RubyGems - rubyneat - Versions diffs - 0.3.5.alpha.3 → 0.3.5.alpha.5 - Mend

rubyneat 0.3.5.alpha.3 → 0.3.5.alpha.5

Files changed (252) hide show

checksums.yaml +4 -4
data/.semver +1 -1
data/Gemfile +19 -19
data/Gemfile.lock +39 -33
data/README.md +66 -0
data/Rakefile +19 -2
data/bin/neat +4 -60
data/lib/rubyneat/cli.rb +5 -0
data/lib/rubyneat/cli/generate.rb +131 -0
data/lib/rubyneat/cli/main.rb +54 -0
data/lib/rubyneat/cli/templates/generate/Gemfile.tt +17 -0
data/lib/rubyneat/cli/templates/generate/README.md.tt +1 -0
data/lib/rubyneat/cli/templates/generate/bin/neat.tt +14 -0
data/{neater/xor_neat.rb → lib/rubyneat/cli/templates/generate/neater.tt} +7 -22
data/rubyneat.gemspec +73 -297
data/rubyneat.gemspec.orig +384 -0
metadata +76 -292
data/.idea/.name +0 -1
data/.idea/.rakeTasks +0 -7
data/.idea/dictionaries/trader.xml +0 -3
data/.idea/encodings.xml +0 -5
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data/.idea/modules.xml +0 -9
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data/.idea/runConfigurations/sigdebug_neat.xml +0 -24
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data/.idea/runConfigurations/xorsin_neat.xml +0 -24
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data/doc/NEAT/Trait.html +0 -169
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data/neater/rnlib/xor.rb +0 -10
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data/neater/xoranalog_neat.rb +0 -138
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data/rdoc/NEAT/Expressor.html +0 -402
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data/rdoc/NEAT/Operator.html +0 -109
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data/rdoc/RubyNEAT.html +0 -98
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data/rdoc/SDL.html +0 -98
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data/rdoc/doc/DSL_html.html +0 -992
data/rdoc/doc/NEAT/BasicNeuronTypes/BiasNeuron_html.html +0 -617
data/rdoc/doc/NEAT/BasicNeuronTypes/CosineNeuron_html.html +0 -413
data/rdoc/doc/NEAT/BasicNeuronTypes/InputNeuron_html.html +0 -498
data/rdoc/doc/NEAT/BasicNeuronTypes/SigmoidNeuron_html.html +0 -413
data/rdoc/doc/NEAT/BasicNeuronTypes/SineNeuron_html.html +0 -413
data/rdoc/doc/NEAT/BasicNeuronTypes/TanhNeuron_html.html +0 -412
data/rdoc/doc/NEAT/BasicNeuronTypes_html.html +0 -310
data/rdoc/doc/NEAT/Controller/NeatSettings_html.html +0 -3324
data/rdoc/doc/NEAT/Controller_html.html +0 -2212
data/rdoc/doc/NEAT/Critter/Genotype/Gene_html.html +0 -997
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data/rdoc/doc/NEAT/Critter/Phenotype_html.html +0 -687
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data/rdoc/doc/NEAT/Evaluator_html.html +0 -556
data/rdoc/doc/NEAT/Evolver/CritterOp_html.html +0 -690
data/rdoc/doc/NEAT/Evolver_html.html +0 -677
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data/rdoc/doc/NEAT/Graph/DependencyResolver_html.html +0 -598
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data/rdoc/doc/NEAT/Population_html.html +0 -1795
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data/doc/NEAT/Operator.html DELETED Viewed

@@ -1,162 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: NEAT::Operator
-    &mdash; Documentation by YARD 0.8.7.4
-</title>
-  <link rel="stylesheet" href="../css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="../css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '../';
-  framesUrl = "../frames.html#!NEAT/Operator.html";
-</script>
-  <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="../_index.html">Index (O)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../NEAT.html" title="NEAT (module)">NEAT</a></span></span>
-     &raquo;
-    <span class="title">Operator</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="../class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="../method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="../file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: NEAT::Operator
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></li>
-            <li class="next">NEAT::Operator</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/rubyneat/rubyneat.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<h1 id="label-Base+class+of+operators+in+RubyNEAT%2C">Base class of operators in RubyNEAT,</h1>
-<p>Such as Evolver, etc.</p>
-  </div>
-</div>
-<div class="tags">
-</div><div id="subclasses">
-  <h2>Direct Known Subclasses</h2>
-  <p class="children"><span class='object_link'><a href="Evaluator.html" title="NEAT::Evaluator (class)">Evaluator</a></span>, <span class='object_link'><a href="Evolver.html" title="NEAT::Evolver (class)">Evolver</a></span>, <span class='object_link'><a href="Expressor.html" title="NEAT::Expressor (class)">Expressor</a></span></p>
-</div>
-  <h2>Instance Attribute Summary</h2>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="NeatOb.html#controller-instance_method" title="NEAT::NeatOb#controller (method)">#controller</a></span>, <span class='object_link'><a href="NeatOb.html#name-instance_method" title="NEAT::NeatOb#name (method)">#name</a></span></p>
-  <h2>Method Summary</h2>
-  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="NeatOb.html#initialize-instance_method" title="NEAT::NeatOb#initialize (method)">#initialize</a></span>, <span class='object_link'><a href="NeatOb.html#log-instance_method" title="NEAT::NeatOb#log (method)">#log</a></span>, <span class='object_link'><a href="NeatOb.html#log-class_method" title="NEAT::NeatOb.log (method)">log</a></span>, <span class='object_link'><a href="NeatOb.html#to_s-instance_method" title="NEAT::NeatOb#to_s (method)">#to_s</a></span></p>
-  <div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <p class="notice">This class inherits a constructor from <span class='object_link'><a href="NeatOb.html#initialize-instance_method" title="NEAT::NeatOb#initialize (method)">NEAT::NeatOb</a></span></p>
-</div>
-</div>
-    <div id="footer">
-  Generated on Sun Apr 13 15:54:02 2014 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.4 (ruby-2.1.1).
-</div>
-  </body>
-</html>

data/doc/NEAT/Population.html DELETED Viewed

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-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
-  <head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<title>
-  Class: NEAT::Population
