y_petri 2.0.7 → 2.0.14.p1

data/test/y_petri_test.rb

@@ -7,1114 +7,23 @@ require_relative '../lib/y_petri'     # tested component itself
 # require 'y_petri'
 # require 'sy'
 
-include Pyper if require 'pyper'
-
-# **************************************************************************
-# Test of Net class.
-# **************************************************************************
-#
-describe ::YPetri::Net do
-  before do
-    # skip "to speed up testing"
-    @tç = tç = Class.new ::YPetri::Transition
-    @pç = pç = Class.new ::YPetri::Place
-    @nç = nç = Class.new ::YPetri::Net
-    [ tç, pç, nç ].each { |ç|
-      ç.namespace!.class_exec {
-        define_method :Place do pç end
-        define_method :Transition do tç end
-        define_method :Net do nç end
-        private :Place, :Transition, :Net
-      }
-    }
-    @p1 = pç.new ɴ: "A", quantum: 0.1, marking: 1.1
-    @p2 = pç.new ɴ: "B", quantum: 0.1, marking: 2.2
-    @p3 = pç.new ɴ: "C", quantum: 0.1, marking: 3.3
-    @net = nç.new
-    [@p1, @p2, @p3].each { |p| @net.include_place! p }
-    @p_not_included = pç.new ɴ: "X", marking: 0
-  end
-
-  describe "net of 3 places and no transitions" do
-    before do
-      @p1.m = 1.1
-      @p2.m = 2.2
-      @p3.m = 3.3
-    end
-
-    it "should expose its elements" do
-      assert_equal [@p1, @p2, @p3], @net.places
-      assert_equal [:A, :B, :C], @net.pp
-      assert_equal [], @net.transitions
-    end
-
-    it "should expose transition groups" do
-      assert_equal [], @net.transitions_with_rate
-      assert_equal [], @net.rateless_transitions
-      assert_equal [], @net.transitions_without_rate
-      assert_equal [], @net.stoichiometric_transitions
-      assert_equal [], @net.nonstoichiometric_transitions
-    end
-
-    it "should tell its qualities" do
-      assert_equal true, @net.functional?
-      assert_equal true, @net.timed?
-      assert @net.include?( @p1 ) && !@net.include?( YPetri::Place.new )
-    end
-
-    it "should have 'standard equipment' methods" do
-      assert @net == @net.dup
-      assert @net.inspect.start_with? "#<Net:"
-      assert @net.include?( @p1 )
-      assert ! @net.include?( @p_not_included )
-      begin
-        @net.exclude_place! @p_not_included
-        @net.include_transition! YPetri::Transition.new( s: { @p_not_included => -1 } )
-        flunk "Attempt to include illegal transition fails to raise"
-      rescue; end
-    end
-
-    describe "plus 1 stoichio. transition with rate" do
-      before do
-        @t1 = @tç.new!( ɴ: "T1",
-                        s: { @p1 => 1, @p2 => -1, @p3 => -1 },
-                        rate: 0.01 )
-        @net.include_transition! @t1
-      end
-
-      it "should expose its elements" do
-        assert_equal [@t1], @net.transitions
-        assert_equal [:T1], @net.tt
-      end
-
-      it "should expose transition groups" do
-        assert_equal true, @t1.has_rate?
-        assert_equal [@t1], @net.transitions_with_rate
-        assert_equal [], @net.rateless_transitions
-        assert_equal [@t1], @net.stoichiometric_transitions
-        assert_equal [], @net.nonstoichiometric_transitions
-      end
-
-      it "should tell its qualities" do
-        assert_equal true, @net.functional?
-        assert_equal true, @net.timed?
