []],
 		["concat", "concat", 1, 'Concatenates NetCDF output files together. File is output in the CR root directory.', ['output file'], [:j, :f, :U, :N]],
 		["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", 0, 'Print a table of all the differences between the input parameters of the filtered 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

@@ -62,9 +62,9 @@ class CodeRunner
   # Cancel the job with the given id. The user is asked interactively for 
   # confirmation and whether they would like to delete the folder for that job 
   # as well.
-  def self.cancel(id, copts={})
+  def self.cancel(copts={})
     runner = fetch_runner(copts)
-    runner.cancel_job(id.to_i)
+    runner.cancel_job(copts)
   end
 
   def self.continue_in_new_folder(folder, copts={})

data/lib/coderunner/instance_methods.rb

@@ -1558,20 +1558,20 @@ EOF
 	# Delete the folders of all runs for whom CodeRunner#filter(run) is true. This will permanently erase the runs. This is an interactive method which asks for confirmation.
 
 	def destroy(options={})
-		ids = @ids.find_all{|id| filter @run_list[id]}
-		unless options[:no_confirm]
-			logf(:destroy)			
-			puts "About to delete:"
-			ids.each{|id| eputs @run_list[id].run_name}
-			return unless Feedback.get_boolean("You are about to DESTROY #{ids.size} jobs. There is no way back. All data will be eliminated. Please confirm the delete.")
-			#gets
-			eputs "Please confirm again. Press Enter to confirm, Ctrl + C to cancel"
-			gets
-		end
-		ids.each{|id| 
-      @run_list[id].clear_cache
-			FileUtils.rm_r @run_list[id].directory if @run_list[id].directory and not ["", ".", ".."].include? @run_list[id].directory
-			@run_list.delete(id); @ids.delete(id); generate_combined_ids}
+      ids = @ids.find_all{|id| filter @run_list[id]}
+      unless options[:no_confirm]
+        logf(:destroy)			
+        puts "About to delete:"
+        ids.each{|id| eputs @run_list[id].run_name}
+        return unless Feedback.get_boolean("You are about to DESTROY #{ids.size} jobs. There is no way back. All data will be eliminated. Please confirm the delete.")
+        eputs "Please confirm again. Press Enter to confirm, Ctrl + C to cancel"
+        gets
+      end
+      ids.each{|id| 
+        @run_list[id].clear_cache
+        FileUtils.rm_r @run_list[id].directory if @run_list[id].directory and not ["", ".", ".."].include? @run_list[id].directory
+        @run_list.delete(id); @ids.delete(id); generate_combined_ids
+      }
     if is_in_repo?
       repo = Repository.open_in_subfolder(@root_folder)
       Dir.chdir(@root_folder){ 
@@ -1579,36 +1579,35 @@ EOF
       }
       repo.autocommit("Deleted simulations with ids #{ids} in folder #{repo.relative_path(@root_folder)}")
     end
-		set_max_id(@ids.max || 0)
-		save_large_cache
-		generate_combined_ids
+      set_max_id(@ids.max || 0)
+      save_large_cache
+      generate_combined_ids
 	end
 
 	# Cancel the job with the given ID. Options are:
 	# 	:no_confirm  ---> true or false, cancel without asking for confirmation if true
 	# 	:delete ---> if (no_confirm and delete), delete cancelled run
 	
-	def cancel_job(id, options={})
-		@run=@run_list[id]
-		raise "Run with id #{id} does not exist" unless @run
-		unless options[:no_confirm]
-			eputs "Cancelling job: #{@run.job_no}: #{@run.run_name}. \n Press enter to confirm"
-	# 		puts 'asfda'
-			gets
-		end
-		@run.cancel_job
-		if options[:no_confirm] 
-			delete =  options[:delete]
-		else
-			delete = Feedback.get_boolean("Do you want to delete the folder (#{@run.directory}) as well?")
-		end
-		FileUtils.rm_r(@run.directory) if delete and @run.directory and not @run.directory == ""
-		update
-		print_out
+	def cancel_job(options={})
+      ids = @ids.find_all{|id| filter @run_list[id]}
+
+      unless options[:no_confirm]
+        puts "About to cancel:"
+        ids.each{|id| eputs "#{@run_list[id].job_no}: #{@run_list[id].run_name}"}
+        return unless Feedback.get_boolean("You are about to cancel "\
+                                           "#{ids.size} jobs. Please confirm.")
+        eputs "Please confirm again. Press Enter to confirm, Ctrl + C to cancel"
+        gets
+      end
+
+      ids.each do |id| 
+        @run_list[id].clear_cache
+        @run_list[id].cancel_job
+        generate_combined_ids
+      end
 	end
 	
