coderunner 0.17.1 → 0.17.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 69f7b07f3dc1008a50a9a630ff006f9f07523276
+  metadata.gz: 2b0abf9dd6e6a60db107f9cb90b1ec2a01da16f3
+  data.tar.gz: 3b748ca1afafeed0d546b6b95701190959291599
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+  metadata.gz: 49075a788f4bffdf23202df136f2319f298674991d8b8b899b9de6ebaeb6ebb3bcc15fe9833ec0f59bf3089532bd60b0458c37bd5b7475b8f49eee1bbb8dd197
+  data.tar.gz: ebe2c25bd99beda5fa353abcbb3e1ede19ff7a27cf2e6aa89dc4487f0eab095a19760ad8e66d75bb04a3de0f84c79837730f2571035924e7bf7bb1e5dc5fe651

data/VERSION

@@ -1 +1 @@
-0.17.1
+0.17.2

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 0.17.1 ruby lib
+# stub: coderunner 0.17.2 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.17.1"
+  s.version = "0.17.2"
 
   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 = "2015-08-16"
+  s.date = "2015-09-04"
   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"]
@@ -99,7 +99,7 @@ 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 = "2.2.2"
   s.summary = "A framework for the automated running and analysis of simulations."
 
   if s.respond_to? :specification_version then

data/lib/coderunner.rb

@@ -203,6 +203,7 @@ EOF
 		["available_defaults_files", "avd", 0, 'List the defaults files for the code module.', [], [:C]],
 		["cancel", "can", 1, 'Cancel the specified job.', ['id'], [:U]],
 		["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]],

data/lib/coderunner/class_methods.rb

@@ -18,7 +18,6 @@ class CodeRunner
   end
 
   # List the available modlets for the given code (copts[:C] or -C on the command line).
-
   def self.available_modlets(copts={})
     process_command_options(copts)
     puts "\nAvailable modlets for #{copts[:C]}:"
@@ -37,7 +36,6 @@ class CodeRunner
   end
 
     # List the available defaults files for the given code (copts[:C] or -C on the command line).
-
   def self.available_defaults_files(copts={})
     process_command_options(copts)
     entries = []
@@ -61,8 +59,9 @@ class CodeRunner
     end
   end
 
-  # 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.
-
+  # 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={})
     runner = fetch_runner(copts)
     runner.cancel_job(id.to_i)
@@ -78,6 +77,29 @@ class CodeRunner
     runner.continue_in_new_folder(folder, options)
   end
 
+  # Method which concatenates NetCDF output files 
+  def self.concat(name, copts={})
+    begin
+      require "numru/netcdf"
+    rescue LoadError
+      eputs "Error: No Ruby NetCDF library (was it installed correctly?): "\
+            "concatenation for netcdf files not possible."
+      return
+    end
+
+    runner = fetch_runner(copts)
+    runs = runner.filtered_ids.map{|id| runner.combined_run_list[id]}
+
+    concat_string = 'ncrcat '
+    runs.each do |r|
+      concat_string += r.directory + '/' + r.run_name + '.out.nc '
+    end
+
+    concat_string += runner.root_folder + '/' + name
+
+    exec "#{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:
   #
@@ -110,11 +132,13 @@ class CodeRunner
               \\begin{itemize}
             EOF
 
-            #Need to call some methods here which reads the graphs we want from gs2crmod, generates the graphs
-            #then generates the latex code to display graphs.
+            # Need to call some methods here which reads the graphs we want 
+            # from gs2crmod, generates the graphs then generates the latex code 
+            # to display graphs.
             latex_code = r.latex_graphs.inject("") do |tmp_latex_code, (kit, latexstring)|
               kit.gnuplot_write(kit.file_name) #write the graph
-              tmp_latex_code += "\\item " + latexstring + " \n\n\\newfig{#{kit.file_name}}"
+              tmp_latex_code += "\\item " + latexstring + 
+                                " \n\n\\newfig{#{kit.file_name}}"
               tmp_latex_code += "\n\n"
               tmp_latex_code
             end
@@ -135,6 +159,7 @@ class CodeRunner
     runner = fetch_runner(copts)
     runner.destroy
   end
+
   def self.differences_between(copts = {})
     runner = fetch_runner(copts)
     runs = runner.filtered_ids.map{|id| runner.combined_run_list[id]}
@@ -180,14 +205,8 @@ class CodeRunner
       kit.gnuplot(eval: string_to_eval)
       sleep(copts[:F][:fr] ? 1.0/copts[:F][:fr] :  0.1)
     end
-  end
-#   def self.executable_name # :nodoc:
-#     ""
-#   end
-#
-#   def self.rcp # :nodoc:
-#     @rcp ||= KitHash.new
-#   end
+  end 
+
   def self.netcdf_plot(netcdf_file, vars, indices, copts={})
     process_command_options(copts)
     begin
@@ -214,8 +233,6 @@ class CodeRunner
     kit.close
   end
 
