trinitycrdriver 0.0.0 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e503fe33b08e9c0fe990649b616e84f6c27e2c17
+  metadata.gz: 49e4039f446adecc1130738a3d689af2a3193c61
+  data.tar.gz: 65142591fe93ea98359f1edf1bd2cdb9043745d3
 SHA512:
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+  metadata.gz: 84b29e1c9e3272fba5a1b4fb5815fc4cfcfec9e8a352b8195d5b0289e2881cfe8d9beaa459083433ace8f63bd8fd38d5aebcfdf922c3bd1dca4052706a4c1353
+  data.tar.gz: ac3d4cf4163d2be4bf1459bf2ef7d8b9d20e478958e0ba82f634704458bfec2cd20e650140ba3acb53d7abd4ef227ae173344d3ef7c550a40b0aaabdc09f4dbe

data/Gemfile

@@ -5,12 +5,17 @@ source "http://rubygems.org"
    gem "text-data-tools", ">= 1.1.3"
 	 gem "gs2crmod", ">=0.11.33"
 	 gem "trinitycrmod", ">= 0.4.7"
+	 gem "ruby-mpi", ">=0.2.0"
+	 gem "cheasecrmod", ">=0.1.0"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", ">= 0"
+  gem "shoulda", " 3.0.1"
   gem "rdoc", "~> 3.12"
   gem "bundler", "> 1.0.0"
-  gem "jeweler", ">= 2.0.0"
+  gem "jeweler", ">= 2.0.1"
+	gem "simplecov", ">=0" 
+	gem "minitest", "~> 4"
+	gem "rake-compiler"
 end

data/Rakefile

@@ -21,6 +21,8 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{A gem to allow coderunner to run the trinity code directly.}
   gem.email = "edmundhighcock@users.sourceforge.net"
   gem.authors = ["Edmund Highcock"]
+	gem.files.exclude 'test/**/*'
+	gem.extensions = %w[ext/trinitycrdriver/extconf.rb]
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new
@@ -49,3 +51,11 @@ Rake::RDocTask.new do |rdoc|
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
 end
+
+NAME = 'trinitycrdriver'
+
+require "rake/extensiontask"
+
+Rake::ExtensionTask.new "trinitycrdriver" do |ext|
+	  ext.lib_dir = "lib/trinitycrdriver"
+end

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.1.0

data/clean.sh

@@ -0,0 +1,9 @@
+rm -rf lib/trinitycrdriver/trinitycrdriver.so
+rm -rf rake_test_opt_chease_defaults.rb
+rm -rf rake_test_opt_defaults.rb
+rm -rf test/chease_opt/.CODE_RUNNER_TEMP_RUN_LIST_CACHE
+rm -rf test/chease_opt/ogyropsi.dat
+rm -rf test/chease_opt/v/
+rm -rf test/chease_opt_chease/.CODE_RUNNER_TEMP_RUN_LIST_CACHE
+rm -rf test/chease_opt_chease/v/
+rm -rf test/trinopt/

