gs2crmod 0.12.16 → 0.12.17

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.
@@ -0,0 +1,7 @@
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+ ---
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+ SHA1:
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+ metadata.gz: 4ddd76f50baa6cdbf11320c1b61a74261843b895
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+ data.tar.gz: c5abd2e4462099887fb01d0695fe628d1b954f3b
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+ SHA512:
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+ metadata.gz: fdd76e6a63c8366c320312b814fa8867beba9f2f3422836fd8edb3bb2a0e31631efbe66baf09e332ca9a69f1647072e39c4cdc4d66ea8e597cc3f131d0c99315
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+ data.tar.gz: 0de7d910910212d819f5c22bfe0284a8053a5642afa878fc4895234b9c9884b78fa0c6b2458d0090396b906a3da604093c098e97805d934fa1f0308af663c092
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.12.16
1
+ 0.12.17
@@ -97,8 +97,8 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
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  /*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
98
98
 
99
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  Check_Type(options, T_HASH);
100
- if(RTEST(CR_HKS(options, "field"))){
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- field = CR_HKS(options, "field");
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+ if(RTEST(CR_HKS(options, "field_netcdf"))){
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+ field = CR_HKS(options, "field_netcdf");
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  CR_CHECK_CLASS(field, cgsl_tensor);
103
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  }
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  else {
@@ -129,7 +129,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
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129
 
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  c_field = ALLOC_N(double, c_shape[0] * c_shape[1] * c_shape[2] * c_shape[3]);
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131
 
132
- /*printf("Allocated stuff\n");*/
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+ /*printf("Allocated stuff\n");*/
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  for (j=0; j<c_shape[2]; j++) /*theta loop*/
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  {
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  for (i=0; i<c_shape[0]; i++) /*ky loop*/
@@ -293,7 +293,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
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  3,
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  ary_ptr[0], ary_ptr[1], ary_ptr[2]);
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  field_real_space_new_narray = RFCALL_10_ON(field_real_space_new, "narray");
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- /*printf("Allocated");*/
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+ /*printf("Allocated");*/
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  /*rb_p(shape_real_space_new);*/
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  for (i=0;i<c_shape_real_space_new[0];i++)
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  for (j=0;j<c_shape_real_space_new[1];j++)
@@ -344,6 +344,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
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  field_real_space = field_real_space_new;
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  }
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+ /*printf("Finished field_real_space_gsl_tensor\n");*/
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  /*rb_p(shape_real_space_new);*/
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  return field_real_space;
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  }
@@ -2,17 +2,20 @@
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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 0.12.17 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 = "0.12.16"
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+ s.name = "gs2crmod".freeze
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+ s.version = "0.12.17"
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- s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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- s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
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- s.date = "2015-12-07"
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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"]
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+ s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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+ s.require_paths = ["lib".freeze]