-
-
   def self.print_queue_status(copts={})
     begin
       eputs queue_status
@@ -227,10 +244,6 @@ class CodeRunner
     end
   end
 
-
-
-
-
   def self.reference(class_or_method, copts={})
     code_folders = Dir.recursive_entries(SCRIPT_FOLDER + '/code_modules').grep(/\/ri$/).map{|fold| ['-d', fold]}.flatten
 #     ep code_folders
@@ -251,11 +264,11 @@ class CodeRunner
 #     trap(1){}
   end
 
-
   def self.directory(id, copts={})
     runner = fetch_runner(copts)
     puts runner.run_list[id.to_i].directory
   end
+
   def self.film(copts={})
     runner = fetch_runner(copts)
     copts[:F][:graphkit_modify] = copts[:w]
@@ -309,7 +322,6 @@ EOF
 
   end
 
-
   def self.generate_cubecalc(copts={})
     #return
     File.open('cubecalc.cc', 'w') do |file|
@@ -372,9 +384,11 @@ EOF
 
     end
   end
+
   def self.launcher_directory
     ENV['HOME'] + "/.coderunner/to_launch/#{ENV['CODE_RUNNER_LAUNCHER']}"
   end
+  
   def self.start_launcher(refresh, max_queue, copts={})
     #eputs "Starting launcher!"
     raise "Raise refresh is #{refresh}: it must be >= 0.1" if refresh.to_f < 0.1
@@ -477,15 +491,16 @@ EOF
 
   end
 
-
   def self.code_runner_execute(ruby_fragment, copts={})
     #eval(ruby_fragment, GLOBAL_BINDING)
     eval(ruby_fragment)
   end
+
   def self.execute(ruby_fragment, copts={})
     eval(ruby_fragment, GLOBAL_BINDING)
     #eval(ruby_fragment)
   end
+  
   def self.load_file(files, copts={})
     process_command_options(copts)
 #     begin
@@ -519,6 +534,7 @@ EOF
     @@psppipe.finish
     @@psppipe = nil
   end
+
   def self.plot_graph(copts = {})
 #     process_copts(copts)
     runner = fetch_runner(copts)
@@ -530,17 +546,18 @@ EOF
     gets
     kit.close
   end
+
   def self.readout(copts={})
-#     process_copts(copts)
     runner = fetch_runner(copts)
     puts runner.readout
   end
+  
   def self.recheck(id, copts={})
-#     process_copts(copts)
     runner = fetch_runner(copts)
     runner.run_list[copts[:R]].recheck
     runner.respond_to_requests
   end
+
   def self.run_class(copts={})
     process_command_options(copts)
     copts[:no_update] = true
@@ -557,12 +574,14 @@ EOF
 
     return setup_run_class(copts[:C], modlet: copts[:m])
   end
+
   def self.code_command(string, copts = {})
     run_class(copts).class_eval(string)
 
 #      runner = fetch_runner(copts)
 #      runner.run_class.class_eval(string)
   end
+  
   def self.run_command(string, copts={})
 #       process_copts(copts)
     runner = fetch_runner(copts)
@@ -606,6 +625,7 @@ EOF
 #     Process.waitall
     runner.respond_to_requests
   end
+
   def self.runner_eval(string, copts = {})
 #      process_copts(copts)
      runner = fetch_runner(copts)
@@ -621,11 +641,13 @@ EOF
      end
 
   end
+  
   def self.scan(scan_string, copts={})
 #       process_copts(copts)
     runner = fetch_runner(copts)
       runner.simple_scan(scan_string, nprocs: copts[:n], version: copts[:v], skip: copts[:k], parameters: copts[:p][0])
   end
+
   def self.submit(copts = {})
 #     process_copts(copts)
     runner = get_submit_runner(copts)
@@ -648,6 +670,7 @@ EOF
     runner.submit(runs, nprocs: copts[:n], version: copts[:v], skip: copts[:k], job_chain: copts[:J], no_update_before_submit: copts[:no_update_before_submit])
     #exit(0)
   end
+
   # Fetch a runner appropriate for submitting simulations. In 
   # all usual cases this is just the default runner for the command
   # but where several folders have been specified and we are dealing
@@ -665,10 +688,9 @@ EOF
       end
     end
   end
+
   def self.resubmit(copts = {})
     runner = get_submit_runner(copts)
-#     process_copts(copts)
-#     raise "something is already submitting" if FileTest.exist? "submitting"
     runs = []
     raise "Parameters must be an array of inspected hashes" unless copts[:p].kind_of? Array
     Dir.chdir(runner.root_folder) do
@@ -688,12 +710,12 @@ EOF
         run
       end
     end
-    #throw(:here)
 
     runner.submit(runs, nprocs: copts[:n], version: copts[:v], skip: copts[:k], job_chain: copts[:J], no_update_before_submit: copts[:no_update_before_submit], replace_existing: copts[:replace_existing], smart_resubmit_name: copts[:smart_resubmit_name], rerun: copts[:rerun])
   end
 