-        assert @net.include?( @t1 )
-      end
-
-      it "should have #place & #transition for safe access to the said elements" do
-        @net.send( :place, @p1 ).must_equal @p1
-        @net.send( :transition, @t1 ).must_equal @t1
-      end
-
-      it "has #new_simulation & #new_timed_simulation constructors" do
-        @net.must_respond_to :new_simulation
-        @net.must_respond_to :new_timed_simulation
-      end
-
-      it "should have other methods" do
-        assert_equal [1.1, 2.2, 3.3], [@p1, @p2, @p3].map( &:marking ).map{ |n| n.round 6 }
-        assert_equal 2.2 * 3.3 * 0.01, @t1.rate_closure.call( @p2.marking, @p3.marking )
-        assert_equal [ @p2, @p3 ], @t1.domain
-        @t1.fire! 1
-        assert_equal [1.1726, 2.1274, 3.2274], [@p1, @p2, @p3].map( &:marking ).map{ |n| n.round 6 }
-      end
-
-      describe "plus 1 more nameless timeless functionless transition" do
-        before do
-          @t2 = @tç.new s: { @p2 => -1, @p3 => 1 }
-          @net.include_transition! @t2
-        end
-
-        it "should expose its elements" do
-          assert_equal [@t1, @t2], @net.transitions
-          assert_equal [:T1, nil], @net.tt
-          @net.tap{ |n| n.exclude_transition! @t1 }.exclude_transition! @t2
-          @net.tap{ |n| n.exclude_place! @p3 }.pp.must_equal [:A, :B]
-        end
-
-        it "should expose transition groups" do
-          assert_equal [], @net.timeless_nonstoichiometric_transitions
-          assert_equal [], @net.timeless_nonstoichiometric_tt
-          assert_equal [@t2], @net.timeless_stoichiometric_transitions
-          assert_equal [nil], @net.timeless_stoichiometric_tt
-          assert_equal [], @net.timed_nonstoichiometric_transitions_without_rate
-          assert_equal [], @net.timed_rateless_nonstoichiometric_transitions
-          assert_equal [], @net.timed_nonstoichiometric_tt_without_rate
-          assert_equal [], @net.timed_rateless_nonstoichiometric_tt
-          assert_equal [], @net.timed_nonstoichiometric_transitions_without_rate
-          assert_equal [], @net.timed_rateless_nonstoichiometric_transitions
-          assert_equal [], @net.timed_nonstoichiometric_tt_without_rate
-          assert_equal [], @net.timed_rateless_nonstoichiometric_tt
-          assert_equal [], @net.nonstoichiometric_transitions_with_rate
-          assert_equal [], @net.nonstoichiometric_tt_with_rate
-          assert_equal [@t1], @net.stoichiometric_transitions_with_rate
-          assert_equal [:T1], @net.stoichiometric_tt_with_rate
-          assert_equal [], @net.assignment_transitions
-          assert_equal [], @net.assignment_tt
-          assert_equal [@t1, @t2], @net.stoichiometric_transitions
-          assert_equal [:T1, nil], @net.stoichiometric_tt
-          assert_equal [], @net.nonstoichiometric_transitions
-          assert_equal [], @net.nonstoichiometric_tt
-          assert_equal [@t1], @net.timed_transitions
-          assert_equal [:T1], @net.timed_tt
-          assert_equal [@t2], @net.timeless_transitions
-          assert_equal [nil], @net.timeless_tt
-          assert_equal [@t1], @net.transitions_with_rate
-          assert_equal [:T1], @net.tt_with_rate
-          assert_equal [@t2], @net.rateless_transitions
-          assert_equal [nil], @net.rateless_tt
-        end
-
-        it "should tell its qualities" do
-          assert_equal false, @net.functional?
-          assert_equal false, @net.timed?
-          @net.exclude_transition! @t2
-          assert_equal true, @net.functional?
-          assert_equal true, @net.timed?
-        end
-      end
-    end
-  end
-end
-
-
-# **************************************************************************
-# Test of Simulation class.
-# **************************************************************************
-#
-describe ::YPetri::Simulation do
-  before do
-    # skip "to make the testing faster"
-    @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
-
-
-# **************************************************************************
-# 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
-
-
-# **************************************************************************
-# Test of Workspace class.
