gs2crmod 0.11.61 → 0.11.62

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (5) hide show
  1. data/VERSION +1 -1
  2. data/gs2crmod.gemspec +5 -7
  3. data/lib/gs2crmod/gs2.rb +36 -0
  4. metadata +42 -64
  5. checksums.yaml +0 -7
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.11.61
1
+ 0.11.62
data/gs2crmod.gemspec CHANGED
@@ -2,17 +2,14 @@
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2
  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: gs2crmod 0.11.61 ruby lib
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- # stub: ext/extconf.rb
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  Gem::Specification.new do |s|
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  s.name = "gs2crmod"
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- s.version = "0.11.61"
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+ s.version = "0.11.62"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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- s.require_paths = ["lib"]
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  s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
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- s.date = "2014-07-28"
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+ s.date = "2014-08-12"
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  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."
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  s.email = "edmundhighcock@sourceforge.net"
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  s.extensions = ["ext/extconf.rb"]
@@ -78,12 +75,13 @@ Gem::Specification.new do |s|
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  ]
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  s.homepage = "http://gs2crmod.sourceforge.net"
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  s.licenses = ["GSLv3"]
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+ s.require_paths = ["lib"]
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  s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
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- s.rubygems_version = "2.2.2"
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+ s.rubygems_version = "1.8.11"
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  s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
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  if s.respond_to? :specification_version then
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- s.specification_version = 4
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+ s.specification_version = 3
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  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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  s.add_runtime_dependency(%q<coderunner>, [">= 0.14.15"])
data/lib/gs2crmod/gs2.rb CHANGED
@@ -1413,6 +1413,42 @@ end
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  =end
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  end
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+
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+ #This section defines a selection of graphs which are written to a latex file when the CR function write_report is called. To add your own, simply copy one a similar looking graph and modify it to your needs.
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+ # The requirements to use the latex report writing is further specified in CodeRunner.
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+ def latex_graphs
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+ #will have a different set of graphs to look at depending on whether linear or nonlinear
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+ if @nonlinear_mode == "off"
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+ #make up a list of graphs that are to be included. The order of the arguments is [code to generate graphkit, LaTeX description and ]
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+ graphs = [
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+ #[(kit = phi2_by_mode_vs_time({kx_index:1, ky_index:1}); kit.xlabel=%[TEST]; kit.gp.term = "post eps color enhanced size 3.5in,2.33in"; kit.gp.output = "test.eps"; kit), "This is a test graph written into a \LaTeX file. \n\n \\myfigure{test.eps}"]
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+ [(kit = phi2tot_vs_time_graphkit; kit.data[0].title=""; kit.gp.logscale="y"; kit.file_name = "phi2tot.eps"; kit), "Total $\\phi^2$ versus time."],
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+ [(kit = growth_rate_vs_ky_graphkit; kit.data[0].title=""; kit.file_name = "growth_rate_vs_ky.eps"; kit), "Growth rate $\\gamma_E$ as a function of $k_y$ averaged over $k_x$ (if applicable)."],
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+ if @grid_option=="range" then [(kit = graphkit('efnmag', {norm:true, kx_index:1, ky_index: :all}); kit.data.each{|dk| dk.title=""}; kit.gp.logscale="y"; kit.file_name = "efnmag.eps"; kit.data.shift; kit), "Normalized magnitude of the eigenfunction as a function of $\\theta$ for all $k_y$'s in the simulation."] end,
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+ if @grid_option=="single" then [(kit = graphkit('efnmag', {norm:true, kx_index:1, ky_index:1}); kit.data.each{|dk| dk.title=""}; kit.gp.logscale="y"; kit.file_name = "efnmag.eps"; kit), "Normalized magnitude of the eigenfunction as a function of $\\theta$ for all $k_y$'s in the simulation."] end,
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+ ].compact
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+ else
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+ graphs = [
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+ [(kit = ky_spectrum_graphkit; kit.gp.logscale="y"; kit.file_name = "ky_spectrum.eps"; kit), "$k_y$ spectrum at the final time step averaged over $k_x$."],
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+ [(kit = kx_spectrum_graphkit; kit.gp.logscale="y"; kit.file_name = "kx_spectrum.eps"; kit), "$k_x$ spectrum at the final time step averaged over $k_y$."],
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+ [(kit = spectrum_graphkit(no_zonal:true); kit.gp.view="map"; kit.gp.logscale="z"; kit.file_name = "spectrum.eps"; kit), "2D spectrum versus $k_x$ and $k_y$ without zonal flows."],
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+ [(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."],
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+ [(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."],
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+ 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,
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+ [(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 $k_y$."],
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+ 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,
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+ [(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 $k_y$."],
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+ [(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."],
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+ [(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."],
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+ 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,
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+ [(kit = es_mom_flux_vs_time_graphkit(species_index:1); kit.file_name = "es_mom_flux_1_vs_time.eps"; kit), "Momentum flux for species 1 as a function of time."],
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+ if @nspec > 1 then [(kit = es_mom_flux_vs_time_graphkit(species_index:2); kit.file_name = "es_mom_flux_2_vs_time.eps"; kit), "Momentum flux for species 2 as a function of time."] end,
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+ [(kit = zonal_spectrum_graphkit; kit.gp.logscale="y"; kit.file_name = "zonal_spectrum.eps"; kit), "Zonal spectrum at the final time step."],
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+ ].compact
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+ end
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+
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+ end
