adding API reference pages for main classes of module

Author: zasexton

docs/api/domain.html

@@ -52,7 +52,7 @@ <h3>Concept Guides</h3>
     <h3>API Reference</h3>
     <p>Detailed signatures and docstrings auto‑generated from the source code.</p>
     <ul>
-      <li><a href="https://github.com/SimVascular/svVascularize">Python API (svv.*)</a></li>
+      <li><a href="api/index_api.html">Python API (svv.*)</a></li>
       <!-- <li><a href="api/cli.html">Command‑line interface (svv CLI)</a></li> -->
     </ul>
 

docs/api/index_api.html

@@ -70,3 +70,68 @@ document.addEventListener('DOMContentLoaded', () => {
     document.head.appendChild(py);
   };
 })();
+
+
+// --- Appended by API reference integration ---
+
+/* =====================
+   API REFERENCE ENHANCEMENTS
+   ===================== */
+(function () {
+  // Build local TOC on the right if #local-toc exists
+  const localToc = document.getElementById('local-toc');
+  const content = document.querySelector('.content');
+  if (localToc && content) {
+    const heads = content.querySelectorAll('h2, h3');
+    const ol = document.createElement('ol');
+    heads.forEach(h => {
+      if (!h.id) h.id = h.textContent.trim().toLowerCase().replace(/[^a-z0-9]+/g, '-');
+      const li = document.createElement('li');
+      const a = document.createElement('a');
+      a.href = '#' + h.id;
+      a.textContent = h.textContent;
+      li.appendChild(a);
+      ol.appendChild(li);
+
+      // Add anchor permalink to headings
+      const anchor = document.createElement('a');
+      anchor.href = '#' + h.id;
+      anchor.className = 'anchor';
+      anchor.setAttribute('aria-label', 'Permalink');
+      anchor.textContent = '¶';
+      h.appendChild(anchor);
+    });
+    localToc.appendChild(ol);
+
+    // Scroll spy to highlight current heading in TOC
+    const tocLinks = localToc.querySelectorAll('a');
+    const obs = new IntersectionObserver((entries) => {
+      entries.forEach(entry => {
+        const id = entry.target.getAttribute('id');
+        const link = localToc.querySelector(`a[href="#${id}"]`);
+        if (entry.isIntersecting) {
+          tocLinks.forEach(l => l.classList.remove('active'));
+          if (link) link.classList.add('active');
+        }
+      });
+    }, { rootMargin: '-40% 0px -55% 0px', threshold: [0, 1.0] });
+    heads.forEach(h => obs.observe(h));
+  }
+
+  // Auto-enable copy-to-clipboard on code blocks
+  document.querySelectorAll('pre').forEach(pre => pre.setAttribute('data-copy', ''));
+
+  // Smooth anchor scrolling with header offset
+  function scrollWithOffset(e) {
+    if (this.hash && this.pathname === location.pathname) {
+      const target = document.querySelector(this.hash);
+      if (target) {
+        e.preventDefault();
+        const top = target.getBoundingClientRect().top + window.pageYOffset - 80;
+        window.scrollTo({ top, behavior: 'smooth' });
+        history.replaceState(null, '', this.hash);
+      }
+    }
+  }
+  document.querySelectorAll('a[href^="#"]').forEach(a => a.addEventListener('click', scrollWithOffset));
+})();