data/ext/trinitycrdriver/extconf.rb

@@ -0,0 +1,42 @@
+require 'mkmf'
+
+#Need to link with C GSL libraries to use in C extensions
+#gsl_inc = `gsl-config --cflags`
+
+#$CFLAGS = " -Wall -I../include #{gsl_inc}"
+
+#srcs = Dir.glob("*.c")
+
+#p ['srcs', srcs]
+                                                                                                         
+#$objs = srcs.collect { |f| f.sub(".c", ".o") }                                                           
+RbConfig::CONFIG['CC'] = CONFIG['CC'] = ENV['CC'] || "mpicc"
+RbConfig::CONFIG['CPP'] = CONFIG['CPP'] = ENV['CPP'] || "mpicc -E"
+p 'CONFIG[CC]', CONFIG['CC']
+crgemspec=Gem::Specification.find_by_name('coderunner')
+crconfig = crgemspec.full_gem_path
+$CPPFLAGS = " -I#{File.join(crconfig, 'include')} "+$CPPFLAGS
+p ['CPPFLAGS', $CPPFLAGS]
+raise "Please set the environment variable TRINITY_DIR" unless ENV['TRINITY_DIR']
+$LOCAL_LIBS = " -L#{ENV['TRINITY_DIR']} " + $LOCAL_LIBS
+$LOCAL_LIBS = " -L#{ENV['GS2']} " + $LOCAL_LIBS
+have_library("gfortran")
+have_library("netcdf")
+have_library("netcdff")
+have_library("fftw3")
+have_library("fftw3f")
+have_library("fftw3_mpi")
+have_library("fftw3f_mpi")
+have_library("simpledataio")
+
+#have_library("gs2", "__gs2_main_MOD_gs2spec_from_trin")
+have_library("gs2")
+have_library("trinity")
+
+dir_config('mpi')
+have_header("mpi.h")
+have_library("mpi")
+have_library("mpi_f90")
+have_library("mpi_f77")
+
+create_makefile("trinitycrdriver/trinitycrdriver")  

data/ext/trinitycrdriver/trinitycrdriver.c

@@ -0,0 +1,69 @@
+#include <math.h>
+#include <string.h>
+#include "code_runner_ext.h"
+#include <mpi.h>
+#include <stdbool.h>
+
+/* Taken from the ruby-mpi gem*/
+struct _Comm {
+	  MPI_Comm Comm;
+		bool free;
+};
+
+static VALUE trinitycrdriver_run_trinity(VALUE class, VALUE input_file_name, VALUE mpi_comm){
+	printf("RUNNING TRINITY!!!\n\n");
+
+	struct _Comm *comm;
+	char * input_file_name_c;
+
+	Data_Get_Struct(mpi_comm, struct _Comm, comm);
+	input_file_name_c = StringValueCStr(input_file_name);
+	run_trinity_c(input_file_name_c, comm->Comm);
+
+	/*printf("input file name was %s\n", input_file_name_c);*/
+	/**/
+	/*free(input_file_name_c);*/
+
+	
+
+	return Qnil;
+
+}
+
+void Init_trinitycrdriver()
+{
+	
+	VALUE ctrinity;
+
+	cgraph_kit = Qnil;
+	ccode_runner_gs2 = Qnil;
+	ccode_runner_ext = Qnil;
+	printf("HERE!!!\n\n");
+	ccode_runner =  RGET_CLASS_TOP("CodeRunner");
+	/*VALUE ctrinity =  RGET_CLASS_TOP("CodeRunner");*/
+  ctrinity	= RGET_CLASS(ccode_runner, "Trinity");
+	rb_define_method(ctrinity, "run_trinity", trinitycrdriver_run_trinity, 2);
+		/*rb_define_class_under(ccode_runner, "Trinity",*/
+		/*RGET_CLASS(*/
+		/*RGET_CLASS(ccode_runner, "Run"), */
+		/*"FortranNamelist"*/
+		/*)*/
+		/*);*/
+
+	/*ccode_runner_gs2_gsl_tensor_complexes = rb_define_module_under(ccode_runner_gs2, "GSLComplexTensors");*/
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensor_complexes);*/
+
+	/*ccode_runner_gs2_gsl_tensors = rb_define_module_under(ccode_runner_gs2, "GSLTensors"); */
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensors);*/
+
+	/*cgsl = RGET_CLASS_TOP("GSL");*/
+	/*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
+	/*cgsl_vector_complex = RGET_CLASS(cgsl_vector, "Complex");*/
+
+	/*rb_define_method(ccode_runner_gs2_gsl_tensor_complexes, "field_gsl_tensor_complex_2", gs2crmod_tensor_complexes_field_gsl_tensor_complex_2, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_real_space_gsl_tensor", gs2crmod_tensor_field_gsl_tensor, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_correlation_gsl_tensor", gs2crmod_tensor_field_correlation_gsl_tensor, 1);*/
+
+	/*rb_define_method(ccode_runner_ext, "hello_world", code_runner_ext_hello_world, 0);*/
+}
+

