ligarb 0.4.0 → 0.6.0

data/assets/serve.js

@@ -0,0 +1,97 @@
+// ligarb serve — SSE-based live reload + reload button
+(function() {
+  'use strict';
+
+  var refreshing = false;
+
+  // Create reload button (hidden by default, shown when build changes)
+  var reloadBtn = document.createElement('button');
+  reloadBtn.id = 'ligarb-reload';
+  reloadBtn.innerHTML = '↻';
+  reloadBtn.title = 'New build available — click to reload';
+  reloadBtn.style.display = 'none';
+  reloadBtn.addEventListener('click', function() {
+    refreshContent();
+  });
+  document.body.appendChild(reloadBtn);
+
+  function showReloadButton() {
+    reloadBtn.style.display = 'flex';
+    reloadBtn.classList.add('has-update');
+    reloadBtn.classList.remove('refreshing');
+  }
+
+  function hideReloadButton() {
+    reloadBtn.style.display = 'none';
+    reloadBtn.classList.remove('has-update', 'refreshing');
+  }
+
+  // Refresh book content without full page reload
+  function refreshContent() {
+    if (refreshing) return;
+    refreshing = true;
+    reloadBtn.classList.remove('has-update');
+    reloadBtn.classList.add('refreshing');
+
+    fetch((window._ligarbBase || '/') + '?_t=' + Date.now())
+      .then(function(r) { return r.text(); })
+      .then(function(html) {
+        var parser = new DOMParser();
+        var doc = parser.parseFromString(html, 'text/html');
+        var newMain = doc.getElementById('content');
+        var oldMain = document.getElementById('content');
+        if (newMain && oldMain) {
+          var scrollY = window.scrollY;
+          oldMain.innerHTML = newMain.innerHTML;
+          var hash = location.hash.replace('#', '');
+          if (hash) {
+            // Show the current chapter without scrolling to top
+            var slug = hash.split('--')[0];
+            var chapters = oldMain.querySelectorAll('.chapter');
+            chapters.forEach(function(el) {
+              el.style.display = el.id === 'chapter-' + slug ? 'block' : 'none';
+            });
+          }
+          window.scrollTo(0, scrollY);
+
+          // Re-initialize syntax highlighting and special blocks
+          if (typeof hljs !== 'undefined') hljs.highlightAll();
+          if (typeof mermaid !== 'undefined') {
+            var unrendered = oldMain.querySelectorAll('.mermaid:not([data-processed])');
+            if (unrendered.length > 0) mermaid.run({nodes: unrendered});
+          }
+          if (typeof katex !== 'undefined') {
+            oldMain.querySelectorAll('.math-block[data-math]').forEach(function(el) {
+              if (el.childNodes.length === 0) {
+                try { katex.render(el.getAttribute('data-math'), el, {displayMode: true, throwOnError: false}); }
+                catch(e) { el.textContent = el.getAttribute('data-math'); }
+              }
+            });
+            oldMain.querySelectorAll('.math-inline[data-math]').forEach(function(el) {
+              if (el.childNodes.length === 0) {
+                try { katex.render(el.getAttribute('data-math'), el, {displayMode: false, throwOnError: false}); }
+                catch(e) { el.textContent = el.getAttribute('data-math'); }
+              }
+            });
+          }
+        }
+        refreshing = false;
+        hideReloadButton();
+      })
+      .catch(function() {
+        refreshing = false;
+        hideReloadButton();
+        location.reload();
+      });
+  }
+
+  // SSE connection
+  var eventSource = new EventSource((window._ligarbAPI || '/_ligarb') + '/events');
+
+  eventSource.addEventListener('build_updated', function() {
+    showReloadButton();
+  });
+
+  // Expose for review.js
+  window._ligarbEvents = eventSource;
+})();

data/assets/style.css

@@ -368,6 +368,18 @@ body {
   margin-right: 0.5rem;
 }
 
+.search-match-count {
+  display: inline-block;
+  background: var(--color-accent);
+  color: #fff;
+  font-size: 0.7rem;
+  padding: 0.05em 0.45em;
+  border-radius: 8px;
+  margin-left: 0.4em;
+  vertical-align: middle;
+  line-height: 1.4;
+}
+
 /* Search highlight */
 mark.search-highlight {
   background: #fef08a;
@@ -435,6 +447,7 @@ mark.search-highlight {
   --color-accent-light: #1c3a5c;
   --color-code-bg: #0f172a;
   --color-code-border: #2d3748;
+  --color-highlight: rgba(255, 243, 205, 0.15);
 }
 