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+ s.authors = ["Edmund Highcock".freeze, "Ferdinand van Wyk".freeze]
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+ s.date = "2017-04-27"
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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.".freeze
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+ s.email = "edmundhighcock@sourceforge.net".freeze
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+ s.extensions = ["ext/extconf.rb".freeze]
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
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  "README.md",
@@ -74,44 +77,43 @@ Gem::Specification.new do |s|
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  "sync_variables_sgk/helper.rb",
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  "sync_variables_sgk/sync_variables_sgk.rb"
76
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  ]
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- s.homepage = "http://gs2crmod.sourceforge.net"
78
- s.licenses = ["GSLv3"]
79
- s.require_paths = ["lib"]
80
- s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
81
- s.rubygems_version = "1.8.23"
82
- s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
80
+ s.homepage = "http://gs2crmod.sourceforge.net".freeze
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+ s.licenses = ["GSLv3".freeze]
82
+ s.required_ruby_version = Gem::Requirement.new(">= 1.9.1".freeze)
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+ s.rubygems_version = "2.6.8".freeze
84
+ s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.".freeze
83
85
 
84
86
  if s.respond_to? :specification_version then
85
- s.specification_version = 3
87
+ s.specification_version = 4
86
88
 
87
89
  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
88
- s.add_runtime_dependency(%q<coderunner>, [">= 0.15.5"])
89
- s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.2"])
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- s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
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- s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
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- s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
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- s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
94
- s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
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- s.add_development_dependency(%q<minitest>, ["~> 4"])
90
+ s.add_runtime_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
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+ s.add_runtime_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
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+ s.add_runtime_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
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+ s.add_development_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
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+ s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
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+ s.add_development_dependency(%q<bundler>.freeze, ["> 1.0.0"])
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+ s.add_development_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
97
+ s.add_development_dependency(%q<minitest>.freeze, ["~> 4"])
96
98
  else
97
- s.add_dependency(%q<coderunner>, [">= 0.15.5"])
98
- s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
99
- s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
100
- s.add_dependency(%q<shoulda>, ["= 3.0.1"])
101
- s.add_dependency(%q<rdoc>, ["~> 3.12"])
102
- s.add_dependency(%q<bundler>, ["> 1.0.0"])
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- s.add_dependency(%q<jeweler>, [">= 1.8.4"])
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- s.add_dependency(%q<minitest>, ["~> 4"])
99
+ s.add_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
100
+ s.add_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
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+ s.add_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
102
+ s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
103
+ s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
104
+ s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
105
+ s.add_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
106
+ s.add_dependency(%q<minitest>.freeze, ["~> 4"])
105
107
  end
106
108
  else
107
- s.add_dependency(%q<coderunner>, [">= 0.15.5"])
108