-    &mdash; Documentation by YARD 0.8.7.4
-</title>
-  <link rel="stylesheet" href="../css/style.css" type="text/css" charset="utf-8" />
-  <link rel="stylesheet" href="../css/common.css" type="text/css" charset="utf-8" />
-<script type="text/javascript" charset="utf-8">
-  hasFrames = window.top.frames.main ? true : false;
-  relpath = '../';
-  framesUrl = "../frames.html#!NEAT/Population.html";
-</script>
-  <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
-  <script type="text/javascript" charset="utf-8" src="../js/app.js"></script>
-  </head>
-  <body>
-    <div id="header">
-      <div id="menu">
-    <a href="../_index.html">Index (P)</a> &raquo;
-    <span class='title'><span class='object_link'><a href="../NEAT.html" title="NEAT (module)">NEAT</a></span></span>
-     &raquo;
-    <span class="title">Population</span>
-  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
-</div>
-      <div id="search">
-    <a class="full_list_link" id="class_list_link"
-        href="../class_list.html">
-      Class List
-    </a>
-    <a class="full_list_link" id="method_list_link"
-        href="../method_list.html">
-      Method List
-    </a>
-    <a class="full_list_link" id="file_list_link"
-        href="../file_list.html">
-      File List
-    </a>
-</div>
-      <div class="clear"></div>
-    </div>
-    <iframe id="search_frame"></iframe>
-    <div id="content"><h1>Class: NEAT::Population
-</h1>
-<dl class="box">
-    <dt class="r1">Inherits:</dt>
-    <dd class="r1">
-      <span class="inheritName"><span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></span>
-        <ul class="fullTree">
-          <li>Object</li>
-            <li class="next"><span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></li>
-            <li class="next">NEAT::Population</li>
-        </ul>
-        <a href="#" class="inheritanceTree">show all</a>
-      </dd>
-    <dt class="r2 last">Defined in:</dt>
-    <dd class="r2 last">lib/rubyneat/population.rb</dd>
-</dl>
-<div class="clear"></div>
-<h2>Overview</h2><div class="docstring">
-  <div class="discussion">
-<h1 id="label-Population+of+NEAT+Critters.">Population of NEAT Critters.</h1>
-<p>The Population  In ourselves we have the pool of neurons the critters all
-use. the pool of neurons are indirects, of course, as during phenotype
-expression, all the phenotypes shall be created individually.</p>
-  </div>
-</div>
-<div class="tags">
-</div>
-  <h2>Instance Attribute Summary <small>(<a href="#" class="summary_toggle">collapse</a>)</small></h2>
-  <ul class="summary">
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#critters-instance_method" title="#critters (instance method)">- (Object) <strong>critters</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>list of critter in this population.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#fitness-instance_method" title="#fitness (instance method)">- (Object) <strong>fitness</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Overall population fitness and novelty.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#hidden_neurons-instance_method" title="#hidden_neurons (instance method)">- (Object) <strong>hidden_neurons</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>List of possible neuron classes for hidden neurons.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#input_neurons-instance_method" title="#input_neurons (instance method)">- (Object) <strong>input_neurons</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Ordered list or hash of input neuron classes  (all critters generated here
-shall have this).</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#novelty-instance_method" title="#novelty (instance method)">- (Object) <strong>novelty</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Overall population fitness and novelty.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#output_neurons-instance_method" title="#output_neurons (instance method)">- (Object) <strong>output_neurons</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Ordered list or hash of output neuron classes (all critters generated here
-shall have this).</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#species-instance_method" title="#species (instance method)">- (Object) <strong>species</strong> </a>
-  </span>
-      <span class="note title readonly">readonly</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Hash list of species lists.</p>
-</div></span>
-</li>
-      <li class="public ">
-  <span class="summary_signature">
-      <a href="#traits-instance_method" title="#traits (instance method)">- (Object) <strong>traits</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Returns the value of attribute traits.</p>
-</div></span>
-</li>
-  </ul>
-  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="NeatOb.html#controller-instance_method" title="NEAT::NeatOb#controller (method)">#controller</a></span>, <span class='object_link'><a href="NeatOb.html#name-instance_method" title="NEAT::NeatOb#name (method)">#name</a></span></p>
-    <h2>
-      Class Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#compactify%21-class_method" title="compactify! (class method)">+ (Object) <strong>compactify!</strong>(parm) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#evaluate%21-class_method" title="evaluate! (class method)">+ (Object) <strong>evaluate!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#member%3F-class_method" title="member? (class method)">+ (Boolean) <strong>member?</strong>(crit) </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>lists keyed by representative critter.</p>
-</div></span>
-</li>
-    </ul>
-    <h2>
-      Instance Method Summary
-      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
-    </h2>
-    <ul class="summary">
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#analyze%21-instance_method" title="#analyze! (instance method)">- (Object) <strong>analyze!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Alalyze evaluation results.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#best_critter-instance_method" title="#best_critter (instance method)">- (Object) <strong>best_critter</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>The “best critter” is the critter with the lowest (closet to zero) fitness
