y_petri 2.4.6 → 2.4.8

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/y_petri/net/data_set.rb

@@ -30,6 +30,26 @@
 # from it or otherwise integrate with it for the purposes of +DataSet+.
 # 
 class YPetri::Net::DataSet < Hash
+  # FIXME: User story:
+  # 
+  # I ran a long simulation (Virginia Tech cell cycle) and then
+  # I found that instead of 200_000 time units, I ran it for
+  # 360_000 time units. As we know, method recording (or
+  # simulation.recording is of DataSet type. I had troubles
+  # cutting down the recording to 200_000 time units.
+  # I had these troubles because there is no special select
+  # method defined for DataSet, or no way to only select
+  # the keys within certain time range, and Hash#select and
+  # other built-in Hash methods return Hash type which no
+  # longer can be plotted easily. Add a way of taking only
+  # certain records, or certain time section
+  #
+  # Finally, I found that #plot method directly accepts
+  # :time alias :time_range parameter, which can be used
+  # to do what I want. But I still think DataSet should have
+  # a method for cutting itself down to only certain lines.
+  # We cannot rely on Gnuplot :x_range parameter only...
+  
   class << self
     alias __new__ new
 
@@ -345,20 +365,28 @@ class YPetri::Net::DataSet < Hash
       map { |lbl, rec| [ lbl, *rec ].join ',' }.join( "\n" )
   end
 
-  # Plots the dataset. Takes several optional arguments: The list of nodes can be
-  # supplied as optional first ordered argument, which are then converted into
-  # features using +Net::State::Features.infer_from_nodes+ method. Similarly,
-  # the features to exclude can be specifies as a list of nodes (or a
-  # feature-specifying hash) supplied under +except:+ keyword. Otherwise, feature
-  # specification can be passed to the method as named arguments. If no feature
-  # specification is explicitly provided, it is assumed that all the features of
-  # this dataset are meant to be plotted.
+  # Plots the dataset using Ruby Gnuplot gem. Takes several
+  # optional arguments: The list of nodes to plot can be
+  # supplied as optional first ordered argument. If supplied,
+  # the nodes are converted into features using
+  # +Net::State::Features.infer_from_nodes+ method. Similarly,
+  # the features to exclude can be specified as a list of
+  # nodes supplied under +except:+ parameter. Under +except:+
+  # parameter, it is also possible to supply a
+  # feature-specifying hash. Otherwise, feature specification
+  # can be passed to the method via named arguments. By
+  # default, it is assumed that the caller means to plot all
+  # the features of this dataset.
+  #
+  # Named arguments admit Gnuplot keywords that control the
+  # plot. These parameters include +title:+, +xlabel:+ and
+  # +ylabel:+.
   # 
   def plot( nodes=nil, except: [], **named_args )
     nn = named_args
     time = nn.may_have :time, syn!: :time_range
     events = events()
-    # Figure out features.
+    # Figure out the features to plot.
     ff = if nodes.nil? then
            nn_ff = nn.slice [ :marking, :flux, :firing,
                               :gradient, :delta, :assignment ]
@@ -366,7 +394,8 @@ class YPetri::Net::DataSet < Hash
          else
            net.State.Features.infer_from_nodes( nodes )
          end
-    # Figure out the features not to plot ("except" features).
+    # Figure out the features to exclude from plotting
+    # ("except" features).
     xff = case except
           when Array then net.State.Features.infer_from_nodes( except )
           when Hash then net.State.Features( except )

