cronoscrmod 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+   gem "coderunner", ">= 0.13.18"
+   #gem "matlab-ruby", "> 2.0.0"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "> 1.0.0"
+  gem "jeweler", ">= 1.8.4"
+  #gem "rcov", ">= 0"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Edmund Highcock
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+cronoscrmod
+===========
+
+A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos
+
+
+cronoscrmod requires matlab-ruby, but for technical reasons, you must install this yourself manually. 
+
+Try:
+
+`gem install matlab-ruby`
+
+If this fails, see the notes below.
+
+
+Notes
+-----
+
+
+Instructions for Mac OS X
+
+You need to install matlab-ruby for cronoscrmod, but `gem install matlab-ruby` does not in general work. It is recommended that you install it yourself like this:
+
+
+`git clone git@github.com:edmundhighcock/matlab-ruby.git`
+
+`cd matlab-ruby`
+
+`ruby setup.rb config -- --with-matlab-include=/Applications/MATLAB_R2012a.app/extern/include/ --with-matlab-lib=/Applications/MATLAB_R2012a.app/bin/maci64/`
+
+`ruby setup.rb setup`
+
+`sudo ruby setup.rb install`
+
+You also need to make sure the Matlab libraries are in the linker path:
+
+Add these lines to your login script:
+
+`export PATH=$PATH:/Applications/MATLAB_R2012a.app/bin/`
+
+`export DYLD_LIBRARY_PATH=/Applications/MATLAB_R2012a.app/bin/maci64:$DYLD_LIBRARY_PATHo`
+

data/README.md.orig

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+cronoscrmod
+===========
+
+A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos

data/README.rdoc

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+= cronoscrmod
+
+Description goes here.
+
+== Contributing to cronoscrmod
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2013 Edmund Highcock. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "cronoscrmod"
+  gem.homepage = "http://github.com/edmundhighcock/cronoscrmod"
+  gem.license = "MIT"
+  gem.summary = %Q{A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos}
+  gem.description = %Q{A module to allow CodeRunner to run the integrated tokamak modelling suite Cronos. Requires matlab and matlab-ruby (Cronos also requires Matlab).}
+  gem.email = "edmundhighcock@users.sourceforge.net"
+  gem.authors = ["Edmund Highcock"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |test|
+  ##test.libs << 'test'
+  ##test.pattern = 'test/**/test_*.rb'
+  ##test.verbose = true
+  ##test.rcov_opts << '--exclude "gems/*"'
+##end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "cronoscrmod #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/cronoscrmod.rb

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+require 'cronoscrmod/cronos.rb'