data/lib/trinitycrdriver/optimisation.rb

@@ -0,0 +1,100 @@
+
+class CodeRunner::Trinity::Optimisation
+	include GSL::MultiMin
+	  # optimisation_spec is a hash of {:code_name => {:variable => [initial_guess, dimension_scale_factor]}}
+	  # dimension_scale_factor is just some estimate of the length scale in which the result
+	  # varies significantly
+	# code_name is either trinity or chease (both can be used simultaneously)
+	  attr_reader :optimisation_spec
+		attr_reader :optimisation_variables
+		attr_accessor :trinity_runner
+		attr_accessor :chease_runner
+		def initialize(optimised_quantity, optimisation_spec)
+			#@folder = folder
+			@optimised_quantity = optimised_quantity
+			@optimisation_spec = optimisation_spec
+			@optimisation_variables = optimisation_spec.map{|code, hash| hash.map{|var, pars| [code, var]}}.flatten(1)
+			@optimisation_starts    = optimisation_spec.map{|code, hash| hash.map{|var, pars| pars[0]}}.flatten(1)
+			@optimisation_steps     = optimisation_spec.map{|code, hash| hash.map{|var, pars| pars[1]}}.flatten(1)
+			#@runner = CodeRunner.fetch_runner(
+			#p ['optimisation_variables', @optimisation_variables]
+		end
+		def dimension
+			@optimisation_variables.size
+		end
+		def serial_optimise(optimisation_method, parameters_obj)
+			optimisation_meth = case optimisation_method
+													when :simplex
+														FMinimizer::NMSIMPLEX
+													else 
+														raise "Unknown optimisation_method"
+													end
+			opt = FMinimizer.alloc(optimisation_meth, @optimisation_variables.size)
+			func = Proc.new{|v, optimiser| optimiser.func(v)}
+			gsl_func = Function.alloc(func, dimension)
+			gsl_func.set_params(self)
+			opt.set(gsl_func, @optimisation_starts.to_gslv, @optimisation_steps.to_gslv)
+			parameters_obj.nit.times do |i|
+				opt.iterate
+				p ['status', opt.x, opt.minimum, i, parameters_obj.nit]
+			end
+
+			p 'heellllllo'
+			MPI.Finalize
+			
+		end
+		def func(v)
+			pars = {}
+			pars[:chease] = {}
+			pars[:trinity] = {}
+			for i in 0...v.size
+				code, varname = @optimisation_variables[i]
+				val = v[i]
+				pars[code][varname] = val
+			end
+			if not @first_run_done
+				pars[:trinity][:ntstep] = 300
+				#@first_run_done = true
+			#else
+				#pars[:trinity][:ntstep] = 100
+			end
+
+			pars[:chease][:ap] = [0.3,0.5,0.4,0.0,0.4,0.0,0.0]
+      pars[:chease][:at] = [0.16,1.0,1.0,-1.1,-1.1]
+
+
+			trinity_runner.run_class.instance_variable_set(:@mpi_communicator, MPI::Comm::WORLD)
+		  if false and trinity_runner.run_list.size > 0
+			else
+				crun = chease_runner.run_class.new(chease_runner)
+				crun.update_submission_parameters(pars[:chease].inspect)
+				if chease_runner.run_list.size > 0
+					crun.restart_id = @cid
+				end
+				chease_runner.submit(crun)
+				crun = chease_runner.run_list[@cid = chease_runner.max_id]
+				crun.recheck
+				chease_runner.update
+				#chease_runner.print_out(0)
+				FileUtils.cp(crun.directory + '/ogyropsi.dat', trinity_runner.root_folder + '/.')
+
+				run = trinity_runner.run_class.new(trinity_runner)
+				run.update_submission_parameters(pars[:trinity].inspect)
+				#trinity_runner.run_class.instance_variable_set(:@delay_execution, true)
+				if trinity_runner.run_list.size > 0
+					#run.restart_id = @id
+				end
+				trinity_runner.submit(run)
+				run = trinity_runner.run_list[@id = trinity_runner.max_id]
+				run.recheck
+				trinity_runner.update
+				#trinity_runner.print_out(0)
+				result =  run.send(@optimised_quantity)
+				p ['result is ', result]
+				return -result
+			end
+
+
+		  #v.square.sum
+		end
+end