data/lib/y_petri/net/own_state.rb

@@ -8,18 +8,50 @@ module YPetri::Net::OwnState
   # class (a subclass of Array), containing marking owned by the net's places.
   # 
   def state
-    State().new( marking )
+    State().new( m )
+  end
+
+  # Like #m method, but instead of returning an array of markings, it returns
+  # a string of the form "A: 1, B: 2, ...", where A, B, ... are the places
+  # and 1, 2, ... their marking. This method is intended to produce output
+  # easy to read by humans, while #m method produces regular output (an
+  # Array) suitable for further processing. Method accepts arbitrary number
+  # of optional arguments, each of which must be a place identifier. If
+  # no arguments are given, full marking of the net is described. If
+  # arguments are given, only marking of the places identified by the
+  # arguments is described.
+  #
+  def marking *place_ids
+    return pp.size == 0 ? "" : marking( *pp ) if place_ids.empty?
+    a = [ place_ids.map { |id| place( id ) },
+          m( place_ids ) ].transpose
+    a.map { |pair| pair.join ": " }.join ', '
   end
 
   # If no argument is supplied, the method returns the array of the markings
   # owned by the net's places. If an array of place identifiers is supplied,
   # the return value is the array of the markings owned by those places.
-  #
-  def marking place_ids=nil
-    return marking( pp ) if place_ids.nil?
+  # 
+  def m place_ids=nil
+    return m( pp ) if place_ids.nil?
     place_ids.map { |id| place( id ).marking }
   end
-  alias m marking
+
+  # If no argument is supplied, the method resets its places to their default
+  # marking. If an array of place identifiers is supplied, only the specified
+  # places are reset. Attempts to reset places that have no default marking
+  # result in +TypeError+.
+  #
+  def reset! place_ids=nil
+    return reset!( pp ) if place_ids.nil?
+    place_ids.map { |id|
+      begin
+        place( id ).reset_marking
+      rescue TypeError => err
+        raise TypeError, "Unable to reset the net! " + err.message
+      end
+    }
+  end
 
   # Takes an array of tS transition identifiers as an optional argument, and
   # returns the array of their firing under current net state. If no argument
@@ -55,7 +87,7 @@ module YPetri::Net::OwnState
     fail NotImplementedError
   end
 
-  # Takes an array of place identifier, and a named argument +:transitions+,
+  # Takes an array of place identifiers, and a named argument +:transitions+,
   # and returns the array of the place delta contribution by the indicated
   # transitions.
   #

data/lib/y_petri/net/state/features.rb

@@ -1,7 +1,7 @@
 # encoding: utf-8
 
 # A feature set. In other words, a set of state features, such as marking,
-# flux etc.
+# flux etc. The supported features are:
 #
 # marking:: Applicable to all places, all places have marking.
 # firing:: Applicable to all stoichiometric transitions, but delta time has

data/lib/y_petri/net.rb

@@ -171,7 +171,7 @@ class YPetri::Net
   # Networks are equal when their places and transitions are equal.
   # 
   def == other
-    return false unless other.class_complies?( self.class )
+    return false unless other.class_complies? self.class
     places == other.places && transitions == other.transitions
   end
 

data/lib/y_petri/place.rb

@@ -151,6 +151,8 @@ class YPetri::Place
   # instance variable).
   # 
   def reset_marking
+    fail TypeError, "No default marking was specified for #{self}!" unless
+      has_default_marking?
     @marking = guard.( @default_marking )
   end
 