- s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
109
- s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
110
- s.add_dependency(%q<shoulda>, ["= 3.0.1"])
111
- s.add_dependency(%q<rdoc>, ["~> 3.12"])
112
- s.add_dependency(%q<bundler>, ["> 1.0.0"])
113
- s.add_dependency(%q<jeweler>, [">= 1.8.4"])
114
- s.add_dependency(%q<minitest>, ["~> 4"])
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+ s.add_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
110
+ s.add_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
111
+ s.add_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
112
+ s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
113
+ s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
114
+ s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
115
+ s.add_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
116
+ s.add_dependency(%q<minitest>.freeze, ["~> 4"])
115
117
  end
116
118
  end
117
119
 
@@ -171,7 +171,6 @@ GRAPHKIT_OPTIONS_HELP = {
171
171
  Rmaj: "The major radius in metres. This has no effect on the shape of the graph: it merely multiplies every length",
172
172
  n0: " The toroidal mode number of the longest y mode. In effect it is the number of periodic copies of the flux tube that will fit in the torus. Periodicity requires that n0 q is also an integer. If you specify :n0 where this is not the case, q will automatically be adjusted until it is",
173
173
  rho_star: " The ratio of the reference Lamour radius to the GS2 normalising length a. Cannot be specified at the same time as n0. If specified, both n0 and q will be adjusted to ensure periodicity",
174
- t_index: "The (1-based) time index",
175
174
  nakx: "The number of radial wave numbers to include in the plot. In effect, it is a low pass filter which reduces the resolution in the radial direction without changing the shape of the final surface. Minimum value is 4",
176
175
  naky: "The number of kys to include in the plot. In effect, it is a low pass filter which reduces the resolution in the y direction without changing the shape of the final surface. Minimum value is 4",
177
176
  gs2_coordinate_factor: "When set to 1, plot the graph in GS2 coordinates. When set to 0 plot the graph in real space. Can be set at any value between 0 and 1: the graph will smoothly distort between the two limits",
@@ -224,7 +224,11 @@ class CodeRunner::Gs2
224
224
 
225
225
  end
226
226
 
227
- arr[0, true, true, true] = 0.0 if options[:no_zonal]
227
+ #if options[:t_index]
228
+ arr[0, true, true, true] = 0.0 if options[:no_zonal]
229
+ #else
230
+ #arr[0, true, true] = 0.0 if options[:no_zonal]
231
+ #end
228
232
  #arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
229
233
  return arr
230
234
 
@@ -374,6 +378,7 @@ class CodeRunner::Gs2
374
378
  end
375
379
  # Order is R0,Z0,a0,Rprim,Zprim,aprim
376
380
  def geometric_factors_gsl_tensor(options)
381
+ #ep 'STARTING'
377
382
  #ops = options.dup; ops.delete :phi
378
383
  #ep ops; gets
379
384
  case @equilibrium_option
@@ -385,7 +390,8 @@ class CodeRunner::Gs2
385
390
  values = File.read(options[:geometry_file]||"#@directory/#@run_name.g").split(/\s*\n\s*/)
386
391
  3.times{values.shift}
387
392
  values = values.map{|str| str.split(/\s+/).map{|s| s.to_f}}.transpose
388
- #ep values
393
+ #ep values[0]
394
+ #ep values[3]
389
395
  shape = factors.shape
390
396
  for i in 0...shape[0]
391
397
  unless options[:interpolate_theta]
@@ -396,7 +402,7 @@ class CodeRunner::Gs2
396
402
  opts = options.dup
397
403
  opts[:interpolate_theta] = nil
398
404
  theta_vec_short = gsl_vector(:theta, {})
399
- interp = GSL::ScatterInterp.alloc(:linear, [values[0], values[i+1].to_gslv], true)
405
+ interp = GSL::ScatterInterp.alloc(:thin_plate_splines, [values[0], values[i+1].to_gslv], false)
400
406
  for j in 0...theta_vec.size
401
407
  factors[i,j] = interp.eval(theta_vec[j])
402
408
  end
@@ -588,7 +588,7 @@
588
588
  :should_include=>"true",
589
589
  :description=>"Major radius/a (Position of magnetic axis)",
590
590
  :tests=>["Tst::FLOAT"],
591
- :autoscanned_defaults=>[1.0, 3, 3.0],
591
+ :autoscanned_defaults=>[1.0, 3.0, 3],
592
592
  :must_pass=>
593
593
  [{:test=>"kind_of? Float or kind_of? Integer",
594
594
  :explanation=>
@@ -947,8 +947,7 @@
947
947
  :should_include=>"true",
948
948
  :description=>nil,
949
949
  :tests=>["Tst::STRING"],
950
- :autoscanned_defaults=>
951
- ["dskeq.cdf", "eqfile_in", "ogyropsi.dat", "test8_efit.dat"],
950
+ :autoscanned_defaults=>["dskeq.cdf", "ogyropsi.dat", "test8_efit.dat"],
952
951
  :must_pass=>
953
952
  [{:test=>"kind_of? String",
954
953
  :explanation=>"This variable must be a string."}],
@@ -960,7 +959,7 @@
960
959
  :should_include=>"true",
961