data/lib/trinitycrdriver.rb

@@ -0,0 +1,35 @@
+
+require 'trinitycrdriver/trinitycrdriver'
+require 'mpi'
+
+class CodeRunner::Trinity
+	# We overwrite the system module's implemenation of this command.
+	# Instead of running trinity via a bash command or a batch script,
+	# we run it directly via its API.
+	@delay_execution = false
+	def execute
+		if rcp.delay_execution
+			return
+		else
+			execute_actual
+		end
+	end
+	def execute_actual
+		Dir.chdir(@directory){
+			if rcp.mpi_communicator?
+				start_mpi = false
+				mpicomm = rcp.mpi_communicator
+			else
+				start_mpi = true
+				MPI.Init
+				mpicomm = MPI::Comm::WORLD
+				puts ["INITIALISED MPI", mpicomm.size ]
+			end
+			run_trinity(@run_name + ".trin", mpicomm)
+			if start_mpi
+				MPI.Finalize
+			end
+
+		}
+	end
+end

data/lib/trinoptcrmod/trinopt.rb

@@ -0,0 +1,174 @@
+
+class CodeRunner
+	#  This is a customised subclass of the CodeRunner::Run  class  which is designed to run the CodeRunner/Trinity optimisation framework
+	#
+	class Trinopt < Run
+
+		# Where this file is
+		@code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+
+
+		################################################
+		# Quantities that are read or determined by CodeRunner
+		# after the simulation has ended
+		###################################################
+
+		@results = [
+		]
+
+		@code_long="CodeRunner/Trinity Optimisation Framework"
+
+		@run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_steps, :percent_complete]
+
+    @variables = [
+      :chease_exec,
+      :output,
+      :search,
+      :trinity_defaults,
+      :gs_defaults,
+      :nit
+    ]
+
+		@uses_mpi = true
+
+		@modlet_required = false
+		
+		@naming_pars = []
+
+		#  Any folders which are a number will contain the results from flux simulations.
+		@excluded_sub_folders = ['trinity_runs', 'chease_runs', 'ecom_runs']
+
+		#  A hook which gets called when printing the standard run information to the screen using the status command.
+		def print_out_line
+			#p ['id', id, 'ctd', ctd]
+			#p rcp.results.zip(rcp.results.map{|r| send(r)})
+			name = @run_name
+			name += " (res: #@restart_id)" if @restart_id
+			beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%")
+			if ctd
+				#beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
+			end
+			beginning += "  ---#{@comment}" if @comment
+			beginning
+		end
+
+
+
+		# Modify new_run so that it becomes a restart of self. Adusts
+		# all the parameters of the new run to be equal to the parameters
+		# of the run that calls this function, and sets up its run name
+		# correctly
+		def restart(new_run)
+			#new_run = self.dup
+			(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
+			new_run.is_a_restart = true
+			new_run.restart_id = @id
+			new_run.restart_run_name = @run_name
+			new_run.nopt = -1
+			new_run.run_name = nil
+			new_run.naming_pars = @naming_pars
+			new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash 
+			new_run.naming_pars.delete(:restart_id)
+			new_run.generate_run_name
