gs2crmod 0.11.28 → 0.11.29
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- checksums.yaml +7 -0
- data/VERSION +1 -1
- data/gs2crmod.gemspec +7 -5
- data/lib/gs2crmod/gs2.rb +19 -19
- data/test/test_gs2crmod.rb +5 -1
- metadata +57 -38
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
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1
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+
---
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+
SHA1:
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+
metadata.gz: 9fc845a7af975cc8918d33678677d6a9daf3b3fe
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4
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+
data.tar.gz: 5911a0644a0aae45ee429a1f9b3370b5692629b7
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+
SHA512:
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6
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+
metadata.gz: 9942d199a0ad3c657e0e5b5b80e4564a86aa0b85c3b13e0fe47475602027796ec2bbb5c6dcc74d30238e8d874a19e372e17e971c76e88fbec55ba68ba1f73f93
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7
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+
data.tar.gz: 1d16ca5efe84d2cc3fa3b9f4da55201416f70a80ab428d94ad13554bbca2234084ad6fcc2f6eb44626553ce232fdbf365e50311527fea92ae0d13058a8e3ad58
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
|
-
0.11.
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1
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+
0.11.29
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data/gs2crmod.gemspec
CHANGED
@@ -2,14 +2,17 @@
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|
2
2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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4
4
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# -*- encoding: utf-8 -*-
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5
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+
# stub: gs2crmod 0.11.29 ruby lib
|
6
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+
# stub: ext/extconf.rb
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5
7
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6
8
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Gem::Specification.new do |s|
|
7
9
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s.name = "gs2crmod"
|
8
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-
s.version = "0.11.
|
10
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+
s.version = "0.11.29"
|
9
11
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10
12
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
13
|
+
s.require_paths = ["lib"]
|
11
14
|
s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
|
12
|
-
s.date = "2014-03-
|
15
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+
s.date = "2014-03-18"
|
13
16
|
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."
|
14
17
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s.email = "edmundhighcock@sourceforge.net"
|
15
18
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s.extensions = ["ext/extconf.rb"]
|
@@ -82,13 +85,12 @@ Gem::Specification.new do |s|
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|
82
85
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]
|
83
86
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s.homepage = "http://gs2crmod.sourceforge.net"
|
84
87
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s.licenses = ["GSLv3"]
|
85
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-
s.require_paths = ["lib"]
|
86
88
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s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
|
87
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-
s.rubygems_version = "
|
89
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+
s.rubygems_version = "2.2.1"
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88
90
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s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
|
89
91
|
|
90
92
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if s.respond_to? :specification_version then
|
91
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-
s.specification_version =
|
93
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+
s.specification_version = 4
|
92
94
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|
93
95
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if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
|
94
96
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s.add_runtime_dependency(%q<coderunner>, [">= 0.14.10"])
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data/lib/gs2crmod/gs2.rb
CHANGED
@@ -524,7 +524,7 @@ def restart(new_run)
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524
524
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#(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
|
525
525
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new_run.is_a_restart = true
|
526
526
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new_run.ginit_option = "many"
|
527
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-
new_run.delt_option = "
|
527
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+
new_run.delt_option = "check_restart"
|
528
528
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#if Dir.entries(@directory).include? "nc"
|
529
529
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#old_restart_run_name = (@restart_run_name or Dir.entries(@directory + '/nc').grep(/\.nc/)[0].sub(/\.nc\.\d+$/, ''))
|
530
530
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#new_run.restart_file = File.expand_path("#@directory/nc/#{old_restart_run_name}.nc")
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@@ -542,6 +542,23 @@ def restart(new_run)
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|
542
542
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new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash
|
543
543
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new_run.naming_pars.delete(:restart_id)
|
544
544
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new_run.generate_run_name
|
545
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+
eputs 'Copying Restart files', ''
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546
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+
FileUtils.makedirs('nc')
|
547
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+
#old_dir = File.dirname(@restart_file)
|
548
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+
new_run.restart_file = "#@run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
|
549
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+
new_run.restart_dir = "nc"
|
550
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+
#files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
|
551
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+
#files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
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552
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+
files = list_of_restart_files.map do |file|
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553
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@directory + "/" + file
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554
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+
end
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555
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+
files.each_with_index do |file , index|
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556
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+
eputs "\033[2A" # Terminal jargon - go back one line
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557
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+
eputs "#{index+1} out of #{files.size}"
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558
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+
num = file.scan(/(?:\.\d+|_ene)$/)[0]
|
559
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+
#FileUtils.cp("#{old_dir}/#{file}", "nc/#@restart_file#{num}")
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560
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+
FileUtils.cp(file, new_run.directory + "/nc/#@restart_file#{num}")
|
561
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+
end
|
545
562
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#@runner.submit(new_run)
|
546
563
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new_run
|
547
564
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end
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@@ -778,25 +795,8 @@ end
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778
795
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def generate_input_file(&block)
|
779
796
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raise CRFatal("No Input Module File Given or Module Corrupted") unless methods.include? (:input_file_text)
|
780
797
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run_namelist_backwards_compatibility
|
781
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-
if @restart_id
|
798
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+
if @restart_id and not @is_a_restart # The second test checks that the restart function has not been called manually earlier (e.g. in Trinity)
|
782
799
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@runner.run_list[@restart_id].restart(self)
|
783
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-
eputs 'Copying Restart files', ''
|
784
|
-
FileUtils.makedirs('nc')
|
785
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-
#old_dir = File.dirname(@restart_file)
|
786
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-
@restart_file = "#@restart_run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
|
787
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-
@restart_dir = "nc"
|
788
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-
#files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
|
789
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-
#files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
|
790
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-
files = @runner.run_list[@restart_id].list_of_restart_files.map do |file|
|
791
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-
@runner.run_list[@restart_id].directory + "/" + file
|
792
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-
end
|
793
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-
files.each_with_index do |file , index|
|
794
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-
eputs "\033[2A" # Terminal jargon - go back one line
|
795
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-
eputs "#{index+1} out of #{files.size}"
|
796
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-
num = file.scan(/(?:\.\d+|_ene)$/)[0]
|
797
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-
#FileUtils.cp("#{old_dir}/#{file}", "nc/#@restart_file#{num}")
|
798
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-
FileUtils.cp(file, "nc/#@restart_file#{num}")
|
799
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-
end
|
800
800
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elsif @save_for_restart and @save_for_restart.fortran_true?
