coderunner 0.14.21 → 0.14.22

data/VERSION

@@ -1 +1 @@
-0.14.21
+0.14.22

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 0.14.21 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.14.21"
+  s.version = "0.14.22"
 
   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 = "2014-07-04"
+  s.date = "2014-08-12"
   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"]
@@ -92,13 +89,14 @@ 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 = "2.2.2"
+  s.rubygems_version = "1.8.11"
   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>, [">= 0.3.2"])

data/lib/coderunner.rb

@@ -231,7 +231,8 @@ EOF
 		["status_loop", "sl", 0, 'Loop, updating the filtered runs, then printing out a summary of the status of the filtered runs.  ', [], [:U, :N, :j, :f, :O]],
 		["submit", "sub", 0, 'Submit a run to be simulated.', [], [:p, :n, :W, :k, :v, :T, :d, :J]],
 		["submit_command", "subcom", 2, 'Submit an arbitrary shell command to the batch queue.', ['job name', 'command'], [:n, :W, :v, :T, :d]],
-		["write_graph", "wg", 1, 'Write a graph to disk.', ['filename'], [:G, :g, :w, :O, :U, :N, :j, :f]]
+		["write_graph", "wg", 1, 'Write a graph to disk.', ['filename'], [:G, :g, :w, :O, :U, :N, :j, :f]],
+		["write_report", "wr", 0, 'Writes out a summary of a given run in a LaTeX document.', [], [:j, :f, :U, :N]],
 	] 
 	
 		# This lists all the commands available on the command line. The first two items in each array indicate the long and short form of the command, and the third indicates the number of arguments the command takes. They are all implemented as Code Runner class methods (the method is named after the long form). The short form of the command is available as a global method in Code Runner interactive mode.

data/lib/coderunner/class_methods.rb

@@ -78,6 +78,59 @@ class CodeRunner
 		runner.continue_in_new_folder(folder, options)
 	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:
+  # 
+  #   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
+  #
+  # 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]}
+
+    #Loop through the runs and write a latex file for each
+    runs.each do |r|
+      Dir.chdir(runner.root_folder) do
+        FileUtils.makedirs("run_docs")
+        FileUtils.makedirs("run_docs/id_#{r.id}")
+        Dir.chdir("run_docs/id_#{r.id}") do
+
+          File.open("summary.tex", 'w') do |file|
+            file.puts r.latex_report_header           
+            file.puts <<-EOF.gsub(/^ {14}/, "")
+              \\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.
+            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 += "\n\n"
+              tmp_latex_code
+            end
+
+            file.puts <<-EOF.gsub(/^ {14}/, "")
+              #{latex_code}
+              \\end{itemize}
+              \\end{document}
+            EOF
+          end #file write
+          system "pdflatex summary.tex" 
+        end
+      end #chdir
+		end # run loop
+  end
+
 	def self.delete(copts={})
 		runner = fetch_runner(copts)
 		runner.destroy

data/lib/coderunner/instance_methods.rb

@@ -1,6 +1,4 @@
 
-# A comment
-
 class CodeRunner # declare the constant
 end
 
@@ -1166,6 +1164,7 @@ Conditions contain a single = sign: #{conditions}
 				# 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
+        p 'test'
 				@submission_script = "cd .. \n" + @submission_script
 				old_job_nos = queue_status.scan(/^\s*(\d+)/).map{|match| match[0].to_i}
 				################ Submit the run
@@ -1727,23 +1726,23 @@ EOF
 				unless FileTest.exist? temp_root +  relative + archive_name
 				eputs "Archiving #{index} out of #{size}" if options[:verbose]
 					Dir.chdir(run.directory + '/..') do
-							command =  "tar -cW#{very_verbose}f #{tar_name} #{File.basename(run.directory)}"
-							eputs command if options[:verbose]
-							unless system command
-								raise "Archiving failed"
-							end
-							break unless comp
-							command = "gzip -4 -vf #{tar_name}"
-							eputs command if options[:verbose]
-							unless system command
-								raise "Compression failed"
-							end
-							command = "gzip -t #{archive_name}"
-							eputs command if options[:verbose]
-							unless system command
-								raise "Compression failed"
-							end
-							#exit
+            command =  "tar -cW#{very_verbose}f #{tar_name} #{File.basename(run.directory)}"
+            eputs command if options[:verbose]
+            unless system command
+              raise "Archiving failed"
+            end
+            break unless comp
+            command = "gzip -4 -vf #{tar_name}"
+            eputs command if options[:verbose]
+            unless system command
+              raise "Compression failed"
+            end
+            command = "gzip -t #{archive_name}"
+            eputs command if options[:verbose]
+            unless system command
+              raise "Compression failed"
+            end
+            #exit
 					end
 					FileUtils.mv(relative.delsubstr('/') + archive_name, temp_root + '/' + relative + archive_name)
 				end
@@ -1770,22 +1769,10 @@ EOF
 			#FileUtils.rm_r(".tmparch")
 		end
 	end
-
-
-
-	
-	
 end
 