960
  :description=>nil,
962
961
  :tests=>["Tst::INT"],
963
- :autoscanned_defaults=>[1, 5, 6],
962
+ :autoscanned_defaults=>[1, 4, 5, 6],
964
963
  :must_pass=>
965
964
  [{:test=>"kind_of? Integer",
966
965
  :explanation=>"This variable must be an integer."}],
@@ -1043,7 +1042,7 @@
1043
1042
  :should_include=>"true",
1044
1043
  :description=>nil,
1045
1044
  :tests=>["Tst::FORTRAN_BOOL"],
1046
- :autoscanned_defaults=>[".false.", ".t.", ".true."],
1045
+ :autoscanned_defaults=>[".false.", ".true."],
1047
1046
  :must_pass=>
1048
1047
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
1049
1048
  :explanation=>
@@ -1067,7 +1066,7 @@
1067
1066
  :should_include=>"true",
1068
1067
  :description=>nil,
1069
1068
  :tests=>["Tst::FORTRAN_BOOL"],
1070
- :autoscanned_defaults=>[".false.", ".t."],
1069
+ :autoscanned_defaults=>[".false.", ".t.", ".true."],
1071
1070
  :must_pass=>
1072
1071
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
1073
1072
  :explanation=>
@@ -1843,7 +1842,87 @@
1843
1842
  :explanation=>
1844
1843
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
1845
1844
  :type=>:Fortran_Bool,
1846
- :autoscanned_defaults=>[".false."]}}},
1845
+ :autoscanned_defaults=>[".false."]},
1846
+ :densfac_lin=>
1847
+ {:should_include=>"true",
1848
+ :description=>"",
1849
+ :help=>"",
1850
+ :code_name=>:densfac_lin,
1851
+ :must_pass=>
1852
+ [{:test=>"kind_of? Numeric",
1853
+ :explanation=>
1854
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1855
+ :type=>:Float},
1856
+ :uparfac_lin=>
1857
+ {:should_include=>"true",
1858
+ :description=>"",
1859
+ :help=>"",
1860
+ :code_name=>:uparfac_lin,
1861
+ :must_pass=>
1862
+ [{:test=>"kind_of? Numeric",
1863
+ :explanation=>
1864
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1865
+ :type=>:Float},
1866
+ :tparfac_lin=>
1867
+ {:should_include=>"true",
1868
+ :description=>"",
1869
+ :help=>"",
1870
+ :code_name=>:tparfac_lin,
1871
+ :must_pass=>
1872
+ [{:test=>"kind_of? Numeric",
1873
+ :explanation=>
1874
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1875
+ :type=>:Float},
1876
+ :tprpfac_lin=>
1877
+ {:should_include=>"true",
1878
+ :description=>"",
1879
+ :help=>"",
1880
+ :code_name=>:tprpfac_lin,
1881
+ :must_pass=>
1882
+ [{:test=>"kind_of? Numeric",
1883
+ :explanation=>
1884
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1885
+ :type=>:Float},
1886
+ :qparfac_lin=>
1887
+ {:should_include=>"true",
1888
+ :description=>"",
1889
+ :help=>"",
1890
+ :code_name=>:qparfac_lin,
1891
+ :must_pass=>
1892
+ [{:test=>"kind_of? Numeric",
1893
+ :explanation=>
1894
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1895
+ :type=>:Float},
1896
+ :qprpfac_lin=>
1897
+ {:should_include=>"true",
1898
+ :description=>"",
1899
+ :help=>"",
1900
+ :code_name=>:qprpfac_lin,
1901
+ :must_pass=>
1902
+ [{:test=>"kind_of? Numeric",
1903
+ :explanation=>
1904
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1905
+ :type=>:Float},
1906
+ :phifac_lin=>
1907
+ {:should_include=>"true",
1908
+ :description=>"",
1909
+ :help=>"",
1910
+ :code_name=>:phifac_lin,
1911
+ :must_pass=>
1912
+ [{:test=>"kind_of? Numeric",
1913
+ :explanation=>
1914
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
1915
+ :type=>:Float},
1916
+ :gf_lo_integrate=>
1917
+ {:should_include=>"true",
1918
+ :description=>"",
1919
+ :help=>"",
1920
+ :code_name=>:gf_lo_integrate,
1921
+ :must_pass=>
1922
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
1923
+ :explanation=>
1924
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
1925
+ :type=>:Fortran_Bool}}},
1847
1926
  :fields_knobs=>
1848
1927
  {:description=>"ALGORITHMIC CHOICES",
1849
1928
  :should_include=>"true",
@@ -1944,7 +2023,7 @@
1944
2023
  [{:test=>"kind_of? Integer",
1945
2024
  :explanation=>"This variable must be an integer."}],
1946
2025
  :type=>:Integer,
1947
- :autoscanned_defaults=>[64]},
2026
+ :autoscanned_defaults=>[]},
1948
2027
  :do_smart_update=>
1949
2028
  {:should_include=>"true",
1950
2029
  :description=>"",
@@ -1980,7 +2059,27 @@
1980
2059
  :explanation=>
1981
2060
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
1982
2061
  :type=>:Fortran_Bool,
1983
- :autoscanned_defaults=>[".false."]}}},
2062
+ :autoscanned_defaults=>[".false."]},
2063
+ :field_local_tuneminnrow=>
2064
+ {:should_include=>"true",
2065
+ :description=>"",
2066
+ :help=>"",
2067
+ :code_name=>:field_local_tuneminnrow,
2068
+ :must_pass=>
2069
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
2070
+ :explanation=>
2071
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2072
+ :type=>:Fortran_Bool},
2073
+ :field_local_nonblocking_collectives=>
2074
+ {:should_include=>"true",
2075
