gs2crmod 0.11.101 → 0.12.0

data/VERSION

@@ -1 +1 @@
-0.11.101
+0.12.0

data/gs2crmod.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: gs2crmod 0.11.101 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.101"
+  s.version = "0.12.0"
 
   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 = "2015-07-03"
+  s.date = "2015-07-28"
   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"]
@@ -79,12 +76,13 @@ 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 = "2.2.2"
+  s.rubygems_version = "1.8.23"
   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 = 4
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.15.5"])

data/lib/gs2crmod/calculations.rb

@@ -279,7 +279,7 @@ def calculate_frequencies
 		logi(f)
 		@frequency_at_ky_at_kx||= FloatHash.new
 		ky_values = []
-		regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f})\s*akx=\\s*(?<akx>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
+		regex = Regexp.new( "^.*ky=\\s*(?<aky>#{f})\s*kx=\\s*(?<akx>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
 		final_timestep_list.scan(regex) do
 			aky = eval($~[:aky])
 			akx = eval($~[:akx])

data/lib/gs2crmod/graphs.rb

@@ -21,8 +21,8 @@ def auto_axiskits(name, options)
     # </MJL>
     'phi2_by_ky_over_time' => ['Phi^2 by ky', ''],
     'phi2_by_kx_over_time' => ['Phi^2 by ky', ''],  
-    'es_heat_by_ky_over_time' => ['Phi^2 by ky', ''],
-    'es_heat_by_kx_over_time' => ['Phi^2 by kx', ''],  
+    'es_heat_flux_by_ky_over_time' => ['Heat flux by ky', ''],
+    'es_heat_flux_by_kx_over_time' => ['Heat flux by kx', ''],  
     'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
     'tpar2_by_mode_over_time' => ["(delta T_parallel)^2 by mode", '%'],
     'tperp2_by_mode_over_time' => ["(delta T_perp)^2 by mode", '%'],
@@ -47,8 +47,8 @@ def auto_axiskits(name, options)
     'spectrum_over_kx_avg' => ["Spectrum Averaged Over Time", '', 1],
     'spectrum_over_ky' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
     'spectrum_over_ky_avg' => ["Spectrum Averaged Over Time", '', 1],
-    'es_heat_over_kx' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
-    'es_heat_over_ky' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
+    'es_heat_flux_over_kx' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
+    'es_heat_flux_over_ky' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
     'es_heat_flux_over_ky_over_kx' => ["Heat flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
     'spectrum_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
     'spectrum_over_ky_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
@@ -267,7 +267,6 @@ module GraphKits
 			kit = GraphKit.autocreate({x: axiskit('t', options), y: phiax})
 			kit.data[0].title = "Phi^2 total: #{kxy} = #{options[kxy]}"	
 			if options[:t_index]
-# 				p 'hello'
 				array_element = options[:t_index_window] ? options[:t_index] - options[:t_index_window][0] : options[:t_index] - 1
 # 				p phiax.data.size, array_element
 # 				p options[:t_index], options[:t_index_window]
@@ -345,7 +344,7 @@ module GraphKits
 
 	alias :eigenfunction_graphkit :efn_graphkit
 		
-	def es_heat_vs_ky_vs_kx_graphkit(options={})
+	def es_heat_flux_vs_ky_vs_kx_graphkit(options={})
 		case options[:command]
 		when :help
 			return  "Graph of electrostatic contribution to heat flux at a given time vs kx and ky"
@@ -362,7 +361,7 @@ module GraphKits
 		end
 	end
 
