initial upload

docs/pylagrit/original/static/alabaster.css

@@ -0,0 +1,701 @@
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: Georgia, serif;
+    font-size: 17px;
+    background-color: #fff;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+
+div.document {
+    width: 940px;
+    margin: 30px auto 0 auto;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 220px;
+}
+
+div.sphinxsidebar {
+    width: 220px;
+    font-size: 14px;
+    line-height: 1.5;
+}
+
+hr {
+    border: 1px solid #B1B4B6;
+}
+
+div.body {
+    background-color: #fff;
+    color: #3E4349;
+    padding: 0 30px 0 30px;
+}
+
+div.body > .section {
+    text-align: left;
+}
+
+div.footer {
+    width: 940px;
+    margin: 20px auto 30px auto;
+    font-size: 14px;
+    color: #888;
+    text-align: right;
+}
+
+div.footer a {
+    color: #888;
+}
+
+p.caption {
+    font-family: inherit;
+    font-size: inherit;
+}
+
+
+div.relations {
+    display: none;
+}
+
+
+div.sphinxsidebar a {
+    color: #444;
+    text-decoration: none;
+    border-bottom: 1px dotted #999;
+}
+
+div.sphinxsidebar a:hover {
+    border-bottom: 1px solid #999;
+}
+
+div.sphinxsidebarwrapper {
+    padding: 18px 10px;
+}
+
+div.sphinxsidebarwrapper p.logo {
+    padding: 0;
+    margin: -10px 0 0 0px;
+    text-align: center;
+}
+
+div.sphinxsidebarwrapper h1.logo {
+    margin-top: -10px;
+    text-align: center;
+    margin-bottom: 5px;
+    text-align: left;
+}
+
+div.sphinxsidebarwrapper h1.logo-name {
+    margin-top: 0px;
+}
+
+div.sphinxsidebarwrapper p.blurb {
+    margin-top: 0;
+    font-style: normal;
+}
+
+div.sphinxsidebar h3,
+div.sphinxsidebar h4 {
+    font-family: Georgia, serif;
+    color: #444;
+    font-size: 24px;
+    font-weight: normal;
+    margin: 0 0 5px 0;
+    padding: 0;
+}
+
+div.sphinxsidebar h4 {
+    font-size: 20px;
+}
+
+div.sphinxsidebar h3 a {
+    color: #444;
+}
+
+div.sphinxsidebar p.logo a,
+div.sphinxsidebar h3 a,
+div.sphinxsidebar p.logo a:hover,
+div.sphinxsidebar h3 a:hover {
+    border: none;
+}
+
+div.sphinxsidebar p {
+    color: #555;
+    margin: 10px 0;
+}
+
+div.sphinxsidebar ul {
+    margin: 10px 0;
+    padding: 0;
+    color: #000;
+}
+
+div.sphinxsidebar ul li.toctree-l1 > a {
+    font-size: 120%;
+}
+
+div.sphinxsidebar ul li.toctree-l2 > a {
+    font-size: 110%;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #CCC;
+    font-family: Georgia, serif;
+    font-size: 1em;
+}
+
+div.sphinxsidebar hr {
+    border: none;
+    height: 1px;
+    color: #AAA;
+    background: #AAA;
+
+    text-align: left;
+    margin-left: 0;
+    width: 50%;
+}
+
+div.sphinxsidebar .badge {
+    border-bottom: none;
+}
+
+div.sphinxsidebar .badge:hover {
+    border-bottom: none;
+}
+
+/* To address an issue with donation coming after search */
+div.sphinxsidebar h3.donation {
+    margin-top: 10px;
+}
+
+/* -- body styles ----------------------------------------------------------- */
+
+a {
+    color: #004B6B;
+    text-decoration: underline;
+}
+
+a:hover {
+    color: #6D4100;
+    text-decoration: underline;
+}
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+    font-family: Georgia, serif;
+    font-weight: normal;
+    margin: 30px 0px 10px 0px;
+    padding: 0;
+}
+
+div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; }
+div.body h2 { font-size: 180%; }
+div.body h3 { font-size: 150%; }
+div.body h4 { font-size: 130%; }
+div.body h5 { font-size: 100%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+    color: #DDD;
+    padding: 0 4px;
+    text-decoration: none;
+}
+
+a.headerlink:hover {
+    color: #444;
+    background: #EAEAEA;
+}
+
+div.body p, div.body dd, div.body li {
+    line-height: 1.4em;
+}
+
+div.admonition {
+    margin: 20px 0px;
+    padding: 10px 30px;
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
+    background-color: #FBFBFB;
+    border-bottom: 1px solid #fafafa;
+}
+
+div.admonition p.admonition-title {
+    font-family: Georgia, serif;
+    font-weight: normal;
+    font-size: 24px;
+    margin: 0 0 10px 0;
+    padding: 0;
+    line-height: 1;
+}
+
+div.admonition p.last {
+    margin-bottom: 0;
+}
+
+div.highlight {
+    background-color: #fff;
+}
+
+dt:target, .highlight {
+    background: #FAF3E8;
+}
+
+div.warning {
+    background-color: #FCC;
+    border: 1px solid #FAA;
+}
+
+div.danger {
+    background-color: #FCC;
