Add markdown provider for YARD documentation

Author: mattruzicka

.yardopts

@@ -1,5 +1,6 @@
 --plugin readme
 --markup markdown
+--markup-provider redcarpet
 --output-dir docs
 
 lib/**/*.rb

docs/Evolvable.html

@@ -14,6 +14,8 @@
 
   <link rel="stylesheet" href="css/common.css" type="text/css" />
 
+  <link rel="stylesheet" href="css/custom.css" type="text/css" />
+
 <script type="text/javascript">
   pathId = "Evolvable";
   relpath = '';
@@ -92,55 +94,60 @@
 
 <h2>Overview</h2><div class="docstring">
   <div class="discussion">
-    <p>The evolutionary process works through these components:
-  1. <strong>Populations</strong>: Groups of the “evolvable” instances you define
-  2. <strong>Genes</strong>: Ruby objects that cache data for evolvables
-  3. <strong>Evaluation</strong>: Sorts evolvables by fitness
-  4. <strong>Evolution</strong>: Selection, combination, and mutation to generate new evolvables</p>
-
-<p>Quick start:
-  1. Include <code>Evolvable</code> in your Ruby class
-  2. Define genes with the macro-style <code>gene</code> method
-  3. Have the <code>#fitness</code> method return a numeric value
-  4. Initialize a population and evolve it</p>
-
-<p>Example population of “shirts” with various colors, buttons, and collars.</p>
-
-<p>```ruby
-  # Step 1
-  class Shirt
-    include Evolvable</p>
-
-<pre class="code ruby"><code class="ruby"># Step 2
-gene :color, type: ColorGene # count: 1 default
-gene :buttons, type: ButtonGene, count: 0..10 # Builds an array of genes that can vary in size
-gene :collar, type: CollarGene, count: 0..1 # Collar optional
-
-# Step 3
-attr_accessor :fitness   end
+    <p>The evolutionary process works through these components:</p>
+
+<ol>
+<li><strong>Populations</strong>: Groups of the &quot;evolvable&quot; instances you define</li>
+<li><strong>Genes</strong>: Ruby objects that cache data for evolvables</li>
+<li><strong>Evaluation</strong>: Sorts evolvables by fitness</li>
+<li><strong>Evolution</strong>: Selection, combination, and mutation to generate new evolvables</li>
+</ol>
+
+<p>Quick start:</p>
+
+<ol>
+<li>Include <code>Evolvable</code> in your Ruby class</li>
+<li>Define genes with the macro-style <code>gene</code> method</li>
+<li>Have the <code>#fitness</code> method return a numeric value</li>
+<li>Initialize a population and evolve it</li>
+</ol>
+
+<p>Example population of &quot;shirts&quot; with various colors, buttons, and collars.</p>
+
+<pre class="code ruby"><code class="ruby">  <span class='comment'># Step 1
+</span>  <span class='kw'>class</span> <span class='const'>Shirt</span>
+    <span class='id identifier rubyid_include'>include</span> <span class='const'>Evolvable</span>
+
+    <span class='comment'># Step 2
+</span>    <span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:color</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>ColorGene</span> <span class='comment'># count: 1 default
+</span>    <span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:buttons</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>ButtonGene</span><span class='comma'>,</span> <span class='label'>count:</span> <span class='int'>0</span><span class='op'>..</span><span class='int'>10</span> <span class='comment'># Builds an array of genes that can vary in size
+</span>    <span class='id identifier rubyid_gene'>gene</span> <span class='symbol'>:collar</span><span class='comma'>,</span> <span class='label'>type:</span> <span class='const'>CollarGene</span><span class='comma'>,</span> <span class='label'>count:</span> <span class='int'>0</span><span class='op'>..</span><span class='int'>1</span> <span class='comment'># Collar optional
+</span>
+    <span class='comment'># Step 3
+</span>    <span class='id identifier rubyid_attr_accessor'>attr_accessor</span> <span class='symbol'>:fitness</span>
+  <span class='kw'>end</span>
+
+  <span class='comment'># Step 4
+</span>  <span class='id identifier rubyid_population'>population</span> <span class='op'>=</span> <span class='const'>Shirt</span><span class='period'>.</span><span class='id identifier rubyid_new_population'>new_population</span><span class='lparen'>(</span><span class='label'>size:</span> <span class='int'>10</span><span class='rparen'>)</span>
+  <span class='id identifier rubyid_population'>population</span><span class='period'>.</span><span class='id identifier rubyid_evolvables'>evolvables</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_shirt'>shirt</span><span class='op'>|</span> <span class='id identifier rubyid_shirt'>shirt</span><span class='period'>.</span><span class='id identifier rubyid_fitness'>fitness</span> <span class='op'>=</span> <span class='id identifier rubyid_tried_it_on_score'>tried_it_on_score</span> <span class='rbrace'>}</span>
 </code></pre>
 
