y_nelson 0.1.5 → 2.0.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -17,4 +17,5 @@ rdoc
 spec/reports
 test/tmp
 test/version_tmp
+test/*.png
 tmp

data/config/mongoid.yml

@@ -0,0 +1,6 @@
+development:
+  sessions:
+    default:
+      database: mongoid
+      hosts:
+        - localhost:27017

data/lib/y_nelson/{manipulator.rb → agent.rb}

@@ -1,30 +1,34 @@
-# -*- coding: utf-8 -*-
-# YNelson user inteface. Ted Nelson, in his introduction of zz structures, has
-# remarks regarding a desired UI, such as:
+# encoding: utf-8
+
+# YNelson's user inteface. As the name suggests, represents an agent that
+# manipulates the YNelson world. In his introduction to zz structures,
+# Ted Nelson has remarks regarding the desired UI, such as:
 #
 # <em>Selection</em> is a pointer to a collection of cells.
 # <em>View</em> consists of selection and a coordinate system.
 # <em>Field<em> is a connected (contiguous) selection.
 # <em>Coordinate system</em> is a collection of oriented dimensions.
 #
-# Apart from that, this manipulator should offer similar functionality as
-# YPetri::Manipulator - that is, should allow constructing a Petri net
-# without much ado about zz aspect, just like YPetri does.
+# Apart from these author's suggestions, the interface should offer similar
+# functionality as YPetri::Agent – that is, should allow constructing a Petri
+# net with the same commands as YPetri does.
 #
-class YNelson::Manipulator
-  attr_reader :workspace
+class YNelson::Agent
+  attr_reader :world
 
-  include YPetri::Manipulator::PetriNetRelatedMethods
-  include YPetri::Manipulator::SimulationRelatedMethods
+  include YPetri::Agent::PetriNetRelated
+  include YPetri::Agent::SimulationRelated
 
+  # Initialization of a YNelson::Agent instance. For YNelson manipulators, the
+  # world is always YNelson itself.
+  # 
   def initialize
-    # For YNelson manipulators, the workspace is always YNelson itself.
-    @workspace = ::YNelson
+    @world = ::YNelson
     super
-    # A hash of sheets. For the moment being, YNelson acts as a spreadsheet.
+    # A hash of sheets. (For the moment being, YNelson acts like a spreadsheet.)
     @sheets = {}
     # Default dimension of this manipulator.
-    @default_dimension = YNelson.Dimension :row
+    @default_dimension = YNelson.Dimension( :row )
     # Zz object pointers of this manipulator.
     @primary_point = YNelson::ZzPoint.new
     @secondary_point = YNelson::ZzPoint.new
@@ -45,7 +49,7 @@ class YNelson::Manipulator
 
   # Dimension convenience constructor from 
   delegate( :Dimension,
-            to: :workspace )
+            to: :world )
   
   # Creation of a single-output formula known well from spreadseets. Given a
   # place, it creates a new assignment transition.
@@ -60,24 +64,38 @@ class YNelson::Manipulator
 
   # Now let's look into the graph visualization.
 
-  def default_dimension; @default_dimension end
+  def default_dimension
+    @default_dimension
+  end
 
-  def primary_point; @primary_point end
+  def primary_point
+    @primary_point
+  end
   alias p1 primary_point
 
-  def secondary_point; @secondary_point end
+  def secondary_point
+    @secondary_point
+  end
   alias p2 secondary_point
 
-  def primary_dimension_point; @primary_dimension_point end
+  def primary_dimension_point
+    @primary_dimension_point
+  end
   alias d1 primary_dimension_point
 
-  def secondary_dimension_point; @secondary_dimension_point end
+  def secondary_dimension_point
+    @secondary_dimension_point
+  end
   alias d2 secondary_dimension_point
 
-  # Define function to display it with kioclient
-  def visualize *args, &block; graphviz *args, &block end
+  # Define function to display it with kioclient.
+  # 
+  def visualize *args, &block
+    graphviz *args, &block
+  end
 