+      raise "This function is not complete"
+		end	
+		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
+		def generate_input_file
+				check_parameters
+				if @restart_id
+					@runner.run_list[@restart_id].restart(self)
+				end
+        File.open("driver_script.rb", "w"){|f| f.puts optimisation_script}
+        FileUtils.makedirs('trinity_runs')
+        FileUtils.makedirs('gs_runs')
+        FileUtils.ln_s("../../#{@trinity_defaults}_defaults.rb", "trinity_runs")
+        FileUtils.ln_s("../../#{@gs_defaults}_defaults.rb", "gs_runs")
+        save
+		end
+
+    def optimisation_script
+      return <<EOF
+      require 'coderunner'
+      CodeRunner.setup_run_class('trinity')
+      CodeRunner.setup_run_class('trinopt')
+      require 'trinitycrdriver'
+      require 'trinitycrdriver/optimisation'
+      CodeRunner::Trinopt.run_optimisation(#@id)
+EOF
+    end
+
+		def check_parameters
+		end
+
+
+    def self.run_optimisation(id = ARGV[-1])
+		  MPI.Init
+      @runner = CodeRunner.fetch_runner(Y: '../../', U: true)
+      #@run = @runner.run_list[id.to_i]
+      @run = self.load(Dir.pwd, @runner)
+      #raise "Can't find run with id #{id}; #{@runner.run_list.keys}" unless @run
+      opt = CodeRunner::Trinity::Optimisation.new(
+        @run.output, @run.search
+      )
+      @trinity_runner = CodeRunner.fetch_runner(Y: 'trinity_runs', X: '/dev/null', C: 'trinity', D: @run.trinity_defaults)
+      @trinity_runner.nprocs = MPI::Comm::WORLD.size
+      @chease_runner = CodeRunner.fetch_runner(Y: 'gs_runs', X: @run.chease_exec, C: 'chease', D: @run.gs_defaults)
+      @chease_runner.nprocs = '1'
+      #Dir.chdir('trinity_runs'){@trinity_runner.run_class.use_new_defaults_file('rake_test_opt', 'ifspppl_chease_input.trin')}
+      #Dir.chdir(tfolderchease){@chease_runner.run_class.use_new_defaults_file('rake_test_opt_chease', 'chease_example.in')}
+      #assert_equal([:trinity, :powerin], opt.optimisation_variables[0])
+      opt.trinity_runner = @trinity_runner
+      opt.chease_runner = @chease_runner
+      opt.serial_optimise(:simplex, @run)
+      MPI.Finalize
+    end
+
+
+
+    def vim_output
+      system "vim -Ro #{output_file} #{error_file}"
+    end
+    alias :vo :vim_output
+
+
+		# Parameters which follow the Trinity executable, in this case just the input file.
+		def parameter_string
+			" driver_script.rb #@id"
+		end
+
+		def parameter_transition
+		end
+
+		def generate_component_runs
+			#puts "HERE"
+		end
+
+		
+
+		@source_code_subfolders = []
+
+		# This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).
+		#
+		def process_directory_code_specific
+			get_status
+			#p ['id is', id, 'ctd is ', ctd]
+			#if ctd
+				#get_global_results 
+			#end
+			#p ['fusionQ is ', fusionQ]
+			#@percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
+      @percent_complete = 0.0
+		end
+
+		def get_status
+			return :Unknown
+		end
+
+
+		def input_file_extension
+			''
+		end
+
+	end
+end
+

data/lib/trinoptcrmod.rb

@@ -0,0 +1 @@
+require 'trinoptcrmod/trinopt'