data/lib/y_petri/simulation/timed.rb

@@ -353,29 +353,34 @@ module YPetri::Simulation::Timed
 
           rk_core.step! Δt
 
-          # TODO: In the above lines, setting rec = recorder and then calling rec!.alert in
-          # the block is a bit weird. It would be nicer to use recorder.alert!, but maybe
+          # TODO: In the above lines, setting rec = recorder and then calling
+          # rec!.alert in the block is a bit weird. It would be nicer to use
+          # recorder.alert!, but maybe
           # wise Ruby closure mechanism does not allow it...
         end # def step!
-      end
-    else
+      end # singleton_class.class_exec
+    else # the method is not :runge_kutta
       @core = if @guarded then
-                YPetri::Core::Timed.new( simulation: self, method: method, guarded: true )
+                YPetri::Core::Timed.new( simulation: self,
+                                         method: method, guarded: true )
               else
-                YPetri::Core::Timed.new( simulation: self, method: method, guarded: false )
+                YPetri::Core::Timed.new( simulation: self,
+                                         method: method, guarded: false )
               end
-      # TODO: But why am I doing it like this? Did I want to emphasize the standalone
-      # nature of Core class? Maybe... And maybe I did it so that the runge-kutta method
-      # with its @rk_core instance variable instead of @core does not have @core and #core.
-      # In this manner, I'm forcing myself to rethink Simulation class.
+      # TODO: But why am I doing it like this? Did I want to
+      # emphasize the standalone nature of Core class? Maybe... And
+      # maybe I did it so that the runge-kutta method with its
+      # @rk_core instance variable instead of @core does not have
+      # @core and #core.  In this manner, I'm forcing myself to
+      # rethink Simulation class.
       singleton_class.class_exec do
         attr_reader :core
         delegate :simulation_method, # this looks quite redundant with simulation.rb
                  :step!,
                  :firing_vector_tS,
                  to: :core
-      end
-    end
+      end # singleton_class.class_exec
+    end 
     @recorder = if features_to_record then
                   # we'll have to figure out features
                   ff = case features_to_record

data/lib/y_petri/transition/types.rb

@@ -5,29 +5,49 @@ require_relative 't'
 require_relative 'A'
 
 module YPetri::Transition::Types
-  # Is this a timed stoichiometric transition?
+  # Is this a transition with assignment action? (Transitions with assignment
+  # action, or "assignment transitions", completely replace the marking of their
+  # codomain with their action closure result, like in spreadsheets.)
   # 
-  def TS?
-    type == :TS
+  def assignment_action?
+    @assignment_action
   end
+  alias assignment? assignment_action?
+  alias A? assignment_action?
 
-  # Is this a timed non-stoichiometric transition?
+  # Is this a non-assignment transition? (Opposite of +#A?+)
   # 
-  def Ts?
-    type == :Ts
+  def a?
+    ! assignment_action?
   end
 
+  # Is this a timeless non-stoichiometric transition?
+  # 
+  def ts?
+    type == :ts
+  end
+  alias B? ts?
+
   # Is this a timeless stoichiometric transition?
   # 
   def tS?
     type == :tS
   end
+  alias C? tS?
 
-  # Is this a timeless non-stoichiometric transition?
+  # Is this a timed non-stoichiometric transition?
   # 
-  def ts?
-    type == :ts
+  def Ts?
+    type == :Ts
   end
+  alias D? Ts?
+
+  # Is this a timed stoichiometric transition?
+  # 
+  def TS?
+    type == :TS
+  end
+  alias E? TS?
 
   # Is this a stoichiometric transition?
   # 
@@ -78,35 +98,50 @@ module YPetri::Transition::Types
     not functional?
   end
 
-  # Reports the transition's membership in one of the 4 basic types:
-  # 
-  # 1. TS .... timed stoichiometric
-  # 2. tS .... timeless stoichiometric
-  # 3. Ts .... timed nonstoichiometric
-  # 4. ts .... timeless nonstoichiometric
+  # Reports the transition's membership in one of the 5 basic types
+  # using one-letter abbreviation:
   #
-  # plus the fifth type
+  # 1. A .... assignment
+  # 2. B .... timeless nonstoichiometric (ts)
+  # 3. C .... timeless stoichiometric (tS)
+  # 4. D .... timed nonstoichiometric (Ts)
+  # 5. E .... timed stoichiometric (TS)
   #
-  # 5. A .... assignment transitions
-  # 
-  def type
+  def t
     return :A if assignment_action?
-    timed? ? ( stoichiometric? ? :TS : :Ts ) : ( stoichiometric? ? :tS : :ts )
+    timed? ? ( stoichiometric? ? :E : :D ) : ( stoichiometric? ? :C : :B )
   end
 