 [data-theme="dark"] .admonition-note {
@@ -624,6 +637,72 @@ mark.search-highlight {
   }
 }
 
+/* === Bibliography === */
+.bibliography-list {
+  list-style: none;
+  padding-left: 0;
+}
+
+.bibliography-list li {
+  margin-bottom: 0.75rem;
+  padding-left: 1.5rem;
+  text-indent: -1.5rem;
+  line-height: 1.5;
+}
+
+.bibliography-list li a {
+  color: var(--color-accent);
+  text-decoration: none;
+}
+
+.bibliography-list li a:hover {
+  text-decoration: underline;
+}
+
+.ligarb-highlight {
+  border-radius: 4px;
+  padding: 4px 6px;
+  animation: ligarb-highlight-fade 3s ease-out forwards;
+}
+
+@keyframes ligarb-highlight-fade {
+  0% { background: var(--color-highlight, #fff3cd); }
+  100% { background: transparent; }
+}
+
+.cite-ref {
+  font-size: 0.8em;
+}
+
+.bib-label {
+  font-weight: 600;
+  color: var(--color-text-muted);
+  margin-right: 0.3em;
+}
+
+.cite-ref a {
+  color: var(--color-accent);
+  text-decoration: none;
+  font-weight: 600;
+}
+
+.cite-ref a:hover {
+  text-decoration: underline;
+}
+
+.cite-missing {
+  color: #d32f2f;
+  background: #ffebee;
+  padding: 0 3px;
+  border-radius: 2px;
+  cursor: help;
+}
+
+[data-theme="dark"] .cite-missing {
+  color: #ef9a9a;
+  background: rgba(211, 47, 47, 0.15);
+}
+
 /* === Index === */
 .index-group {
   margin-bottom: 1.5rem;
@@ -748,3 +827,27 @@ mark.search-highlight {
     }
   }
 }
+
+/* === Mermaid source toggle === */
+details.mermaid-source {
+  margin-top: 0.3em;
+  font-size: 0.8em;
+}
+details.mermaid-source summary {
+  cursor: pointer;
+  color: #888;
+  user-select: none;
+}
+details.mermaid-source pre {
+  margin-top: 0.3em;
+  padding: 0.5em;
+  background: #f5f5f5;
+  border: 1px solid #ddd;
+  border-radius: 4px;
+  overflow-x: auto;
+  white-space: pre-wrap;
+}
+.dark-mode details.mermaid-source pre {
+  background: #2a2a2a;
+  border-color: #444;
+}

data/lib/ligarb/asset_manager.rb

@@ -9,7 +9,7 @@ module Ligarb
   class AssetManager
     ASSETS = {
       highlight: {
-        fence_pattern: /language-(?!mermaid|math)(\w+)/,
+        fence_pattern: /language-(?!mermaid|math|functionplot)(\w+)/,
         files: {
           "js/highlight.min.js" => "https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.11.1/highlight.min.js",
           "css/highlight.css" => "https://cdnjs.cloudflare.com/ajax/libs/highlight.js/11.11.1/styles/github.min.css",
@@ -28,6 +28,13 @@ module Ligarb
           "css/katex.min.css" => "https://cdn.jsdelivr.net/npm/katex@0.16/dist/katex.min.css",
         },
       },
+      functionplot: {
+        fence_pattern: /class="functionplot"/,
+        files: {
+          "js/d3.min.js" => "https://cdn.jsdelivr.net/npm/d3@7/dist/d3.min.js",
+          "js/function-plot.min.js" => "https://cdn.jsdelivr.net/npm/function-plot@1/dist/function-plot.js",
+        },
+      },
     }.freeze
 
     def initialize(output_path)
@@ -60,6 +67,8 @@ module Ligarb
 
     private
 
+    MAX_ASSET_SIZE = 5 * 1024 * 1024 # 5MB
+
     def download(url, dest)
       FileUtils.mkdir_p(File.dirname(dest))
       $stderr.print "Downloading #{File.basename(dest)}... "
@@ -68,6 +77,9 @@ module Ligarb
       response = fetch_with_redirects(uri)
 