data/lib/cronoscrmod/cronos.rb

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+eputs "The Cronos CodeRunner module is written by Edmund Highcock, based on MatLab tools written by Jonathan Citrin" unless $has_put_startup_message_for_coderunner
+
+require 'matlab'
+class CodeRunner
+	class Cronos < Run
+		# Where this file is
+		@code_module_folder = folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+
+		class EngineHandler
+			def initialize(engine)
+				@engine = engine
+				@cronos_path_set = false
+				@pathc
+			end
+			def start_cronos(path)
+				return
+				return if @cronos_path_set
+				raise "cronos not found in #{path}" unless FileTest.exist?("#{path}/cronos.m")
+				@engine.eval_string("addpath #{File.expand_path(path)};")
+				@engine.eval_string("addpath #{File.expand_path(path)}/interface;")
+				@engine.eval_string("addpath #{File.expand_path(path)}/op;")
+				@engine.eval_string("cronos")
+				@engine.eval_string("zuidirect")
+				@cronos_path_set = true
+			end
+
+			def new_file
+				@engine.eval_string("zuicreate")
+				STDIN.gets
+			end
+		end
+
+		def run_command
+			"echo 'manual run'"
+		end 
+
+		module CodeRunner::InteractiveMethods
+			def cronos(*args)
+				if args.size > 0
+					args.each do |com|
+					CodeRunner::Cronos.rcp.engine_handler.cronos.puts(com)
+					end
+				end
+			end
+		end
+
+
+
+		class CronosHandler
+			def initialize(runner)
+				if runner and runner.executable
+					start_cronos(runner.executable)
+				end
+			end
+			attr_reader :cronos
+
+			def start_cronos(path)
+				return if @cronos_started
+				raise "cronos not found in #{path}" unless FileTest.exist?("#{path}/cronos.m")
+				@cronos = IO.popen("#{path}/cronos 3>&2 2>&1 1>&3 | grep -v 'Time Machine' 3>&2 2>&1 1>&3 ",  'w')
+				@cronos_started = true
+			end
+			def new_file
+				@cronos.puts("zuicreate")
+			end
+		end
+
+		begin
+	  	#@engine = Matlab::Engine.new("matlab -nodesktop -nosplash")
+			#@engine_handler = EngineHandler.new(@engine)
+			@engine_handler = CronosHandler.new((rcp.runner? ? rcp.runner : nil))
+		#rescue => err
+			#if err.to_s =~ /driver for matlab/
+				#puts "Please make sure matlab is in your path"
+
+				#raise
+			#else
+				#raise 
+			#end
+		end
+
+		def set_cronos_path
+			rcp.engine_handler.start_cronos(@runner.executable.sub(/cronos$/, ""))
+		end
+
+		
+
+
+
+
+		################################################
+		# Quantities that are read or determined by CodeRunner
+		# after the simulation has ended
+		###################################################
+
+		@results = [
+		]
+
+		@variables = [
+			:aim,
+			:duplicate_id,
+
+		]
+
+		@code_long="Cronos Integrated Tokamak Modeller"
+
+		@run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_timesteps, :percent_complete]
+
+		@uses_mpi = false
+
+		@modlet_required = false
+		
+		@naming_pars = []
+
+		#  Any subfolders of the main run folder
+		@excluded_sub_folders = ["rapsauve_#{ENV['USER']}"]
+
+		#  A hook which gets called when printing the standard run information to the screen using the status command.
+		def print_out_line
+			#p ['id', id, 'ctd', ctd]
+			#p rcp.results.zip(rcp.results.map{|r| send(r)})
+			name = @run_name
+			name += " (res: #@restart_id)" if @restart_id
+			name += " real_id: #@real_id" if @real_id
+			beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s)",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s)
+			if @status == :Incomplete and @completed_timesteps
+				beginning += sprintf(" %d steps ", @completed_timesteps)
+			elsif @percent_complete
+ 				beginning+=sprintf(" %3s%1s ", percent_complete, "%")
+			end
+			if ctd
+				#beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
+			end
+			beginning += "  ---#{@comment}" if @comment
+			beginning
+		end
+
+
+		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
+		def generate_input_file
+			#FileUtils.touch("#@run_name.mat")
+			#cronos.new_file
+			#eputs "Make sure you save the file as #@run_name.mat... overwrite the existing empty place holder. When you have saved the file press enter."
+			if @duplicate_id
+				old = @runner.run_list[@duplicate_id]
+				system "cp #{old.directory}/#{old.run_name}.mat #@directory/#@run_name.mat"
+				load
+			elsif @restart_id
+				old = @runner.run_list[@restart_id]
+				system "cp #{old.directory}/#{old.run_name}_resultat.mat #@directory/#@run_name.mat"
+				load
+			else
+				sz = Terminal.terminal_size[1]
+				eputs((str = "When you have created the file press enter. Don't save it (CodeRunner will automatically save it in the right place. You can edit parameters later as well. CodeRunner will not submit the file... submit it manually using a batch or interactive run."; ["-"*sz, str, "-"*sz]))
+				cronos.puts("zuicreate")
+				STDIN.gets
+			end
+			cronos.puts("param.gene.origine = '#@directory/#@run_name.mat'")
+			cronos.puts("param.gene.file = '#@directory/#{@run_name}_resultat.mat'")
+			cronos.puts("param.gene.rapsauve = '#@directory/#{@run_name}_resultat'")
+			cronos.puts("param.edit.currentfile= '#@directory/#@run_name.mat'")
+			cronos.puts("param.from.creation.com = '#@comment'")
+			cronos.puts("zuisavedata('force')")
+			#cronos.eval("zuicreate")
+			refresh_gui
+			
+		end
+
+		def refresh_gui
+			cronos.puts(["[hfig,h] = zuiformhandle('direct');",
+								   "if ishandle(hfig)
+									 set(h.text_loadfile, 'string', param.gene.origine)
+									 set(h.text_nom_machine, 'string', param.from.machine)
+									 set(h.text_numchoc, 'string', sprintf('%d', param.from.shot.num))
+
+									end"])	
+		end
+
+		def load
+			cronos.puts("zuiload('#@directory/#@run_name.mat')")
+			refresh_gui
+		end
+
+		def cronos
+			set_cronos_path
+			rcp.engine_handler.cronos
+		end
+
+
+
+		# Parameters which follow the Trinity executable, in this case just the input file.
+		def parameter_string
+		end
+
+		def parameter_transition
+		end
+
+
+		@source_code_subfolders = []
+
+		# This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).
+		#
+		def process_directory_code_specific
+			get_status
+			#p ['fusionQ is ', fusionQ]
+			#@percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
+		end
+
+		def results_file_name
+			"#{@run_name}_resultat.mat"
+		end
+
+		def get_status
+			Dir.chdir(@directory) do
+				if FileTest.exist? results_file_name
+					@status = :Complete
+					@percent_complete = 100.0
+				elsif temps = Dir.entries.grep(/resultat_\d+/) and temps.size > 1
+					@status = :Incomplete
+					@completed_timesteps = temps.map{|f| f.scan(/resultat_(\d+)/)[0][0].to_i}.max
+				else 
+					@status = :Unknown
+					@percent_complete = 0
+				end
+			end
+		end
+
+	end
+end
+

