genecrmod 0.1.6 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 9ab1ac6f44e2a2d2d050cf1ba0be1aaca50fe84e
+  metadata.gz: 5fdad6ba5f5786ffe8c504ccf813636d9860c611
+  data.tar.gz: a56f41d321bc965adc3505062e380750675ea475
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+  data.tar.gz: def19cf656f3291b7ee2ce5f7b3de4425e3a9217e5698baf4fdc7d527228de77e25c8ea088198a8b04c3dcf9a451cdd8bd6a2c40935192317c93c78fc775d642

data/Gemfile

@@ -3,6 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
    gem "coderunner", ">= 0.14.2"
+   gem "hdf5"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/Rakefile

@@ -20,6 +20,7 @@ Jeweler::Tasks.new do |gem|
   gem.summary = %Q{A module which allows the GENE gyrokinetic code to be run using the CodeRunner framework. }
   gem.description = %Q{A module which allows the GENE gyrokinetic code to be run using the CodeRunner framework. }
   gem.email = "edmundhighcock@users.sourceforge.net"
+	gem.files.exclude 'test/**/*'
   gem.authors = ["Edmund Highcock"]
   # dependencies defined in Gemfile
 end

data/VERSION

@@ -1 +1 @@
-0.1.6
+0.2.0

data/genecrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: genecrmod 0.1.6 ruby lib
+# stub: genecrmod 0.2.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "genecrmod"
-  s.version = "0.1.6"
+  s.version = "0.2.0"
 
   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 = "2014-07-22"
+  s.date = "2014-07-23"
   s.description = "A module which allows the GENE gyrokinetic code to be run using the CodeRunner framework. "
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [
@@ -27,12 +27,13 @@ Gem::Specification.new do |s|
     "VERSION",
     "genecrmod.gemspec",
     "lib/genecrmod.rb",
+    "lib/genecrmod/check_parameters.rb",
     "lib/genecrmod/gene.rb",
+    "lib/genecrmod/hdf5.rb",
     "lib/genecrmod/namelists.rb",
     "sync_variables/helper.rb",
     "sync_variables/sync_variables.rb",
-    "test/helper.rb",
-    "test/test_genecrmod.rb"
+    "test/linear_run/.CODE_RUNNER_TEMP_RUN_LIST_CACHE"
   ]
   s.homepage = "http://github.com/edmundhighcock/genecrmod"
   s.licenses = ["GPLv3"]
@@ -44,6 +45,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_runtime_dependency(%q<hdf5>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["~> 1.0"])
@@ -52,6 +54,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<minitest>, ["~> 4"])
     else
       s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_dependency(%q<hdf5>, [">= 0"])
       s.add_dependency(%q<shoulda>, ["= 3.0.1"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["~> 1.0"])
@@ -61,6 +64,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+    s.add_dependency(%q<hdf5>, [">= 0"])
     s.add_dependency(%q<shoulda>, ["= 3.0.1"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["~> 1.0"])

data/lib/genecrmod/check_parameters.rb

@@ -0,0 +1,89 @@
+
+class CodeRunner::Gene
+      def run_namelist_tests(namelist, hash, enum = nil)
+        ext = enum ? "_#{enum}" : ""
+        hash[:must_pass].each do |tst|
+          error(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
+        end if hash[:must_pass]
+        hash[:should_pass].each do |tst|
+          warning(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
+        end if hash[:should_pass]
+        hash[:variables].each do |var, var_hash|
+          #gs2_var = (var_hash[:gs2_name] or var)
+          cr_var = var+ext.to_sym 
+          value = send(cr_var)
+          if value.kind_of? Array
+            value.each{|v| test_variable(namelist, var, var_hash, ext, v)}
+          else
+            test_variable(namelist, var, var_hash, ext, value)
+          end
+        end
+      end
+    def check_parameters
+      rcp.namelists.each do |namelist, hash|
+        next if hash[:should_include].kind_of? String and not eval(hash[:should_include])
+        if en = hash[:enumerator]
+          #ep 'en', en, namelist
+          next unless send(en[:name])
+          send(en[:name]).times do |i|
+            run_namelist_tests(namelist, hash, i+1)
+          end
+        else
+          run_namelist_tests(namelist, hash)
+        end
+      end
+      warning("Very little analysis will be possible without write_h5 = '.true.'") if not (@write_h5 and @write_h5.fortran_true?)
+    end
+def test_failed(namelist, var, gs2_var, tst)
+	return  <<EOF
+
+---------------------------
+	Test Failed
+---------------------------
+
+Namelist: #{namelist}	
+Variable: #{var}
+GS2 Name: #{gs2_var}
+Value: #{send(var)}
+Test: #{tst[:test]}
+Explanation: #{tst[:explanation]}
+
+---------------------------
+EOF
+
+end
+
+
+def namelist_test_failed(namelist, tst)
+	return  <<EOF
+
+---------------------------
+	Test Failed
+---------------------------
+
+Namelist: #{namelist}	
+Test: #{tst[:test]}
+Explanation: #{tst[:explanation]}
+
+---------------------------
+EOF
+
+end
+def test_variable(namelist, var, var_hash, ext, value)
+		gs2_var = (var_hash[:gs2_name] or var)
+		cr_var = var+ext.to_sym 
+		if value and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
+			var_hash[:must_pass].each do |tst|
+				error(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
+			end if var_hash[:must_pass]
+			var_hash[:should_pass].each do |tst|
+				warning(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
+			end if var_hash[:should_pass]
+			if (var_hash[:allowed_values] or var_hash[:text_options])
+				tst = {test: "#{(var_hash[:allowed_values] or var_hash[:text_options]).inspect}.include? self", explanation: "The variable must have one of these values"}
+				error(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
+			end
+
+		end
+end
+end

data/lib/genecrmod/gene.rb

@@ -13,6 +13,9 @@ class CodeRunner
     # Where this file is
     @code_module_folder =  File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
 