-rating.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#dump_s-instance_method" title="#dump_s (instance method)">- (Object) <strong>dump_s</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'></div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#evaluate%21-instance_method" title="#evaluate! (instance method)">- (Object) <strong>evaluate!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Called for each sequence.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#evolve-instance_method" title="#evolve (instance method)">- (Object) <strong>evolve</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Call this after evaluation.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#express%21-instance_method" title="#express! (instance method)">- (Object) <strong>express!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Express the entire population.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize-instance_method" title="#initialize (instance method)">- (Population) <strong>initialize</strong>(c, &amp;block) </a>
-  </span>
-    <span class="note title constructor">constructor</span>
-    <span class="summary_desc"><div class='inline'>
-<p>Create initial (ramdom) population of critters.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#initialize_for_recurrence%21-instance_method" title="#initialize_for_recurrence! (instance method)">- (Object) <strong>initialize_for_recurrence!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Make sure all critters are reset and prepared for recurrent network
-evaluation.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#mutate%21-instance_method" title="#mutate! (instance method)">- (Object) <strong>mutate!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Mutate the genes and neurons.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#report-instance_method" title="#report (instance method)">- (Object) <strong>report</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<h2 id="label-Generate+a+report+on+the+state+of+this+population.">Generate a report on the state of this population.</h2>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#speciate%21-instance_method" title="#speciate! (instance method)">- (Object) <strong>speciate!</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>Group critters into species Note that the @species objects have useful
-singleton methods: * @species.member? – checks all of the lists for
-membership, not just the hash * @<a href="crit">species</a>.fitness –
-fitness of the entire species.</p>
-</div></span>
-</li>
-        <li class="public ">
-  <span class="summary_signature">
-      <a href="#worst_critter-instance_method" title="#worst_critter (instance method)">- (Object) <strong>worst_critter</strong> </a>
-  </span>
-    <span class="summary_desc"><div class='inline'>
-<p>The “worst critter” is the critter with the highest (away from zero)
-fitness rating.</p>
-</div></span>
-</li>
-    </ul>
-  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="NeatOb.html" title="NEAT::NeatOb (class)">NeatOb</a></span></h3>
-  <p class="inherited"><span class='object_link'><a href="NeatOb.html#log-instance_method" title="NEAT::NeatOb#log (method)">#log</a></span>, <span class='object_link'><a href="NeatOb.html#log-class_method" title="NEAT::NeatOb.log (method)">log</a></span>, <span class='object_link'><a href="NeatOb.html#to_s-instance_method" title="NEAT::NeatOb#to_s (method)">#to_s</a></span></p>
-  <div id="constructor_details" class="method_details_list">
-  <h2>Constructor Details</h2>
-    <div class="method_details first">
-  <h3 class="signature first" id="initialize-instance_method">
-    - (<tt><span class='object_link'><a href="" title="NEAT::Population (class)">Population</a></span></tt>) <strong>initialize</strong>(c, &amp;block)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Create initial (ramdom) population of critters</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-49
-50</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 37</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize'>initialize</span><span class='lparen'>(</span><span class='id identifier rubyid_c'>c</span><span class='comma'>,</span> <span class='op'>&amp;</span><span class='id identifier rubyid_block'>block</span><span class='rparen'>)</span>
-  <span class='kw'>super</span>
-  <span class='ivar'>@input_neurons</span> <span class='op'>=</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_neural_inputs'>neural_inputs</span><span class='period'>.</span><span class='id identifier rubyid_clone'>clone</span>
-  <span class='ivar'>@output_neurons</span> <span class='op'>=</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_neural_outputs'>neural_outputs</span><span class='period'>.</span><span class='id identifier rubyid_clone'>clone</span>
-  <span class='ivar'>@hidden_neurons</span> <span class='op'>=</span> <span class='kw'>unless</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_neural_hidden'>neural_hidden</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-                      <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_neural_hidden'>neural_hidden</span>
-                    <span class='kw'>else</span>
-                      <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_neuron_catalog'>neuron_catalog</span><span class='period'>.</span><span class='id identifier rubyid_keep_if'>keep_if</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_n'>n</span><span class='op'>|</span> <span class='kw'>not</span> <span class='id identifier rubyid_n'>n</span><span class='period'>.</span><span class='id identifier rubyid_input?'>input?</span><span class='rbrace'>}</span>
-                    <span class='kw'>end</span>
-  <span class='ivar'>@critters</span> <span class='op'>=</span> <span class='lparen'>(</span><span class='int'>0</span> <span class='op'>...</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_parms'>parms</span><span class='period'>.</span><span class='id identifier rubyid_start_population_size'>start_population_size</span> <span class='op'>||</span> <span class='id identifier rubyid_c'>c</span><span class='period'>.</span><span class='id identifier rubyid_parms'>parms</span><span class='period'>.</span><span class='id identifier rubyid_population_size'>population_size</span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='kw'>do</span>