-  # Define graphviz places
+  # Define graphviz places.
+  # 
   def graphviz dim1=primary_dimension_point, dim2=secondary_dimension_point
     γ = GraphViz.new :G, type: :digraph  # Create a new graph
 

data/lib/y_nelson/dimension.rb

@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# encoding: utf-8
+
 # Zz dimension can in principle be any object, in YNelson, special class
 # Dimension is used.
 # 

data/lib/y_nelson/dsl.rb

@@ -0,0 +1,77 @@
+# encoding: utf-8
+
+module YNelson
+  # YNelson DSL.
+  # 
+  module DSL
+    def y_nelson_agent
+      @y_nelson_agent ||= Agent.new
+        .tap { puts "Defining YNelson agent for #{self}" if YNelson::DEBUG }
+    end
+  end
+
+  delegate :world, to: :y_nelson_agent
+
+  # Petri net aspect.
+  delegate( :Place,
+            :Transition, :T, :A,
+            :Net,
+            :place, :transition, :pl, :tr,
+            :places, :transitions, :nets,
+            :pn, :tn, :nn,
+            :net_point,
+            :net_selection,
+            :net, :nnet,
+            :net_point_reset,
+            :net_point=,
+            to: :y_nelson_agent )
+
+  # Simulation aspect.
+  delegate( :simulation_point, :ssc_point, :cc_point, :imc_point,
+            :simulation_selection, :ssc_selection,
+            :cc_selection, :imc_selection,
+            :simulations,
+            :clamp_collections,
+            :initial_marking_collections,
+            :simulation_settings_collections,
+            :clamp_collection_names, :ncc,
+            :initial_marking_collection_names, :nimc,
+            :simulation_settings_collection_names, :nssc,
+            :set_clamp_collection, :set_cc,
+            :set_initial_marking_collection, :set_imc,
+            :set_simulation_settings_collection, :set_ssc,
+            :new_simulation,
+            :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
+            :simulation_point_position,
+            :simulation,
+            :clamp_collection, :cc,
+            :initial_marking_collection, :imc,
+            :simulation_settings_collection, :ssc,
+            :clamp,
+            :initial_marking,
+            :set_step, :set_step_size,
+            :set_time, :set_target_time,
+            :set_sampling,
+            :set_simulation_method,
+            :new_timed_simulation,
+            :run!,
+            :print_recording,
+            :plot,
+            :plot_selected,
+            :plot_state,
+            :plot_flux,
+            to: :y_nelson_agent )
+
+
+  # Zz aspect.
+  delegate( :Dimension,
+            :ϝ,
+            :default_dimension,
+            :primary_point, :p1,
+            :secondary_point, :p2,
+            :primary_dimension_point, :d1,
+            :secondary_dimension_point, :d2,
+            :visualize,
+            :graphviz,
+            to: :y_nelson_agent )
+end # module YNelson

data/lib/y_nelson/net.rb

@@ -1,12 +1,4 @@
 # Represents Petri nets inside the Nelson net.
 # 
 class YNelson::Net < YPetri::Net
-
-  private
-
-  # Place, Transition, Net class
-  # 
-  def Place; ::YNelson::Place end
-  def Transition; ::YNelson::Transition end
-  def Net; ::YNelson::Net end
 end # class YNelson::Net

data/lib/y_nelson/place.rb

@@ -3,26 +3,29 @@
 # 
 class YNelson::Place < YPetri::Place
   include YNelson::Yzz
+
+  # include Mongoid::Document
+  # store_in collection: "places", database: "y_nelson"
+
   alias call along # .( :dim ) instead of .along( :dim )
 
   class << self
+    private :new
+  end
+
+  def initialize( *args )
+    super
+    
   end
 
