y_petri 2.0.15 → 2.1.3

data/test/timed_simulation_test.rb

@@ -1,153 +0,0 @@
-#! /usr/bin/ruby
-# -*- coding: utf-8 -*-
-
-require 'minitest/spec'
-require 'minitest/autorun'
-require_relative '../lib/y_petri'     # tested component itself
-# require 'y_petri'
-# require 'sy'
-
-include Pyper if require 'pyper'
-
-# **************************************************************************
-# Test of TimedSimulation class.
-# **************************************************************************
-#
-describe YPetri::Simulation::Timed do  
-  before do
-    # skip "to speed up testing"
-    @a = YPetri::Place.new default_marking: 1.0
-    @b = YPetri::Place.new default_marking: 2.0
-    @c = YPetri::Place.new default_marking: 3.0
-  end
-
-  describe "timed assembly a + b >> c" do
-    before do
-      @t1 = YPetri::Transition.new s: { @a => -1, @b => -1, @c => 1 }, rate: 0.1
-      @net = YPetri::Net.new << @a << @b << @c << @t1
-      @im_collection = [@a, @b, @c].τBmχHτ &:default_marking
-    end
-
-    describe "simulation with step size 1" do
-      before do
-        @sim = YPetri::Simulation.new net: @net,
-                                      initial_marking: @im_collection,
-                                      step: 1,
-                                      sampling: 10,
-                                      time: 0..100
-      end
-
-      it "should #step! with expected results" do
-        m = @sim.step!.marking
-        assert_in_delta 0.8, m[0]
-        assert_in_delta 1.8, m[1]
-        assert_in_delta 3.2, m[2]
-      end
-
-      it "should behave" do
-        expect = Matrix.column_vector [-0.02, -0.02, 0.02]
-        ( expect - @sim.ΔE( 0.1 ) ).column( 0 ).norm.must_be_within_delta 0
-        @sim.Euler_step! 0.1
-        expect = Matrix.column_vector [0.98, 1.98, 3.02]
-        ( expect - @sim.marking_vector ).column( 0 ).norm.must_be_within_delta 0
-        @sim.method.must_equal :pseudo_Euler
-        @sim.send :reset!
-        @sim.step! 0.1
-        expect = Matrix.column_vector [0.98, 1.98, 3.02]
-        ( expect - @sim.marking_vector ).column( 0 ).norm.must_be_within_delta 0
-      end
-    end
-
-    describe "simulation with step size 0.1" do
-      before do
-        @sim = YPetri::Simulation.new net: @net,
-                                      initial_marking: @im_collection,
-                                      step: 0.1,
-                                      sampling: 10,
-                                      time: 0..100
-      end
-
-      it "should behave" do
-        m = @sim.step!.marking
-        assert_equal 10, @sim.sampling_period
-        assert_in_delta 0.98, m[ 0 ], 1e-9
-        assert_in_delta 1.98, m[ 1 ], 1e-9
-        assert_in_delta 3.02, m[ 2 ], 1e-9
-      end
-
-      it "should behave" do
-        @sim.run_until 31
-        expected_recording = {
-          0 => [ 1, 2, 3 ],
-          10 => [ 0.22265, 1.22265, 3.77735 ],
-          20 => [ 0.07131, 1.07131, 3.92869 ],
-          30 => [ 0.02496, 1.02496, 3.97503 ]
-        }
-        assert_equal expected_recording.keys, @sim.recording.keys
-        assert_in_delta 0, expected_recording.values.zip( @sim.recording.values )
-          .map{ |expected, actual| ( Vector[ *expected ] -
-                                     Vector[ *actual ] ).norm }.reduce( :+ ), 1e-4
-        expected_recording_string =
-          "0.0,1.0,2.0,3.0\n" +
-          "10.0,0.22265,1.22265,3.77735\n" +
-          "20.0,0.07131,1.07131,3.92869\n" +
-          "30.0,0.02496,1.02496,3.97504\n"
-        assert_equal expected_recording_string, @sim.recording_csv_string
-      end
-    end
-  end
-
-  describe "timed 'isomerization' with given as λ" do
-    before do
-      @t2 = YPetri::Transition.new s: { @a => -1, @c => 1 },
-                                     rate_closure: -> a { a * 0.5 }
-      @net = YPetri::Net.new << @a << @b << @c << @t2
-    end
-
-    describe "behavior of #step" do
-      before do
-        @sim = YPetri::Simulation.new net: @net,
-                 initial_marking: [ @a, @b, @c ].τBᴍHτ( &:default_marking ),
-                 step: 1,
-                 sampling: 10
-      end
-
-      it "should have expected stoichiometry matrix" do
-        @sim.S.must_equal Matrix[ [-1, 0, 1] ].t
-        m = @sim.step!.marking
-        m[ 0 ].must_be_within_epsilon( 0.5, 1e-6 )
-        m[ 1 ].must_equal 2
-        m[ 2 ].must_be_within_delta( 3.5, 1e-9 )
-      end
-    end
-  end
-
-  describe "timed controlled isomerization" do
-    before do
-      @t3 = YPetri::Transition.new s: { @a => -1, @c => 1 },
-                                     domain: @b,
-                                     rate: -> a { a * 0.5 }
-      @net = YPetri::Net.new << @a << @b << @c << @t3
-      @sim = YPetri::Simulation.new net: @net,
-                                    initial_marking: { @a => 1, @b => 0.6, @c => 3 },
-                                    step: 1,
-                                    sampling: 10,
-                                    time: 0..2
-    end
-
-    it "should exhibit correct behavior of #step" do
-      @sim.marking.must_equal [1.0, 0.6, 3.0]
-      @t3.stoichiometric?.must_equal true
-      @t3.timed?.must_equal true
-      @t3.has_rate?.must_equal true
-      @sim.gradient.must_equal Matrix.cv [-0.3, 0.0, 0.3]
-      @sim.Δ_Euler.must_equal Matrix.cv [-0.3, 0.0, 0.3]
-      @sim.step!
-      @sim.marking_vector.must_equal Matrix.cv [0.7, 0.6, 3.3]
-      @sim.euler_step!
-      @sim.run!
-      @sim.marking_vector.map( &[:round, 5] )
-        .must_equal Matrix.cv [0.4, 0.6, 3.6]
-    end
-  end
-end