-# **************************************************************************
-#
-describe ::YPetri::Workspace do
-  before do
-    # skip "to speed up testing"
-    @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
-
-# **************************************************************************
-# Test of Manipulator class.
-# **************************************************************************
-#
-describe ::YPetri::Manipulator do
-  before do
-    # skip "for now"
-    @m = ::YPetri::Manipulator.new
-  end
-  
-  it "has net basic points" do
-    # --- net point related assets ---
-    @m.net_point_reset
-    @m.net_point_set @m.workspace.net( :Top )
-    @m.net.must_equal @m.workspace.Net::Top
-    # --- simulation point related assets ---
-    @m.simulation_point.reset
-    @m.simulation.must_equal nil
-    @m.simulation_point.key.must_equal nil
-    # --- cc point related assets ---
-    @m.cc_point.reset
-    @m.cc_point.set :Base
-    @m.cc.must_equal @m.workspace.clamp_collection
-    @m.cc.wont_equal :Base
-    @m.cc_point.key.must_equal :Base
-    # --- imc point related assets ---
-    @m.imc_point.reset
-    @m.imc_point.set :Base
-    @m.imc.must_equal @m.workspace.initial_marking_collection
-    @m.imc.wont_equal :Base
-    @m.imc_point.key.must_equal :Base
-    # --- ssc point related assets ---
-    @m.ssc_point.reset
-    @m.ssc_point.set :Base
-    @m.ssc.must_equal @m.workspace.simulation_settings_collection
-    @m.ssc.wont_equal :Base
-    @m.ssc_point.key.must_equal :Base
-  end
-
-  it "has basic selections" do
-    @m.net_selection.clear
-    @m.simulation_selection.clear
-    @m.cc_selection.clear
-    @m.imc_selection.clear
-    @m.ssc_selection.clear
-    @m.net_selection.get.must_equal []
-    @m.simulation_selection.get.must_equal []
-    @m.ssc_selection.get.must_equal []
-    @m.cc_selection.get.must_equal []
-    @m.imc_selection.get.must_equal []
-  end
-
-  it "presents some methods from workspace" do
-    [ @m.places, @m.transitions, @m.nets, @m.simulations ].map( &:size )
-      .must_equal [ 0, 0, 1, 0 ]
-    [ @m.clamp_collections,
-      @m.initial_marking_collections,
-      @m.simulation_settings_collections ].map( &:size ).must_equal [ 1, 1, 1 ]
-    [ @m.clamp_collections,
-      @m.initial_marking_collections,
-      @m.simulation_settings_collections ]
-    .map( &:keys ).must_equal [[:Base]] * 3
-    @m.pp.must_equal []
-    @m.tt.must_equal []
-    @m.nn.must_equal [ :Top ]       # ie. :Top net spanning whole workspace
-  end
-  
-  describe "slightly more complicated case" do
-    before do
-      @p = @m.Place ɴ: "P", default_marking: 1
-      @q = @m.Place ɴ: "Q", default_marking: 1
-      @decay_t = @m.Transition ɴ: "Tp", s: { P: -1 }, rate: 0.1
-      @constant_flux_t = @m.Transition ɴ: "Tq", s: { Q: 1 }, rate: -> { 0.02 }
-      @m.initial_marking @p => 1.2
-      @m.initial_marking @q => 2
-      @m.set_step 0.01
-      @m.set_sampling 1
-      @m.set_time 30
-    end
-    
-    it "works" do
-      @m.run!
-      @m.simulation.places.must_equal [ @p, @q ]
-      @m.simulation.transitions.must_equal [ @decay_t, @constant_flux_t ]
-      @m.simulation.SR_tt.must_equal [ :Tp, :Tq ]
-      @m.simulation.sparse_stoichiometry_vector( :Tp )
-        .must_equal Matrix.column_vector( [-1, 0] )
-      @m.simulation.stoichiometry_matrix_for( @m.transitions ).column_size
-        .must_equal 2
-      @m.simulation.stoichiometry_matrix_for( @m.transitions ).row_size
-        .must_equal 2
-      @m.simulation.flux_vector.row_size.must_equal 2
-      # @m.plot_recording
-    end
-  end
-end
-
-
-# **************************************************************************
-# Test of YPetri class itself.