       if response.is_a?(Net::HTTPSuccess)
+        if response.body.bytesize > MAX_ASSET_SIZE
+          abort "Error: downloaded file too large: #{File.basename(dest)} (#{response.body.bytesize} bytes, limit #{MAX_ASSET_SIZE})"
+        end
         File.write(dest, response.body)
         $stderr.puts "done"
       else
@@ -77,11 +89,14 @@ module Ligarb
 
     def fetch_with_redirects(uri, limit = 5)
       raise "Too many redirects" if limit == 0
+      raise "Only HTTPS URLs are supported for asset downloads" unless uri.scheme == "https"
 
       response = Net::HTTP.get_response(uri)
       case response
       when Net::HTTPRedirection
-        fetch_with_redirects(URI(response["location"]), limit - 1)
+        new_uri = URI(response["location"])
+        raise "Redirect to non-HTTPS URL: #{new_uri}" unless new_uri.scheme == "https"
+        fetch_with_redirects(new_uri, limit - 1)
       else
         response
       end

data/lib/ligarb/builder.rb

@@ -30,9 +30,12 @@ module Ligarb
         }
       }
 
+      bibliography = resolve_citations!(all_chapters)
+
       html = Template.new.render(config: @config, chapters: all_chapters,
                                  structure: structure, assets: assets,
-                                 index_entries: index_entries)
+                                 index_entries: index_entries,
+                                 bibliography: bibliography)
 
       FileUtils.mkdir_p(@config.output_path)
       output_file = File.join(@config.output_path, "index.html")
@@ -145,6 +148,178 @@ module Ligarb
       end
     end
 