-<p># Step 4
-  population = Shirt.new_population(size: 10)
-  population.evolvables.each { |shirt| shirt.fitness = tried_it_on_score }
-  ```</p>
-
-<p>You are free to tailor the genes to your needs and “try it on” yourself.</p>
+<p>You are free to tailor the genes to your needs and &quot;try it on&quot; yourself.</p>
 
 <p>The <code>ColorGene</code> could be as simple as this:</p>
 
-<p>```ruby
-  class ColorGene
-    include Evolvable::Gene</p>
+<pre class="code ruby"><code class="ruby">  <span class='kw'>class</span> <span class='const'>ColorGene</span>
+    <span class='id identifier rubyid_include'>include</span> <span class='const'>Evolvable</span><span class='op'>::</span><span class='const'><span class='object_link'><a href="Evolvable/Gene.html" title="Evolvable::Gene (module)">Gene</a></span></span>
 
-<pre class="code ruby"><code class="ruby">def to_s
-  @to_s ||= %w[red green blue].sample
-end   end   ```
+    <span class='kw'>def</span> <span class='id identifier rubyid_to_s'>to_s</span>
+      <span class='ivar'>@to_s</span> <span class='op'>||=</span> <span class='qwords_beg'>%w[</span><span class='tstring_content'>red</span><span class='words_sep'> </span><span class='tstring_content'>green</span><span class='words_sep'> </span><span class='tstring_content'>blue</span><span class='tstring_end'>]</span></span><span class='period'>.</span><span class='id identifier rubyid_sample'>sample</span>
+    <span class='kw'>end</span>
+  <span class='kw'>end</span>
 </code></pre>
 
 <p>Not into shirts?</p>
 
-<p>Here’s a <a href="https://github.com/mattruzicka/evolvable/blob/main/exe/hello_evolvable_world">Hello World</a> command line demo.</p>
+<p>Here&#39;s a <a href="https://github.com/mattruzicka/evolvable/blob/main/exe/hello_evolvable_world">Hello World</a> command line demo.</p>
 
 
   </div>
@@ -348,8 +355,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -394,8 +400,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -440,8 +445,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -463,8 +467,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -555,7 +558,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'><p>Merges another genome into this evolvable’s genome.</p>
+    <span class="summary_desc"><div class='inline'><p>Merges another genome into this evolvable&#39;s genome.</p>
 </div></span>
 
 </li>
@@ -1486,7 +1489,7 @@ <h3 class="signature " id="merge_genome!-instance_method">
 
 </h3><div class="docstring">
   <div class="discussion">
-    <p>Merges another genome into this evolvable’s genome.
+    <p>Merges another genome into this evolvable&#39;s genome.
 Useful for combining genetic traits from different evolvables.</p>
 
 
@@ -1557,7 +1560,7 @@ <h3 class="signature " id="merge_genome!-instance_method">
 </div>
 
       <div id="footer">
-  Generated on Thu May  8 23:57:27 2025 by
+  Generated on Fri May  9 00:09:34 2025 by
   <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.9.37 (ruby-3.4.2).
 </div>

docs/Evolvable/ClassMethods.html

@@ -14,6 +14,8 @@
 
   <link rel="stylesheet" href="../css/common.css" type="text/css" />
 
+  <link rel="stylesheet" href="../css/custom.css" type="text/css" />
+
 <script type="text/javascript">
   pathId = "Evolvable::ClassMethods";
   relpath = '../';
@@ -625,11 +627,14 @@ <h3 class="signature " id="cluster-instance_method">
   <div class="discussion">
     <p>The <code>.cluster</code> macro applies a pre-defined group of related genes.</p>
 
-<p>Clusters promote code organization through:
-  - Modularity: Define related genes once, reuse them
-  - Organization: Group genes by function
-  - Maintenance: Update in one place
-  - Accessibility: Access via a single accessor</p>
+<p>Clusters promote code organization through:</p>
+
+<ul>
+<li>Modularity: Define related genes once, reuse them</li>
+<li>Organization: Group genes by function</li>
+<li>Maintenance: Update in one place</li>
+<li>Accessibility: Access via a single accessor</li>
+</ul>
 
 
   </div>
@@ -766,10 +771,13 @@ <h3 class="signature " id="gene-instance_method">
     <p>The <code>.gene</code> macro defines traits that can mutate and evolve over time.
 Syntactically similar to ActiveRecord-style macros, it sets up the genetic structure of your model.</p>
 
-<p>Key features:
-- Fixed or variable gene counts
-- Automatic accessor methods
-- Optional clustering for related genes</p>
+<p>Key features:</p>
+
+<ul>
+<li>Fixed or variable gene counts</li>
+<li>Automatic accessor methods</li>
+<li>Optional clustering for related genes</li>
+</ul>
 
 
   </div>
@@ -1070,12 +1078,12 @@ <h3 class="signature " id="new_evolvable-instance_method">
 </h3><div class="docstring">
   <div class="discussion">
     <p>Initializes a new instance. Accepts a population object, an array of gene objects,
-and the instance’s population index. This method is useful for re-initializing
+and the instance&#39;s population index. This method is useful for re-initializing
 instances and populations that have been saved.</p>
 
 <p><em>It is not recommended that you override this method</em> as it is used by
 Evolvable internals. If you need to customize how your instances are
-initialized you can override either of the following two “initialize_instance”
+initialized you can override either of the following two &quot;initialize_instance&quot;
 methods.</p>
 
 
@@ -1217,7 +1225,7 @@ <h3 class="signature " id="new_population-instance_method">
 </div>
 
       <div id="footer">
-  Generated on Thu May  8 23:57:27 2025 by
+  Generated on Fri May  9 00:09:34 2025 by
   <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.9.37 (ruby-3.4.2).
 </div>

docs/Evolvable/Community.html

@@ -14,6 +14,8 @@
 
   <link rel="stylesheet" href="../css/common.css" type="text/css" />
 
+  <link rel="stylesheet" href="../css/custom.css" type="text/css" />
+
 <script type="text/javascript">
   pathId = "Evolvable::Community";
   relpath = '../';
@@ -93,18 +95,18 @@ <h2>Overview</h2><div class="docstring">
 <p><strong>Key Features</strong></p>
 
 <ul>
-  <li>Define a community with multiple population types</li>
-  <li>Manage relationships between different evolvable types</li>
-  <li>Coordinate evolution across multiple populations</li>
-  <li>Access populations and instances through a unified interface</li>
+<li>Define a community with multiple population types</li>
+<li>Manage relationships between different evolvable types</li>
+<li>Coordinate evolution across multiple populations</li>
+<li>Access populations and instances through a unified interface</li>
 </ul>
 
 <p><strong>Example Use Cases</strong></p>
 
 <ul>
-  <li><strong>Ecosystems</strong>: Simulate interactions between plants, herbivores, and predators</li>
-  <li><strong>Multi-component Systems</strong>: Design systems where components evolve together</li>
-  <li><strong>Layered Optimization</strong>: Solve problems with different optimization levels</li>
+<li><strong>Ecosystems</strong>: Simulate interactions between plants, herbivores, and predators</li>
+<li><strong>Multi-component Systems</strong>: Design systems where components evolve together</li>
+<li><strong>Layered Optimization</strong>: Solve problems with different optimization levels</li>
 </ul>
 
 
@@ -176,8 +178,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -1185,7 +1186,7 @@ <h3 class="signature " id="reset_populations-instance_method">
 </div>
 
       <div id="footer">
-  Generated on Thu May  8 23:57:27 2025 by
+  Generated on Fri May  9 00:09:35 2025 by
   <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.9.37 (ruby-3.4.2).
 </div>

docs/Evolvable/Community/ClassMethods.html

@@ -14,6 +14,8 @@
 
   <link rel="stylesheet" href="../../css/common.css" type="text/css" />
 
+  <link rel="stylesheet" href="../../css/custom.css" type="text/css" />
+
 <script type="text/javascript">
   pathId = "Evolvable::Community::ClassMethods";
   relpath = '../../';
@@ -215,8 +217,7 @@ <h2>
 
 
 
-    <span class="summary_desc"><div class='inline'>
-</div></span>
+    <span class="summary_desc"><div class='inline'></div></span>
 
 </li>
 
@@ -699,7 +700,7 @@ <h3 class="signature " id="populations_by_name-instance_method">
 </div>
 
       <div id="footer">
-  Generated on Thu May  8 23:57:27 2025 by
+  Generated on Fri May  9 00:09:35 2025 by
   <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.9.37 (ruby-3.4.2).
 </div>

docs/Evolvable/CountGene.html

@@ -14,6 +14,8 @@
 
   <link rel="stylesheet" href="../css/common.css" type="text/css" />
 
+  <link rel="stylesheet" href="../css/custom.css" type="text/css" />
+
 <script type="text/javascript">
   pathId = "Evolvable::CountGene";
   relpath = '../';
@@ -151,8 +153,8 @@ <h2>
 These lambdas determine how two count genes are merged during evolution.</p>
 
 <ol>
-  <li>Random selection with slight mutation (-1, 0, or +1)</li>
-  <li>Average of the two counts</li>
+<li>Random selection with slight mutation (-1, 0, or +1)</li>
+<li>Average of the two counts</li>
 </ol>
 
 
@@ -874,7 +876,7 @@ <h3 class="signature " id="min_count-instance_method">
 </div>
 
       <div id="footer">
-  Generated on Thu May  8 23:57:27 2025 by
+  Generated on Fri May  9 00:09:35 2025 by
   <a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
   0.9.37 (ruby-3.4.2).
 </div>