-# **************************************************************************
-#
-describe ::YPetri do
-  before do
-    # skip "to speed up testing"
-  end
-
+# Unit tests for the YPetri module.
+# 
+describe YPetri do
   it "should have basic classes" do
-    [ :Place, :Transition, :Net,
-      :Simulation, :TimedSimulation,
-      :Workspace, :Manipulator ].each { |ß|
-      assert_kind_of Module, ::YPetri.const_get( ß ) }
+    assert [ :Place, :Transition, :Net,
+             :Simulation, :TimedSimulation,
+             :Workspace, :Manipulator
+           ].all? { |ß| YPetri.const_get( ß ).is_a? Module }
   end
 end
 
-
-# **************************************************************************
-# ACCEPTANCE TESTS
-# **************************************************************************
-
-# describe "Token game" do
-#   before do
-#     @m = YPetri::Manipulator.new
-#     @m.Place name: "A"
-#     @m.Place name: "B"
-#     @m.Place name: "C", marking: 7.77
-#     @m.Transition name: "A2B", stoichiometry: { A: -1, B: 1 }
-#     @m.Transition name: "C_decay", stoichiometry: { C: -1 }, rate: 0.05
-#   end
-
-#   it "should work" do
-#     @m.place( :A ).marking = 2
-#     @m.place( :B ).marking = 5
-#     @m.places.map( &:name ).must_equal [:A, :B, :C]
-#     @m.places.map( &:marking ).must_equal [2, 5, 7.77]
-#     @m.transition( :A2B ).arcs.must_equal [ @m.place( :A ), @m.place( :B ) ]
-#     @m.transition( :A2B ).fire!
-#     @m.places.map( &:marking ).must_equal [1, 6, 7.77]
-#     @m.transition( :A2B ).fire!
-#     @m.place( :A ).marking.must_equal 0
-#     @m.place( :B ).marking.must_equal 7
-#     2.times do @m.transition( :C_decay ).fire! 1 end
-#     @m.transition( :C_decay ).fire! 0.1
-#     200.times do @m.transition( :C_decay ).fire! 1 end
-#     assert_in_delta @m.place( :C ).marking, 0.00024, 0.00001
-#   end
-# end
-
-# describe "Basic use of TimedSimulation" do
-#   before do
-#     @m = YPetri::Manipulator.new
-#     @m.Place( name: "A", default_marking: 0.5 )
-#     @m.Place( name: "B", default_marking: 0.5 )
-#     @m.Transition( name: "A_pump",
-#                    stoichiometry: { A: -1 },
-#                    rate: proc { 0.005 } )
-#     @m.Transition( name: "B_decay",
-#                    stoichiometry: { B: -1 },
-#                    rate: 0.05 )
-#   end
-
-#   it "should work" do
-#     @m.net.must_be_kind_of ::YPetri::Net
-#     @m.run!
