y_petri 2.0.7 → 2.0.14.p1

data/test/simulation_test.rb

@@ -0,0 +1,280 @@
+#! /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'
+
+describe ::YPetri::Simulation do
+  before do
+    @pç = pç = Class.new( ::YPetri::Place )
+    @tç = tç = Class.new( ::YPetri::Transition )
+    @nç = nç = Class.new( ::YPetri::Net )
+    [ @pç, @tç, @nç ].each { |klass|
+      klass.namespace!.class_exec {
+        private
+        define_method :Place do pç end
+        define_method :Transition do tç end
+        define_method :Net do nç end
+      }
+    }
+    @p1 = @pç.new name: "P1", default_marking: 1
+    @p2 = @pç.new name: "P2", default_marking: 2
+    @p3 = @pç.new name: "P3", default_marking: 3
+    @p4 = @pç.new name: "P4", default_marking: 4
+    @p5 = @pç.new name: "P5", default_marking: 5
+    @t1 = @tç.new name: "T1",
+                  s: { @p1 => -1, @p2 => -1, @p4 => 1 },
+                  rate: 0.1
+    @t2 = @tç.new name: "T2",
+                  s: { @p1 => -1, @p3 => 1 },
+                  rate: -> a { a * 0.5 }
+    @t3 = @tç.new name: "T3",
+                  s: { @p1 => -1, @p2 => -1, @p4 => 1 },
+                  domain: @p3,
+                  rate: -> a { a * 0.5 }
+    @net = @nç.new << @p1 << @p2 << @p3 << @p4 << @p5
+    @net.include_transition! @t1
+    @net.include_transition! @t2
+    @net << @t3
+    @s = YPetri::Simulation.new net: @net,
+                                marking_clamps: { @p1 => 2.0, @p5 => 2.0 },
+                                initial_marking: { @p2 => @p2.default_marking,
+                                                   @p3 => @p3.default_marking,
+                                                   @p4 => @p4.default_marking }
+  end
+
+  it "exposes the net" do
+    @s.net.must_equal @net
+    @s.net.places.size.must_equal 5
+    @s.net.transitions.size.must_equal 3
+    assert @net.include? @t1
+    assert @s.net.include? @t1
+    assert @net.include? @t2
+    assert @s.net.include? @t2
+    assert @net.include? @t3
+    assert @s.net.include? @t3
+    @s.net.transitions.size.must_equal 3
+  end
+
+  it "exposes Petri net places" do
+    @s.places.must_equal [ @p1, @p2, @p3, @p4, @p5 ]
+    @s.pp.must_equal [ :P1, :P2, :P3, :P4, :P5 ]
+    @s.places( :pp ).must_equal( { @p1 => :P1, @p2 => :P2, @p3 => :P3,
+                                   @p4 => :P4, @p5 => :P5 } )
+    @s.pp( :pp ).must_equal( { P1: :P1, P2: :P2, P3: :P3, P4: :P4, P5: :P5 } )
+  end
+
+  it "exposes Petri net transitions" do
+    @s.transitions.must_equal [ @t1, @t2, @t3 ]
+    @s.tt.must_equal [ :T1, :T2, :T3 ]
+    @s.transitions( :tt ).must_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 } )
+    @s.tt( :tt ).must_equal( { T1: :T1, T2: :T2, T3: :T3 } )
+  end
+
+  it "exposes place clamps" do
+    @s.clamped_places( :place_clamps ).must_equal( { @p1 => 2, @p5 => 2 } )
+    @s.clamped_pp( :place_clamps ).must_equal( { P1: 2, P5: 2 } )
+  end
+
+  it "presents free places" do
+    @s.free_places.must_equal [ @p2, @p3, @p4 ]
+    @s.free_pp.must_equal [ :P2, :P3, :P4 ]