 	# Needs to be fixed.
-
 # 	def rename_variable(old, new)
 # 		puts "Please confirm complete renaming of #{old} to #{new}"
 # 		gets

data/lib/coderunner/system_modules/generic_linux.rb

@@ -1,91 +1,86 @@
 class CodeRunner
-require SCRIPT_FOLDER + '/system_modules/launcher.rb'
-module GenericLinux
-  include Launcher
+  require SCRIPT_FOLDER + '/system_modules/launcher.rb'
+  module GenericLinux
+    include Launcher
 
+    # @@ruby_command = "ruby1.9"
 
-# @@ruby_command = "ruby1.9"
-
-def queue_status
-		if use_launcher
-      queue_status_launcher
-    else
-      if methods.include?(:rcp) and rcp.uses_mpi? and rcp.uses_mpi
-        return %x[ps -e -U #{Process.uid} | grep mpi] + %x[ps -e -U #{Process.uid} | grep -G '\\bsh\\b'] + %x[ps -e -U #{Process.uid} -o pid,user,cmd | grep coderunner].grep(/launch/)
+    def queue_status
+      if use_launcher
+        queue_status_launcher
       else
-    # 		ep executable_name
-        return %x[ps -e -U #{Process.uid} | grep '#{executable_name}'] + %x[ps -e -U #{Process.uid} | grep -G '\\bsh\\b']
+        if methods.include?(:rcp) and rcp.uses_mpi? and rcp.uses_mpi
+          return %x[ps -e -U #{Process.uid} | grep mpi] + %x[ps -e -U #{Process.uid} | grep -G '\\bsh\\b'] + %x[ps -e -U #{Process.uid} -o pid,user,cmd | grep coderunner].grep(/launch/)
+        else
+          return %x[ps -e -U #{Process.uid} | grep '#{executable_name}'] + %x[ps -e -U #{Process.uid} | grep -G '\\bsh\\b']
+        end
       end
     end
-end
-
-def run_command
-  crenv = @code_run_environment ? @code_run_environment + ";" : nil
-	if rcp.uses_mpi
-    raise "Number of processors (nprocs) not specified" unless @nprocs
-		return %[#{crenv} time mpirun -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
-	else
-		return %[#{crenv} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
-	end
-end		
 
-def execute
-	log 'execute_submission'
-# 	ppipe = PPipe.new(2, false)
-#   trap(0){}
-# 	ppipe.fork do
-#     trap(0, 'IGNORE')
-# 		trap(2, 'IGNORE')
-# 		pid =  system(run_command + " & ") #  fork{exec run_command}
-# 		ppipe.w_send(:pid, pid, tp: 0)
-# 		Thread.new{Process.wait(pid)} # Need to pick up the dead process when it finishes
-# 	end
-# 	pid = ppipe.w_recv(:pid)
-# 	ppipe.die
-#   eputs "HERE"
-  
-#   trap(0){}
-#   trap(2, 'IGNORE')
-# 	pid = spawn("trap '' 2 && trap '' 0 && " + run_command + " & ")
-  if prefix = ENV['CODE_RUNNER_LAUNCHER']
-    launch_id = "#{Time.now.to_i}#{$$}"
-    fname = CodeRunner.launcher_directory + "/#{launch_id}"
-    File.open(fname + '.start', 'w'){|file| file.puts "cd '#{Dir.pwd}';#{run_command}"}
-    sleep 1 until FileTest.exist? fname + '.pid'
-    pid = File.read(fname + '.pid').to_i
-    FileUtils.rm fname + '.pid'
-  else
-    #pid = Kernel.spawn(run_command + " ")
-    system run_command
-		pid = -1
-  end
-  
-#   require 'rbconfig'
-#   pid = spawn %[#{Config::CONFIG['bindir']}/#{Config::CONFIG['ruby_install_name']} -e 'puts fork{exec("#{run_command}")}' &]
-  
-#   eputs "THERE"
-# 	Thread.new{Process.wait(pid)}
-#  	sleep 0.2
-	return pid
-end
+    def run_command
+      crenv = @code_run_environment ? @code_run_environment + ";" : nil
+        if rcp.uses_mpi
+        raise "Number of processors (nprocs) not specified" unless @nprocs
+            return %[#{crenv} time mpirun -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
+        else
+            return %[#{crenv} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
+        end
+    end		
 