-#     @m.simulation.must_be_kind_of ::YPetri::TimedSimulation
-#     @m.plot_state
-#     sleep 3
-#   end
-# end
-
-# describe "Graphviz visualization" do
-#   before do
-#     @m = YPetri::Manipulator.new
-#     @m.Place name: :A, m!: 1
-#     @m.Place name: :B, m!: 1.5
-#     @m.Place name: :C, m!: 2
-#     @m.Place name: :D, m!: 2.5
-#     @m.Transition name: :A_pump, s: { A: -1 }, rate: proc { 0.005 }
-#     @m.Transition name: :B_decay, s: { B: -1 }, rate: 0.05
-#     @m.Transition name: :C_guard, assignment: true, codomain: :C, action: λ { 2 }
-#   end
-
-#   it "should work" do
-#     @m.net.visualize
-#   end
-# end
-
-# describe "Simplified dTTP pathway used for demo with Dr. Chang" do
-#   before do
-#     @m = YPetri::Manipulator.new
-#     Cytoplasm_volume_in_litres = 5.0e-11
-#     NA = 6.022e23
-#     Pieces_per_micromolar = NA / 1_000_000 * Cytoplasm_volume_in_litres
-#     @m.set_step 60
-#     @m.set_sampling 300
-#     @m.set_target_time 60 * 60 * 2
-#     AMP = @m.Place( name: :AMP, m!: 8695.0 )
-#     ADP = @m.Place( name: :ADP, m!: 6521.0 )
-#     ATP = @m.Place( name: :ATP, m!: 3152.0 )
-#     Deoxycytidine = @m.Place( name: :Deoxycytidine, m!: 0.5 )
-#     DeoxyCTP = @m.Place( name: :DeoxyCTP, m!: 1.0 )
-#     DeoxyGMP = @m.Place( name: :DeoxyGMP, m!: 1.0 )
-#     UMP_UDP_pool = @m.Place( name: :UMP_UDP_pool, m!: 2737.0 )
-#     DeoxyUMP_DeoxyUDP_pool = @m.Place( name: :DeoxyUMP_DeoxyUDP_pool, m!: 0.0 )
-#     DeoxyTMP = @m.Place( name: :DeoxyTMP, m!: 3.3 )
-#     DeoxyTDP_DeoxyTTP_pool = @m.Place( name: :DeoxyTDP_DeoxyTTP_pool, m!: 5.0 )
-#     Thymidine = @m.Place( name: :Thymidine, m!: 0.5 )
-#     TK1 = @m.Place( name: :TK1, m!: 100_000 )
-#     TYMS = @m.Place( name: :TYMS, m!: 100_000 )
-#     RNR = @m.Place( name: :RNR, m!: 100_000 )
-#     TMPK = @m.Place( name: :TMPK, m!: 100_000 )
-#     TK1_kDa = 24.8
-#     TYMS_kDa = 66.0
-#     RNR_kDa = 140.0
-#     TMPK_kDa = 50.0
-#     TK1_a = 5.40
-#     TYMS_a = 3.80
-#     RNR_a = 1.00
-#     TMPK_a = 0.83
-#     @m.clamp AMP: 8695.0, ADP: 6521.0, ATP: 3152.0
-#     @m.clamp Deoxycytidine: 0.5, DeoxyCTP: 1.0, DeoxyGMP: 1.0
-#     @m.clamp Thymidine: 0.5
-#     @m.clamp UMP_UDP_pool: 2737.0
-#     # Functions
-#     Vmax_per_minute_per_enzyme_molecule =
-#       lambda { |enzyme_specific_activity_in_micromol_per_minute_per_mg,
-#                 enzyme_molecular_mass_in_kDa|
-#                   enzyme_specific_activity_in_micromol_per_minute_per_mg *
-#                     enzyme_molecular_mass_in_kDa }
-#     Vmax_per_minute =
-#       lambda { |specific_activity, kDa, enzyme_molecules_per_cell|
-#                Vmax_per_minute_per_enzyme_molecule.( specific_activity, kDa ) *
-#                  enzyme_molecules_per_cell }
-#     Vmax_per_second =
-#       lambda { |specific_activity, kDa, enzyme_molecules_per_cell|
-#                Vmax_per_minute.( specific_activity,
-#                                  kDa,
-#                                  enzyme_molecules_per_cell ) / 60 }
-#     Km_reduced =
-#       lambda { |km, ki_hash={}|
-#                ki_hash.map { |concentration, ci_Ki|
-#                              concentration / ci_Ki
-#                            }.reduce( 1, :+ ) * km }
-#     Occupancy =
-#       lambda { |concentration, reactant_Km, compet_inh_w_Ki_hash={}|
-#                concentration / ( concentration +
-#                                  Km_reduced.( reactant_Km,
