test

Author: mikemartinez99

build_site.py

@@ -292,6 +292,16 @@ def markdown_to_html(md_content, base_path='.'):
 
     return html
 
+def normalize_anchor(filename):
+    """Normalize filename to create consistent anchor."""
+    anchor = filename.replace('/', '-').replace('.md', '').replace('&', '-').replace(' ', '-')
+    # Replace multiple dashes with single dash
+    while '--' in anchor:
+        anchor = anchor.replace('--', '-')
+    # Remove leading/trailing dashes
+    anchor = anchor.strip('-')
+    return anchor
+
 def build_navigation(structure):
     """Build navigation HTML from book structure."""
     nav_items = []
@@ -304,13 +314,13 @@ def build_navigation(structure):
                 nav_items.append(f'<div class="part-title">{part_title}</div>')
                 nav_items.append('<ul>')
                 for chapter_file, chapter_title in chapters:
-                    anchor = chapter_file.replace('/', '-').replace('.md', '').replace('&', '-').replace(' ', '-')
+                    anchor = normalize_anchor(chapter_file)
                     nav_items.append(f'<li><a href="#{anchor}">{chapter_title}</a></li>')
                 nav_items.append('</ul>')
             else:
                 # It's a single chapter
                 chapter_file, chapter_title = item
-                anchor = chapter_file.replace('/', '-').replace('.md', '').replace('&', '-').replace(' ', '-')
+                anchor = normalize_anchor(chapter_file)
                 nav_items.append(f'<li><a href="#{anchor}">{chapter_title}</a></li>')
 
     return '\n'.join(nav_items)
@@ -332,7 +342,7 @@ def build_content(structure, base_path='.'):
                             md_content = f.read()
 
                         _, content = extract_frontmatter(md_content)
-                        anchor = chapter_file.replace('/', '-').replace('.md', '').replace('&', '-').replace(' ', '-')
+                        anchor = normalize_anchor(chapter_file)
                         html_content = markdown_to_html(content, base_path)
                         content_sections.append(f'<section id="{anchor}">')
                         content_sections.append(f'<h2>{chapter_title}</h2>')
@@ -347,7 +357,7 @@ def build_content(structure, base_path='.'):
                         md_content = f.read()
 
                     _, content = extract_frontmatter(md_content)
-                    anchor = chapter_file.replace('/', '-').replace('.md', '').replace('&', '-').replace(' ', '-')
+                    anchor = normalize_anchor(chapter_file)
                     html_content = markdown_to_html(content, base_path)
                     content_sections.append(f'<section id="{anchor}">')
                     content_sections.append(f'<h1>{chapter_title}</h1>')

docs/index.html

@@ -193,7 +193,7 @@
         <nav class="sidebar">
             <h1>RNA-seq DE Workshop</h1>
             <li><a href="#index">Introduction</a></li>
-<li><a href="#welcome---setup">Welcome and Setup</a></li>
+<li><a href="#welcome-setup">Welcome and Setup</a></li>
 <li><a href="#schedule">Schedule</a></li>
 <li><a href="#useful_links">Useful Links</a></li>
 <div class="part-title">Day 1</div>
@@ -214,7 +214,7 @@ <h1>RNA-seq DE Workshop</h1>
 <div class="part-title">Day 3</div>
 <ul>
 <li><a href="#Day-3-01-differential-expression-analysis">Differential Expression Analysis</a></li>
-<li><a href="#Day-3-02-annotation---visulaization">Annotation & Visualization</a></li>
+<li><a href="#Day-3-02-annotation-visulaization">Annotation & Visualization</a></li>
 <li><a href="#Day-3-03-putting-it-together">Putting It Together</a></li>
 <li><a href="#Day-3-further-reading">Further Reading</a></li>
 </ul>
@@ -227,7 +227,7 @@ <h1 id="welcome">Welcome</h1>
 <p>Welcome to the RNA-seq Differential Expression Analysis Workshop. This workshop covers statistical methods and R/Bioconductor tools for analyzing differential gene expression from RNA-seq data.</p>
 <p>Use the navigation menu on the left to explore the workshop materials organized by day.</p>
 </section>
-<section id="welcome---setup">
+<section id="welcome-setup">
 <h1>Welcome and Setup</h1>
 <h1 id="welcome-set-up-instructions">Welcome &amp; set-up instructions</h1>
 <p>Welcome to the Data Analytics Core (DAC) bulk RNA-seq differential expression analysis workshop. Before you attend the workshop, we ask that you familiarize yourself with the dataset we will be using, and install the software we will be using.</p>
@@ -3138,7 +3138,7 @@ <h4 id="how-does-independent-filtering-work">How does Independent filtering work
 <span class="nf">saveRDS</span><span class="p">(</span><span class="n">dds</span><span class="p">,</span><span class="w"> </span><span class="n">file</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s">&quot;DESeq2.rds&quot;</span><span class="p">)</span>
 </code></pre></div>
 </section>
-<section id="Day-3-02-annotation---visulaization">
+<section id="Day-3-02-annotation-visulaization">
 <h2>Annotation & Visualization</h2>
 <h1 id="results-annotation-visualization">Results annotation &amp; visualization</h1>
 <h3 id="learning-objectives">Learning objectives:</h3>