|
801
801
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@restart_dir = "nc"
|
802
802
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#if CODE_OPTIONS[:gs2] and CODE_OPTIONS[:gs2][:list]
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data/test/test_gs2crmod.rb
CHANGED
@@ -36,7 +36,11 @@ if ENV['GS2_EXEC']
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36
36
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FileUtils.rm_r(tfolder)
|
37
37
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end
|
38
38
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def test_submission
|
39
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-
CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '
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39
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+
CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '2', Y: tfolder, p: '{write_moments: ".true.", write_line: ".true.", save_for_restart: ".true.", nsave: 40}')
|
40
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+
CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '2', Y: tfolder, p: '{restart_id: 1}')
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41
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+
runs = CodeRunner.fetch_runner(Y: tfolder).run_list
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42
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+
assert_equal(50, runs[1].completed_timesteps)
|
43
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+
assert_equal(runs[1].gsl_vector('phi2tot_over_time')[-1].round(4), runs[2].gsl_vector('phi2tot_over_time')[0].round(4))
|
40
44
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CodeRunner.status(Y: tfolder)
|
41
45
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end
|
42
46
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end
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metadata
CHANGED
@@ -1,8 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: gs2crmod
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.11.
|
5
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-
prerelease:
|
4
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+
version: 0.11.29
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5
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platform: ruby
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7
6
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authors:
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8
7
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- Edmund Highcock
|
@@ -10,85 +9,106 @@ authors:
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10
9
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autorequire:
|
11
10
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bindir: bin
|
12
11
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cert_chain: []
|
13
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-
date: 2014-03-
|
12
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+
date: 2014-03-18 00:00:00.000000000 Z
|
14
13
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dependencies:
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15
14
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- !ruby/object:Gem::Dependency
|
16
15
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name: coderunner
|
17
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-
requirement:
|
18
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-
none: false
|
16
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+
requirement: !ruby/object:Gem::Requirement
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19
17
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requirements:
|
20
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-
- -
|
18
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+
- - ">="
|
21
19
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- !ruby/object:Gem::Version
|
22
20
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version: 0.14.10
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23
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type: :runtime
|
24
22
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prerelease: false
|
25
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-
version_requirements:
|
23
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+
version_requirements: !ruby/object:Gem::Requirement
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+
requirements:
|
25
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+
- - ">="
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26
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+
- !ruby/object:Gem::Version
|
27
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+
version: 0.14.10
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26
28
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- !ruby/object:Gem::Dependency
|
27
29
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name: rubyhacks
|
28
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-
requirement:
|
29
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-
none: false
|
30
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+
requirement: !ruby/object:Gem::Requirement
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30
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requirements:
|
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-
- -
|
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+
- - ">="
|
32
33
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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
|
36
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-
version_requirements:
|
37
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+
version_requirements: !ruby/object:Gem::Requirement
|
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+
requirements:
|
39
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+
- - ">="
|
40
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+
- !ruby/object:Gem::Version
|
41
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+
