coderunner 0.18.2 → 0.18.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 1b236a2f425a38db491d1229ad78ec52d7e0ddbc
+  metadata.gz: c7e746354a851207811dad7279189cebc4ac944d
+  data.tar.gz: 45c5ef152cab46c28f24e647497d992c857aa9b2
 SHA512:
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+  metadata.gz: 2cfc3d4250b200e60317d1a27fa26da96555272dd95d389917086eebe5bc91a4fcd0775a865202f3ea9474349d0044ccabe0e244018890397c59fec7d4a8e888
+  data.tar.gz: 540db0835ff130b11ffb2adfabfdb1bd79514a49be8c95490ddd44d75c7ed563965511d29c9c92bb324d6c2f28e97c98fd2102911a3816e3ff852ae1d0279fd6

data/.travis.yml

@@ -0,0 +1,37 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.2.0
+notifications:
+    email:
+        on_success: change
+        on_failure: change
+
+addons:
+    apt:
+        packages:
+        - gsl-bin
+        - libgsl0-dev
+        - libnetcdf-dev
+        - libhdf5-serial-dev
+        - libyaml-dev
+        - libreadline-dev
+        - libncurses5-dev
+
+before_install:
+    - rvm use 2.2.0 --install --binary --fuzzy --default
+
+install:
+    - bundle install
+    - rake install
+    - mkdir -m 700 -p -v $HOME/.ssh
+    - ssh-keygen -t rsa -N '' -f $HOME/.ssh/id_rsa
+    - cat $HOME/.ssh/id_rsa.pub > $HOME/.ssh/authorized_keys
+    - cat $HOME/.ssh/id_rsa.pub > $HOME/.ssh/known_hosts
+    - echo "Host *" >> $HOME/.ssh/config &&
+      echo "  NoHostAuthenticationForLocalhost yes" >> $HOME/.ssh/config
+    - echo "export CODE_RUNNER_SYSTEM=generic_linux" >> $HOME/.bashrc
+    - source $HOME/.bashrc
+
+script:
+    - export CPP=g++ && rake test

data/VERSION

@@ -1 +1 @@
-0.18.2
+0.18.3

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 0.18.2 ruby lib
+# stub: coderunner 0.18.3 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.18.2"
+  s.version = "0.18.3"
 
   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 = "2016-04-03"
+  s.date = "2016-05-11"
   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"]
@@ -23,6 +23,7 @@ Gem::Specification.new do |s|
   ]
   s.files = [
     ".document",
+    ".travis.yml",
     "CONTRIBUTING.md",
     "Gemfile",
     "LICENSE.txt",
@@ -35,11 +36,15 @@ Gem::Specification.new do |s|
     "dependencies/Makefile",
     "dependencies/README.md",
     "dependencies/download_dependencies.sh",
+    "dependencies/system_config_files/archer.sh",
+    "dependencies/system_config_files/bluejoule.sh",
+    "dependencies/system_config_files/helios.sh",
     "ext/code_runner_ext.c",
     "ext/extconf.rb",
     "ext/graph_kit.c",
     "include/code_runner_ext.h",
     "include/graph_kit.h",
+    "index.html",
     "lib/code_runner_extension.rb",
     "lib/coderunner.rb",
     "lib/coderunner/class_methods.rb",
@@ -103,7 +108,7 @@ 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 = "2.2.0"
+  s.rubygems_version = "2.4.8"
   s.summary = "A framework for the automated running and analysis of simulations."
 
   if s.respond_to? :specification_version then

data/dependencies/Makefile

@@ -13,7 +13,7 @@ HDF5="hdf5-1.8.9"
 YAML="yaml-0.1.4"
 READLINE="readline-6.2"
 NCURSES="ncurses-5.9"
-RUBY="ruby-2.1-stable"
+RUBY="ruby-2.1.0"
 
 help:
 	@echo

data/dependencies/README.md

@@ -27,7 +27,7 @@ Manual Installation
 2. To compile all the packages, run `make hd all rb PREFIX=/path/to/install/dir`.
 3. If you only want to build one package see the makefile for the short name
    of the package. If you find any of these out of date, please open an
-   issue of GitHub.
+   issue on GitHub.
 4. Finally, export these to the system PATH by adding the following to your
    `.bashrc`:
 