   # Subclass of YTed::Zz::Side.
   # 
   class Side < Side
-    # "Budding": creation of new cells from the cell sides
+    # "Budding": creation of new cells from the cell sides.
+    # 
     def bud( value: L!, f: nil )
       # FIXME
     end
     alias :>> :bud
   end
-
-  private
-
-  # Place, Transition, Net class
-  # 
-  def Place; ::YNelson::Place end
-  def Transition; ::YNelson::Transition end
-  def Net; ::YNelson::Net end
 end

data/lib/y_nelson/transition.rb

@@ -29,10 +29,4 @@ class YNelson::Transition < YPetri::Transition
     }
     super
   end
-
-  # Place, Transition, Net class.
-  # 
-  def Place; ::YNelson::Place end
-  def Transition; ::YNelson::Transition end
-  def Net; ::YNelson::Net end
 end

data/lib/y_nelson/version.rb

@@ -1,4 +1,4 @@
 module YNelson
   DEBUG = false
-  VERSION = "0.1.5"
+  VERSION = "2.0.1"
 end

data/lib/y_nelson/yzz.rb

@@ -8,4 +8,4 @@ module YNelson::Yzz
       args.size == 1 && args[0].is_a?( ::YNelson::Dimension )
     super( ::YNelson.Dimension *args )
   end
-end # module YzzPrepend
+end # module Yzz

data/lib/y_nelson.rb

@@ -1,4 +1,5 @@
-# -*- coding: utf-8 -*-
+# encoding: utf-8
+
 require 'yzz'
 require 'y_petri'
 require 'y_support/kde'
@@ -13,134 +14,73 @@ require_relative 'y_nelson/transition'
 require_relative 'y_nelson/net'
 require_relative 'y_nelson/zz_point'
 require_relative 'y_nelson/dimension_point'
-require_relative 'y_nelson/manipulator'
+require_relative 'y_nelson/agent'
+require_relative 'y_nelson/dsl'
 
 # YNelson is an implementation of a cross between Ted Nelson's Zz structure, and
-# a functional Petri net (FPN). The resulting data structure, which combines
-# qualities of FPNs with those of relational databases, I refer to as Nelson net
-# throughout this text.
+# the functional Petri net (FPN). The resulting data structure, which combines
+# the qualities of FPNs with those of relational databases, I refer to as Nelson
+# net throughout this text.
 # 
-# One way to understand Nelson nets is as a genralization of a spreadsheet. In
-# his explanations of Zz structures, Ted Nelson makes wide use of spreadsheet
-# metaphors: cells, ranks, rows, columns, cursors, selections... Nelson net
-# implemented here adds "formulas" to the mix, represented by FPN transitions.
+# A Nelson net, from a certain point of view, is as a genralization of a
+# spreadsheet software. In his explanations of Zz structures, Ted Nelson makes
+# wide use of metaphors well known from spreadsheets: cells, ranks, rows,
+# columns, cursors, selections... Nelson net, as implemented here, adds
+# "formulas" to the mix: Spreadsheet "formulas" are simply represented by FPN
+# transitions.
 # 
-# Nelson net disposes of the arbitrary constraints on FPNs as well as the
-# orthogonal structure of "cells" seen in most practical spreadsheet
-# implementations:
+# Nelson net disposes of the arbitrary constraints on FPNs, and also extends the
+# plain orthogonal structure of spreadsheet "cells", as can be seen in the
+# existing spreadsheet implementations:
 # 
 # 1. Both places and transitions of the FPN take part in zz structure.
 # 2. Formula-based transitions are upgraded to standalone FPN transitions.
 # 
-# The implications of the zz structure differences from ordinary hyperorthogonal
-# structures hav been, to a degree, explained by Ted Nelson himself. There is a
-# growing body of literature on zz structure applications, including in
-# bioinformatics.
+# The implications of the differences of a zz structure from ordinary
+# hyperorthogonal structures have been, to a degree, explained by Ted Nelson
+# himself. There is a growing body of literature on zz structure applications,
+# including the applications in bioinformatics.
 #
 # As for functional Petri nets, their power in computing is well recognized (eg.
 # Funnel, Odersky 2000). FPNs are sometimes just called functional nets, because
 # Petri originally described his nets as timeless and functionless. However, in
 # special-purpose applications, such as biochemical applications, to which I
 # incline, it is appropriate to honor Petri, who designed his nets specifically
-# with chemical modeling in mind as one of their main applications. In
-# biochemistry, it is common to call functional nets Petri nets (Miyano, 200?).
+# with chemical modeling in mind. In biochemistry, it is common to call
+# functional nets Petri nets (Miyano, 200?).
 # 
 module YNelson
-  # Singleton class of YNelson is partial descendant of YPetri::Workspace. More
-  # specifically, it mixes in most YPetri::Workspace instance methods and
-  # provides interface, which should be a superset of YPetri::Workspace. The
-  # difference is, that while YPetri::Workspace can have multiple instances,
-  # representing workdesks, YNelson is a singleton representing relational
-  # database.
+  # Singleton class of YNelson is a partial descendant of YPetri::World. It
+  # aspires to be a database that represents the world. More specifically, it
+  # mixes in most of the YPetri::World methods, and provides interface, which
+  # is a superset of YPetri::World interface. The difference is, that while
+  # YPetri::World can have multiple instances – workspaces in which we possibly
+  # represent the world in different ways – YNelson::World is a singleton.
   # 
   class << self
-    # YNelson metaclass includes instance methods of YPetri::Workspace.
-    include YPetri::Workspace::PetriNetRelatedMethods
-    include YPetri::Workspace::SimulationRelatedMethods
+    attr_reader :dimensions
+
+    # Including instance methods of YPetri::World:
+    include YPetri::World::PetriNetRelated
+    include YPetri::World::SimulationRelated
 
