fathom 0.3.4 → 0.3.6

data/VERSION

@@ -1 +1 @@
-0.3.4
+0.3.6

data/lib/fathom.rb

@@ -19,39 +19,6 @@ module Fathom
   lib = File.expand_path(File.dirname(__FILE__))
   $LOAD_PATH.unshift(lib)
   
-  Fathom.autoload :Node, "node"
-  Fathom.autoload :BeliefNode, "node/belief_node"
-  Fathom.autoload :DataCollection, "node/data_collection"
-  Fathom.autoload :DataNode, "node/data_node"
-  Fathom.autoload :DiscreteNode, "node/discrete_node"
-  Fathom.autoload :MCNode, "node/mc_node"
-  Fathom.autoload :PlausibleRange, "node/plausible_range"
-  Fathom.autoload :Fact, "node/fact"
-  Fathom.autoload :Decision, "node/decision"
-  Fathom.autoload :CPMNode, 'node/cpm_node'
-  
-  Fathom.autoload :ValueDescription, "value_description"
-  Fathom.autoload :MonteCarloSet, "monte_carlo_set"
-  Fathom.autoload :KnowledgeBase, "knowledge_base"
-  
-  Fathom.autoload :Import, "import"
-  Fathom.autoload :ImportNode, "import/import_node"
-  Fathom.autoload :YAMLImport, 'import/yaml_import'
-  Fathom.autoload :CSVImport, 'import/csv_import'
-  
-  Fathom.autoload :Simulation, 'simulation'
-  Fathom.autoload :TickMethods, 'simulation/tick_methods'
-  Fathom.autoload :TickSimulation, 'simulation/tick_simulation'
-  
-  Fathom.autoload :Agent, 'agent'
-  Fathom.autoload :Properties, 'agent/properties'
-  Fathom.autoload :AgentCluster, 'agent/agent_cluster'
-  
-  Fathom.autoload :EnforcedName, 'node/node_extensions/enforced_name'
-  Fathom.autoload :NumericMethods, 'node/node_extensions/numeric_methods'
-  
-  
-  
   # Autoload classes and modules so that we only load as much of the library as we're using.
   # This allows us to have a fairly large library without taking up a lot of memory unless we need it.
   # autoload :Node, "node"
@@ -103,3 +70,34 @@ end
 
 # Temporary
 # include Fathom
+
+Fathom.autoload :Node, "node"
+Fathom.autoload :BeliefNode, "node/belief_node"
+Fathom.autoload :DataCollection, "node/data_collection"
+Fathom.autoload :DataNode, "node/data_node"
+Fathom.autoload :DiscreteNode, "node/discrete_node"
+Fathom.autoload :MCNode, "node/mc_node"
+Fathom.autoload :PlausibleRange, "node/plausible_range"
+Fathom.autoload :Fact, "node/fact"
+Fathom.autoload :Decision, "node/decision"
+Fathom.autoload :CPMNode, 'node/cpm_node'
+
+Fathom.autoload :ValueDescription, "value_description"
+Fathom.autoload :MonteCarloSet, "monte_carlo_set"
+Fathom.autoload :KnowledgeBase, "knowledge_base"
+
+Fathom.autoload :Import, "import"
+Fathom.autoload :ImportNode, "import/import_node"
+Fathom.autoload :YAMLImport, 'import/yaml_import'
+Fathom.autoload :CSVImport, 'import/csv_import'
+
+Fathom.autoload :Simulation, 'simulation'
+Fathom.autoload :TickMethods, 'simulation/tick_methods'
+Fathom.autoload :TickSimulation, 'simulation/tick_simulation'
+
+Fathom.autoload :Agent, 'agent'
+Fathom.autoload :Properties, 'agent/properties'
+Fathom.autoload :AgentCluster, 'agent/agent_cluster'
+
+Fathom.autoload :EnforcedName, 'node/node_extensions/enforced_name'
+Fathom.autoload :NumericMethods, 'node/node_extensions/numeric_methods'

data/lib/fathom/node/mc_node.rb

@@ -1,7 +1,8 @@
 require File.expand_path(File.join(File.dirname(__FILE__), '..', '..', 'fathom'))
 class Fathom::MCNode < Fathom::Node
   