+    def resolve_citations!(all_chapters)
+      bib_path = @config.bibliography_path
+      return [] unless bib_path
+
+      unless File.exist?(bib_path)
+        abort "Error: bibliography file not found: #{bib_path}"
+      end
+
+      bib_data = load_bibliography(bib_path)
+
+      # Validate all cite keys exist
+      cited_keys = {}
+      all_chapters.each do |ch|
+        ch.cite_entries.each do |entry|
+          unless bib_data.key?(entry.key)
+            warn "Warning: unknown bibliography key '#{entry.key}' in chapter #{File.basename(ch.instance_variable_get(:@path))}"
+            next
+          end
+          cited_keys[entry.key] = true
+        end
+      end
+
+      # Post-process each chapter's HTML to insert [author, year] citations
+      all_chapters.each do |ch|
+        ch.instance_variable_set(:@html, ch.html.gsub(%r{<span id="([^"]+)" data-cite-key="([^"]+)">(.*?)</span>}m) do
+          anchor_id = $1
+          key = $2
+          display_text = $3
+          ref = bib_data[key]
+          unless ref
+            next %(<span id="#{anchor_id}">#{display_text}<sup class="cite-ref cite-missing" title="Bibliography entry '#{encode_attr(key)}' not found">[#{encode_attr(key)}?]</sup></span>)
+          end
+          cite_label = format_cite_label(ref)
+          title_text = format_bib_hover(ref)
+          %(<span id="#{anchor_id}">#{display_text}<sup class="cite-ref"><a href="#bib-#{key}" title="#{encode_attr(title_text)}" onclick="showChapterAndScroll('__bibliography__', 'bib-#{key}'); return false;">[#{encode_attr(cite_label)}]</a></sup></span>)
+        end)
+      end
+
+      # Build bibliography list sorted by author then year (only cited entries)
+      cited_keys.keys.map do |key|
+        ref = bib_data[key]
+        {
+          key: key,
+          author: ref["author"],
+          title: ref["title"],
+          year: ref["year"],
+          url: ref["url"],
+          label: format_cite_label(ref),
+          formatted_html: format_bib_html(ref),
+        }
+      end.sort_by { |e| [e[:author].to_s, e[:year].to_s] }
+    end
+
+    def load_bibliography(path)
+      if path.end_with?(".bib")
+        parse_bibtex(File.read(path))
+      else
+        YAML.safe_load_file(path)
+      end
+    end
+
+    def parse_bibtex(source)
+      result = {}
+      # Remove comment lines
+      lines = source.each_line.reject { |l| l.match?(/\A\s*%/) }.join
+
+      # Extract @type{key, ...} blocks
+      lines.scan(/@(\w+)\s*\{\s*([^,]+)\s*,(.*?)\n\s*\}/m) do |type, key, body|
+        entry = {"_type" => type.downcase}
+        body.scan(/(\w+)\s*=\s*(?:\{((?:[^{}]|\{(?:[^{}]|\{[^{}]*\})*\})*)\}|"([^"]*)")/) do |field, brace_val, quote_val|
+          value = (brace_val || quote_val).strip
+          # Remove BibTeX case-protection braces (e.g. {LaTeX} -> LaTeX)
+          value = value.gsub(/\{([^{}]*)\}/, '\1')
+          entry[field.downcase] = value
+        end
+        result[key.strip] = entry
+      end
+
+      result
+    end
+
+    def format_bib_html(ref)
+      type = ref["_type"] || "misc"
+      parts = []
+
+      author = ref["author"]
+      parts << encode_html(author) if author
+
+      title = ref["title"]
+      if title
+        title_html = if ref["url"]
+                       %(<em><a href="#{encode_attr(ref["url"])}" target="_blank" rel="noopener">#{encode_html(title)}</a></em>)
+                     elsif type == "article" || type == "inproceedings"
+                       %("#{encode_html(title)}")
+                     else
+                       "<em>#{encode_html(title)}</em>"
+                     end
+        parts << title_html
+      end
+
+      case type
+      when "book"
+        parts << "#{encode_html(ref["edition"])}" if ref["edition"]
+        parts << encode_html(ref["publisher"]) if ref["publisher"]
+      when "article"
+        journal_parts = []
+        journal_parts << "<em>#{encode_html(ref["journal"])}</em>" if ref["journal"]
+        vol_num = []
+        vol_num << ref["volume"] if ref["volume"]
+        vol_num << "(#{ref["number"]})" if ref["number"]
+        journal_parts << vol_num.join("") unless vol_num.empty?
+        journal_parts << "pp. #{ref["pages"]}" if ref["pages"]
+        parts << journal_parts.join(", ") unless journal_parts.empty?
+      when "inproceedings"
+        conf_parts = []
+        conf_parts << "In <em>#{encode_html(ref["booktitle"])}</em>" if ref["booktitle"]
+        conf_parts << "pp. #{ref["pages"]}" if ref["pages"]
+        parts << conf_parts.join(", ") unless conf_parts.empty?
+      else
+        parts << encode_html(ref["publisher"]) if ref["publisher"]
+        parts << "<em>#{encode_html(ref["journal"])}</em>" if ref["journal"]
+        parts << "Vol. #{ref["volume"]}" if ref["volume"]
+        parts << "pp. #{ref["pages"]}" if ref["pages"]
+      end
+
+      parts << ref["year"].to_s if ref["year"]
+      parts << encode_html(ref["editor"]) if ref["editor"]
+      parts << encode_html(ref["note"]) if ref["note"]
+
+      # Strip trailing dots from parts to avoid double periods
+      html = parts.map { |p| p.sub(/\.\z/, "") }.join(". ") + "."
+
+      if ref["doi"] && !ref["url"]
+        doi_url = ref["doi"].start_with?("http") ? ref["doi"] : "https://doi.org/#{ref["doi"]}"
+        html += %( <a href="#{encode_attr(doi_url)}" target="_blank" rel="noopener">DOI</a>)
+      elsif ref["doi"] && ref["url"]
+        doi_url = ref["doi"].start_with?("http") ? ref["doi"] : "https://doi.org/#{ref["doi"]}"
+        html += %( <a href="#{encode_attr(doi_url)}" target="_blank" rel="noopener">DOI</a>)
+      end
+
+      html
+    end
+
+    def format_cite_label(ref)
+      author = ref["author"].to_s.split(/[,\s]/).first || "?"
+      year = ref["year"] ? ref["year"].to_s : "n.d."
+      "#{author}, #{year}"
+    end
+
+    def format_bib_hover(ref)
+      parts = []
+      parts << ref["author"] if ref["author"]
+      parts << ref["title"] if ref["title"]
+      parts << ref["publisher"] if ref["publisher"]
+      parts << ref["journal"] if ref["journal"]
+      parts << "Vol. #{ref["volume"]}" if ref["volume"]
+      parts << "No. #{ref["number"]}" if ref["number"]
+      parts << "pp. #{ref["pages"]}" if ref["pages"]
+      parts << ref["edition"] if ref["edition"]
+      parts << ref["year"].to_s if ref["year"]
+      parts << ref["note"] if ref["note"]
+      parts.join(". ") + "."
+    end
+
+    def encode_attr(text)
+      text.gsub("&", "&amp;").gsub("<", "&lt;").gsub(">", "&gt;").gsub('"', "&quot;")
+    end
+
+    def encode_html(text)
+      text.to_s.gsub("&", "&amp;").gsub("<", "&lt;").gsub(">", "&gt;")
+    end
+
     def copy_images
       images_dir = File.join(@config.base_dir, "images")
       return unless Dir.exist?(images_dir)