-  # This method allows the straightforward submission of a single command using the batch queue on any system.
+  # This method allows the straightforward submission of a single command using 
+  # the batch queue on any system.
   def self.submit_command(jid, comm, copts={})
     process_command_options(copts)
     submitter = Object.new
@@ -717,25 +739,27 @@ EOF
     submitter.execute
   end
 
-
-
   def self.readout(copts={})
     runner = fetch_runner(copts)
     runner.readout
   end
+
   def self.show_values_of(expression, copts={})
     runner = fetch_runner(copts)
     p runner.filtered_ids.map{|id| runner.combined_run_list[id].instance_eval(expression)}.uniq.sort
   end
+  
   def self.status_with_comments(copts={})
     copts[:with_comments] = true
     status(copts)
   end
+  
   def self.status(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     runner.print_out(0, with_comments: copts[:with_comments]) unless copts[:interactive_start] or copts[:Z] or copts[:no_print_out]
   end
+  
   def self.status_loop(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
@@ -758,6 +782,7 @@ EOF
       #ep "end sleep"
     end
   end
+
   def self.status_loop_running(copts={})
     copts[:f] = "@running"
     runner = fetch_runner(copts)
@@ -766,6 +791,7 @@ EOF
     copts[:j] = nil
     status_loop(copts)
   end
+  
   def self.status_loop(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
@@ -788,6 +814,7 @@ EOF
       #ep "end sleep"
     end
   end
+
   def self.write_graph(name, copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
@@ -808,11 +835,13 @@ EOF
     raise "kit doesn't have a file_name and no filename specified; can't write graph" unless name or (kit.file_name.class == String and kit.file_name =~ /\S/)
     Dir.chdir(COMMAND_FOLDER){kit.gnuplot_write((name or kit.file_name), {eval: copts[:w]})}
   end
+
   def self.read_default_command_options(copts)
     DEFAULT_COMMAND_OPTIONS.each do |key, value|
       copts[key] ||= value
     end
   end
+  
   def self.process_command_options(copts)
     if copts[:true]
       copts[:true].to_s.split(//).each do |letter|
@@ -869,8 +898,8 @@ EOF
 
   end
 
-  # Analyse copts[:Y], the choice of the root folder for the runner, and make appropriate
-  # modifications to the command options for running remotely, etc.
+  # Analyse copts[:Y], the choice of the root folder for the runner, and make 
+  # appropriate modifications to the command options for running remotely, etc.
   def self.process_root_folder(copts)
     copts[:Y] ||= DEFAULT_COMMAND_OPTIONS[:Y] if DEFAULT_COMMAND_OPTIONS[:Y]
     if copts[:Y] and copts[:Y].kind_of? Array
@@ -890,8 +919,8 @@ EOF
 
   CODE_OPTIONS={}
 
-  # Retrieve the runner with the folder (and possibly server) given in copts[:Y]. If no runner has been loaded for that folder, load one.
-
+  # Retrieve the runner with the folder (and possibly server) given in 
+  # copts[:Y]. If no runner has been loaded for that folder, load one.
   def self.fetch_runner(copts={})
 #     ep copts
     #read_default_command_options(copts)
@@ -943,20 +972,19 @@ EOF
     return runner
 #     @r.read_defaults
   end
+
   def self.update_runners
     @runners ||= {}
     @runners.each{|runner| runner.update}
   end
 
-
   def self.runner
     @runners ||={}
     @runners.values[0]
   end
 
-
-    def self.manual(copts={})
-      help = <<EOF
+  def self.manual(copts={})
+    help = <<EOF
 
 
 -------------CodeRunner Manual---------------
@@ -1018,12 +1046,4 @@ EOF
      help.paginate
     end
 
-
-
-
-
 end
-
-
-
-

data/test/helper.rb

@@ -16,6 +16,3 @@ require 'coderunner'
 require 'cubecalccrmod'
 require 'cubecalccrmod/sleep'
 
-
-#class Test::Unit::TestCase
-#end

data/test/test_coderunner.rb

@@ -3,8 +3,6 @@ require 'helper'
 require 'rbconfig'
 CodeRunner::RemoteCodeRunner::DISPLAY_REMOTE_INVOCATION = true
 
-
-
 module MiniTest::Assertions
 	def assert_system(string)
 		assert(system(string), "System Command: '#{string}'")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.17.1
+  version: 0.17.2
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-16 00:00:00.000000000 Z
+date: 2015-09-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -286,7 +286,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: coderunner
-rubygems_version: 2.4.8
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: A framework for the automated running and analysis of simulations.