data/trinitycrdriver.gemspec

@@ -0,0 +1,92 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: trinitycrdriver 0.1.0 ruby lib
+# stub: ext/trinitycrdriver/extconf.rb
+
+Gem::Specification.new do |s|
+  s.name = "trinitycrdriver"
+  s.version = "0.1.0"
+
+  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 = "2015-07-23"
+  s.description = "A gem to allow coderunner to run the trinity code directly."
+  s.email = "edmundhighcock@users.sourceforge.net"
+  s.extensions = ["ext/trinitycrdriver/extconf.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "clean.sh",
+    "ext/trinitycrdriver/extconf.rb",
+    "ext/trinitycrdriver/trinitycrdriver.c",
+    "lib/trinitycrdriver.rb",
+    "lib/trinitycrdriver/optimisation.rb",
+    "lib/trinoptcrmod.rb",
+    "lib/trinoptcrmod/trinopt.rb",
+    "trinitycrdriver.gemspec"
+  ]
+  s.homepage = "http://github.com/edmundhighcock/trinitycrdriver"
+  s.licenses = ["GPLv3"]
+  s.rubygems_version = "2.4.8"
+  s.summary = "A gem to allow coderunner to run the trinity code directly via a C interface."
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    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<text-data-tools>, [">= 1.1.3"])
+      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.33"])
+      s.add_runtime_dependency(%q<trinitycrmod>, [">= 0.4.7"])
+      s.add_runtime_dependency(%q<ruby-mpi>, [">= 0.2.0"])
+      s.add_runtime_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+      s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, [">= 2.0.1"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<minitest>, ["~> 4"])
+      s.add_development_dependency(%q<rake-compiler>, [">= 0"])
+    else
+      s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
+      s.add_dependency(%q<gs2crmod>, [">= 0.11.33"])
+      s.add_dependency(%q<trinitycrmod>, [">= 0.4.7"])
+      s.add_dependency(%q<ruby-mpi>, [">= 0.2.0"])
+      s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+      s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>, [">= 2.0.1"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<minitest>, ["~> 4"])
+      s.add_dependency(%q<rake-compiler>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+    s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
+    s.add_dependency(%q<gs2crmod>, [">= 0.11.33"])
+    s.add_dependency(%q<trinitycrmod>, [">= 0.4.7"])
+    s.add_dependency(%q<ruby-mpi>, [">= 0.2.0"])
+    s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+    s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>, [">= 2.0.1"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<minitest>, ["~> 4"])
+    s.add_dependency(%q<rake-compiler>, [">= 0"])
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrdriver
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.1.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-23 00:00:00.000000000 Z
+date: 2015-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -67,19 +67,47 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.4.7
 - !ruby/object:Gem::Dependency
-  name: shoulda
+  name: ruby-mpi
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
+        version: 0.2.0
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.2.0
+- !ruby/object:Gem::Dependency
+  name: cheasecrmod
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.0.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.0.1
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
@@ -114,18 +142,61 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 2.0.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.0.0
+        version: 2.0.1
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+- !ruby/object:Gem::Dependency
+  name: rake-compiler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 description: A gem to allow coderunner to run the trinity code directly.
 email: edmundhighcock@users.sourceforge.net
 executables: []
-extensions: []
+extensions:
+- ext/trinitycrdriver/extconf.rb
 extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
@@ -136,9 +207,14 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
+- clean.sh
+- ext/trinitycrdriver/extconf.rb
+- ext/trinitycrdriver/trinitycrdriver.c
 - lib/trinitycrdriver.rb
-- test/helper.rb
-- test/test_trinitycrdriver.rb
+- lib/trinitycrdriver/optimisation.rb
+- lib/trinoptcrmod.rb
+- lib/trinoptcrmod/trinopt.rb
+- trinitycrdriver.gemspec
 homepage: http://github.com/edmundhighcock/trinitycrdriver
 licenses:
 - GPLv3
@@ -159,7 +235,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.8
 signing_key: 
 specification_version: 4
 summary: A gem to allow coderunner to run the trinity code directly via a C interface.

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 'trinitycrdriver'
-
-class Test::Unit::TestCase
-end

data/test/test_trinitycrdriver.rb

@@ -1,6 +0,0 @@
-require 'helper'
-
-class TestTrinitycrdriver < Test::Unit::TestCase
-	def test_run
-	end
-end