+ :description=>"",
2076
+ :help=>"",
2077
+ :code_name=>:field_local_nonblocking_collectives,
2078
+ :must_pass=>
2079
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
2080
+ :explanation=>
2081
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2082
+ :type=>:Fortran_Bool}}},
1984
2083
  :knobs=>
1985
2084
  {:description=>"",
1986
2085
  :should_include=>"true",
@@ -2280,7 +2379,19 @@
2280
2379
  :explanation=>
2281
2380
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2282
2381
  :type=>:Fortran_Bool,
2283
- :autoscanned_defaults=>[".false."]}}},
2382
+ :autoscanned_defaults=>[".false.", ".true."]},
2383
+ :trinity_ql_fluxes=>
2384
+ {:should_include=>"true",
2385
+ :description=>
2386
+ "If linear and trinity_linear_fluxes is true, return quasilinear flux estimate to trinity",
2387
+ :help=>
2388
+ "If linear and trinity_linear_fluxes is true, return quasilinear flux estimate to trinity",
2389
+ :code_name=>:trinity_ql_fluxes,
2390
+ :must_pass=>
2391
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
2392
+ :explanation=>
2393
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2394
+ :type=>:Fortran_Bool}}},
2284
2395
  :reinit_knobs=>
2285
2396
  {:description=>"",
2286
2397
  :should_include=>"true",
@@ -2442,7 +2553,7 @@
2442
2553
  :explanation=>
2443
2554
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2444
2555
  :type=>:Fortran_Bool,
2445
- :autoscanned_defaults=>[".false."]},
2556
+ :autoscanned_defaults=>[".true."]},
2446
2557
  :opt_redist_init=>
2447
2558
  {:should_include=>"true",
2448
2559
  :description=>
@@ -2553,7 +2664,27 @@
2553
2664
  [{:test=>"kind_of? String",
2554
2665
  :explanation=>"This variable must be a string."}],
2555
2666
  :type=>:String,
2556
- :autoscanned_defaults=>["default"]}}},
2667
+ :autoscanned_defaults=>["default"]},
2668
+ :simple_gf_decomposition=>
2669
+ {:should_include=>"true",
2670
+ :description=>"",
2671
+ :help=>"",
2672
+ :code_name=>:simple_gf_decomposition,
2673
+ :must_pass=>
2674
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
2675
+ :explanation=>
2676
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2677
+ :type=>:Fortran_Bool},
2678
+ :gf_local_fields=>
2679
+ {:should_include=>"true",
2680
+ :description=>"",
2681
+ :help=>"",
2682
+ :code_name=>:gf_local_fields,
2683
+ :must_pass=>
2684
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
2685
+ :explanation=>
2686
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
2687
+ :type=>:Fortran_Bool}}},
2557
2688
  :collisions_knobs=>
2558
2689
  {:description=>"COLLISIONS",
2559
2690
  :should_include=>"true",
@@ -3147,7 +3278,67 @@
3147
3278
  :explanation=>
3148
3279
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
3149
3280
  :type=>:Fortran_Bool,
3150
- :autoscanned_defaults=>[]}}},
3281
+ :autoscanned_defaults=>[]},
3282
+ :densfac=>
3283
+ {:should_include=>"true",
3284
+ :description=>"",
3285
+ :help=>"",
3286
+ :code_name=>:densfac,
3287
+ :must_pass=>
3288
+ [{:test=>"kind_of? Numeric",
3289
+ :explanation=>
3290
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3291
+ :type=>:Float},
3292
+ :uparfac=>
3293
+ {:should_include=>"true",
3294
+ :description=>"",
3295
+ :help=>"",
3296
+ :code_name=>:uparfac,
3297
+ :must_pass=>
3298
+ [{:test=>"kind_of? Numeric",
3299
+ :explanation=>
3300
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3301
+ :type=>:Float},
3302
+ :tparfac=>
3303
+ {:should_include=>"true",
3304
+ :description=>"",
3305
+ :help=>"",
3306
+ :code_name=>:tparfac,
3307
+ :must_pass=>
3308
+ [{:test=>"kind_of? Numeric",
3309
+ :explanation=>
3310
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3311
+ :type=>:Float},
3312
+ :tprpfac=>
3313
+ {:should_include=>"true",
3314
+ :description=>"",
3315
+ :help=>"",
3316
+ :code_name=>:tprpfac,
3317
+ :must_pass=>
3318
+ [{:test=>"kind_of? Numeric",
3319
+ :explanation=>
3320
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3321
+ :type=>:Float},
3322
+ :qparfac=>
3323
+ {:should_include=>"true",
3324
+ :description=>"",
3325
+ :help=>"",
3326
+ :code_name=>:qparfac,
3327
+ :must_pass=>
3328
+ [{:test=>"kind_of? Numeric",
3329
+ :explanation=>
3330
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3331
+ :type=>:Float},
3332
+ :qprpfac=>
3333
+ {:should_include=>"true",
3334
+ :description=>"",
3335
+ :help=>"",
3336
+ :code_name=>:qprpfac,
3337
+ :must_pass=>
3338
+ [{:test=>"kind_of? Numeric",
3339
+ :explanation=>
3340
+ "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
3341
+ :type=>:Float}}},
3151
3342
  :additional_linear_terms_knobs=>
3152
3343
  {:description=>"ADDITIONAL LINEAR TERMS",
3153
3344
  :should_include=>"true",
@@ -3179,7 +3370,7 @@
3179
3370
  :should_include=>"true",