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'coderunner'
+
+class Test::Unit::TestCase
+end

data/test/test_cronoscrmod.rb

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+require 'helper'
+
+raise "Please specify $CRONOS_EXEC" unless ENV['CRONOS_EXEC']
+
+class TestCronoscrmod < Test::Unit::TestCase
+  def setup
+		FileUtils.mkdir('test/jet') rescue 0
+    @runner = CodeRunner.fetch_runner(Y: 'test/jet', C: 'cronos', X: ENV['CRONOS_EXEC'])
+  end
+  def teardown
+    FileUtils.rm('test/jet/.code_runner_script_defaults.rb')
+    #FileUtils.rm('test/jet/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+  end
+  def test_basics
+    assert_equal(@runner.run_class, CodeRunner::Cronos)
+		@runner.print_out(0)
+  end
+	def test_matlab
+
+		#require 'matlab'
+		  
+		##engine = Matlab::Engine.new(command = "#{ENV['MATLAB_BINDIR']}matlab  -nodesktop -nosplash")
+	  #p ['output', CodeRunner::Cronos.rcp.engine.put_variable("x", 124.456)]
+		#p ['output', CodeRunner::Cronos.rcp.engine.get_variable("x")]
+	end
+	def test_create
+		CodeRunner.submit(Y: 'test/jet', p: '{aim: "test_cronos"}', T: true)
+	end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: cronoscrmod
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Edmund Highcock
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-10-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: coderunner
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.13.18
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.13.18
+- !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: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+description: A module to allow CodeRunner to run the integrated tokamak modelling
+  suite Cronos. Requires matlab and matlab-ruby (Cronos also requires Matlab).
+email: edmundhighcock@users.sourceforge.net
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.md.orig
+- README.rdoc
+files:
+- .document
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/cronoscrmod.rb
+- lib/cronoscrmod/cronos.rb
+- lib/cronoscrmod/defaults_files/cronos_defaults.rb
+- test/helper.rb
+- test/test_cronoscrmod.rb
+- README.md.orig
+homepage: http://github.com/edmundhighcock/cronoscrmod
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 3245162892836041727
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: A module to allow CodeRunner to run the integrated tokamak modelling suite
+  Cronos
+test_files: []