-def cancel_job
-	children = `ps --ppid #@job_no`.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
-	system "kill #{@job_no}"
-	children.each do |pid|
-		 system "kill #{pid}"
-	end
-# 	`kill #{@job_no}`
-end
-
-def error_file
-		return "#{executable_name}.#{job_identifier}.e"
-end
+    def execute
+        log 'execute_submission'
+    # 	ppipe = PPipe.new(2, false)
+    #   trap(0){}
+    # 	ppipe.fork do
+    #     trap(0, 'IGNORE')
+    # 		trap(2, 'IGNORE')
+    # 		pid =  system(run_command + " & ") #  fork{exec run_command}
+    # 		ppipe.w_send(:pid, pid, tp: 0)
+    # 		Thread.new{Process.wait(pid)} # Need to pick up the dead process when it finishes
+    # 	end
+    # 	pid = ppipe.w_recv(:pid)
+    # 	ppipe.die
+    #   eputs "HERE"
+      
+    #   trap(0){}
+    #   trap(2, 'IGNORE')
+    # 	pid = spawn("trap '' 2 && trap '' 0 && " + run_command + " & ")
+      if prefix = ENV['CODE_RUNNER_LAUNCHER']
+        launch_id = "#{Time.now.to_i}#{$$}"
+        fname = CodeRunner.launcher_directory + "/#{launch_id}"
+        File.open(fname + '.start', 'w'){|file| file.puts "cd '#{Dir.pwd}';#{run_command}"}
+        sleep 1 until FileTest.exist? fname + '.pid'
+        pid = File.read(fname + '.pid').to_i
+        FileUtils.rm fname + '.pid'
+      else
+        #pid = Kernel.spawn(run_command + " ")
+        system run_command
+            pid = -1
+      end
+      
+    #   require 'rbconfig'
+    #   pid = spawn %[#{Config::CONFIG['bindir']}/#{Config::CONFIG['ruby_install_name']} -e 'puts fork{exec("#{run_command}")}' &]
+      
+    #   eputs "THERE"
+    # 	Thread.new{Process.wait(pid)}
+    #  	sleep 0.2
+        return pid
+    end
 
-def output_file
-		return "#{executable_name}.#{job_identifier}.o"
-end
+    def cancel_job
+      children = `ps --ppid #@job_no`.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
+      system "kill #{@job_no}"
+      children.each do |pid|
+        system "kill #{pid}"
+      end
+    end
 
+    def error_file
+            return "#{executable_name}.#{job_identifier}.e"
+    end
 
-end
+    def output_file
+            return "#{executable_name}.#{job_identifier}.o"
+    end
+  end
 end

metadata

@@ -1,181 +1,206 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.17.3
+  version: 0.17.4
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-09 00:00:00.000000000 Z
+date: 2015-09-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.4.2
 - !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
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.4
 - !ruby/object:Gem::Dependency
   name: rb-gsl
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.12.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.12.0
 - !ruby/object:Gem::Dependency
   name: gsl_extras
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.3.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.3.0
 - !ruby/object:Gem::Dependency
   name: hostmanager
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 0.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: command-line-flunky
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 0.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: git
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.2.9
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.2.9
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 2.0.0
 description: CodeRunner is a framework for the automated running and analysis of simulations.
@@ -195,7 +220,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -269,25 +294,26 @@ files:
 homepage: http://coderunner.sourceforge.net
 licenses:
 - GPLv3
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: coderunner
-rubygems_version: 2.4.8
+rubygems_version: 1.8.23
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: A framework for the automated running and analysis of simulations.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
----
-SHA1:
-  metadata.gz: 554e5c730407b32651cda8ce43cd5453fad35132
-  data.tar.gz: f34ed6190f5f242e748ecfbf24270ae60b92b9a0
-SHA512:
-  metadata.gz: a1692edb1e21f67c49f4a720e52e2d7b1bf4738f41a9263d61714eec25c35b804ec8a9552d38f312e6400394dc804cfe5832d4ae5edad69501e740a1ca2c1a1d
-  data.tar.gz: 67e773d77563e726b2d0f0f13573532c6a707d37ad76cce08c6ed9bec1ee7850e9783bc6943a9a49be35da6f4144c04eec2ee4828604b2fa99d0994ed492ba71