-	def es_heat_vs_kx_graphkit(options={})
+	def es_heat_flux_vs_kx_graphkit(options={})
 		case options[:command]
 		when :help
 			return "Heat flux vs kx"
@@ -372,7 +371,7 @@ module GraphKits
 			return es_heat_flux_vs_kxy_graphkit(options.absorb({direction: :kx}))
 		end
 	end
-	def es_heat_vs_ky_graphkit(options={})
+	def es_heat_flux_vs_ky_graphkit(options={})
 		case options[:command]
 		when :help
 			return "Heat flux vs ky"
@@ -391,7 +390,7 @@ module GraphKits
 			return [:ky_index, :species_index]
 		else
 			kxy = options[:direction]||options[:kxy] 
-			kit = GraphKit.autocreate({x: axiskit(kxy.to_s, options), y: axiskit("es_heat_over_#{kxy}", options)})
+			kit = GraphKit.autocreate({x: axiskit(kxy.to_s, options), y: axiskit("es_heat_flux_over_#{kxy}", options)})
 			kit.title  = "Heat flux vs #{kxy} for species #{options[:species_index]}"
 			kit.file_name = options[:graphkit_name] + options[:t_index].to_s
 			kit.data[0].with = 'lp'
@@ -2012,25 +2011,25 @@ module GraphKits
       end
 # </MJL>
 
-	def es_heat_by_mode_vs_time_graphkit(options={})
+	def es_heat_flux_by_mode_vs_time_graphkit(options={})
 		options[:direction] = :mode
-		es_heat_by_kxy_or_mode_vs_time_graphkit(options)
+		es_heat_flux_by_kxy_or_mode_vs_time_graphkit(options)
 	end
 
-	def es_heat_by_kx_vs_time_graphkit(options={})
+	def es_heat_flux_by_kx_vs_time_graphkit(options={})
 		options[:direction] = :kx
-		es_heat_by_kxy_or_mode_vs_time_graphkit(options)
+		es_heat_flux_by_kxy_or_mode_vs_time_graphkit(options)
 	end
 
-	def es_heat_by_ky_vs_time_graphkit(options={})
+	def es_heat_flux_by_ky_vs_time_graphkit(options={})
 		options[:direction] = :ky
-		es_heat_by_kxy_or_mode_vs_time_graphkit(options)
+		es_heat_flux_by_kxy_or_mode_vs_time_graphkit(options)
 	end
 
-	def es_heat_by_kxy_or_mode_vs_time_graphkit(options={})
+	def es_heat_flux_by_kxy_or_mode_vs_time_graphkit(options={})
 		case options[:command]
 		when :help
-			return  "'es_heat_by_ky_vs_time' or 'es_heat_by_kx_vs_time': Electrostatic Heat Flux vs Time for a given kx or ky, integrated over the other direction"
+			return  "'es_heat_flux_by_ky_vs_time' or 'es_heat_flux_by_kx_vs_time': Electrostatic Heat Flux vs Time for a given kx or ky, integrated over the other direction"
 		when :options
 			return  [:ky, :ky_index, :kx, :kx_index, :species_index]
 		else
@@ -2038,7 +2037,7 @@ module GraphKits
 			nt_options = options.dup # 'no time' options
 			#nt_options.delete(:t_index) if nt_options[:t_index]
 			#nt_options.delete(:frame_index) if nt_options[:frame_index]
-			phiax = axiskit("es_heat_by_#{kxy}_over_time", nt_options)	
+			phiax = axiskit("es_heat_flux_by_#{kxy}_over_time", nt_options)	
 			kit = GraphKit.autocreate({x: axiskit('t', options), y: phiax})
 			kit.data[0].title = "ES Heat Flux: #@run_name #{kxy} = #{options[kxy]}"	
 			kit.log_axis = 'y'
@@ -2081,7 +2080,6 @@ module GraphKits
 			kit = GraphKit.autocreate({x: axiskit('t', options), y: phiax})
 			kit.data[0].title = "Phi^2 total: #{kxy} = #{options[kxy]}"	
 			if options[:t_index]
-# 				p 'hello'
 				array_element = options[:t_index_window] ? options[:t_index] - options[:t_index_window][0] : options[:t_index] - 1
 # 				p phiax.data.size, array_element
 # 				p options[:t_index], options[:t_index_window]
@@ -2133,7 +2131,6 @@ module GraphKits
 			kit = GraphKit.autocreate({x: axiskit('t', options), y: tparax})
 			kit.data[0].title = "Tpar^2 total: #{kxy} = #{options[kxy]}"	
 			if options[:t_index]
-# 				p 'hello'
 				array_element = options[:t_index_window] ? options[:t_index] - options[:t_index_window][0] : options[:t_index] - 1
 # 				p tparax.data.size, array_element
 # 				p options[:t_index], options[:t_index_window]
@@ -2175,7 +2172,6 @@ module GraphKits
 			kit = GraphKit.autocreate({x: axiskit('t', options), y: tperpax})
 			kit.data[0].title = "Tperp^2 total: #{kxy} = #{options[kxy]}"	
 			if options[:t_index]
-# 				p 'hello'
 				array_element = options[:t_index_window] ? options[:t_index] - options[:t_index_window][0] : options[:t_index] - 1
 # 				p tparax.data.size, array_element
 # 				p options[:t_index], options[:t_index_window]