-    <span class='const'>Critter</span><span class='period'>.</span><span class='id identifier rubyid_new'>new</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span>
-  <span class='kw'>end</span>
-  <span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='lparen'>(</span><span class='kw'>self</span><span class='rparen'>)</span> <span class='kw'>unless</span> <span class='id identifier rubyid_block'>block</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-</div>
-  <div id="instance_attr_details" class="attr_details">
-    <h2>Instance Attribute Details</h2>
-      <span id="critters=-instance_method"></span>
-      <div class="method_details first">
-  <h3 class="signature first" id="critters-instance_method">
-    - (<tt>Object</tt>) <strong>critters</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>list of critter in this population</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-25
-26
-27</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 25</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_critters'>critters</span>
-  <span class='ivar'>@critters</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="fitness-instance_method">
-    - (<tt>Object</tt>) <strong>fitness</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Overall population fitness and novelty</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-28
-29
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 28</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_fitness'>fitness</span>
-  <span class='ivar'>@fitness</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="hidden_neurons=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="hidden_neurons-instance_method">
-    - (<tt>Object</tt>) <strong>hidden_neurons</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>List of possible neuron classes for hidden neurons.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-16
-17
-18</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 16</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_hidden_neurons'>hidden_neurons</span>
-  <span class='ivar'>@hidden_neurons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="input_neurons=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="input_neurons-instance_method">
-    - (<tt>Object</tt>) <strong>input_neurons</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Ordered list or hash of input neuron classes  (all critters generated here
-shall have this)</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-13
-14
-15</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 13</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_input_neurons'>input_neurons</span>
-  <span class='ivar'>@input_neurons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="novelty-instance_method">
-    - (<tt>Object</tt>) <strong>novelty</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Overall population fitness and novelty</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-28
-29
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 28</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_novelty'>novelty</span>
-  <span class='ivar'>@novelty</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="output_neurons=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="output_neurons-instance_method">
-    - (<tt>Object</tt>) <strong>output_neurons</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Ordered list or hash of output neuron classes (all critters generated here
-shall have this)</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-20
-21
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 20</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_output_neurons'>output_neurons</span>
-  <span class='ivar'>@output_neurons</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id=""></span>
-      <div class="method_details ">
-  <h3 class="signature " id="species-instance_method">
-    - (<tt>Object</tt>) <strong>species</strong>  <span class="extras">(readonly)</span>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Hash list of species lists</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-31
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 31</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_species'>species</span>
-  <span class='ivar'>@species</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <span id="traits=-instance_method"></span>
-      <div class="method_details ">
-  <h3 class="signature " id="traits-instance_method">
-    - (<tt>Object</tt>) <strong>traits</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Returns the value of attribute traits</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 22</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_traits'>traits</span>
-  <span class='ivar'>@traits</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="class_method_details" class="method_details_list">
-    <h2>Class Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="compactify!-class_method">
-    + (<tt>Object</tt>) <strong>compactify!</strong>(parm)
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 102</span>
-<span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_compactify!'>compactify!</span><span class='lparen'>(</span><span class='id identifier rubyid_parm'>parm</span><span class='rparen'>)</span>
-  <span class='id identifier rubyid_mutt'>mutt</span> <span class='op'>=</span> <span class='kw'>self</span><span class='lbracket'>[</span><span class='symbol'>:mutt</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reject'>reject</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span>
-    <span class='id identifier rubyid_splist'>splist</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_parm'>parm</span><span class='period'>.</span><span class='id identifier rubyid_smallest_species'>smallest_species</span>
-  <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span>
-    <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span> <span class='id identifier rubyid_k'>k</span>
-    <span class='id identifier rubyid_splist'>splist</span>
-  <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-  <span class='comment'># FIXME this code is not dry!!!!
