gs2crmod 0.11.28 → 0.11.29

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9fc845a7af975cc8918d33678677d6a9daf3b3fe
+  data.tar.gz: 5911a0644a0aae45ee429a1f9b3370b5692629b7
+SHA512:
+  metadata.gz: 9942d199a0ad3c657e0e5b5b80e4564a86aa0b85c3b13e0fe47475602027796ec2bbb5c6dcc74d30238e8d874a19e372e17e971c76e88fbec55ba68ba1f73f93
+  data.tar.gz: 1d16ca5efe84d2cc3fa3b9f4da55201416f70a80ab428d94ad13554bbca2234084ad6fcc2f6eb44626553ce232fdbf365e50311527fea92ae0d13058a8e3ad58

data/VERSION

@@ -1 +1 @@
-0.11.28
+0.11.29

data/gs2crmod.gemspec

@@ -2,14 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: gs2crmod 0.11.29 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.28"
+  s.version = "0.11.29"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-03-17"
+  s.date = "2014-03-18"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]
@@ -82,13 +85,12 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"
   s.licenses = ["GSLv3"]
-  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.11"
+  s.rubygems_version = "2.2.1"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.14.10"])

data/lib/gs2crmod/gs2.rb

@@ -524,7 +524,7 @@ def restart(new_run)
 	#(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
 	new_run.is_a_restart = true
 	new_run.ginit_option = "many"
-	new_run.delt_option = "default"
+	new_run.delt_option = "check_restart"
 	#if Dir.entries(@directory).include? "nc"
 		#old_restart_run_name =  (@restart_run_name or Dir.entries(@directory + '/nc').grep(/\.nc/)[0].sub(/\.nc\.\d+$/, ''))
 		#new_run.restart_file = File.expand_path("#@directory/nc/#{old_restart_run_name}.nc")
@@ -542,6 +542,23 @@ def restart(new_run)
 	new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash 
 	new_run.naming_pars.delete(:restart_id)
 	new_run.generate_run_name
+	eputs 'Copying Restart files', ''
+	FileUtils.makedirs('nc')
+	#old_dir = File.dirname(@restart_file)
+	new_run.restart_file = "#@run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
+	new_run.restart_dir = "nc"
+	#files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
+	#files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
+	files = list_of_restart_files.map do |file|
+		@directory + "/" + file
+	end
+	files.each_with_index do |file , index|
+		eputs "\033[2A" # Terminal jargon - go back one line
+		eputs "#{index+1} out of #{files.size}"
+		num = file.scan(/(?:\.\d+|_ene)$/)[0]
+		#FileUtils.cp("#{old_dir}/#{file}", "nc/#@restart_file#{num}")
+		FileUtils.cp(file, new_run.directory + "/nc/#@restart_file#{num}")
+	end
 	#@runner.submit(new_run)
 	new_run
 end	
@@ -778,25 +795,8 @@ end
 def generate_input_file(&block)
 	raise CRFatal("No Input Module File Given or Module Corrupted") unless methods.include? (:input_file_text)
 	run_namelist_backwards_compatibility
-	if @restart_id
+	if @restart_id and not @is_a_restart  # The second test checks that the restart function has not been called manually earlier (e.g. in Trinity)
 		@runner.run_list[@restart_id].restart(self)
-		eputs 'Copying Restart files', ''
-		FileUtils.makedirs('nc')
-		#old_dir = File.dirname(@restart_file)
-		@restart_file = "#@restart_run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
-		@restart_dir = "nc"
-		#files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
-		#files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
-		files = @runner.run_list[@restart_id].list_of_restart_files.map do |file|
-			@runner.run_list[@restart_id].directory + "/" + file
-		end
-		files.each_with_index do |file , index|
-			eputs "\033[2A" # Terminal jargon - go back one line
-			eputs "#{index+1} out of #{files.size}"
-			num = file.scan(/(?:\.\d+|_ene)$/)[0]
-			#FileUtils.cp("#{old_dir}/#{file}", "nc/#@restart_file#{num}")
-			FileUtils.cp(file, "nc/#@restart_file#{num}")
-		end
 	elsif @save_for_restart and @save_for_restart.fortran_true?
 		@restart_dir = "nc"
 		#if CODE_OPTIONS[:gs2] and CODE_OPTIONS[:gs2][:list]

data/test/test_gs2crmod.rb

@@ -36,7 +36,11 @@ if ENV['GS2_EXEC']
 			FileUtils.rm_r(tfolder)
 		end
 		def test_submission
-			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '1', Y: tfolder, p: '{write_moments: ".true.", write_line: ".true."}')
+			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '2', Y: tfolder, p: '{write_moments: ".true.", write_line: ".true.", save_for_restart: ".true.", nsave: 40}')
+			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '2', Y: tfolder, p: '{restart_id: 1}')
+			runs = CodeRunner.fetch_runner(Y: tfolder).run_list
+			assert_equal(50, runs[1].completed_timesteps)
+			assert_equal(runs[1].gsl_vector('phi2tot_over_time')[-1].round(4), runs[2].gsl_vector('phi2tot_over_time')[0].round(4))
 			CodeRunner.status(Y: tfolder)
 		end
 	end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.28
-  prerelease: 
+  version: 0.11.29
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,85 +9,106 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-17 00:00:00.000000000 Z
+date: 2014-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &17007920 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: *17007920
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.14.10
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &16911540 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *16911540
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &16910940 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *16910940
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &16910320 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *16910320
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &16909700 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *16909700
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &16909060 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>'
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *16909060
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &16907780 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *16907780
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
   be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
   running and analysis of large simulations. This module allows GS2 (and its sister
@@ -102,7 +122,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -165,26 +185,25 @@ files:
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
+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: 
-rubygems_version: 1.8.11
+rubygems_version: 2.2.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []