coderunner 0.16.19 → 0.16.20

checksums.yaml

@@ -1,7 +1,7 @@
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-  metadata.gz: 72930ce4dd1fb18fc037992914665d924a285358
-  data.tar.gz: 0b72724ad98ba0948b68415ac92c828fd53c4871
+  metadata.gz: 825e5b87d1a775c0aa8b34d9e27cb7595682d626
+  data.tar.gz: f612840765798803fd028d4f0614c7744792c64b
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+  metadata.gz: 865f31135fd908b570f36bac6c6e51feb8ffba0b0385ae224135f0d9956da9b2f8e20f5b1671e0fbdafc65455f6f5216e7be90119a8d5da2575d0f8cc86f883d
+  data.tar.gz: ba330a49dd1e0fbd6f4998d4cf12469bb5a2b46973bdab7b20f6b162a8b151234600275d56782ab3539c8483dff7e71e1d97d8c5aeda68ed38a977931e92bb42

data/Gemfile

@@ -5,7 +5,7 @@ source "http://rubygems.org"
   gem "graphkit", ">= 0.4.2"
   gem "parallelpipes", ">= 1.0.0"
   gem "rubyhacks", ">= 0.1.4"
-  gem "rb-gsl", ">= 1.12.0"
+  gem "rb-gsl", "> 1.12.0"
   gem "gsl_extras", ">= 0.3.0"
   #gem "ruby-netcdf", ">= 0.6.6"
 	gem "hostmanager", "> 0.1.0"

data/VERSION

@@ -1 +1 @@
-0.16.19
+0.16.20

data/coderunner.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: coderunner 0.16.19 ruby lib
+# stub: coderunner 0.16.20 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.16.19"
+  s.version = "0.16.20"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock"]
-  s.date = "2015-07-21"
+  s.date = "2015-07-28"
   s.description = "CodeRunner is a framework for the automated running and analysis of simulations. It automatically generates any necessary input files, organises the output data and analyses it. Because it is a modular system, it can easily be customised to work with any system and any simulation code. One of its greatest strengths is that it is independent of any one simulation code; thus it can easily plot and compare the data from different codes."
   s.email = "edmundhighcock@sourceforge.net"
   s.executables = ["coderunner", "coderunnerrepo"]
@@ -109,7 +109,7 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<graphkit>, [">= 0.4.2"])
       s.add_runtime_dependency(%q<parallelpipes>, [">= 1.0.0"])
       s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.4"])
-      s.add_runtime_dependency(%q<rb-gsl>, [">= 1.12.0"])
+      s.add_runtime_dependency(%q<rb-gsl>, ["> 1.12.0"])
       s.add_runtime_dependency(%q<gsl_extras>, [">= 0.3.0"])
       s.add_runtime_dependency(%q<hostmanager>, ["> 0.1.0"])
       s.add_runtime_dependency(%q<command-line-flunky>, ["> 0.1.0"])
@@ -122,7 +122,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<graphkit>, [">= 0.4.2"])
       s.add_dependency(%q<parallelpipes>, [">= 1.0.0"])
       s.add_dependency(%q<rubyhacks>, [">= 0.1.4"])
-      s.add_dependency(%q<rb-gsl>, [">= 1.12.0"])
+      s.add_dependency(%q<rb-gsl>, ["> 1.12.0"])
       s.add_dependency(%q<gsl_extras>, [">= 0.3.0"])
       s.add_dependency(%q<hostmanager>, ["> 0.1.0"])
       s.add_dependency(%q<command-line-flunky>, ["> 0.1.0"])
@@ -136,7 +136,7 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<graphkit>, [">= 0.4.2"])
     s.add_dependency(%q<parallelpipes>, [">= 1.0.0"])
     s.add_dependency(%q<rubyhacks>, [">= 0.1.4"])
-    s.add_dependency(%q<rb-gsl>, [">= 1.12.0"])
+    s.add_dependency(%q<rb-gsl>, ["> 1.12.0"])
     s.add_dependency(%q<gsl_extras>, [">= 0.3.0"])
     s.add_dependency(%q<hostmanager>, ["> 0.1.0"])
     s.add_dependency(%q<command-line-flunky>, ["> 0.1.0"])

data/lib/coderunner/fortran_namelist.rb

@@ -776,7 +776,8 @@ def self.use_new_defaults_file(name=ARGV[-2], input_file=ARGV[-1])
 
 	#modlet = rcp.modlet? ? rcp.modlet : nil
 	#executable = rcp.executable? ? rcp.executable : CodeRunner::DEFAULT_RUNNER_OPTIONS
-	CodeRunner.fetch_runner(D: name) #(C: rcp.code, m: rcp.modlet, D: name, CodeRunner)
+	#CodeRunner.fetch_runner(D: name) #(C: rcp.code, m: rcp.modlet, D: name, CodeRunner)
+	CodeRunner.fetch_runner(C: rcp.code, m: (rcp.modlet? ? rcp.modlet : nil), D: name) #CodeRunner)
 end
 
 # The name is self-explanatory: this method takes an input file and generates a CodeRunner defaults file. The first argument is the name of the new defaults file.

data/lib/coderunner/repository.rb

@@ -1,7 +1,11 @@
 require 'git'
 class CodeRunner
   def is_in_repo?(folder=@root_folder)
-    Repository.repo_folder(folder) ?  true : false
+    if ENV['CODE_RUNNER_NO_REPO']
+      return false
+    else
+      Repository.repo_folder(folder) ?  true : false
+    end
   end
   class Run
     # Add CodeRunner files within the run folder to git. If

data/lib/coderunner/system_modules/generic_linux.rb

@@ -14,11 +14,12 @@ def queue_status
 end
 
 def run_command
+  crenv = @code_run_environment ? @code_run_environment + ";" : nil
 	if rcp.uses_mpi
     raise "Number of processors (nprocs) not specified" unless @nprocs
-		return %[time mpirun -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
+		return %[#{crenv} time mpirun -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
 	else
-		return %[#{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
+		return %[#{crenv} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
 	end
 end		
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.16.19
+  version: 0.16.20
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-21 00:00:00.000000000 Z
+date: 2015-07-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -56,14 +56,14 @@ dependencies:
   name: rb-gsl
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.12.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.12.0
 - !ruby/object:Gem::Dependency