-</span>  <span class='kw'>def</span> <span class='id identifier rubyid_mutt'>mutt</span><span class='period'>.</span><span class='id identifier rubyid_fitness='>fitness=</span><span class='lparen'>(</span><span class='id identifier rubyid_fit'>fit</span><span class='rparen'>)</span>
-    <span class='ivar'>@fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_fit'>fit</span>
-  <span class='kw'>end</span>
-  <span class='kw'>def</span> <span class='id identifier rubyid_mutt'>mutt</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span>
-    <span class='ivar'>@fitness</span>
-  <span class='kw'>end</span>
-  <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span> <span class='symbol'>:mutt</span> <span class='kw'>if</span> <span class='kw'>self</span><span class='lbracket'>[</span><span class='symbol'>:mutt</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="evaluate!-class_method">
-    + (<tt>Object</tt>) <strong>evaluate!</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-96
-97
-98
-99
-100</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 96</span>
-<span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_evaluate!'>evaluate!</span>
-  <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_sp'>sp</span><span class='op'>|</span>
-    <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_crit'>crit</span><span class='op'>|</span> <span class='id identifier rubyid_crit'>crit</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span><span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='op'>+</span><span class='id identifier rubyid_b'>b</span><span class='rbrace'>}</span> <span class='op'>/</span> <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="member?-class_method">
-    + (<tt>Boolean</tt>) <strong>member?</strong>(crit)
-</h3><div class="docstring">
-  <div class="discussion">
-<p>lists keyed by representative critter</p>
-  </div>
-</div>
-<div class="tags">
-<p class="tag_title">Returns:</p>
-<ul class="return">
-    <li>
-        <span class='type'>(<tt>Boolean</tt>)</span>
-    </li>
-</ul>
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-92
-93
-94</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 92</span>
-<span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_crit'>crit</span><span class='rparen'>)</span>
-  <span class='kw'>super</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_crit'>crit</span><span class='rparen'>)</span> <span class='kw'>or</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_li'>li</span><span class='op'>|</span> <span class='id identifier rubyid_li'>li</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_crit'>crit</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_t1'>t1</span><span class='comma'>,</span> <span class='id identifier rubyid_t2'>t2</span><span class='op'>|</span> <span class='id identifier rubyid_t1'>t1</span> <span class='kw'>or</span> <span class='id identifier rubyid_t2'>t2</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-  <div id="instance_method_details" class="method_details_list">
-    <h2>Instance Method Details</h2>
-      <div class="method_details first">
-  <h3 class="signature first" id="analyze!-instance_method">
-    - (<tt>Object</tt>) <strong>analyze!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Alalyze evaluation results.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-74
-75
-76</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 74</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_analyze!'>analyze!</span>
-   <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_critter'>critter</span><span class='op'>|</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_evaluator'>evaluator</span><span class='period'>.</span><span class='id identifier rubyid_analyze_for_fitness!'>analyze_for_fitness!</span> <span class='id identifier rubyid_critter'>critter</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="best_critter-instance_method">
-    - (<tt>Object</tt>) <strong>best_critter</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>The “best critter” is the critter with the lowest (closet to zero) fitness
-rating.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-181
-182</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 176</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_best_critter'>best_critter</span>
-  <span class='kw'>unless</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_compare_func'>compare_func</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-    <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_min'>min</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_compare_func'>compare_func</span><span class='period'>.</span><span class='lparen'>(</span><span class='id identifier rubyid_a'>a</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
-  <span class='kw'>else</span>
-    <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_min'>min</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span> <span class='op'>&lt;=&gt;</span> <span class='id identifier rubyid_b'>b</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rbrace'>}</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="dump_s-instance_method">
-    - (<tt>Object</tt>) <strong>dump_s</strong>
-</h3><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-194
-195
-196</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 194</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_dump_s'>dump_s</span>
-  <span class='id identifier rubyid_to_s'>to_s</span> <span class='op'>+</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\npopulation:\n</span><span class='tstring_end'>&quot;</span></span> <span class='op'>+</span> <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_crit'>crit</span><span class='op'>|</span> <span class='id identifier rubyid_crit'>crit</span><span class='period'>.</span><span class='id identifier rubyid_dump_s'>dump_s</span> <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\n</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="evaluate!-instance_method">