+    require @code_module_folder + '/hdf5.rb'
+    require @code_module_folder + '/check_parameters.rb'
+
     # Use the Run::FortranNamelist tools to process the variable database
     setup_namelists(@code_module_folder)
 
@@ -156,8 +159,6 @@ class CodeRunner
       text
     end
 
-    def check_parameters
-    end
 
 
 
@@ -204,7 +205,7 @@ class CodeRunner
     end
 
     def get_status
-			if @running 
+			if @running
         if @status != :Queueing
           get_completed_timesteps
           if completed_timesteps == 0
@@ -228,7 +229,11 @@ class CodeRunner
     end
 		def get_completed_timesteps
 			Dir.chdir(@directory) do
-        @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat 2>/dev/null].split("\n").size
+        if FileTest.exist?('nrg.dat.h5')
+          @completed_timesteps = get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').shape[0]
+        else
+          @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat 2>/dev/null].split("\n").size
+        end
 			end
 		end
 
@@ -282,7 +287,11 @@ EOF1
 
     def get_growth_rates
       Dir.chdir(@directory) do
-        if FileTest.exist?('omega.dat')
+        if FileTest.exist?(ofile = 'omega.dat.h5')
+          @kyvals = get_h5_narray_all(ofile, '/ky').to_gslv
+          @growth_rates = get_h5_narray_all(ofile, '/gamma').to_gslv
+          @frequencies = get_h5_narray_all(ofile, '/omega').to_gslv
+        elsif FileTest.exist?('omega.dat')
           @kyvals, @growth_rates, @frequencies = GSL::Vector.filescan('omega.dat')
         else
           @kyvals, @growth_rates, @frequencies = [[]] * 3

data/lib/genecrmod/hdf5.rb

@@ -0,0 +1,9 @@
+require 'hdf5'
+class CodeRunner::Gene
+  def get_h5_narray_all(file, dataset)
+    Dir.chdir(@directory) do
+      file = Hdf5::H5File.new(file)
+      return file.dataset(dataset).narray_all
+    end
+  end
+end

data/lib/genecrmod/namelists.rb

@@ -461,18 +461,20 @@
        :help=>nil,
        :code_name=>:kymin,
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String},
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :lv=>
       {:should_include=>"true",
        :description=>nil,
        :help=>nil,
        :code_name=>:lv,
        :must_pass=>
-        [{:test=>"kind_of? Integer",
-          :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :lw=>
       {:should_include=>"true",
        :description=>nil,
@@ -537,9 +539,10 @@
        :help=>nil,
        :code_name=>:x0,
        :must_pass=>
-        [{:test=>"kind_of? Integer",
-          :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :mu_grid_type=>
       {:should_include=>"true",
        :description=>nil,
@@ -618,10 +621,9 @@
        :help=>nil,
        :code_name=>:comp_type,
        :must_pass=>
-        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
-          :explanation=>
-           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
-       :type=>:Fortran_Bool},
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String},
      :perf_vec=>
       {:should_include=>"true",
        :description=>nil,
@@ -3157,9 +3159,10 @@
        :help=>nil,
        :code_name=>:bref,
        :must_pass=>
-        [{:test=>"kind_of? Integer",
-          :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :mref=>
       {:should_include=>"true",
        :description=>nil,

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: genecrmod
 version: !ruby/object:Gem::Version
-  version: 0.1.6
+  version: 0.2.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-22 00:00:00.000000000 Z
+date: 2014-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -24,6 +24,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.14.2
+- !ruby/object:Gem::Dependency
+  name: hdf5
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -125,12 +139,13 @@ files:
 - VERSION
 - genecrmod.gemspec
 - lib/genecrmod.rb
+- lib/genecrmod/check_parameters.rb
 - lib/genecrmod/gene.rb
+- lib/genecrmod/hdf5.rb
 - lib/genecrmod/namelists.rb
 - sync_variables/helper.rb
 - sync_variables/sync_variables.rb
-- test/helper.rb
-- test/test_genecrmod.rb
+- test/linear_run/.CODE_RUNNER_TEMP_RUN_LIST_CACHE
 homepage: http://github.com/edmundhighcock/genecrmod
 licenses:
 - GPLv3

data/test/helper.rb

@@ -1,34 +0,0 @@
-require 'simplecov'
-
-module SimpleCov::Configuration
-  def clean_filters
-    @filters = []
-  end
-end
-
-SimpleCov.configure do
-  clean_filters
-  load_adapter 'test_frameworks'
-end
-
-ENV["COVERAGE"] && SimpleCov.start do
-  add_filter "/.rvm/"
-end
-require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'test/unit'
-require 'shoulda'
-
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'genecrmod'
-
-class Test::Unit::TestCase
-end

data/test/test_genecrmod.rb

@@ -1,7 +0,0 @@
-require 'helper'
-
-class TestGenecrmod < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
-  end
-end