-    # Allows summoning DSL by 'include YNelson' (like YPetri does).
+    # Allows summoning YNelson::DSL by 'include YNelson'.
     # 
     def included receiver
-      # receiver.instance_variable_set :@NelsonManipulator, Manipulator.new
-      # puts "included in #{receiver}"
-      receiver.module_exec {
-        define_method :nelson_manipulator do
-          singleton_class.instance_variable_get :@NelsonManipulator or
-            ( puts "defining Manipulator for #{self} singleton class" if YNelson::DEBUG
-              singleton_class.instance_variable_set :@NelsonManipulator, Manipulator.new )
-        end
-      }
+      receiver.extend YNelson::DSL
+      receiver.delegate :y_nelson_agent, to: "self.class"
     end
-
-    def dimensions; @dimensions end
   end # class << self
 
-  # Instance variables @Place, @Transition, @Net are expected by
-  # YPetri::Workspace module.
-  @Place, @Transition, @Net = self::Place, self::Transition, self::Net
+  # Parametrize the Place / Transition / Net classes.
+  param_class!( { Place: YNelson::Place,
+                  Transition: YNelson::Transition,
+                  Net: YNelson::Net },
+                with: { world: self } )
 
-  # Atypical call to #initialize in the course of module execution.
-  initialize
-  
-  delegate( :workspace, to: :nelson_manipulator )
+  # Make them their own namespaces.
+  [ Place(), Transition(), Net() ].each &:namespace!
 