-    - (<tt>Object</tt>) <strong>evaluate!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Called for each sequence.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-69
-70
-71</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 69</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_evaluate!'>evaluate!</span>
-   <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_critter'>critter</span><span class='op'>|</span> <span class='id identifier rubyid_critter'>critter</span><span class='period'>.</span><span class='id identifier rubyid_evaluate!'>evaluate!</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="evolve-instance_method">
-    - (<tt>Object</tt>) <strong>evolve</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Call this after evaluation. Returns a newly-evolved population.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-80
-81
-82</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 80</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_evolve'>evolve</span>
-  <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_evolver'>evolver</span><span class='period'>.</span><span class='id identifier rubyid_evolve'>evolve</span> <span class='kw'>self</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="express!-instance_method">
-    - (<tt>Object</tt>) <strong>express!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Express the entire population.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-64
-65
-66</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 64</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_express!'>express!</span>
-   <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_critter'>critter</span><span class='op'>|</span> <span class='id identifier rubyid_critter'>critter</span><span class='period'>.</span><span class='id identifier rubyid_express!'>express!</span> <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="initialize_for_recurrence!-instance_method">
-    - (<tt>Object</tt>) <strong>initialize_for_recurrence!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Make sure all critters are reset and prepared for recurrent network
-evaluation.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-54
-55
-56</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 54</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_initialize_for_recurrence!'>initialize_for_recurrence!</span>
-  <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_crit'>crit</span><span class='op'>|</span> <span class='id identifier rubyid_crit'>crit</span><span class='period'>.</span><span class='id identifier rubyid_initialize_neurons!'>initialize_neurons!</span><span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="mutate!-instance_method">
-    - (<tt>Object</tt>) <strong>mutate!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Mutate the genes and neurons.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-59
-60
-61</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 59</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_mutate!'>mutate!</span>
-  <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_evolver'>evolver</span><span class='period'>.</span><span class='id identifier rubyid_mutate!'>mutate!</span> <span class='kw'>self</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="report-instance_method">
-    - (<tt>Object</tt>) <strong>report</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<h2 id="label-Generate+a+report+on+the+state+of+this+population.">Generate a report on the state of this population.</h2>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-165
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 165</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_report'>report</span>
-  <span class='lbrace'>{</span>
-      <span class='label'>fitness:</span>         <span class='id identifier rubyid_report_fitness'>report_fitness</span><span class='comma'>,</span>
-      <span class='label'>fitness_species:</span> <span class='id identifier rubyid_report_fitness_species'>report_fitness_species</span><span class='comma'>,</span>
-      <span class='label'>best_critter:</span>    <span class='id identifier rubyid_report_best_fit'>report_best_fit</span><span class='comma'>,</span>
-      <span class='label'>worst_critter:</span>   <span class='id identifier rubyid_report_worst_fit'>report_worst_fit</span><span class='comma'>,</span>
-  <span class='rbrace'>}</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="speciate!-instance_method">
-    - (<tt>Object</tt>) <strong>speciate!</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>Group critters into species Note that the @species objects have useful
-singleton methods:</p>
-<ul><li>
-<p>@species.member? – checks all of the lists for membership, not just the
-hash</p>
-</li><li>
-<p>@<a href="crit">species</a>.fitness – fitness of the entire species</p>
-</li></ul>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
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-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 89</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_speciate!'>speciate!</span>
-  <span class='comment'># We blow away existing species and create our own member? function
-</span>  <span class='ivar'>@species</span> <span class='op'>=</span> <span class='lbrace'>{</span><span class='rbrace'>}</span> <span class='comment'># lists keyed by representative critter
-</span>  <span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_crit'>crit</span><span class='rparen'>)</span>