3180
3371
  :description=>"Charge",
3181
3372
  :tests=>["Tst::FLOAT"],
3182
- :autoscanned_defaults=>[1],
3373
+ :autoscanned_defaults=>[0.0, 1],
3183
3374
  :must_pass=>
3184
3375
  [{:test=>"kind_of? Float or kind_of? Integer",
3185
3376
  :explanation=>
@@ -5116,7 +5307,8 @@
5116
5307
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5117
5308
  :explanation=>
5118
5309
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5119
- :type=>:Fortran_Bool},
5310
+ :type=>:Fortran_Bool,
5311
+ :autoscanned_defaults=>[".false."]},
5120
5312
  :serial_netcdf4=>
5121
5313
  {:should_include=>"true",
5122
5314
  :description=>"",
@@ -5126,7 +5318,8 @@
5126
5318
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5127
5319
  :explanation=>
5128
5320
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5129
- :type=>:Fortran_Bool},
5321
+ :type=>:Fortran_Bool,
5322
+ :autoscanned_defaults=>[".false."]},
5130
5323
  :write_ntot_over_time=>
5131
5324
  {:should_include=>"true",
5132
5325
  :description=>"",
@@ -5136,7 +5329,8 @@
5136
5329
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5137
5330
  :explanation=>
5138
5331
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5139
- :type=>:Fortran_Bool},
5332
+ :type=>:Fortran_Bool,
5333
+ :autoscanned_defaults=>[".false."]},
5140
5334
  :write_density_over_time=>
5141
5335
  {:should_include=>"true",
5142
5336
  :description=>"",
@@ -5146,7 +5340,8 @@
5146
5340
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5147
5341
  :explanation=>
5148
5342
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5149
- :type=>:Fortran_Bool},
5343
+ :type=>:Fortran_Bool,
5344
+ :autoscanned_defaults=>[".false."]},
5150
5345
  :write_upar_over_time=>
5151
5346
  {:should_include=>"true",
5152
5347
  :description=>"",
@@ -5156,7 +5351,8 @@
5156
5351
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5157
5352
  :explanation=>
5158
5353
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5159
- :type=>:Fortran_Bool},
5354
+ :type=>:Fortran_Bool,
5355
+ :autoscanned_defaults=>[".false."]},
5160
5356
  :write_tperp_over_time=>
5161
5357
  {:should_include=>"true",
5162
5358
  :description=>"",
@@ -5166,7 +5362,8 @@
5166
5362
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5167
5363
  :explanation=>
5168
5364
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5169
- :type=>:Fortran_Bool},
5365
+ :type=>:Fortran_Bool,
5366
+ :autoscanned_defaults=>[".false."]},
5170
5367
  :write_fluxes=>
5171
5368
  {:should_include=>"true",
5172
5369
  :description=>"",
@@ -5176,7 +5373,8 @@
5176
5373
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5177
5374
  :explanation=>
5178
5375
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5179
- :type=>:Fortran_Bool},
5376
+ :type=>:Fortran_Bool,
5377
+ :autoscanned_defaults=>[".true."]},
5180
5378
  :write_fluxes_by_mode=>
5181
5379
  {:should_include=>"true",
5182
5380
  :description=>"",
@@ -5186,7 +5384,8 @@
5186
5384
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5187
5385
  :explanation=>
5188
5386
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5189
- :type=>:Fortran_Bool},
5387
+ :type=>:Fortran_Bool,
5388
+ :autoscanned_defaults=>[".true."]},
5190
5389
  :ncheck=>
5191
5390
  {:should_include=>"true",
5192
5391
  :description=>"",
@@ -5195,7 +5394,8 @@
5195
5394
  :must_pass=>
5196
5395
  [{:test=>"kind_of? Integer",
5197
5396
  :explanation=>"This variable must be an integer."}],
5198
- :type=>:Integer},
5397
+ :type=>:Integer,
5398
+ :autoscanned_defaults=>[10, 100]},
5199
5399
  :write_heating=>
5200
5400
  {:should_include=>"true",
5201
5401
  :description=>"",
@@ -5205,12 +5405,34 @@
5205
5405
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5206
5406
  :explanation=>
5207
5407
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5208
- :type=>:Fortran_Bool},
5408
+ :type=>:Fortran_Bool,
5409
+ :autoscanned_defaults=>[".false."]},
5209
5410
  :write_jext=>
5210
5411
  {:should_include=>"true",
5211
5412
  :description=>"",
5212
5413
  :help=>"",
5213
5414
  :code_name=>:write_jext,
5415
+ :must_pass=>
5416
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5417
+ :explanation=>
5418
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5419
+ :type=>:Fortran_Bool,
5420
+ :autoscanned_defaults=>[".false."]},
5421
+ :write_zonal_transfer=>
5422
+ {:should_include=>"true",
5423
+ :description=>"",
5424
+ :help=>"",
5425
+ :code_name=>:write_zonal_transfer,
5426
+ :must_pass=>
5427
+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5428
+ :explanation=>
5429
+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
5430
+ :type=>:Fortran_Bool},
5431
+ :write_collisional=>
5432
+ {:should_include=>"true",