data/lib/gs2crmod/gs2.rb

@@ -1273,9 +1273,9 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
         [(kit = hflux_tot_vs_time_graphkit; kit.file_name = "hflux_tot_vs_time.eps"; kit), "Total heat flux $Q_{tot}$ as a function of time."],
         [(kit = es_heat_flux_vs_time_graphkit(species_index:1); kit.file_name = "es_heat_1_vs_time.eps"; kit), "Heat flux of species 1 versus time."],
         if @nspec > 1 then [(kit = es_heat_flux_vs_time_graphkit(species_index:2); kit.file_name = "es_heat_2_vs_time.eps"; kit), "Heat flux of species 2 versus time."] end,
-        [(kit = es_heat_vs_ky_graphkit(species_index:1); kit.gp.logscale="y" ; kit.file_name = "es_heat_1_vs_ky.eps"; kit), "Heat flux of species 1 as a function of $k_y$."],
-        if @nspec > 1 then [(kit = es_heat_vs_ky_graphkit(species_index:2); kit.gp.logscale="y" ; kit.file_name = "es_heat_2_vs_ky.eps"; kit), "Heat flux of species 2 as a function of $k_y$."] end,
-        [(kit = es_heat_vs_ky_vs_kx_graphkit; kit.gp.view="map" ; kit.file_name = "es_heat_vs_ky_vs_kx.eps"; kit), "2D total heat flux spectrum as a function of $k_x$ and $k_y$."],
+        [(kit = es_heat_flux_vs_ky_graphkit(species_index:1); kit.gp.logscale="y" ; kit.file_name = "es_heat_1_vs_ky.eps"; kit), "Heat flux of species 1 as a function of $k_y$."],
+        if @nspec > 1 then [(kit = es_heat_flux_vs_ky_graphkit(species_index:2); kit.gp.logscale="y" ; kit.file_name = "es_heat_2_vs_ky.eps"; kit), "Heat flux of species 2 as a function of $k_y$."] end,
+        [(kit = es_heat_flux_vs_ky_vs_kx_graphkit; kit.gp.view="map" ; kit.file_name = "es_heat_vs_ky_vs_kx.eps"; kit), "2D total heat flux spectrum as a function of $k_x$ and $k_y$."],
         [(kit = phi_real_space_graphkit(n0:1, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "phi_real_space.eps"; kit), "Potential fluctuations at the final time step vs GS2 $x$ and $y$ at the outboard midplane."],
         [(kit = density_real_space_graphkit(n0:1, species_index:1, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "density_real_space.eps"; kit), "Density fluctuations for species 1 at the final time step vs GS2 $x$ and $y$ at the outboard midplane."],
         if @nspec > 1 then [(kit = density_real_space_graphkit(n0:1, species_index:2, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "density_real_space.eps"; kit), "Density fluctuations for species 2 at the final time step vs GS2 $x$ and $y$ at the outboard midplane."] end,

data/lib/gs2crmod/gsl_data.rb

@@ -304,7 +304,7 @@ module GSLVectors
       return fix_norm(dphi/gsl_vector('dt'), 0, options)
     end
 
-# <MJL edits on 2013-09-19>
+  # <MJL edits on 2013-09-19>
                   # The real frequency of the fluctuations, read from the .out file, indexed by time and normalised to vth_1/a.
                   # :ky_index or :kx_index must be specified in options.
 