-#                                               compet_inh_w_Ki_hash ) ) }
-#     MM_with_inh_micromolars_per_second =
-#       lambda { |reactant_concentration,
-#                 enzyme_specific_activity,
-#                 enzyme_mass_in_kDa,
-#                 enzyme_molecules_per_cell,
-#                 reactant_Km,
-#                 competitive_inh_w_Ki_hash={}|
-#                 Vmax_per_second.( enzyme_specific_activity,
-#                                   enzyme_mass_in_kDa,
-#                                   enzyme_molecules_per_cell ) *
-#                   Occupancy.( reactant_concentration,
-#                               reactant_Km,
-#                               competitive_inh_w_Ki_hash ) }
-#     MMi = MM_with_inh_micromolars_per_second
-#     TK1_Thymidine_Km = 5.0
-#     TYMS_DeoxyUMP_Km = 2.0
-#     RNR_UDP_Km = 1.0
-#     DNA_creation_speed = 3_000_000_000 / ( 12 * 3600 )
-#     TMPK_DeoxyTMP_Km = 12.0
-
-#     # transitions
-#     @m.Transition name: :TK1_Thymidine_DeoxyTMP,
-#                   domain: [ Thymidine, TK1, DeoxyTDP_DeoxyTTP_pool, DeoxyCTP, Deoxycytidine, AMP, ADP, ATP ],
-#                   stoichiometry: { Thymidine: -1, DeoxyTMP: 1 },
-#                   rate: proc { |rc, e, pool1, ci2, ci3, master1, master2, master3|
-#                                ci1 = pool1 * master3 / ( master2 + master3 )
-#                                MMi.( rc, TK1_a, TK1_kDa, e, TK1_Thymidine_Km,
-#                                      ci1 => 13.5, ci2 => 0.8, ci3 => 40.0 ) }
-#     @m.Transition name: :TYMS_DeoxyUMP_DeoxyTMP,
-#                   domain: [ DeoxyUMP_DeoxyUDP_pool, TYMS, AMP, ADP, ATP ],
-#                   stoichiometry: { DeoxyUMP_DeoxyUDP_pool: -1, DeoxyTMP: 1 },
-#                   rate: proc { |pool, e, master1, master2, master3|
-#                           rc = pool * master2 / ( master1 + master2 )
-#                           MMi.( rc, TYMS_a, TYMS_kDa, e, TYMS_DeoxyUMP_Km ) }
-#     @m.Transition name: :RNR_UDP_DeoxyUDP,
-#                   domain: [ UMP_UDP_pool, RNR, DeoxyUMP_DeoxyUDP_pool, AMP, ADP, ATP ],
-#                   stoichiometry: { UMP_UDP_pool: -1, DeoxyUMP_DeoxyUDP_pool: 1 },
-#                   rate: proc { |pool, e, master1, master2, master3|
-#                                rc = pool * master2 / ( master1 + master2 )
-#                                MMi.( rc, RNR_a, RNR_kDa, e, RNR_UDP_Km ) }
-#     @m.Transition name: :DNA_polymerase_consumption_of_DeoxyTTP,
-#                   stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1 },
-#                   rate: proc { DNA_creation_speed / 4 }
-#     @m.Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
-#                   domain: [ DeoxyTMP, TMPK, ADP,
-#                             DeoxyTDP_DeoxyTTP_pool,
-#                             DeoxyGMP, AMP, ATP ],
-#                   stoichiometry: { DeoxyTMP: -1, TMPK: 0, DeoxyTDP_DeoxyTTP_pool: 1 },
-#                   rate: proc { |rc, e, ci1, pool, ci4, master1, master3|
-#                                master2 = ci1
-#                                ci2 = pool * master2 / ( master2 + master3 )
-#                                ci3 = pool * master3 / ( master2 + master3 )
-#                                MMi.( rc, TMPK_a, TMPK_kDa, e, TMPK_DeoxyTMP_Km,
-#                                      ci1 => 250.0, ci2 => 30.0, ci3 => 750, ci4 => 117 ) }
-#   end
-
-#   it "should work" do
-#     @m.run!