-  attr_reader :value_description, :samples_taken
+  attr_reader :samples_taken
+  attr_accessor :value_description
   
   def initialize(opts={}, &block) 
     super(opts)

data/spec/fathom/distributions/gaussian_spec.rb

@@ -18,7 +18,7 @@ describe Gaussian do
   end
   
   it "should be able to generate an inverse CDF" do
-    Gaussian.inverse_cdf(@opts).should be_close(-0.16448, 0.00001)
+    Gaussian.inverse_cdf(@opts).should be_within(0.00001).of(-0.16448)
   end
   
   it "should require mean as an option for an inverse CDF" do
@@ -33,20 +33,20 @@ describe Gaussian do
   
   it "should take std as an alias for sd when creating an inverse CDF" do
     @opts.delete(:sd)
-    Gaussian.inverse_cdf(@opts.merge(:std => 0.1)).should be_close(-0.16448, 0.00001)
+    Gaussian.inverse_cdf(@opts.merge(:std => 0.1)).should be_within(0.00001).of(-0.16448)
   end
 
   it "should take standard_deviation as an alias for sd when creating an inverse CDF" do
     @opts.delete(:sd)
-    Gaussian.inverse_cdf(@opts.merge(:standard_deviation => 0.1)).should be_close(-0.16448, 0.00001)
+    Gaussian.inverse_cdf(@opts.merge(:standard_deviation => 0.1)).should be_within(0.00001).of(-0.16448)
   end
   
   it "should be able to set upper to true and get Q instead of P" do
-    Gaussian.inverse_cdf(@opts.merge(:upper =>true)).should be_close(0.16448, 0.00001)
+    Gaussian.inverse_cdf(@opts.merge(:upper =>true)).should be_within(0.00001).of(0.16448)
   end
   
   it "should be able to take a different confidence interval" do
-    Gaussian.inverse_cdf(@opts.merge(:confidence_interval => 0.1)).should be_close(-0.12815, 0.00001)
+    Gaussian.inverse_cdf(@opts.merge(:confidence_interval => 0.1)).should be_within(0.00001).of(-0.12815)
   end
 
   it "should have a lower_bound alias for inverse_cdf" do

data/spec/fathom/import/import_node_spec.rb

@@ -5,6 +5,6 @@ include Fathom
 describe ImportNode do
   it "should record the time of the import" do
     i = ImportNode.new
-    i.imported_at.should be_close(Time.now, 0.01)
+    i.imported_at.should be_within(0.01).of(Time.now)
   end
 end

data/spec/fathom/node/cpm_node_spec.rb

@@ -46,24 +46,24 @@ describe CPMNode do
     # GSL::Matrix
     # [  8.000e-02  1.200e-01 
     #    3.200e-01  4.800e-01 ]
-    @cpm.probability(:color => :red, :child => :asher).should be_close(0.08, 1e-10)
-    @cpm.probability(:color => :red, :child => :stella).should be_close(0.32, 1e-10)
-    @cpm.probability(:color => :green, :child => :asher).should be_close(0.12, 1e-10)
-    @cpm.probability(:color => :green, :child => :stella).should be_close(0.48, 1e-10)
+    @cpm.probability(:color => :red, :child => :asher).should be_within(1e-10).of(0.08)
+    @cpm.probability(:color => :red, :child => :stella).should be_within(1e-10).of(0.32)
+    @cpm.probability(:color => :green, :child => :asher).should be_within(1e-10).of(0.12)
+    @cpm.probability(:color => :green, :child => :stella).should be_within(1e-10).of(0.48)
   end
   
   it "should look for all children values, if no child is provided" do
-    @cpm.probability(:child => :asher).should be_close(0.2, 1e-10)
-    @cpm.probability(:child => :stella).should be_close(0.8, 1e-10)
+    @cpm.probability(:child => :asher).should be_within(1e-10).of(0.2)
+    @cpm.probability(:child => :stella).should be_within(1e-10).of(0.8)
   end
   
   it "should look for all parent values, if no parent is provided" do
-    @cpm.probability(:color => :red).should be_close(0.4, 1e-10)
-    @cpm.probability(:color => :green).should be_close(0.6, 1e-10)
+    @cpm.probability(:color => :red).should be_within(1e-10).of(0.4)
+    @cpm.probability(:color => :green).should be_within(1e-10).of(0.6)
   end
   
   it "should provide a probability of 1 if no filter is set" do
-    @cpm.probability.should be_close(1.0, 1e-10)
+    @cpm.probability.should be_within(1e-10).of(1.0)
   end
   
   it "should give a description in a hash, if description is turned on" do
@@ -79,38 +79,38 @@ describe CPMNode do
   end
   