version: 0.1.2
|
37
42
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- !ruby/object:Gem::Dependency
|
38
43
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name: ruby-netcdf-updated
|
39
|
-
requirement:
|
40
|
-
none: false
|
44
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+
requirement: !ruby/object:Gem::Requirement
|
41
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requirements:
|
42
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-
- -
|
46
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+
- - ">="
|
43
47
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- !ruby/object:Gem::Version
|
44
48
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version: 0.6.6.1
|
45
49
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type: :runtime
|
46
50
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prerelease: false
|
47
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-
version_requirements:
|
51
|
+
version_requirements: !ruby/object:Gem::Requirement
|
52
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+
requirements:
|
53
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+
- - ">="
|
54
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+
- !ruby/object:Gem::Version
|
55
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+
version: 0.6.6.1
|
48
56
|
- !ruby/object:Gem::Dependency
|
49
57
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name: shoulda
|
50
|
-
requirement:
|
51
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-
none: false
|
58
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+
requirement: !ruby/object:Gem::Requirement
|
52
59
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requirements:
|
53
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-
- -
|
60
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+
- - ">="
|
54
61
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- !ruby/object:Gem::Version
|
55
62
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version: '0'
|
56
63
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type: :development
|
57
64
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prerelease: false
|
58
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-
version_requirements:
|
65
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+
version_requirements: !ruby/object:Gem::Requirement
|
66
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+
requirements:
|
67
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+
- - ">="
|
68
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+
- !ruby/object:Gem::Version
|
69
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+
version: '0'
|
59
70
|
- !ruby/object:Gem::Dependency
|
60
71
|
name: rdoc
|
61
|
-
requirement:
|
62
|
-
none: false
|
72
|
+
requirement: !ruby/object:Gem::Requirement
|
63
73
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requirements:
|
64
|
-
- - ~>
|
74
|
+
- - "~>"
|
65
75
|
- !ruby/object:Gem::Version
|
66
76
|
version: '3.12'
|
67
77
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type: :development
|
68
78
|
prerelease: false
|
69
|
-
version_requirements:
|
79
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+
version_requirements: !ruby/object:Gem::Requirement
|
80
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+
requirements:
|
81
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+
- - "~>"
|
82
|
+
- !ruby/object:Gem::Version
|
83
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+
version: '3.12'
|
70
84
|
- !ruby/object:Gem::Dependency
|
71
85
|
name: bundler
|
72
|
-
requirement:
|
73
|
-
none: false
|
86
|
+
requirement: !ruby/object:Gem::Requirement
|
74
87
|
requirements:
|
75
|
-
- -
|
88
|
+
- - ">"
|
76
89
|
- !ruby/object:Gem::Version
|
77
90
|
version: 1.0.0
|
78
91
|
type: :development
|
79
92
|
prerelease: false
|
80
|
-
version_requirements:
|
93
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+
version_requirements: !ruby/object:Gem::Requirement
|
94
|
+
requirements:
|
95
|
+
- - ">"
|
96
|
+
- !ruby/object:Gem::Version
|
97
|
+
version: 1.0.0
|
81
98
|
- !ruby/object:Gem::Dependency
|
82
99
|
name: jeweler
|
83
|
-
requirement:
|
84
|
-
none: false
|
100
|
+
requirement: !ruby/object:Gem::Requirement
|
85
101
|
requirements:
|
86
|
-
- -
|
102
|
+
- - ">="
|
87
103
|
- !ruby/object:Gem::Version
|
88
104
|
version: 1.8.4
|
89
105
|
type: :development
|
90
106
|
prerelease: false
|
91
|
-
version_requirements:
|
107
|
+
version_requirements: !ruby/object:Gem::Requirement
|
108
|
+
requirements:
|
109
|
+
- - ">="
|
110
|
+
- !ruby/object:Gem::Version
|
111
|
+
version: 1.8.4
|
92
112
|
description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
|
93
113
|
be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
|
94
114
|
running and analysis of large simulations. This module allows GS2 (and its sister
|
@@ -102,7 +122,7 @@ extra_rdoc_files:
|
|
102
122
|
- README.md
|
103
123
|
- README.rdoc
|
104
124
|
files:
|
105
|
-
- .document
|
125
|
+
- ".document"
|
106
126
|
- Gemfile
|
107
127
|
- LICENSE.txt
|
108
128
|
- README.md
|
@@ -165,26 +185,25 @@ files:
|
|
165
185
|
homepage: http://gs2crmod.sourceforge.net
|
166
186
|
licenses:
|
167
187
|
- GSLv3
|
188
|
+
metadata: {}
|
168
189
|
post_install_message:
|
169
190
|
rdoc_options: []
|
170
191
|
require_paths:
|
171
192
|
- lib
|
172
193
|
required_ruby_version: !ruby/object:Gem::Requirement
|
173
|
-
none: false
|
174
194
|
requirements:
|
175
|
-
- -
|
195
|
+
- - ">="
|
176
196
|
- !ruby/object:Gem::Version
|
177
197
|
version: 1.9.1
|
178
198
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
179
|
-
none: false
|
180
199
|
requirements:
|
181
|
-
- -
|
200
|
+
- - ">="
|
182
201
|
- !ruby/object:Gem::Version
|
183
202
|
version: '0'
|
184
203
|
requirements: []
|
185
204
|
rubyforge_project:
|
186
|
-
rubygems_version:
|
205
|
+
rubygems_version: 2.2.1
|
187
206
|
signing_key:
|
188
|
-
specification_version:
|
207
|
+
specification_version: 4
|
189
208
|
summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
|
190
209
|
test_files: []
|