data/dependencies/download_dependencies.sh

@@ -16,5 +16,5 @@ wget -nc ftp://ftp.gnu.org/gnu/ncurses/ncurses-5.9.tar.gz -P $DIR
 wget -nc ftp://ftp.unidata.ucar.edu/pub/netcdf/old/netcdf-4.2.1.1.tar.gz -P $DIR
 wget -nc ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz -P $DIR
 wget -nc http://pyyaml.org/download/libyaml/yaml-0.1.4.tar.gz -P $DIR
-wget -nc https://cache.ruby-lang.org/pub/ruby/ruby-2.1-stable.tar.gz -P $DIR
+wget -nc https://cache.ruby-lang.org/pub/ruby/ruby-2.1.0.tar.gz -P $DIR
 

data/dependencies/system_config_files/archer.sh

@@ -0,0 +1,8 @@
+export CODE_RUNNER_SYSTEM=archer
+export CODE_RUNNER_NO_ANALYSIS=false
+eval `modulecmd bash unload PrgEnv-cray`
+eval `modulecmd bash load PrgEnv-gnu`
+eval `modulecmd bash load fftw`
+export XTPE_LINK_TYPE=dynamic
+export LD_LIBRARY_PATH=/opt/xt-libsci/10.4.1/gnu/lib/44:$LD_LIBRARY_PATH
+echo "Confiuration is now complete."

data/dependencies/system_config_files/bluejoule.sh

@@ -0,0 +1,3 @@
+
+export CFLAGS='-dynamic'
+echo "Confiuration is now complete."

data/dependencies/system_config_files/helios.sh

@@ -0,0 +1,3 @@
+echo "No configuration is necessary for helios!"
+echo "However, all libraries need to be installed:"
+echo "  make hd all rb PREFIX=<yourprefix>"

data/index.html

@@ -0,0 +1 @@
+hello world

data/lib/coderunner/remote_code_runner.rb

@@ -2,14 +2,14 @@ class RemoteCodeRunner < CodeRunner
 	(CodeRunner.instance_methods - (Object.instance_methods + Log.instance_methods)).each do |meth|
 		next if [:sort_runs, :print_out, :filter, :similar_runs, :get_max, :get_min, :generate_combined_ids, :setup_run_class, :get_run_class_name, :readout, :graphkit_from_lists, :graphkit, :graphkit_shorthand, :run_graphkit_shorthand, :axiskit, :filtered_ids,  :filtered_run_list, :make_film_from_lists, :sweep_graphkits, :cache, :merged_runner_info].include? meth
 		next if CodeRunner::DEFAULT_RUNNER_OPTIONS.keys.include? meth
-		next if CodeRunner::DEFAULT_RUNNER_OPTIONS.keys.map{|meth| (meth.to_s + '=').to_sym}.include? meth
+		next if CodeRunner::DEFAULT_RUNNER_OPTIONS.keys.map{|method| (method.to_s + '=').to_sym}.include? meth
 
 		undef_method meth
 	end
 # 	class << self
 # 		undef_method :graphkit_multiple_runners_from_frame_array
 # 			def method_missing(method, *args)
-# 		raise "Not a CodeRunner class method #{method}" unless (CodeRunner.methods + [:puts]).include? method 
+# 		raise "Not a CodeRunner class method #{method}" unless (CodeRunner.methods + [:puts]).include? method
 # 		if method.to_s =~ /=$/
 # 			raise NoMethodError.new("unknown set method: #{method}")
 # # 			@attributes[method] = args[0]
@@ -18,14 +18,14 @@ class RemoteCodeRunner < CodeRunner
 # 		data = retrieve(method, *args)
 # 		if method.to_s =~ /graphkit/
 # 			return Marshal.load(data)
-# 		else 
+# 		else
 # 			puts data
 # 		end
-# 	end	
 # 	end
-		
+# 	end
+
 	attr_accessor :combined_ids, :component_ids, :ids, :combined_run_list, :component_run_list, :run_list, :remote_cache, :libraries
-	
+
 # 	include Log
 # 	puts instance_methods; exit
 # 	SHOULD_NOT_BE_CALLED = :add_component
@@ -61,13 +61,13 @@ class RemoteCodeRunner < CodeRunner
 					runner =  old_new(host, folder, copts)
 					runner.update
 					runner.remote_cache = copts[:cache]
-					unless FileTest.exist? cache_folder(host, folder) 
+					unless FileTest.exist? cache_folder(host, folder)
 						FileUtils.makedirs cache_folder(host, folder)
 					end
 					File.open(cache_file(host, folder), 'w') do |file|
 						file.puts Marshal.dump(runner)
 					end
-					return runner					
+					return runner
 				end
 			else
 				return old_new(host, folder, copts)
@@ -81,7 +81,7 @@ class RemoteCodeRunner < CodeRunner
 			cache_folder(host, folder) + '/runner.msl'
 		end
 	end
-	
+
 	DISPLAY_REMOTE_INVOCATION = false
 