5433
+ :description=>"",
5434
+ :help=>"",
5435
+ :code_name=>:write_collisional,
5214
5436
  :must_pass=>
5215
5437
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
5216
5438
  :explanation=>
@@ -7459,7 +7681,8 @@
7459
7681
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
7460
7682
  :explanation=>
7461
7683
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
7462
- :type=>:Fortran_Bool},
7684
+ :type=>:Fortran_Bool,
7685
+ :autoscanned_defaults=>[".false."]},
7463
7686
  :auto=>
7464
7687
  {:should_include=>"true",
7465
7688
  :description=>
@@ -7471,7 +7694,8 @@
7471
7694
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
7472
7695
  :explanation=>
7473
7696
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
7474
- :type=>:Fortran_Bool},
7697
+ :type=>:Fortran_Bool,
7698
+ :autoscanned_defaults=>[".true."]},
7475
7699
  :measure_all=>
7476
7700
  {:should_include=>"true",
7477
7701
  :description=>"",
@@ -7481,7 +7705,8 @@
7481
7705
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
7482
7706
  :explanation=>
7483
7707
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
7484
- :type=>:Fortran_Bool},
7708
+ :type=>:Fortran_Bool,
7709
+ :autoscanned_defaults=>[".false."]},
7485
7710
  :warm_up=>
7486
7711
  {:should_include=>"true",
7487
7712
  :description=>"Experimental, set to false.",
@@ -7491,7 +7716,8 @@
7491
7716
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
7492
7717
  :explanation=>
7493
7718
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
7494
- :type=>:Fortran_Bool},
7719
+ :type=>:Fortran_Bool,
7720
+ :autoscanned_defaults=>[".false."]},
7495
7721
  :estimate_timing_error=>
7496
7722
  {:should_include=>"true",
7497
7723
  :description=>
@@ -7503,7 +7729,8 @@
7503
7729
  [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
7504
7730
  :explanation=>
7505
7731
  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
7506
- :type=>:Fortran_Bool},
7732
+ :type=>:Fortran_Bool,
7733
+ :autoscanned_defaults=>[".true."]},
7507
7734
  :nstep_measure=>
7508
7735
  {:should_include=>"true",
7509
7736
  :description=>
@@ -7514,7 +7741,8 @@
7514
7741
  :must_pass=>
7515
7742
  [{:test=>"kind_of? Integer",
7516
7743
  :explanation=>"This variable must be an integer."}],
7517
- :type=>:Integer},
7744
+ :type=>:Integer,
7745
+ :autoscanned_defaults=>[5]},
7518
7746
  :max_imbalance=>
7519
7747
  {:should_include=>"true",
7520
7748
  :description=>
@@ -7525,7 +7753,8 @@
7525
7753
  :must_pass=>
7526
7754
  [{:test=>"kind_of? Integer",
7527
7755
  :explanation=>"This variable must be an integer."}],
7528
- :type=>:Integer},
7756
+ :type=>:Integer,
7757
+ :autoscanned_defaults=>[-1]},
7529
7758
  :max_unused_procs=>
7530
7759
  {:should_include=>"true",
7531
7760
  :description=>
@@ -7536,7 +7765,8 @@
7536
7765
  :must_pass=>
7537
7766
  [{:test=>"kind_of? Integer",
7538
7767
  :explanation=>"This variable must be an integer."}],
7539
- :type=>:Integer},
7768
+ :type=>:Integer,
7769
+ :autoscanned_defaults=>[0]},
7540
7770
  :min_efficiency=>
7541
7771
  {:should_include=>"true",
7542
7772
  :description=>
@@ -7548,4 +7778,5 @@
7548
7778
  [{:test=>"kind_of? Numeric",
7549
7779
  :explanation=>
7550
7780
  "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
7551
- :type=>:Float}}}}
7781
+ :type=>:Float,
7782
+ :autoscanned_defaults=>[-1.0]}}}}
@@ -7,12 +7,12 @@ rescue Bundler::BundlerError => e
7
7
  $stderr.puts "Run `bundle install` to install missing gems"
8
8
  exit e.status_code
9
9
  end
10
- require 'test/unit'
11
- require 'shoulda'
10
+ #require 'test/unit'
11
+ #require 'shoulda'
12
12
 
13
13
  $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
14
14
  $LOAD_PATH.unshift(File.dirname(__FILE__))
15
15
  require 'coderunner'
16
16
 
17
- class Test::Unit::TestCase
18
- end
17
+ #class Test::Unit::TestCase
18
+ #end
metadata CHANGED
@@ -1,8 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: gs2crmod
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.12.16
5
- prerelease:
4
+ version: 0.12.17
6
5
  platform: ruby
7
6
  authors:
8
7
  - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
10
9
  autorequire:
11
10
  bindir: bin
12
11
  cert_chain: []
13
- date: 2015-12-07 00:00:00.000000000 Z
12
+ date: 2017-04-27 00:00:00.000000000 Z
14
13
  dependencies:
15
14
  - !ruby/object:Gem::Dependency
16
15
  name: coderunner
17
16
  requirement: !ruby/object:Gem::Requirement
18
- none: false
19
17
  requirements:
20
- - - ! '>='
18
+ - - ">="
21
19
  - !ruby/object:Gem::Version
22
20
  version: 0.15.5
23
21
  type: :runtime
24
22
  prerelease: false
25
23
  version_requirements: !ruby/object:Gem::Requirement
26
- none: false
27
24
  requirements:
28