docs/api/patch.html

@@ -291,3 +291,149 @@ footer {
   body { padding: 0 2rem; }
   .hero h2 { font-size: 2.75rem; }
 }
+
+
+/* --- Appended by API reference integration --- */
+
+/* =====================
+   API REFERENCE LAYOUT
+   ===================== */
+
+/* Header (maps our .site-header to the existing .topnav look & feel) */
+.site-header {
+  position: sticky;
+  top: 0;
+  z-index: 1000;
+  background-color: var(--clr-primary-700);
+  color: var(--clr-surface);
+  box-shadow: var(--shadow-sm);
+  transition: background-color var(--ease-fast), box-shadow var(--ease-fast);
+}
+.site-header .header-inner {
+  display: flex;
+  align-items: center;
+  justify-content: space-between;
+  padding: 0.9rem 0;
+}
+.site-header .brand {
+  color: var(--clr-surface);
+  font-weight: 700;
+  letter-spacing: -.3px;
+}
+.site-header .primary-nav a {
+  color: var(--clr-surface);
+  font-weight: 600;
+  margin-left: 1rem;
+  position: relative;
+}
+.site-header .primary-nav a::after {
+  content: "";
+  position: absolute;
+  left: 0; right: 0; bottom: -6px;
+  height: 2px;
+  background: var(--clr-primary-200);
+  transform: scaleX(0);
+  transform-origin: left;
+  transition: transform var(--ease-fast);
+}
+.site-header .primary-nav a:hover::after,
+.site-header .primary-nav a:focus::after,
+.site-header .primary-nav a.active::after {
+  transform: scaleX(1);
+}
+
+/* Grid layout: left nav / content / right toc */
+.doc-grid {
+  display: grid;
+  grid-template-columns: 260px 1fr 260px;
+  gap: 2rem;
+  padding: 1.5rem 0 0;
+}
+.sidebar { position: sticky; top: 5.5rem; align-self: start; }
+.sidebar .sidebar-title { margin: 0 0 .5rem; font-size: 0.95rem; text-transform: uppercase; letter-spacing: .06em; color: var(--clr-grey-500); }
+.sidebar .sidebar-section {
+  background: var(--clr-surface);
+  border: 1px solid var(--clr-grey-300);
+  border-radius: var(--radius-sm);
+  box-shadow: var(--shadow-sm);
+  padding: 0.75rem 0.85rem;
+}
+.left-nav .toc, .on-this-page .toc {
+  margin: 0;
+  padding-left: 1rem;
+}
+.left-nav .toc ol, .on-this-page .toc ol { list-style: none; margin: 0; padding-left: 0; }
+.left-nav .toc li, .on-this-page .toc li { margin: .25rem 0; }
+.left-nav .toc a, .on-this-page .toc a {
+  color: var(--clr-grey-700);
+  font-size: .92rem;
+}
+.left-nav .toc a.active, .on-this-page .toc a.active { color: var(--clr-primary-600); font-weight: 700; }
+
+/* Content area */
+.content {
+  background: var(--clr-surface);
+  border: 1px solid var(--clr-grey-300);
+  border-radius: var(--radius-sm);
+  box-shadow: var(--shadow-sm);
+  padding: 1.25rem 1.25rem;
+}
+.doc-header h1 { margin-top: 0; }
+.muted { color: var(--clr-grey-500); font-size: 0.9rem; }
+
+/* Autosummary table */
+.api-table { border-collapse: collapse; width: 100%; margin: 1rem 0 1.5rem; }
+.api-table thead th {
+  position: sticky;
+  top: 0;
+  background: var(--clr-grey-100);
+  z-index: 1;
+}
+.api-table th, .api-table td { border: 1px solid var(--clr-grey-300); padding: .5rem .6rem; }
+.api-table tbody tr:nth-child(even) { background: rgba(0,0,0,.015); }
+
+/* Signature blocks & field lists */
+.sig { font-family: Consolas, monospace; font-weight: 600; }
+.field-list { column-gap: 2rem; }
+.field-list dt { font-weight: 700; }
+.field-list dd { margin: 0 0 .6rem 0; color: var(--clr-grey-700); }
+
+/* Admonitions (SciPy-like) */
+.admonition {
+  border-left: 4px solid var(--clr-grey-300);
+  background: var(--clr-grey-100);
+  padding: .75rem 1rem;
+  margin: 1.25rem 0;
+  border-radius: var(--radius-sm);
+}
+.admonition p { margin: 0; }
+.admonition.info { border-left-color: var(--clr-primary-400); background: rgba(26,163,255,.12); }
+.admonition.warning { border-left-color: var(--clr-danger); background: rgba(255,107,107,.12); }
+.admonition.note { border-left-color: var(--clr-warning); background: rgba(255,182,39,.12); }
+.admonition.seealso { border-left-color: var(--clr-success); background: rgba(46,204,113,.12); }
+
+/* Heading anchor permalink */
+.anchor {
+  margin-left: .3rem;
+  opacity: 0;
+  text-decoration: none;
+  font-weight: 700;
+}
+.content h2:hover .anchor,
+.content h3:hover .anchor,
+.content h4:hover .anchor { opacity: .8; }
+
+/* Code blocks: add space for copy badge */
+pre[data-copy] { cursor: pointer; }
+pre[data-copy]::after { right: .75rem; top: .5rem; }
+
+/* Responsive collapse */
+@media (max-width: 1100px) {
+  .doc-grid { grid-template-columns: 220px 1fr; }
+  .on-this-page { display: none; }
+}
+@media (max-width: 800px) {
+  .doc-grid { grid-template-columns: 1fr; }
+  .left-nav { display: none; }
+  .content { padding: 1rem; }
+}