@@ -354,7 +354,7 @@ module GSLVectors
                      raise "No real frequencies found in the .out file for the desired k" if (omega_reals.size==0)
                      GSL::Vector.alloc(omega_reals)
                 end
-# </MJL>
+  # </MJL>
 
 
     # The size of each time step,  indexed by time, normalised to a/v_th1.
@@ -412,16 +412,16 @@ module GSLVectors
       return GSL::Vector.alloc(gsl_vector('ky').to_a.map{|ky| frequency_at_ky_at_kx[ky].values[options[:kx_index]-1]})
   end
 
-  def es_heat_by_kx_over_time_gsl_vector(options)
+  def es_heat_flux_by_kx_over_time_gsl_vector(options)
     options[:direction] = :kx
-    es_heat_by_kxy_over_time_gsl_vector(options)
+    es_heat_flux_by_kxy_over_time_gsl_vector(options)
   end
-  def es_heat_by_ky_over_time_gsl_vector(options)
+  def es_heat_flux_by_ky_over_time_gsl_vector(options)
     options[:direction] = :ky
-    es_heat_by_kxy_over_time_gsl_vector(options)
+    es_heat_flux_by_kxy_over_time_gsl_vector(options)
   end
 
-  def es_heat_by_kxy_over_time_gsl_vector(options)
+  def es_heat_flux_by_kxy_over_time_gsl_vector(options)
     Dir.chdir(@directory) do
       kxy = options[:direction]
       #kxy_index = kxy + :_index
@@ -430,7 +430,7 @@ module GSLVectors
       if kxy==:ky
         lkx = list(:kx)
         es_heat_av = (lkx.keys.map do |kx_index|
-          es_heat =  netcdf_file.var('es_heat_by_k').get({'start' => [kx_index-1,options[:ky_index]-1,options[:species_index]-1, 0], 'end' => [kx_index-1,options[:ky_index]-1,options[:species_index]-1, -1]})
+          es_heat =  netcdf_file.var('es_heat_flux_by_mode').get({'start' => [kx_index-1,options[:ky_index]-1,options[:species_index]-1, 0], 'end' => [kx_index-1,options[:ky_index]-1,options[:species_index]-1, -1]})
           #ep phi.shape
           es_heat.reshape(*es_heat.shape.values_at(3))
         end).sum / lkx.size
@@ -438,7 +438,7 @@ module GSLVectors
       else
         lky = list(:ky)
         es_heat_av = (lky.keys.map do |ky_index|
-          es_heat =  netcdf_file.var('es_heat_by_k').get({'start' => [options[:kx_index]-1,ky_index-1,options[:species_index]-1, 0], 'end' => [options[:kx_index]-1,ky_index-1,options[:species_index]-1, -1]})
+          es_heat =  netcdf_file.var('es_heat_flux_by_mode').get({'start' => [options[:kx_index]-1,ky_index-1,options[:species_index]-1, 0], 'end' => [options[:kx_index]-1,ky_index-1,options[:species_index]-1, -1]})
           #ep phi.shape
           es_heat.reshape(*es_heat.shape.values_at(3))
         end).sum / lky.size
@@ -447,25 +447,25 @@ module GSLVectors
 
     end
   end
-  private :es_heat_by_kxy_over_time_gsl_vector
+  private :es_heat_flux_by_kxy_over_time_gsl_vector
 
-  def es_heat_over_kx_gsl_vector(options)
+  def es_heat_flux_over_kx_gsl_vector(options)
     options[:direction] = :kx
-    es_heat_over_kxy_gsl_vector(options)
+    es_heat_flux_over_kxy_gsl_vector(options)
   end
-  def es_heat_over_ky_gsl_vector(options)
+  def es_heat_flux_over_ky_gsl_vector(options)
     options[:direction] = :ky
-    es_heat_over_kxy_gsl_vector(options)
+    es_heat_flux_over_kxy_gsl_vector(options)
   end
 