 	RUNNER_CACHE = ENV['HOME'] + '/.coderunner/remote_cache/'
@@ -117,7 +117,7 @@ class RemoteCodeRunner < CodeRunner
 		@copts.delete(:E)
 	end
 	def method_missing(method, *args)
-		raise "Not a CodeRunner method #{method}" unless (CodeRunner.instance_methods + [:puts]).include? method 
+		raise "Not a CodeRunner method #{method}" unless (CodeRunner.instance_methods + [:puts]).include? method
 # 		ep method; STDIN.gets
 
 		if method.to_s =~ /=$/
@@ -133,10 +133,10 @@ class RemoteCodeRunner < CodeRunner
 			end
 			#return Marshal.load(data)
 			return data
-		else 
+		else
 			puts data
 		end
-	end	
+	end
 	def retrieve_method(method, *args)
 		eputs "Calling Remote Method: #{method}"
     retrieve("#{method.to_s}(*#{args.inspect})")
@@ -157,42 +157,38 @@ class RemoteCodeRunner < CodeRunner
 
 		eputs "Connecting to server using '#{@ssh_command}'..."
 		eputs "Loading folder #{@folder}..."
-# 		eval = 
-# 		> /dev/null 2> /dev/null > /dev/null 2> /dev/null
-#{%w{ ~/.bashrc ~/.bash_login ~/.bash_profile ~/.profile}.map{|w| "source #{w} > /dev/null 2> /dev/null "}.join(" && ")}
 		shell_script = <<EOF
 cd #@folder
 export ROWS=#{Terminal.terminal_size[0]}
-export COLS=#{Terminal.terminal_size[1]} 
+export COLS=#{Terminal.terminal_size[1]}
 source /etc/bashrc /etc/profile > /dev/null 2> /dev/null
-#{%w{ ~/.bashrc ~/.bash_login ~/.bash_profile ~/.profile}.map{|w| "source #{w} > /dev/null 2> /dev/null "}.join(" ; ")}
+#{%w{ .bash_login .bash_profile .profile .bashrc .rvm/scripts/rvm}.map{|w| "source $HOME/#{w} > /dev/null 2> /dev/null "}.join(" ; ")}
 if [ "$CODE_RUNNER_COMMAND" ]
 	then
-		$CODE_RUNNER_COMMAND runner_eval #{string.inspect} -Z #{@copts.inspect.inspect}	
+		$CODE_RUNNER_COMMAND runner_eval #{string.inspect} -Z #{@copts.inspect.inspect}
 	else
 		coderunner runner_eval #{string.inspect} -Z #{@copts.inspect.inspect}
 fi
 