+    @s.free_places( :free_pp )
+      .must_equal( { @p2 => :P2, @p3 => :P3, @p4 => :P4 } )
+    @s.free_pp( :free_pp )
+      .must_equal( { P2: :P2, P3: :P3, P4: :P4 } )
+  end
+
+  it "presents clamped places" do
+    @s.clamped_places.must_equal [ @p1, @p5 ]
+    @s.clamped_pp.must_equal [ :P1, :P5 ]
+    @s.clamped_places( :clamped_pp ).must_equal( { @p1 => :P1, @p5 => :P5 } )
+    @s.clamped_pp( :clamped_pp ).must_equal( { P1: :P1, P5: :P5 } )
+  end
+
+  it "exposes initial marking" do
+    @s.free_places( :im ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
+    @s.free_pp( :im ).must_equal( { P2: 2, P3: 3, P4: 4 } )
+    @s.im.must_equal [ 2, 3, 4 ]
+    @s.im_vector.must_equal Matrix[[2], [3], [4]]
+    @s.im_vector.must_equal @s.iᴍ
+  end
+
+  it "exposes marking (simulation state)" do
+    @s.m.must_equal [2, 3, 4] # (we're after reset)
+    @s.free_places( :m ).must_equal( { @p2 => 2, @p3 => 3, @p4 => 4 } )
+    @s.free_pp( :m ).must_equal( { P2: 2, P3: 3, P4: 4 } )
+    @s.ᴍ.must_equal Matrix[[2], [3], [4]]
+  end
+
+  it "separately exposes marking of clamped places" do
+    @s.m_clamped.must_equal [ 2, 2 ]
+    @s.clamped_places( :m_clamped ).must_equal( { @p1 => 2, @p5 => 2 } )
+    @s.clamped_pp( :m_clamped ).must_equal( { P1: 2, P5: 2 } )
+    @s.ᴍ_clamped.must_equal Matrix[[2], [2]]
+  end
+
+  it "exposes marking of all places (with capitalized M)" do
+    @s.marking.must_equal [ 2, 2, 3, 4, 2 ]
+    @s.places( :marking )
+      .must_equal( { @p1 => 2, @p2 => 2, @p3 => 3, @p4 => 4, @p5 => 2 } )
+    @s.pp( :marking ).must_equal( { P1: 2, P2: 2, P3: 3, P4: 4, P5: 2 } )
+    @s.marking_vector.must_equal Matrix[[2], [2], [3], [4], [2]]
+  end
+
+  it "has #S_for / #stoichiometry_matrix_for" do
+    assert_equal Matrix.empty(3, 0), @s.S_for( [] )
+    assert_equal Matrix[[-1], [0], [1]], @s.S_for( [@t1] )
+    x = Matrix[[-1, -1], [0, 0], [1, 1]]
+    x.must_equal @s.S_for( [@t1, @t3] )
+    x.must_equal( @s.S_for( [@t1, @t3] ) )
+    @s.stoichiometry_matrix_for( [] ).must_equal Matrix.empty( 5, 0 )
+  end
+
+  it "has stoichiometry matrix for 3. tS transitions" do
+    @s.S_for_tS.must_equal Matrix.empty( 3, 0 )
+  end
+
+  it "has stoichiometry matrix for 4. Sr transitions" do
+    @s.S_for_TSr.must_equal Matrix.empty( 3, 0 )
+  end
+
+  it "has stoichiometry matrix for 6. SR transitions" do
+    @s.S_for_SR.must_equal Matrix[[-1,  0, -1], [0, 1, 0], [1, 0, 1]]
+    @s.S.must_equal @s.S_for_SR
+  end
+
+  it "presents 1. ts" do
+    assert_equal [], @s.ts_transitions
+    assert_equal( {}, @s.ts_transitions( :ts_transitions ) )
+    assert_equal [], @s.ts_tt
+    assert_equal( {}, @s.ts_tt( :ts_tt ) )
+  end
+
+  it "presents 2. tS transitions" do
+    assert_equal [], @s.tS_transitions
+    assert_equal( {}, @s.tS_transitions( :tS_transitions ) )
+    assert_equal [], @s.tS_tt
+    assert_equal( {}, @s.tS_tt( :tS_tt ) )
+  end
+
+  it "presents 3. Tsr transitions" do
+    assert_equal [], @s.Tsr_transitions
+    assert_equal( {}, @s.Tsr_transitions( :Tsr_transitions ) )