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+
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  end # class GS2
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  # For backwards compatibility
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metadata CHANGED
@@ -1,7 +1,8 @@
1
1
  --- !ruby/object:Gem::Specification
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  name: gs2crmod
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  version: !ruby/object:Gem::Version
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- version: 0.11.61
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+ version: 0.11.62
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+ prerelease:
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  platform: ruby
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  authors:
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  - Edmund Highcock
@@ -9,120 +10,96 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-07-28 00:00:00.000000000 Z
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+ date: 2014-08-12 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: coderunner
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15321180 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 0.14.15
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: 0.14.15
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+ version_requirements: *15321180
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  - !ruby/object:Gem::Dependency
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  name: rubyhacks
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15320220 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 0.1.2
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: 0.1.2
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+ version_requirements: *15320220
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  - !ruby/object:Gem::Dependency
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  name: ruby-netcdf-updated
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15319300 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 0.6.6.1
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  type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: 0.6.6.1
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+ version_requirements: *15319300
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  - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15318680 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - '='
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+ - - =
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  - !ruby/object:Gem::Version
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  version: 3.0.1
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - '='
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- - !ruby/object:Gem::Version
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- version: 3.0.1
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+ version_requirements: *15318680
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  - !ruby/object:Gem::Dependency
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  name: rdoc
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15317940 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - "~>"
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+ - - ~>
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  - !ruby/object:Gem::Version
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  version: '3.12'
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - "~>"
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- - !ruby/object:Gem::Version
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- version: '3.12'
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+ version_requirements: *15317940
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15333600 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">"
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+ - - ! '>'
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  - !ruby/object:Gem::Version
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">"
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- - !ruby/object:Gem::Version
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- version: 1.0.0
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+ version_requirements: *15333600
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15332820 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 1.8.4
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: 1.8.4
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+ version_requirements: *15332820
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  - !ruby/object:Gem::Dependency
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  name: minitest
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- requirement: !ruby/object:Gem::Requirement
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+ requirement: &15331440 !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - "~>"
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+ - - ~>
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  - !ruby/object:Gem::Version
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  version: '4'
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  type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
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- - - "~>"
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- - !ruby/object:Gem::Version
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- version: '4'
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+ version_requirements: *15331440
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  description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
127
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  be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
128
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  running and analysis of large simulations. This module allows GS2 (and its sister
@@ -136,7 +113,7 @@ extra_rdoc_files:
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  - README.md
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  - README.rdoc
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  files:
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- - ".document"
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+ - .document
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  - Gemfile
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  - LICENSE.txt
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  - README.md
@@ -192,25 +169,26 @@ files:
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  homepage: http://gs2crmod.sourceforge.net
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  licenses:
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  - GSLv3
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- metadata: {}
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  post_install_message:
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  rdoc_options: []
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  require_paths:
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  - lib
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  required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: 1.9.1
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  required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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- - - ">="
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+ - - ! '>='
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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  rubyforge_project:
212
- rubygems_version: 2.2.2
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+ rubygems_version: 1.8.11
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  signing_key:
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- specification_version: 4
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+ specification_version: 3
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  summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
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  test_files: []
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