 EOF
-# coderunner runner_eval #{"#{method.to_s}(*#{args.inspect})".inspect} -Z #{@copts.inspect.inspect}
 
 		eputs shell_script if DISPLAY_REMOTE_INVOCATION
 		data = %x[#@ssh_command '#{shell_script}']
  		#ep data
-		eputs "\nDisconnecting from server..."	
+		eputs "\nDisconnecting from server..."
 		eprint "Extracting data..."
 		data_arr = []
 		in_dump = false
 		i = 0
 		loop do
-			
+
 			if  i>=80 #data.size
 				break
-			
-			else  #if data[i-1] == "E" and data[i-2] == "_" 
+
+			else  #if data[i-1] == "E" and data[i-2] == "_"
 # 				ep data[i...(i + "code_runner_server_dump_start_E".size)], '.....'
 # 			ep data[(-"code_runner_server_dump_end_E\n".size-i+1)..-i] if in_dump
-		
+
 # 				string = data[0...i]
 	# 			p string
 				if !in_dump and data[i...(i + "code_runner_server_dump_start_E".size)] == "code_runner_server_dump_start_E" #   =~ /.*Begin Output\n\Z/
@@ -200,7 +196,7 @@ EOF
 					data = data[(i + "code_runner_server_dump_start_E".size)..-1]
 					in_dump = true
 					i = 0
-				elsif in_dump and data[(-"code_runner_server_dump_end_E\n".size-i+1)..-i] == "code_runner_server_dump_end_E\n" #  
+				elsif in_dump and data[(-"code_runner_server_dump_end_E\n".size-i+1)..-i] == "code_runner_server_dump_end_E\n" #
 					data_arr.push data[0...(data.size - ("code_runner_server_dump_end_E\n".size+i-1))]
 # 					ep "OUT DUMP"
 	# 				ep data_arr
@@ -212,11 +208,11 @@ EOF
 			end
 			i+=1
 		end
-		
+
 		eputs "done"
 # 		ep data_arr; exit
-		
-		
+
+
 		begin
 			case data_arr.size
 			when 0

data/test/test_coderunner.rb

@@ -44,7 +44,7 @@ class TestSubmission  < MiniTest::Test
 	end
 	def test_status_loop
 		unless ENV['SHORT_TEST']
-			ENV['CODE_RUNNER_LAUNCHER'] = '42323490qw4q4432407Q2342U3'
+			CodeRunner::GLOBAL_OPTIONS[:launcher] = '42323490qw4q4432407Q2342U3'
 			#@mutex = Mutex.new
 			#@launcher_started =
 			@thread = Thread.new{CodeRunner.start_launcher(0.5,10)}
@@ -52,7 +52,7 @@ class TestSubmission  < MiniTest::Test
 			CodeRunner.submit(Y: 'test/submission_results', C: 'cubecalc', m: 'sleep', X: Dir.pwd + '/test/submission_results/cubecalc', p: '{sleep_time: 2}')
 			CodeRunner.status_loop(Y: 'test/submission_results')
 			#@thread.kill # This is commented out because it causes a Heisenbug... the kill signal can get trapped and cause the deletion of the 'submitting' lock file. This line is unnecessary because the thread will die when the program exits
-			ENV.delete('CODE_RUNNER_LAUNCHER')
+      CodeRunner::GLOBAL_OPTIONS[:launcher] = nil
 		end
 	end
 	def testanalysis
@@ -384,7 +384,7 @@ end # if false/true
 #end
 #
 #
-ENV['CR_NON_INTERACTIVE'] = 'true'
+CodeRunner::GLOBAL_OPTIONS[:non_interactive] = true
 class TestFortranNamelistC < MiniTest::Test
 	def setup
 	end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.18.2
+  version: 0.18.3
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-03 00:00:00.000000000 Z
+date: 2016-05-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -195,6 +195,7 @@ extra_rdoc_files:
 - README.md
 files:
 - ".document"
+- ".travis.yml"
 - CONTRIBUTING.md
 - Gemfile
 - LICENSE.txt
@@ -207,11 +208,15 @@ files:
 - dependencies/Makefile
 - dependencies/README.md
 - dependencies/download_dependencies.sh
+- dependencies/system_config_files/archer.sh
+- dependencies/system_config_files/bluejoule.sh
+- dependencies/system_config_files/helios.sh
 - ext/code_runner_ext.c
 - ext/extconf.rb
 - ext/graph_kit.c
 - include/code_runner_ext.h
 - include/graph_kit.h
+- index.html
 - lib/code_runner_extension.rb
 - lib/coderunner.rb
 - lib/coderunner/class_methods.rb
@@ -290,7 +295,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: coderunner
-rubygems_version: 2.2.0
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: A framework for the automated running and analysis of simulations.