+    assert_equal [], @s.Tsr_tt
+    assert_equal( {}, @s.Tsr_tt( :Tsr_tt ) )
+  end
+
+  it "presents 4. TSr transitions" do
+    assert_equal [], @s.TSr_transitions
+    assert_equal( {}, @s.TSr_transitions( :TSr_tt ) )
+    assert_equal [], @s.TSr_tt
+    assert_equal( {}, @s.TSr_tt( :TSr_tt ) )
+  end
+
+  it "presents 5. sR transitions" do
+    assert_equal [], @s.sR_transitions
+    assert_equal( {}, @s.sR_transitions( :sR_transitions ) )
+    assert_equal [], @s.sR_tt
+    assert_equal( {}, @s.sR_tt( :sR_tt ) )
+  end
+
+  it "presents SR transitions" do
+    assert_equal [@t1, @t2, @t3], @s.SR_transitions
+    assert_equal( { @t1 => :T1, @t2 => :T2, @t3 => :T3 },
+                  @s.SR_transitions( :SR_tt ) )
+    assert_equal [:T1, :T2, :T3], @s.SR_tt
+    assert_equal( { T1: :T1, T2: :T2, T3: :T3 }, @s.SR_tt( :SR_tt ) )
+  end
+
+  it "presents A transitions" do
+    assert_equal [], @s.A_transitions
+    assert_equal( {}, @s.A_transitions( :A_tt ) )
+    assert_equal [], @s.A_tt
+    assert_equal( {}, @s.A_tt( :A_tt ) )
+  end
+
+  it "presents S transitions" do
+    assert_equal [@t1, @t2, @t3], @s.S_transitions
+    assert_equal [:T1, :T2, :T3], @s.S_tt
+    assert_equal( { T1: :T1, T2: :T2, T3: :T3 }, @s.S_tt( :S_tt ) )
+  end
+
+  it "presents s transitions" do
+    assert_equal [], @s.s_transitions
+    assert_equal [], @s.s_tt
+    assert_equal( {}, @s.s_tt( :s_tt ) )
+  end
+
+  it "presents R transitions" do
+    assert_equal [@t1, @t2, @t3], @s.R_transitions
+    assert_equal [:T1, :T2, :T3], @s.R_tt
+    assert_equal( { T1: :T1, T2: :T2, T3: :T3 }, @s.R_tt( :R_tt ) )
+  end
+
+  it "presents r transitions" do
+    assert_equal [], @s.r_transitions
+    assert_equal [], @s.r_tt
+  end
+
+  it "1. handles ts transitions" do
+    @s.Δ_closures_for_tsa.must_equal []
+    @s.Δ_if_tsa_fire_once.must_equal Matrix.zero( @s.free_pp.size, 1 )
+  end
+
+  it "2. handles Tsr transitions" do
+    @s.Δ_closures_for_Tsr.must_equal []
+    @s.Δ_for_Tsr( 1.0 ).must_equal Matrix.zero( @s.free_pp.size, 1 )
+  end
+
+  it "3. handles tS transitions" do
+    @s.action_closures_for_tS.must_equal []
+    @s.action_vector_for_tS.must_equal Matrix.column_vector( [] )
+    @s.α_for_t.must_equal Matrix.column_vector( [] )
+    @s.Δ_if_tS_fire_once.must_equal Matrix.zero( @s.free_pp.size, 1 )
+  end
+
+  it "4. handles TSr transitions" do
+    @s.action_closures_for_TSr.must_equal []
+    @s.action_closures_for_Tr.must_equal []
+    @s.action_vector_for_TSr( 1.0 ).must_equal Matrix.column_vector( [] )
+    @s.action_vector_for_Tr( 1.0 ).must_equal Matrix.column_vector( [] )
+    @s.Δ_for_TSr( 1.0 ).must_equal Matrix.zero( @s.free_pp.size, 1 )
+  end
+
+  it "5. handles sR transitions" do
+    assert_equal [], @s.rate_closures_for_sR
+    assert_equal [], @s.rate_closures_for_s
+    # @s.gradient_for_sR.must_equal Matrix.zero( @s.free_pp.size, 1 )
+    @s.Δ_Euler_for_sR( 1.0 ).must_equal Matrix.zero( @s.free_pp.size, 1 )
+  end
+
+  it "6. handles stoichiometric transitions with rate" do