-    <span class='kw'>super</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span><span class='lparen'>(</span><span class='id identifier rubyid_crit'>crit</span><span class='rparen'>)</span> <span class='kw'>or</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_li'>li</span><span class='op'>|</span> <span class='id identifier rubyid_li'>li</span><span class='period'>.</span><span class='id identifier rubyid_member?'>member?</span> <span class='id identifier rubyid_crit'>crit</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_t1'>t1</span><span class='comma'>,</span> <span class='id identifier rubyid_t2'>t2</span><span class='op'>|</span> <span class='id identifier rubyid_t1'>t1</span> <span class='kw'>or</span> <span class='id identifier rubyid_t2'>t2</span> <span class='rbrace'>}</span>
-  <span class='kw'>end</span>
-  <span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_evaluate!'>evaluate!</span>
-    <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_sp'>sp</span><span class='op'>|</span>
-      <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_crit'>crit</span><span class='op'>|</span> <span class='id identifier rubyid_crit'>crit</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reduce'>reduce</span><span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span><span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='op'>+</span><span class='id identifier rubyid_b'>b</span><span class='rbrace'>}</span> <span class='op'>/</span> <span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='kw'>def</span> <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_compactify!'>compactify!</span><span class='lparen'>(</span><span class='id identifier rubyid_parm'>parm</span><span class='rparen'>)</span>
-    <span class='id identifier rubyid_mutt'>mutt</span> <span class='op'>=</span> <span class='kw'>self</span><span class='lbracket'>[</span><span class='symbol'>:mutt</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span> <span class='lbracket'>[</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='rbracket'>]</span><span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_reject'>reject</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span>
-      <span class='id identifier rubyid_splist'>splist</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span> <span class='op'>&gt;=</span> <span class='id identifier rubyid_parm'>parm</span><span class='period'>.</span><span class='id identifier rubyid_smallest_species'>smallest_species</span>
-    <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_map'>map</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_splist'>splist</span><span class='op'>|</span>
-      <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span> <span class='id identifier rubyid_k'>k</span>
-      <span class='id identifier rubyid_splist'>splist</span>
-    <span class='rbrace'>}</span><span class='period'>.</span><span class='id identifier rubyid_flatten'>flatten</span>
-    <span class='comment'># FIXME this code is not dry!!!!
-</span>    <span class='kw'>def</span> <span class='id identifier rubyid_mutt'>mutt</span><span class='period'>.</span><span class='id identifier rubyid_fitness='>fitness=</span><span class='lparen'>(</span><span class='id identifier rubyid_fit'>fit</span><span class='rparen'>)</span>
-      <span class='ivar'>@fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_fit'>fit</span>
-    <span class='kw'>end</span>
-    <span class='kw'>def</span> <span class='id identifier rubyid_mutt'>mutt</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span>
-      <span class='ivar'>@fitness</span>
-    <span class='kw'>end</span>
-    <span class='kw'>self</span><span class='period'>.</span><span class='id identifier rubyid_delete'>delete</span> <span class='symbol'>:mutt</span> <span class='kw'>if</span> <span class='kw'>self</span><span class='lbracket'>[</span><span class='symbol'>:mutt</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_empty?'>empty?</span>
-  <span class='kw'>end</span>
-  <span class='comment'># Some convience parms
-</span>  <span class='id identifier rubyid_parm'>parm</span> <span class='op'>=</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_parms'>parms</span>
-  <span class='comment'># And so now we iterate...
-</span>  <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_crit'>crit</span><span class='op'>|</span>
-    <span class='id identifier rubyid_wearein'>wearein</span> <span class='op'>=</span> <span class='kw'>false</span>
-    <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_ck'>ck</span><span class='comma'>,</span> <span class='id identifier rubyid_list'>list</span><span class='op'>|</span>
-      <span class='id identifier rubyid_delta'>delta</span> <span class='op'>=</span> <span class='id identifier rubyid_crit'>crit</span><span class='period'>.</span><span class='id identifier rubyid_compare'>compare</span><span class='lparen'>(</span><span class='id identifier rubyid_ck'>ck</span><span class='rparen'>)</span>
-      <span class='comment'>#log.debug { &quot;delta for #{crit} and #{ck} is #{delta}&quot; }
-</span>      <span class='kw'>if</span> <span class='id identifier rubyid_delta'>delta</span> <span class='op'>&lt;</span> <span class='id identifier rubyid_parm'>parm</span><span class='period'>.</span><span class='id identifier rubyid_compatibility_threshold'>compatibility_threshold</span>
-        <span class='id identifier rubyid_list'>list</span> <span class='op'>&lt;&lt;</span> <span class='id identifier rubyid_crit'>crit</span>
-        <span class='id identifier rubyid_wearein'>wearein</span> <span class='op'>=</span> <span class='kw'>true</span>
-        <span class='kw'>break</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-    <span class='comment'># New species?