-  # Petri net aspect.
-  delegate( :Place, :Transition, :Net,
-            :place, :transition, :pl, :tr,
-            :places, :transitions, :nets,
-            :pp, :tt, :nn,
-            :net_point,
-            :net_selection,
-            :net, :ne,
-            :net_point_reset,
-            :net_point_set,
-            to: :nelson_manipulator )
-
-  # Simulation aspect.
-  delegate( :simulation_point, :ssc_point, :cc_point, :imc_point,
-            :simulation_selection, :ssc_selection,
-            :cc_selection, :imc_selection,
-            :simulations,
-            :clamp_collections,
-            :initial_marking_collections,
-            :simulation_settings_collections,
-            :clamp_collection_names, :cc_names,
-            :initial_marking_collection_names, :imc_names,
-            :simulation_settings_collection_names, :ssc_names,
-            :set_clamp_collection, :set_cc,
-            :set_initial_marking_collection, :set_imc,
-            :set_simulation_settings_collection, :set_ssc,
-            :new_timed_simulation,
-            :clamp_cc, :initial_marking_cc, :simulation_settings_cc,
-            :simulation_point_position,
-            :simulation,
-            :clamp_collection, :cc,
-            :initial_marking_collection, :imc,
-            :simulation_settings_collection, :ssc,
-            :clamp,
-            :initial_marking,
-            :set_step, :set_step_size,
-            :set_time, :set_target_time,
-            :set_sampling,
-            :set_simulation_method,
-            :new_timed_simulation,
-            :run!,
-            :print_recording,
-            :plot,
-            :plot_selected,
-            :plot_state,
-            :plot_flux,
-            to: :nelson_manipulator )
-
-  # Zz aspect.
-  delegate( :Dimension,
-            :ϝ,
-            :default_dimension,
-            :primary_point, :p1,
-            :secondary_point, :p2,
-            :primary_dimension_point, :d1,
-            :secondary_dimension_point, :d2,
-            :visualize,
-            :graphviz,
-            to: :nelson_manipulator )
+  # Atypical initialize call.
+  initialize
 end

data/test/mongoid_example.rb

@@ -0,0 +1,100 @@
+require 'y_support/all'
+
+# Places are basically glorified variables, with current contents (marking), and
+# default contents (default_marking).
+#
+class Place
+  attr_reader :name, :default_marking
+  attr_accessor :marking
+  def initialize name, default_marking=0
+    @name, @default_marking = name, default_marking
+  end
+  def reset!; @marking = default_marking end
+end
+
+# Transitions specify how marking changes when the transition "fires" (activates).
+# "Arcs" attribute is a hash of { place => change } pairs.
+#
+class Transition
+  attr_reader :name, :arcs
+  def initialize( name, arcs: {} )
+    @name, @arcs = name, arcs
+  end
+  def fire!
+    arcs.each { |place, change| place.marking = place.marking + change }
+  end
+end
+
+A, B, C = Place.new( "A" ), Place.new( "B" ), Place.new( "C" )
+
+# Marking of A is incremented by 1
+AddA = Transition.new( "AddA", arcs: { A => 1 } )
+
+# 1 piece of A dissociates into 1 piece of B and 1 piece of C
+DissocA = Transition.new( "DissocA", arcs: { A => -1, B => +1, C => +1 } )
+
+[ A, B, C ].each &:reset!
+[ A, B, C ].map &:marking #=> [0, 0, 0]
+AddA.fire!
+[ A, B, C ].map &:marking #=> [1, 0, 0]
+DissocA.fire!
+[ A, B, C ].map &:marking #=> [0, 1, 1]
+
+require 'yaml'
+
+class Place
+  def to_yaml
+    YAML.dump( { name: name, default_marking: default_marking } )
+  end
+
+  def to_ruby
+    "Place( name: #{name}, default_marking: #{default_marking} )\n"
+  end
+end
+
+puts A.to_yaml
+puts B.to_yaml
+puts C.to_yaml
+puts A.to_ruby
+puts B.to_ruby
+puts C.to_ruby
+
+class Transition
+  def to_yaml
+    YAML.dump( { name: name, arcs: arcs.modify { |k, v| [k.name, v] } } )
+  end
+
+  def to_ruby
+    "Transition( name: #{name}, default_marking: #{arcs.modify { |k, v| [k.name.to_sym, v] }} )\n"
+  end
+end
+
+puts AddA.to_yaml
+puts DissocA.to_yaml
+puts AddA.to_ruby
+puts DissocA.to_ruby
+
+# Now save that to a file
+# and use
+
+Place.from_yaml YAML.load( yaml_place_string )
+Transition.from_yaml YAML.load( yaml_transition_string )
+# or
+YNelson::Manipulator.load( yaml: YAML.load( system_definition ) )
+
+# then decorate #to_yaml and #to_ruby methods with Zz-structure-specific parts.
+
+class Zz
+  def to_yaml
+    super + "\n" +
+      YAML.dump( { along: dump_connectivity() } )
+  end
+
+  def to_ruby
+    super + "\n" +
+      "#{name}.along( #{dimension} ).posward #{along( dimension ).posward.name}\n" +
+      "#{name}.along( #{dimension} ).negward #{along( dimension ).negward.name}"
+  end
+end
+
+# etc.