-#     @m.plot_state
-#     sleep 3
-#   end
-# end
-
-# describe "Use of TimedSimulation with units" do
-#   before do
-#     require 'sy'
-
-#     @m = YPetri::Manipulator.new
-
-#     # === General assumptions
-#     Cytoplasm_volume = 5.0e-11.l
-#     Pieces_per_concentration = SY::Nᴀ * Cytoplasm_volume
-
-#     # === Simulation settings
-#     @m.set_step 60.s
-#     @m.set_target_time 10.min
-#     @m.set_sampling 120.s
-
-#     # === Places
-#     AMP = @m.Place m!: 8695.0.µM
-#     ADP = @m.Place m!: 6521.0.µM
-#     ATP = @m.Place m!: 3152.0.µM
-#     Deoxycytidine = @m.Place m!: 0.5.µM
-#     DeoxyCTP = @m.Place m!: 1.0.µM
-#     DeoxyGMP = @m.Place m!: 1.0.µM
-#     U12P = @m.Place m!: 2737.0.µM
-#     DeoxyU12P = @m.Place m!: 0.0.µM
-#     DeoxyTMP = @m.Place m!: 3.3.µM
-#     DeoxyT23P = @m.Place m!: 5.0.µM
-#     Thymidine = @m.Place m!: 0.5.µM
-#     TK1 = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
-#     TYMS = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
-#     RNR = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
-#     TMPK = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
-
-#     # === Enzyme molecular masses
-#     TK1_m = 24.8.kDa
-#     TYMS_m = 66.0.kDa
-#     RNR_m = 140.0.kDa
-#     TMPK_m = 50.0.kDa
-
-#     # === Specific activities of the enzymes
-#     TK1_a = 5.40.µmol.min⁻¹.mg⁻¹
-#     TYMS_a = 3.80.µmol.min⁻¹.mg⁻¹
-#     RNR_a = 1.00.µmol.min⁻¹.mg⁻¹
-#     TMPK_a = 0.83.µmol.min⁻¹.mg⁻¹
-
-#     # === Clamps
-#     @m.clamp AMP: 8695.0.µM, ADP: 6521.0.µM, ATP: 3152.0.µM
-#     @m.clamp Deoxycytidine: 0.5.µM, DeoxyCTP: 1.0.µM, DeoxyGMP: 1.0.µM
-#     @m.clamp Thymidine: 0.5.µM
-#     @m.clamp U12P: 2737.0.µM
-
-#     # === Function closures
-
-#     # Vmax of an enzyme.
-#     # 
-#     Vmax_enzyme = lambda { |specific_activity, mass, enzyme_conc|
-#       specific_activity * mass * enzyme_conc.( SY::Molecularity )
-#     }
-
-#     # Michaelis constant reduced for competitive inhibitors.
-#     # 
-#     Km_reduced = lambda { |km, ki_hash={}|
-#       ki_hash.map { |concentration, ci_Ki|
-#         concentration / ci_Ki }
-#         .reduce( 1, :+ ) * km
-#     }
-
-#     # Occupancy of enzyme active sites at given concentration of reactants
-#     # and competitive inhibitors.
-#     # 
-#     Occupancy = lambda { |ʀ_conc, ʀ_Km, cɪ_Kɪ={}|
-#       ʀ_conc / ( ʀ_conc + Km_reduced.( ʀ_Km, cɪ_Kɪ ) )
-#     }
-
-#     # Michaelis and Menten equation with competitive inhibitors.
-#     # 
-#     MMi = MM_equation_with_inhibitors = lambda {
-#       |ʀ_conc, ᴇ_specific_activity, ᴇ_mass, ᴇ_conc, ʀ_Km, cɪ_Kɪ={}|
-#       Vmax_enzyme.( ᴇ_specific_activity, ᴇ_mass, ᴇ_conc ) *
-#         Occupancy.( ʀ_conc, ʀ_Km, cɪ_Kɪ )
-#     }
-
-#     # === Michaelis constants of the enzymes involved.
