Merge pull request #17 from zasexton/main

Add interactive GUI (PySide6/VTK), .dmn IO, sphere refinement, and Mesa setup

Author: zasexton

.gitignore

@@ -0,0 +1,29 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C/C++ artifacts from Cython builds
+*.so
+*.pyd
+*.dll
+*.dylib
+*.o
+*.a
+*.cpp
+
+# Build and packaging
+build/
+dist/
+*.egg-info/
+
+# Local caches and temp
+tmp/
+.idea/
+
+# Local binaries and downloads
+svv/bin/
+svZeroDSolver*
+
+# Sample artifacts
+cube.dmn

docs/algorithm.html

@@ -35,7 +35,7 @@ <h1>svVascularize</h1>
         <a href="index.html#about">About</a>
         <a href="install.html">Installation</a>
         <a class="active" href="doc.html">Documentation</a>
-        <a href="#simulation">Simulation</a>
+        <a href="index.html#simulation">Simulation</a>
         <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
         <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
       </nav>

docs/api/domain.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>

docs/api/forest.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>

docs/api/index_api.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>
@@ -388,6 +388,15 @@ <h5>1D Models</h5>
                             </div>
                         </div>
 
+                        <div class="api-classes">
+                            <h4>Main Classes</h4>
+                            <ul class="api-class-list">
+                                <li>
+                                    <a href="simulation.html"><code>Simulation</code></a> - Container for generating meshes and simulation files
+                                </li>
+                            </ul>
+                        </div>
+
                         <div class="api-example">
                             <h4>Example Usage</h4>
                             <pre data-copy><code class="language-python">from svv.simulation import Simulation

docs/api/patch.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>

docs/api/simulation.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>

docs/api/tree.html

@@ -18,7 +18,7 @@ <h1>svVascularize</h1>
                 <a href="../index.html#about">About</a>
                 <a href="../install.html">Installation</a>
                 <a href="../doc.html">Documentation</a>
-                <a href="#simulation">Simulation</a>
+                <a href="../index.html#simulation">Simulation</a>
                 <a href="https://pypi.org/project/svv/" target="_blank" rel="noopener">PyPI</a>
                 <a href="https://github.com/SimVascular/svVascularize" target="_blank" rel="noopener">GitHub</a>
             </nav>

docs/doc.html

@@ -71,6 +71,20 @@ <h3>Community & Support</h3>
       <li><a href="https://github.com/SimVascular/svVascularize/issues" target="_blank" rel="noopener">GitHub Issues</a></li>
     </ul>
 
+    <h3 id="simulation">Simulation Overview</h3>
+    <p>The <code>Simulation</code> module mirrors the capabilities in the library today:</p>
+    <ul>
+      <li><a href="pipeline.html">3-D CFD pipeline</a> &mdash; full workflow from <code>build_meshes()</code> through
+        <code>write_3d_fluid_simulation()</code>, including boundary layer options and multi-tree exports.</li>
+      <li><a href="api/simulation.html">Simulation API reference</a> &mdash; method-by-method detail on mesh storage,
+        face extraction, and svFSI XML generation.</li>
+      <li><a href="quickstart.html#export-0d-simulation-files">0-D exports</a> &mdash; use
+        <code>svv.simulation.fluid.rom.zero_d</code> helpers for fast circuit models; 1-D parameter builders are also
+        included in <code>Simulation.construct_1d_fluid_simulation()</code> for multiscale coupling.</li>
+    </ul>
+    <div class="callout info"><strong>Tip:</strong> 0-D and 1-D solvers are shipped separately; see the installation
+      guide&rsquo;s <a href="install.html#simulation">simulation extras</a> for setup notes.</div>
+
   </main>
 
   <!-- Footer -->

docs/index.html

@@ -46,11 +46,31 @@ <h3>About<code>svVascularize</code> </h3>
   </section>
 
 
+  <section id="simulation" class="content">
+    <div class="container">
+      <h3>Simulation Workflows</h3>
+      <p>The <code>svv.simulation.Simulation</code> container turns generated trees and forests into ready-to-run
+        solver input. It automates mesh generation, boundary extraction, and svFSI configuration so you can move from a
+        synthetic network to a 3-D CFD job without leaving Python.</p>
+      <ul>
+        <li><strong>3D CFD:</strong> build watertight tet meshes, optional boundary layers, extract wall/outlet faces,
+          and emit svFSI XML plus surface/volume mesh files.</li>
+        <li><strong>Multi-tree support:</strong> forests are handled tree-by-tree, letting you select which networks to
+          mesh and export.</li>
+        <li><strong>Reduced-order:</strong> direct helpers in <code>svv.simulation.fluid.rom</code> export matching 0-D
+          circuits today, with 1-D parameter generation available for coupling work.</li>
+      </ul>
+      <div class="callout info"><strong>Need details?</strong> The <a href="pipeline.html">3-D pipeline</a> and <a href="api/simulation.html">Simulation API</a> pages walk through every step, from
+        <code>build_meshes()</code> to writing solver files.</div>
+    </div>
+  </section>
+
+
   <footer>
     <div class="container">
       <p>&copy; 2025 SimVascular, Stanford University, The Regents of the University of California, and others —
       <a href="https://opensource.org/license/BSD-3-Clause">BSD 3-Clause License</a><br></p>
     </div>
   </footer>
 </body>
-</html>
+</html>