   it "should alias p for probability" do
-    @cpm.p(:color => :red, :child => :asher).should be_close(0.08, 1e-10)
-    @cpm.p(:color => :red, :child => :stella).should be_close(0.32, 1e-10)
-    @cpm.p(:color => :green, :child => :asher).should be_close(0.12, 1e-10)
-    @cpm.p(:color => :green, :child => :stella).should be_close(0.48, 1e-10)
-    @cpm.p(:child => :asher).should be_close(0.2, 1e-10)
-    @cpm.p(:child => :stella).should be_close(0.8, 1e-10)
-    @cpm.p(:color => :red).should be_close(0.4, 1e-10)
-    @cpm.p(:color => :green).should be_close(0.6, 1e-10)
-    @cpm.p.should be_close(1.0, 1e-10)
+    @cpm.p(:color => :red, :child => :asher).should be_within(1e-10).of(0.08)
+    @cpm.p(:color => :red, :child => :stella).should be_within(1e-10).of(0.32)
+    @cpm.p(:color => :green, :child => :asher).should be_within(1e-10).of(0.12)
+    @cpm.p(:color => :green, :child => :stella).should be_within(1e-10).of(0.48)
+    @cpm.p(:child => :asher).should be_within(1e-10).of(0.2)
+    @cpm.p(:child => :stella).should be_within(1e-10).of(0.8)
+    @cpm.p(:color => :red).should be_within(1e-10).of(0.4)
+    @cpm.p(:color => :green).should be_within(1e-10).of(0.6)
+    @cpm.p.should be_within(1e-10).of(1.0)
   end
   
   it "should have odds for any query" do
-    @cpm.odds(:color => :red, :child => :asher).should be_close(0.087, 1e-3)
-    @cpm.odds(:color => :red, :child => :stella).should be_close(0.471, 1e-3)
-    @cpm.odds(:color => :green, :child => :asher).should be_close(0.136, 1e-3)
-    @cpm.odds(:color => :green, :child => :stella).should be_close(0.923, 1e-3)
-    @cpm.odds(:child => :asher).should be_close(0.25, 1e-3)
-    @cpm.odds(:child => :stella).should be_close(4.0, 1e-3)
-    @cpm.odds(:color => :red).should be_close(0.666, 1e-3)
-    @cpm.odds(:color => :green).should be_close(1.5, 1e-3)
+    @cpm.odds(:color => :red, :child => :asher).should be_within(1e-3).of(0.087)
+    @cpm.odds(:color => :red, :child => :stella).should be_within(1e-3).of(0.471)
+    @cpm.odds(:color => :green, :child => :asher).should be_within(1e-3).of(0.136)
+    @cpm.odds(:color => :green, :child => :stella).should be_within(1e-3).of(0.923)
+    @cpm.odds(:child => :asher).should be_within(1e-3).of(0.25)
+    @cpm.odds(:child => :stella).should be_within(1e-3).of(4.0)
+    @cpm.odds(:color => :red).should be_within(1e-3).of(0.666)
+    @cpm.odds(:color => :green).should be_within(1e-3).of(1.5)
     @cpm.odds.should eql(1 / 0.0)
   end
   
   it "should alias o for odds" do
-    @cpm.o(:color => :red, :child => :asher).should be_close(0.087, 1e-3)
-    @cpm.o(:color => :red, :child => :stella).should be_close(0.471, 1e-3)
-    @cpm.o(:color => :green, :child => :asher).should be_close(0.136, 1e-3)
-    @cpm.o(:color => :green, :child => :stella).should be_close(0.923, 1e-3)
-    @cpm.o(:child => :asher).should be_close(0.25, 1e-3)
-    @cpm.o(:child => :stella).should be_close(4.0, 1e-3)
-    @cpm.o(:color => :red).should be_close(0.666, 1e-3)
-    @cpm.o(:color => :green).should be_close(1.5, 1e-3)
+    @cpm.o(:color => :red, :child => :asher).should be_within(1e-3).of(0.087)
+    @cpm.o(:color => :red, :child => :stella).should be_within(1e-3).of(0.471)
+    @cpm.o(:color => :green, :child => :asher).should be_within(1e-3).of(0.136)
+    @cpm.o(:color => :green, :child => :stella).should be_within(1e-3).of(0.923)
+    @cpm.o(:child => :asher).should be_within(1e-3).of(0.25)
+    @cpm.o(:child => :stella).should be_within(1e-3).of(4.0)
+    @cpm.o(:color => :red).should be_within(1e-3).of(0.666)
+    @cpm.o(:color => :green).should be_within(1e-3).of(1.5)
     @cpm.o.should eql(1 / 0.0)
   end
   

data/spec/fathom/node/plausible_range_spec.rb

@@ -68,7 +68,7 @@ describe PlausibleRange do
   end
   
   it "should be able to calculate the standard deviation" do
-    @pr.standard_deviation.should be_close( 2.7358, 0.0001)
+    @pr.standard_deviation.should be_within(0.0001).of( 2.7358)
   end
   
   it "should be able to use std instead of standard_deviation" do

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: fathom
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 31
   prerelease: 
   segments: 
   - 0
   - 3
-  - 4
-  version: 0.3.4
+  - 6
+  version: 0.3.6
 platform: ruby
 authors: 
 - David