- - - ! '>='
25
+ - - ">="
29
26
  - !ruby/object:Gem::Version
30
27
  version: 0.15.5
31
28
  - !ruby/object:Gem::Dependency
32
29
  name: rubyhacks
33
30
  requirement: !ruby/object:Gem::Requirement
34
- none: false
35
31
  requirements:
36
- - - ! '>='
32
+ - - ">="
37
33
  - !ruby/object:Gem::Version
38
34
  version: 0.1.2
39
35
  type: :runtime
40
36
  prerelease: false
41
37
  version_requirements: !ruby/object:Gem::Requirement
42
- none: false
43
38
  requirements:
44
- - - ! '>='
39
+ - - ">="
45
40
  - !ruby/object:Gem::Version
46
41
  version: 0.1.2
47
42
  - !ruby/object:Gem::Dependency
48
43
  name: ruby-netcdf
49
44
  requirement: !ruby/object:Gem::Requirement
50
- none: false
51
45
  requirements:
52
- - - ! '>='
46
+ - - ">="
53
47
  - !ruby/object:Gem::Version
54
48
  version: 0.7.1
55
49
  type: :runtime
56
50
  prerelease: false
57
51
  version_requirements: !ruby/object:Gem::Requirement
58
- none: false
59
52
  requirements:
60
- - - ! '>='
53
+ - - ">="
61
54
  - !ruby/object:Gem::Version
62
55
  version: 0.7.1
63
56
  - !ruby/object:Gem::Dependency
64
57
  name: shoulda
65
58
  requirement: !ruby/object:Gem::Requirement
66
- none: false
67
59
  requirements:
68
60
  - - '='
69
61
  - !ruby/object:Gem::Version
@@ -71,7 +63,6 @@ dependencies:
71
63
  type: :development
72
64
  prerelease: false
73
65
  version_requirements: !ruby/object:Gem::Requirement
74
- none: false
75
66
  requirements:
76
67
  - - '='
77
68
  - !ruby/object:Gem::Version
@@ -79,65 +70,57 @@ dependencies:
79
70
  - !ruby/object:Gem::Dependency
80
71
  name: rdoc
81
72
  requirement: !ruby/object:Gem::Requirement
82
- none: false
83
73
  requirements:
84
- - - ~>
74
+ - - "~>"
85
75
  - !ruby/object:Gem::Version
86
76
  version: '3.12'
87
77
  type: :development
88
78
  prerelease: false
89
79
  version_requirements: !ruby/object:Gem::Requirement
90
- none: false
91
80
  requirements:
92
- - - ~>
81
+ - - "~>"
93
82
  - !ruby/object:Gem::Version
94
83
  version: '3.12'
95
84
  - !ruby/object:Gem::Dependency
96
85
  name: bundler
97
86
  requirement: !ruby/object:Gem::Requirement
98
- none: false
99
87
  requirements:
100
- - - ! '>'
88
+ - - ">"
101
89
  - !ruby/object:Gem::Version
102
90
  version: 1.0.0
103
91
  type: :development
104
92
  prerelease: false
105
93
  version_requirements: !ruby/object:Gem::Requirement
106
- none: false
107
94
  requirements:
108
- - - ! '>'
95
+ - - ">"
109
96
  - !ruby/object:Gem::Version
110
97
  version: 1.0.0
111
98
  - !ruby/object:Gem::Dependency
112
99
  name: jeweler
113
100
  requirement: !ruby/object:Gem::Requirement
114
- none: false
115
101
  requirements:
116
- - - ! '>='
102
+ - - ">="
117
103
  - !ruby/object:Gem::Version
118
104
  version: 1.8.4
119
105
  type: :development
120
106
  prerelease: false
121
107
  version_requirements: !ruby/object:Gem::Requirement
122
- none: false
123
108
  requirements:
124
- - - ! '>='
109
+ - - ">="
125
110
  - !ruby/object:Gem::Version
126
111
  version: 1.8.4
127
112
  - !ruby/object:Gem::Dependency
128
113
  name: minitest
129
114
  requirement: !ruby/object:Gem::Requirement
130
- none: false
131
115
  requirements:
132
- - - ~>
116
+ - - "~>"
133
117
  - !ruby/object:Gem::Version
134
118
  version: '4'
135
119
  type: :development
136
120
  prerelease: false
137
121
  version_requirements: !ruby/object:Gem::Requirement
138
- none: false
139
122
  requirements:
140
- - - ~>
123
+ - - "~>"
141
124
  - !ruby/object:Gem::Version
142
125
  version: '4'
143
126
  description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
@@ -153,7 +136,7 @@ extra_rdoc_files:
153
136
  - README.md
154
137
  - README.rdoc
155
138
  files:
156
- - .document
139
+ - ".document"
157
140
  - Gemfile
158
141
  - LICENSE.txt
159
142
  - README.md
@@ -210,26 +193,25 @@ files:
210
193
  homepage: http://gs2crmod.sourceforge.net
211
194
  licenses:
212
195
  - GSLv3
196
+ metadata: {}
213
197
  post_install_message:
214
198
  rdoc_options: []
215
199
  require_paths:
216
200
  - lib
217
201
  required_ruby_version: !ruby/object:Gem::Requirement
218
- none: false
219
202
  requirements:
220
- - - ! '>='
203
+ - - ">="
221
204
  - !ruby/object:Gem::Version
222
205
  version: 1.9.1
223
206
  required_rubygems_version: !ruby/object:Gem::Requirement
224
- none: false
225
207
  requirements:
226
- - - ! '>='
208
+ - - ">="
227
209
  - !ruby/object:Gem::Version
228
210
  version: '0'
229
211
  requirements: []
230
212
  rubyforge_project:
231
- rubygems_version: 1.8.23
213
+ rubygems_version: 2.6.8
232
214
  signing_key:
233
- specification_version: 3
215
+ specification_version: 4
234
216
  summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
235
217
  test_files: []