-  # Is this a transition with assignment action? (Transitions with assignment
-  # action, or "assignment transitions", completely replace the marking of their
-  # codomain with their action closure result, like in spreadsheets.)
+  # Reports the transition's membership in one of the 5 basic types
+  # using two-letter abbreviation + A for assignment transition.
+  # This methods reflects the fact that the new users may take time
+  # to memorize the meaning of A, B, C, D, E transition types.
+  # Two-letter abbreviations may be easier to figure out.
+  #
+  # 1. A .... assignment transitions (A-type)
+  # 2. ts .... timeless nonstoichiometric (B-type)
+  # 3. tS .... timeless stoichiometric (C-type)
+  # 4. Ts .... timed nonstoichiometric (D-type)
+  # 5. TS .... timed stoichiometric (E-type)
   # 
-  def assignment_action?
-    @assignment_action
+  def type
+    { A: :A, B: :ts, C: :tS, D: :Ts, E: :TS }[ t ]
   end
-  alias assignment? assignment_action?
-  alias A? assignment_action?
 
-  # Is this a non-assignment transition? (Opposite of +#A?+)
-  # 
-  def a?
-    ! assignment_action?
+  # Reports the transition's membership in one of the 5 basic types
+  # as a full string.
+  #
+  # 1. assignment (A-type)
+  # 2. timeless nonstoichiometric (B-type)
+  # 3. timeless stoichiometric (C-type)
+  # 4. timed nonstoichiometric (D-type)
+  # 5. timed stoichiometric (E-type)
+  #
+  def type_full
+    { A: "assignment",
+      ts: "timeless nonstoichiometric",
+      tS: "timeless stoichiometric",
+      Ts: "timed nonstoichiometric",
+      TS: "timed stoichiometric" }[ type ]
   end
 end # class YPetri::Transition::Types

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.4.6"
+  VERSION = "2.4.8"
   DEBUG = false
 end

data/test/net_test.rb

@@ -35,6 +35,24 @@ describe YPetri::Net do
       @net.Places( [] ).must_equal []
       @net.places( :A ).must_equal [ p ]
     end
+
+    describe "#reset!" do
+      it "should work as expected" do
+        place_with_default_marking =
+          @w.Place.send :new, name: "A", default_marking: 42
+        place_without_default_marking =
+          @w.Place.send :new, name: "B", marking: 43
+        @net.include_place( place_with_default_marking )
+        place_with_default_marking.marking = 0
+        @net.reset!
+        assert place_with_default_marking.marking == 42
+        @net.include_place( place_without_default_marking )
+        place_with_default_marking.marking = 0
+        -> { @net.reset! }.must_raise TypeError
+        @net.reset! [ :A ]
+        assert place_with_default_marking.marking == 42
+      end
+    end
   end
 
   describe "world with 3 places" do
@@ -78,10 +96,9 @@ describe YPetri::Net do
       it "should know its state (marking owned by the places)" do
         @net.state.must_be_kind_of YPetri::Net::State
         @net.state.must_equal [ @p1, @p2, @p3 ].map( &:marking )
-        @net.marking.must_equal [ @p1, @p2, @p3 ].map( &:marking )
-        @net.marking.must_be_kind_of Array
-        # User-expected #m alias for #marking
-        @net.m.must_equal @net.marking
+        @net.m.must_equal [ @p1, @p2, @p3 ].map( &:marking )
+        # Easy-to-read marking information.
+        @net.marking.must_equal "A: 1.1, B: 2.2, C: 3.3"
       end
 
       it "should have standard equipment expected of a class" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.4.6
+  version: 2.4.8
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-24 00:00:00.000000000 Z
+date: 2016-06-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -131,9 +131,7 @@ files:
 - ACKNOWLEDGMENT.txt
 - Gemfile
 - Introduction_to_Ruby_for_YPetri_and_YNelson_Users.pdf
-- Introduction_to_YNelson_and_YPetri.pdf
 - LICENSE.txt
-- Object_model_of_YNelson_and_YPetri.pdf
 - README.md
 - Rakefile
 - lib/y_petri.rb