gs2crmod 0.11.63 → 0.11.64

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Files changed (6) hide show
  1. data/VERSION +1 -1
  2. data/gs2crmod.gemspec +5 -7
  3. data/lib/gs2crmod/calculations.rb +13 -0
  4. data/lib/gs2crmod/gs2.rb +1 -0
  5. metadata +40 -22
  6. checksums.yaml +0 -7
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.11.63
1
+ 0.11.64
data/gs2crmod.gemspec CHANGED
@@ -2,17 +2,14 @@
2
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  # 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 0.11.63 ruby lib
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- # stub: ext/extconf.rb
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5
 
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  Gem::Specification.new do |s|
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  s.name = "gs2crmod"
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- s.version = "0.11.63"
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+ s.version = "0.11.64"
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9
 
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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 = "2014-08-20"
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+ s.date = "2014-09-02"
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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 = "1.8.23"
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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/calculations.rb CHANGED
@@ -22,6 +22,7 @@ def calculate_time_averaged_fluxes
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  return unless FileTest.exist?(netcdf_filename)
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  @hflux_tot_stav = saturated_time_average('hflux_tot_over_time', {})
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  @hflux_tot_stav_error = saturated_time_average_error('hflux_tot_over_time', {})
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+ @hflux_tot_stav_std_dev = saturated_time_average_std_dev('hflux_tot_over_time', {})
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  @phi2_tot_stav = saturated_time_average('phi2tot_over_time', {})
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  #@par_mom_flux_stav = saturated_time_average('par_mom_flux_over_time', {}) rescue nil
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  #@perp_mom_flux_stav = saturated_time_average('perp_mom_flux_over_time', {}) rescue nil
@@ -99,6 +100,18 @@ def saturated_time_average_error(name, options)
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  return tavg.sd
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  end
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+ def saturated_time_average_std_dev(name, options)
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+ # calculate_saturation_time_index unless @saturation_time_index
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+ options[:t_index_window] = [@saturation_time_index, list(:t).keys.max]
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+ begin
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+ vec = gsl_vector(name, options)
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+ rescue NoMethodError
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+ eputs "Warning: could not calculate #{name} saturated_time_average_std_dev"
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+ return nil
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+ end
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+ return vec.sd
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+ end
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+
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  # I.e. the time at which the primary modes are saturated and the fluxes settle around a long term average.
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data/lib/gs2crmod/gs2.rb CHANGED
@@ -154,6 +154,7 @@ eval(%[
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  :es_heat_flux_stav,
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  :es_mom_flux_stav,
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  :hflux_tot_stav_error,
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+ :hflux_tot_stav_std_dev,
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  :es_heat_flux_stav_error,
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  :es_mom_flux_stav_error,
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  :saturated,
metadata CHANGED
@@ -1,7 +1,8 @@
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  --- !ruby/object:Gem::Specification
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  name: gs2crmod
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  version: !ruby/object:Gem::Version
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- version: 0.11.63
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+ version: 0.11.64
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+ prerelease:
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  platform: ruby
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  authors:
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  - Edmund Highcock
@@ -9,53 +10,60 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-08-20 00:00:00.000000000 Z
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+ date: 2014-09-02 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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+ 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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+ 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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  - !ruby/object:Gem::Dependency
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  name: rubyhacks
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  requirement: !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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+ 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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  - !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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+ 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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+ 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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  - !ruby/object:Gem::Dependency
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  name: shoulda
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  requirement: !ruby/object:Gem::Requirement
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+ none: false
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  requirements:
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  - - '='
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  - !ruby/object:Gem::Version
@@ -63,6 +71,7 @@ dependencies:
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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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+ none: false
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  requirements:
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  - - '='
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  - !ruby/object:Gem::Version
@@ -70,57 +79,65 @@ dependencies:
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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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+ 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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+ 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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  - !ruby/object:Gem::Dependency
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  name: bundler
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  requirement: !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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+ 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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  - !ruby/object:Gem::Dependency
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  name: jeweler
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  requirement: !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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+ 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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  - !ruby/object:Gem::Dependency
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  name: minitest
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  requirement: !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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+ 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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  description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
@@ -136,7 +153,7 @@ 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 +209,26 @@ 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:
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- rubygems_version: 2.2.2
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+ rubygems_version: 1.8.23
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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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@@ -1,7 +0,0 @@
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