-
-#     TK1_Thymidine_Km = 5.0.µM
-#     TYMS_DeoxyUMP_Km = 2.0.µM
-#     RNR_UDP_Km = 1.0.µM
-#     TMPK_DeoxyTMP_Km = 12.0.µM
-
-#     # === DNA synthesis speed.
-
-#     DNA_creation_speed = 3_000_000_000.unit.( SY::MoleAmount ) / 12.h / Cytoplasm_volume
-
-#     # === Transitions
-
-#     # Synthesis of TMP by TK1.
-#     # 
-#     TK1_Thymidine_DeoxyTMP = @m.Transition s: { Thymidine: -1, DeoxyTMP: 1 },
-#       domain: [ Thymidine, TK1, DeoxyT23P, DeoxyCTP, Deoxycytidine, AMP, ADP, ATP ],
-#         rate: proc { |rc, e, pool1, ci2, ci3, master1, master2, master3|
-#                 ci1 = pool1 * master3 / ( master2 + master3 )
-#                 MMi.( rc, TK1_a, TK1_m, e, TK1_Thymidine_Km,
-#                       ci1 => 13.5.µM, ci2 => 0.8.µM, ci3 => 40.0.µM )
-#               }
-
-#     # Methylation of DeoxyUMP into TMP by TYMS.
-#     TYMS_DeoxyUMP_DeoxyTMP = @m.Transition s: { DeoxyU12P: -1, DeoxyTMP: 1 },
-#       domain: [ DeoxyU12P, TYMS, AMP, ADP, ATP ],
-#         rate: proc { |pool, e, master1, master2, master3|
-#                 rc = pool * master2 / ( master1 + master2 )
-#                 MMi.( rc, TYMS_a, TYMS_m, e, TYMS_DeoxyUMP_Km )
-#               }
-
-#     # Reduction of UDP into DeoxyUDP by RNR.
-#     RNR_UDP_DeoxyUDP = @m.Transition s: { U12P: -1, DeoxyU12P: 1 },
-#       domain: [ U12P, RNR, DeoxyU12P, AMP, ADP, ATP ],
-#         rate: proc { |pool, e, master1, master2, master3|
-#                 rc = pool * master2 / ( master1 + master2 )
-#                 MMi.( rc, RNR_a, RNR_m, e, RNR_UDP_Km )
-#               }
-
-#     # Consumption of TTP by DNA synthesis.
-#     DeoxyTTP_to_DNA = @m.Transition s: { DeoxyT23P: -1 },
-#         rate: proc { DNA_creation_speed / 4 }
-
-#     # Phosphorylation of TMP into TDP-TTP pool.
-#     TMPK_DeoxyTMP_DeoxyTDP = @m.Transition s: { DeoxyTMP: -1, TMPK: 0, DeoxyT23P: 1 },
-#       domain: [ DeoxyTMP, TMPK, ADP, DeoxyT23P, DeoxyGMP, AMP, ATP ],
-#         rate: proc { |rc, e, ci1, pool, ci4, master1, master3|
-#                 master2 = ci1
-#                 ci2 = pool * master2 / ( master2 + master3 )
-#                 ci3 = pool * master3 / ( master2 + master3 )
-#                 MMi.( rc, TMPK_a, TMPK_m, e, TMPK_DeoxyTMP_Km,
-#                       ci1 => 250.0.µM, ci2 => 30.0.µM, ci3 => 750.µM, ci4 => 117.µM )
-#               }
-#   end
-
-#   it "should work" do
-#     # === Simulation execution
-#     @m.run!
-#     # === Plotting of the results
-#     @m.plot_state
-#     sleep 20
-#   end
-# end
+# Run all other unit tests.
+# 
+require_relative 'place_test'
+require_relative 'transition_test'
+require_relative 'net_test'
+require_relative 'simulation_test'
+require_relative 'timed_simulation_test'
+require_relative 'workspace_test'
+require_relative 'manipulator_test'