data/lib/ligarb/chapter.rb

@@ -7,11 +7,12 @@ module Ligarb
   class Chapter
     class CrossReferenceError < StandardError; end
 
-    attr_reader :title, :slug, :html, :headings, :number, :appendix_letter, :index_entries
+    attr_reader :title, :slug, :html, :headings, :number, :appendix_letter, :index_entries, :cite_entries
     attr_accessor :part_title, :cover, :relative_path
 
     Heading = Struct.new(:level, :text, :id, :display_text, keyword_init: true)
     IndexEntry = Struct.new(:term, :display_text, :chapter_slug, :anchor_id, keyword_init: true)
+    CiteEntry = Struct.new(:key, :display_text, :chapter_slug, :anchor_id, keyword_init: true)
 
     def initialize(path, base_dir)
       @path     = path
@@ -63,7 +64,9 @@ module Ligarb
         target_path = File.expand_path(href_path, source_dir)
         entry = chapter_map[target_path]
         unless entry
-          raise CrossReferenceError, "cross-reference target not found: #{href_path} (from #{File.basename(@path)})"
+          line_no = @source.each_line.with_index(1) { |line, i| break i if line.include?(href_path) }
+          loc = line_no ? "#{@path}:#{line_no}" : File.basename(@path)
+          raise CrossReferenceError, "cross-reference target not found: #{href_path} (from #{loc})\n  link text: #{link_text.empty? ? "(auto)" : link_text}\n  resolved to: #{target_path}"
         end
 
         if fragment && !fragment.empty?
@@ -106,6 +109,8 @@ module Ligarb
       @html = scope_footnote_ids(@html)
       @index_entries = []
       @html = extract_index_markers(@html)
+      @cite_entries = []
+      @html = extract_cite_markers(@html)
       @title = @headings.first&.text || @slug
     end
 
@@ -161,14 +166,18 @@ module Ligarb
     end
 
     def convert_special_code_blocks(html)
-      html.gsub(%r{<pre><code class="language-(mermaid|math)">(.*?)</code></pre>}m) do
+      html.gsub(%r{<pre><code class="language-(mermaid|math|functionplot)">(.*?)</code></pre>}m) do
         lang = $1
         raw = decode_entities($2)
         case lang
         when "mermaid"
-          %(<div class="mermaid">\n#{raw}</div>)
+          escaped = raw.gsub("&", "&amp;").gsub("<", "&lt;").gsub(">", "&gt;")
+          %(<div class="mermaid">\n#{raw}</div>) +
+            %(<details class="mermaid-source"><summary>mermaid source</summary><pre>#{escaped}</pre></details>)
         when "math"
           %(<div class="math-block" data-math="#{encode_attr(raw)}"></div>)
+        when "functionplot"
+          %(<div class="functionplot" data-plot="#{encode_attr(raw)}"></div>)
         end
       end
     end
@@ -258,6 +267,25 @@ module Ligarb
       end
     end
 
+    def extract_cite_markers(html)
+      cite_count = 0
+      html.gsub(%r{<a\s+href="#cite:([^"]+)">(.*?)</a>}m) do
+        key = $1
+        display_text = $2
+        anchor_id = "#{@slug}--cite-#{cite_count}"
+        cite_count += 1
+
+        @cite_entries << CiteEntry.new(
+          key: key,
+          display_text: display_text,
+          chapter_slug: @slug,
+          anchor_id: anchor_id
+        )
+
+        %(<span id="#{anchor_id}" data-cite-key="#{key}">#{display_text}</span>)
+      end
+    end
+
     def rewrite_image_paths(html)
       html.gsub(/(<img\s[^>]*src=")([^"]+)(")/) do
         prefix = $1