-</span>    <span class='kw'>unless</span> <span class='id identifier rubyid_wearein'>wearein</span>
-      <span class='ivar'>@species</span><span class='lbracket'>[</span><span class='id identifier rubyid_crit'>crit</span><span class='rbracket'>]</span> <span class='op'>=</span> <span class='id identifier rubyid_species'>species</span> <span class='op'>=</span> <span class='lbracket'>[</span><span class='id identifier rubyid_crit'>crit</span><span class='rbracket'>]</span>
-      <span class='kw'>def</span> <span class='id identifier rubyid_species'>species</span><span class='period'>.</span><span class='id identifier rubyid_fitness='>fitness=</span><span class='lparen'>(</span><span class='id identifier rubyid_fit'>fit</span><span class='rparen'>)</span>
-        <span class='ivar'>@fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_fit'>fit</span>
-      <span class='kw'>end</span>
-      <span class='kw'>def</span> <span class='id identifier rubyid_species'>species</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span>
-        <span class='ivar'>@fitness</span>
-      <span class='kw'>end</span>
-    <span class='kw'>end</span>
-  <span class='kw'>end</span>
-  <span class='comment'># Compactify the species if less than smallest_species
-</span>  <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_compactify!'>compactify!</span> <span class='id identifier rubyid_parm'>parm</span>
-  <span class='comment'># And now we evaluate all species for fitness...
-</span>  <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_evaluate!'>evaluate!</span>
-  <span class='comment'># Dump for debugging reasons
-</span>  <span class='ivar'>@species</span><span class='period'>.</span><span class='id identifier rubyid_each'>each</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_k'>k</span><span class='comma'>,</span> <span class='id identifier rubyid_sp'>sp</span><span class='op'>|</span>
-    <span class='id identifier rubyid_log'>log</span><span class='period'>.</span><span class='id identifier rubyid_debug'>debug</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>&gt;&gt; Species </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_k'>k</span><span class='embexpr_end'>}</span><span class='tstring_content'> has </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_size'>size</span><span class='embexpr_end'>}</span><span class='tstring_content'> members with a </span><span class='embexpr_beg'>#{</span><span class='id identifier rubyid_sp'>sp</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='embexpr_end'>}</span><span class='tstring_content'> fitness</span><span class='tstring_end'>&quot;</span></span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-      <div class="method_details ">
-  <h3 class="signature " id="worst_critter-instance_method">
-    - (<tt>Object</tt>) <strong>worst_critter</strong>
-</h3><div class="docstring">
-  <div class="discussion">
-<p>The “worst critter” is the critter with the highest (away from zero)
-fitness rating.</p>
-  </div>
-</div>
-<div class="tags">
-</div><table class="source_code">
-  <tr>
-    <td>
-      <pre class="lines">
-186
-187
-188
-189
-190
-191
-192</pre>
-    </td>
-    <td>
-      <pre class="code"><span class="info file"># File 'lib/rubyneat/population.rb', line 186</span>
-<span class='kw'>def</span> <span class='id identifier rubyid_worst_critter'>worst_critter</span>
-  <span class='kw'>unless</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_compare_func'>compare_func</span><span class='period'>.</span><span class='id identifier rubyid_nil?'>nil?</span>
-    <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='ivar'>@controller</span><span class='period'>.</span><span class='id identifier rubyid_compare_func'>compare_func</span><span class='period'>.</span><span class='lparen'>(</span><span class='id identifier rubyid_a'>a</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rparen'>)</span> <span class='rbrace'>}</span>
-  <span class='kw'>else</span>
-    <span class='ivar'>@critters</span><span class='period'>.</span><span class='id identifier rubyid_max'>max</span> <span class='lbrace'>{</span><span class='op'>|</span><span class='id identifier rubyid_a'>a</span><span class='comma'>,</span> <span class='id identifier rubyid_b'>b</span><span class='op'>|</span> <span class='id identifier rubyid_a'>a</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span> <span class='op'>&lt;=&gt;</span> <span class='id identifier rubyid_b'>b</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span><span class='rbrace'>}</span>
-  <span class='kw'>end</span>
-<span class='kw'>end</span></pre>
-    </td>
-  </tr>
-</table>
-</div>
-  </div>
-</div>
-    <div id="footer">
-  Generated on Sun Apr 13 15:54:03 2014 by
-  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
-  0.8.7.4 (ruby-2.1.1).
-</div>
-  </body>
-</html>