+    @s.rate_closures_for_SR.size.must_equal 3
+    @s.rate_closures_for_S.size.must_equal 3
+    @s.rate_closures.size.must_equal 3
+    @s.flux_vector_for_SR.must_equal Matrix.column_vector( [ 0.4, 1.0, 1.5 ] )
+    @s.φ_for_SR.must_equal @s.flux_vector
+    @s.SR_tt( :φ_for_SR ).must_equal( { T1: 0.4, T2: 1.0, T3: 1.5 } )
+    @s.Euler_action_vector_for_SR( 1 )
+      .must_equal Matrix.column_vector [ 0.4, 1.0, 1.5 ]
+    @s.SR_tt( :Euler_action_for_SR, 1 ).must_equal( T1: 0.4, T2: 1.0, T3: 1.5 )
+    @s.Δ_Euler_for_SR( 1 ).must_equal Matrix[[-1.9], [1.0], [1.9]]
+    @s.free_pp( :Δ_Euler_for_SR, 1 ).must_equal( { P2: -1.9, P3: 1.0, P4: 1.9 } )
+  end
+
+  it "presents sparse stoichiometry vectors for its transitions" do
+    @s.sparse_σ( @t1 ).must_equal Matrix.cv( [-1, 0, 1] )
+    @s.sparse_stoichiometry_vector( @t1 )
+      .must_equal Matrix.cv( [-1, -1, 0, 1, 0] )
+  end
+
+  it "presents correspondence matrices free, clamped => all places" do
+    @s.F2A.must_equal Matrix[[0, 0, 0], [1, 0, 0], [0, 1, 0],
+                                    [0, 0, 1], [0, 0, 0]]
+    @s.C2A.must_equal Matrix[[1, 0], [0, 0], [0, 0], [0, 0], [0, 1]]
+  end
+end

data/test/timed_simulation_test.rb

@@ -0,0 +1,149 @@
+#! /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::TimedSimulation 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::TimedSimulation.new net: @net,
+                                           initial_marking: @im_collection,
+                                           step: 1,
+                                           sampling: 10,
+                                           target_time: 100
+      end
+
+      it "should #step! with expected results" do
+        m = @sim.step!.marking
+        assert_in_delta 0.8, m[ 0 ], 1e-9
+        assert_in_delta 1.8, m[ 1 ], 1e-9
+        assert_in_delta 3.2, m[ 2 ], 1e-9
+      end
+
+      it "should behave" do
+        assert_in_delta 0, ( Matrix.column_vector( [-0.02, -0.02, 0.02] ) -
+                             @sim.ΔE( 0.1 ) ).column( 0 ).norm, 1e-9
+        @sim.step! 0.1
+        assert_in_delta 0, ( Matrix.column_vector( [0.98, 1.98, 3.02] ) -
+                             @sim.marking_vector ).column( 0 ).norm, 1e-9
+
+      end
+    end
+
+    describe "simulation with step size 0.1" do
+      before do
+        @sim = YPetri::TimedSimulation.new net: @net,
+                                           initial_marking: @im_collection,
+                                           step: 0.1,
+                                           sampling: 10,
+                                           target_time: 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_target_time! 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::TimedSimulation.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::TimedSimulation.new net: @net,
+               initial_marking: { @a => 1, @b => 0.6, @c => 3 },
+               step: 1,
+               sampling: 10,
+               target_time: 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

data/test/transition_test.rb