data/test/y_nelson_test.rb

@@ -1,7 +1,5 @@
-#! /usr/bin/ruby
-# -*- coding: utf-8 -*-
+# encoding: utf-8
 
-require 'minitest/spec'
 require 'minitest/autorun'
 # tested component itself
 require './../lib/y_nelson'
@@ -9,11 +7,10 @@ require './../lib/y_nelson'
 # **************************************************************************
 # Nelson net test
 # **************************************************************************
-#
+# 
 describe YNelson do
   before do
-    skip
-    @m = YNelson::Manipulator.new
+    @m = YNelson::Agent.new
     @p = @m.Place default_marking: 3.2,
                   marking: 1.1,
                   quantum: 0.1
@@ -29,9 +26,11 @@ describe YNelson do
     it "should work as expected" do
       assert_equal [], @p.neighbors
       assert_equal [], @p.connectivity # 'connectivity' now exclusively a zz keyword
-      t = @m.Transition codomain: @p, action: lambda { 0.1 }, assignment: true
+      t = @m.Transition codomain: @p,
+                        action: -> { 0.1 },
+                        assignment: true
       assert_equal [ @p ], t.neighbors
-      dim = @m.Dimension( :codomain, 0 )
+      dim = @m.Dimension( t, :codomain, 0 )
       assert_equal @p, t.along( dim ).posward.neighbor
       # And then, it would be the job of dimension reduction to determine if
       # some dimensions should be visualized or otherwise used together.
@@ -77,7 +76,7 @@ end
 
 describe "visualization" do
   before do
-    @m = YNelson::Manipulator.new
+    @m = YNelson::Agent.new
     @m.Place name: :A, m!: 3.2
     @m.Place name: :B, m!: 5
     @m.Transition name: :T1, s: { A: -1, B: 1 }, rate: 1
@@ -86,8 +85,11 @@ describe "visualization" do
   end
 
   it "should work" do
-    dim1 = YNelson::Dimension( :domain, 0 )
-    dim2 = YNelson::Dimension( :codomain, 1 )
+    dim1 = YNelson::Dimension( @m.transition( :T1 ), :domain, 0 )
+    dim2 = YNelson::Dimension( @m.transition( :T2 ), :domain, 0 )
+    @m.visualize dim1, dim2
+    dim1 = YNelson::Dimension( @m.transition( :T1 ), :codomain, 0 )
+    dim2 = YNelson::Dimension( @m.transition( :T2 ), :codomain, 0 )
     @m.visualize dim1, dim2
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_nelson
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 2.0.1
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-05-14 00:00:00.000000000 Z
+date: 2013-08-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: yzz
@@ -78,10 +78,12 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
+- config/mongoid.yml
 - lib/y_nelson.rb
+- lib/y_nelson/agent.rb
 - lib/y_nelson/dimension.rb
 - lib/y_nelson/dimension_point.rb
-- lib/y_nelson/manipulator.rb
+- lib/y_nelson/dsl.rb
 - lib/y_nelson/net.rb
 - lib/y_nelson/place.rb
 - lib/y_nelson/transition.rb
@@ -89,9 +91,11 @@ files:
 - lib/y_nelson/yzz.rb
 - lib/y_nelson/zz.png
 - lib/y_nelson/zz_point.rb
+- test/mongoid_example.rb
 - test/y_nelson_test.rb
 - test/zz.png
 - y_nelson.gemspec
+- zz.png
 homepage: ''
 licenses:
 - MIT
@@ -117,5 +121,6 @@ signing_key:
 specification_version: 4
 summary: A fusion of functional Petri net with a zz structure.
 test_files:
+- test/mongoid_example.rb
 - test/y_nelson_test.rb
 - test/zz.png