-
-
-
-
-
-
-
 [
-	"/graphs_and_films.rb", 
+  "/graphs_and_films.rb",
 	"/remote_code_runner.rb", 
 	"/merged_code_runner.rb",
 	'/run.rb', 

data/lib/coderunner/run.rb

@@ -1078,6 +1078,38 @@ def actual_number_of_processors
 		  @nprocs.split('x').slice(0..1).map{|n| n.to_i}.inject(1){|ntot, n| ntot*n}
 end
 
+def latex_report_header
+#gsub is a hack which removes 14 spaces from the beginning of the file. This allows nice code indentation here.
+<<-EOF.gsub(/^ {4}/, "")
+    % Set up  
+    \\documentclass[11pt, twocolumn]{report}
+    \\usepackage{amsmath}
+    \\usepackage{amsthm}
+    \\usepackage{amssymb}
+    \\usepackage{graphicx}
+    \\usepackage{caption}
+    \\usepackage{subcaption}
+    \\usepackage{wrapfig}
+    \\usepackage{epstopdf}
+    \\usepackage{fullpage}
+
+    \\newcommand{\\newfig}[1]{
+    \\includegraphics[width=\\linewidth]{#1}
+    }
+
+    \\begin{document}
+
+    % Title Page
+    \\title{Run summary for run number #{id}}
+    \\date{#{Time.now}}
+    \\author{CodeRunner}
+                  
+    \\maketitle
+
+EOF
+
+end
+
 end
 
 end

data/test/test_coderunner.rb

@@ -128,6 +128,7 @@ class TestCodeRunner < Test::Unit::TestCase
 	def test_remote_coderunner
 		puts 'testing remote coderunner'
 		rc = RemoteCodeRunner.new(ENV['USER'] + '@localhost', Dir.pwd + '/test/results', U: true, N: true).update
+    p rc
 		assert_equal(@runner.ids.sort, rc.ids.sort)
 		rc.print_out(0)
 		wdvh = rc.graphkit("width:height:depth:volume;;;height")

metadata

@@ -1,155 +1,126 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.14.21
+  version: 0.14.22
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-04 00:00:00.000000000 Z
+date: 2014-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18535160 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.3.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.3.2
+  version_requirements: *18535160
 - !ruby/object:Gem::Dependency
   name: parallelpipes
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18550940 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *18550940
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18550140 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.1.4
+  version_requirements: *18550140
 - !ruby/object:Gem::Dependency
   name: rb-gsl
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18549500 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.12.0
+  version_requirements: *18549500
 - !ruby/object:Gem::Dependency
   name: gsl_extras
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18548880 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.3.0
+  version_requirements: *18548880
 - !ruby/object:Gem::Dependency
   name: hostmanager
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18547920 !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
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 0.1.0
+  version_requirements: *18547920
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18546220 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+  version_requirements: *18546220
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18544440 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *18544440
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18559040 !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
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *18559040
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &18557720 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 2.0.0
+  version_requirements: *18557720
 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
@@ -166,7 +137,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -235,25 +206,26 @@ 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: 2.2.2
+rubygems_version: 1.8.11
 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: f31da7c1a3066436f1928a1e63927d1ae159c7c1
-  data.tar.gz: 2fbf034e17fffa91edb9f7e1b6cccb303d96d5b2
-SHA512:
-  metadata.gz: c9210fef0749606da3dbe287e1b7ea262ae709be197eda71410b2a4f4e68c414ec1bca67c859f29b05fe302ae0634b743990ce29687e1b47d17f0730c147da37
-  data.tar.gz: 842086ee9b7c6e62d144bb68724b83797040bb3b6bb8a90c06102ce40baa48bb658e0c508526e79717c14f77fa52bea6da3cb02b9fb77751a74aa42a5ba1971c