@@ -155,15 +155,13 @@ describe ::YPetri::Transition do
         assert @tt.all? { |t| t.action == [1] }
         # #zero_action
         assert @tt.all? { |t| t.zero_action }
-        # #action_after_feasibility_check
-        assert @tt.all? { |t| t.action_after_feasibility_check == [1] }
         # #domain_marking
         assert @tt.all? { |t| t.domain_marking == [] }
         # #codomain_marking
         assert @tt.all? { |t| t.codomain_marking == [@p1.m] }
         # #enabled?
         @p1.m.must_equal 1
-        @p1.guard.( 1 ).must_equal true
+        @p1.guard.( 1 ).must_equal 1
         @tt.each { |t| t.enabled?.must_equal true }
       end
     end
@@ -248,7 +246,7 @@ describe ::YPetri::Transition do
       @SR2.fire! 1.0
       [@p1, @p3].map( &:marking ).must_equal [0.4, 3.4]
       # the action t3 cannot fire with delta time 1.0
-      -> { @SR3.fire! 1.0 }.must_raise RuntimeError
+      -> { @SR3.fire! 1.0 }.must_raise YPetri::GuardError
       [@p1, @p2, @p3, @p4].map( &:marking ).must_equal [0.4, 1.8, 3.4, 4.2]
       # but it can fire with eg. delta time 0.1
       @SR3.fire! 0.1

data/test/workspace_test.rb

@@ -0,0 +1,72 @@
+#! /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'
+
+describe YPetri::Workspace do
+  before do
+    @w = YPetri::Workspace.new
+    a = @w.Place.new!( default_marking: 1.0, name: "AA" )
+    b = @w.Place.new!( default_marking: 2.0, name: "BB" )
+    c = @w.Place.new!( ɴ: "CC", default_marking: 3.0 )
+    t1 = @w.Transition.new! s: { a => -1, b => -1, c => 1 },
+                            rate: 0.1,
+                            ɴ: "AA_BB_assembly"
+    t2 = @w.Transition.new! ɴ: "AA_appearing",
+                            codomain: a,
+                            rate: -> { 0.1 },
+                            stoichiometry: 1
+    @pp, @tt = [a, b, c], [t1, t2]
+    @f_name = "test_output.csv"
+    @w.set_imc @pp.τBᴍHτ( &:default_marking )
+    @w.set_ssc step: 0.1, sampling: 10, target_time: 50
+    @w.set_cc( {} )
+    @sim = @w.new_timed_simulation
+    File.delete @f_name rescue nil
+  end
+
+  it "should present places, transitions, nets, simulations" do
+    assert_kind_of YPetri::Net, @w.Net::Top
+    assert_equal @pp[0], @w.place( "AA" )
+    assert_equal :AA, @w.pl( @pp[0] )
+    assert_equal @tt[0], @w.transition( "AA_BB_assembly" )
+    assert_equal :AA_appearing, @w.tr( @tt[1] )
+    assert_equal @pp, @w.places
+    assert_equal @tt, @w.transitions
+    assert_equal 1, @w.nets.size
+    assert_equal 1, @w.simulations.size
+    assert_equal 0, @w.cc.size
+    assert_equal 3, @w.imc.size
+    assert [0.1, 10, 50].each { |e| @w.ssc.include? e }
+    assert_equal @sim, @w.simulation
+    assert_equal [:Base], @w.clamp_collections.keys
+    assert_equal [:Base], @w.initial_marking_collections.keys
+    assert_equal [:Base], @w.simulation_settings_collections.keys
+    assert_equal [:AA, :BB, :CC], @w.pp
+    assert_equal [:AA_BB_assembly, :AA_appearing], @w.tt
+    assert_equal [:Top], @w.nn
+  end
+
+  it "should simulate" do
+    assert_equal 1, @w.simulations.size
+    assert_kind_of( YPetri::Simulation, @w.simulation )
+    assert_equal 2, @w.simulation.SR_transitions.size
+    @tt[0].domain.must_equal [ @pp[0], @pp[1] ]
+    @tt[1].domain.must_equal []
+    assert_equal [0.2, 0.1], @w.simulation.φ.column_to_a
+    @w.simulation.step!
+    @w.simulation.run!
+    rec_string = @w.simulation.recording_csv_string
+    expected_recording_string =
+      "0.0,1.0,2.0,3.0\n" +
+      "10.0,0.86102,0.86102,4.13898\n" +
+      "20.0,1.29984,0.29984,4.70016\n"
+    assert rec_string.start_with?( expected_recording_string )
+  end
+end