   #This function will output the heat flux as a function of kx or ky.
   #Default behaviour will be to average the heat flux over the time domain.
-  def es_heat_over_kxy_gsl_vector(options)
+  def es_heat_flux_over_kxy_gsl_vector(options)
     Dir.chdir(@directory) do
       kxy = options[:direction]
       raise "Please provide species_index " unless options[:species_index]
       if kxy==:ky
-        es_heat = (netcdf_file.var('es_heat_by_k').get({'start' => [0,0,options[:species_index]-1, 0], 'end' => [-1,-1,options[:species_index]-1, -1]})) #index = [kx,ky,spec,t]
+        es_heat = (netcdf_file.var('es_heat_flux_by_mode').get({'start' => [0,0,options[:species_index]-1, 0], 'end' => [-1,-1,options[:species_index]-1, -1]})) #index = [kx,ky,spec,t]
         #Need to average over time and sum over kx
         shape = es_heat.shape
         es_heat_av = []; temp = [];
@@ -477,7 +477,7 @@ module GSLVectors
         end
         return es_heat_av.to_gslv
       else
-        es_heat = (netcdf_file.var('es_heat_by_k').get({'start' => [0,0,options[:species_index]-1, 0], 'end' => [-1,-1,options[:species_index]-1, -1]})) #index = [kx,ky,spec,t]
+        es_heat = (netcdf_file.var('es_heat_flux_by_mode').get({'start' => [0,0,options[:species_index]-1, 0], 'end' => [-1,-1,options[:species_index]-1, -1]})) #index = [kx,ky,spec,t]
         shape = es_heat.shape
         es_heat_av = []; temp = [];
         for ix in 0...shape[0]
@@ -1039,12 +1039,11 @@ module GSLVectors
     #This is v_ZF = kxfac*IFT(i k_x phi_imag), where kxfac = (qinp/rhoc)*grho(rhoc).
     def zf_velocity_over_x_gsl_vector(options)
       Dir.chdir(@directory) do
-        raise CRFatal.new("Need to specify a theta_index.") unless options[:theta_index]
         raise CRFatal.new("Need either qinp or pk and epsl specified in order to calculate kxfac.
                           If using numerical equil use the option :kxfac to override calculation.") unless @qinp or (@pk and @epsl or options[:kxfac])
 
         kx = gsl_vector(:kx).to_box_order
-        grho = gsl_vector('grho')[options[:theta_index]]
+        grho = gsl_vector('grho')[get_list_of(:theta).length/2]
 
         phi = GSL::Vector.alloc(kx.size)
         for it in 0...gsl_vector(:t).size
@@ -1172,7 +1171,7 @@ module GSLVectorComplexes
     Dir.chdir(@directory) do
         raise CRFatal.new("write_eigenfunc is not enabled so this function won't work") unless @write_eigenfunc
         options.convert_to_index(self, :t)
-        a = netcdf_file.var('phi0').get({
+        a = netcdf_file.var('phi_igomega_by_mode').get({
           'start' => [0,0,0, options[:t_index] - 1],
           'end' => [-1,-1,0, options[:t_index] - 1]
         })
@@ -1217,7 +1216,7 @@ module GSLMatrices
       options.convert_to_index(:t) if options[:t] or options[:t_element]
       options[:t_index] ||= list(:t).keys.max
       #es_heat_by_k index order (in Fortran) is kx, ky, t
-      es_heat_narray = netcdf_file.var("es_heat_by_k").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [-1, -1, 0, options[:t_index] - 1])
+      es_heat_narray = netcdf_file.var("es_heat_flux_by_mode").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [-1, -1, 0, options[:t_index] - 1])
       es_heat_narray.reshape!(*es_heat_narray.shape.slice(0..1))
 
       gm =  es_heat_narray.to_gm.move_cols_from_box_order

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.101
+  version: 0.12.0
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,53 +10,60 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-03 00:00:00.000000000 Z
+date: 2015-07-28 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: 0.15.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.15.5
 - !ruby/object:Gem::Dependency
   name: rubyhacks
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -63,6 +71,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -70,57 +79,65 @@ dependencies:
 - !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
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
@@ -136,7 +153,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -193,25 +210,26 @@ 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: 2.2.2
+rubygems_version: 1.8.23
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
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-  data.tar.gz: 58c57e1fee6e4f6c6fc2b00bfa1fdae0c000958d
-SHA512:
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