+    border: 1px solid #FAA;
+    -moz-box-shadow: 2px 2px 4px #D52C2C;
+    -webkit-box-shadow: 2px 2px 4px #D52C2C;
+    box-shadow: 2px 2px 4px #D52C2C;
+}
+
+div.error {
+    background-color: #FCC;
+    border: 1px solid #FAA;
+    -moz-box-shadow: 2px 2px 4px #D52C2C;
+    -webkit-box-shadow: 2px 2px 4px #D52C2C;
+    box-shadow: 2px 2px 4px #D52C2C;
+}
+
+div.caution {
+    background-color: #FCC;
+    border: 1px solid #FAA;
+}
+
+div.attention {
+    background-color: #FCC;
+    border: 1px solid #FAA;
+}
+
+div.important {
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.note {
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.tip {
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.hint {
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.seealso {
+    background-color: #EEE;
+    border: 1px solid #CCC;
+}
+
+div.topic {
+    background-color: #EEE;
+}
+
+p.admonition-title {
+    display: inline;
+}
+
+p.admonition-title:after {
+    content: ":";
+}
+
+pre, tt, code {
+    font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+    font-size: 0.9em;
+}
+
+.hll {
+    background-color: #FFC;
+    margin: 0 -12px;
+    padding: 0 12px;
+    display: block;
+}
+
+img.screenshot {
+}
+
+tt.descname, tt.descclassname, code.descname, code.descclassname {
+    font-size: 0.95em;
+}
+
+tt.descname, code.descname {
+    padding-right: 0.08em;
+}
+
+img.screenshot {
+    -moz-box-shadow: 2px 2px 4px #EEE;
+    -webkit-box-shadow: 2px 2px 4px #EEE;
+    box-shadow: 2px 2px 4px #EEE;
+}
+
+table.docutils {
+    border: 1px solid #888;
+    -moz-box-shadow: 2px 2px 4px #EEE;
+    -webkit-box-shadow: 2px 2px 4px #EEE;
+    box-shadow: 2px 2px 4px #EEE;
+}
+
+table.docutils td, table.docutils th {
+    border: 1px solid #888;
+    padding: 0.25em 0.7em;
+}
+
+table.field-list, table.footnote {
+    border: none;
+    -moz-box-shadow: none;
+    -webkit-box-shadow: none;
+    box-shadow: none;
+}
+
+table.footnote {
+    margin: 15px 0;
+    width: 100%;
+    border: 1px solid #EEE;
+    background: #FDFDFD;
+    font-size: 0.9em;
+}
+
+table.footnote + table.footnote {
+    margin-top: -15px;
+    border-top: none;
+}
+
+table.field-list th {
+    padding: 0 0.8em 0 0;
+}
+
+table.field-list td {
+    padding: 0;
+}
+
+table.field-list p {
+    margin-bottom: 0.8em;
+}
+
+/* Cloned from
+ * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68
+ */
+.field-name {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
+
+table.footnote td.label {
+    width: .1px;
+    padding: 0.3em 0 0.3em 0.5em;
+}
+
+table.footnote td {
+    padding: 0.3em 0.5em;
+}
+
+dl {
+    margin: 0;
+    padding: 0;
+}
+
+dl dd {
+    margin-left: 30px;
+}
+
+blockquote {
+    margin: 0 0 0 30px;
+    padding: 0;
+}
+
+ul, ol {
+    /* Matches the 30px from the narrow-screen "li > ul" selector below */
+    margin: 10px 0 10px 30px;
+    padding: 0;
+}
+
+pre {
+    background: #EEE;
+    padding: 7px 30px;
+    margin: 15px 0px;
+    line-height: 1.3em;
+}
+
+div.viewcode-block:target {
+    background: #ffd;
+}
+
+dl pre, blockquote pre, li pre {
+    margin-left: 0;
+    padding-left: 30px;
+}
+
+tt, code {
+    background-color: #ecf0f3;
+    color: #222;
+    /* padding: 1px 2px; */
+}
+
+tt.xref, code.xref, a tt {
+    background-color: #FBFBFB;
+    border-bottom: 1px solid #fff;
+}
+
+a.reference {
+    text-decoration: none;
+    border-bottom: 1px dotted #004B6B;
+}
+
+/* Don't put an underline on images */
+a.image-reference, a.image-reference:hover {
+    border-bottom: none;
+}
+
+a.reference:hover {
+    border-bottom: 1px solid #6D4100;
+}
+
+a.footnote-reference {
+    text-decoration: none;
+    font-size: 0.7em;
+    vertical-align: top;
+    border-bottom: 1px dotted #004B6B;
+}
+
+a.footnote-reference:hover {
+    border-bottom: 1px solid #6D4100;
+}
+
+a:hover tt, a:hover code {
+    background: #EEE;
+}
+
+
+@media screen and (max-width: 870px) {
+
+    div.sphinxsidebar {
+    	display: none;
+    }
+
+    div.document {
+       width: 100%;
+
+    }
+
+    div.documentwrapper {
+    	margin-left: 0;
+    	margin-top: 0;
+    	margin-right: 0;
+    	margin-bottom: 0;
+    }
+
+    div.bodywrapper {
+    	margin-top: 0;
+    	margin-right: 0;
+    	margin-bottom: 0;
+    	margin-left: 0;
+    }
+
+    ul {
+    	margin-left: 0;
+    }
+
+	li > ul {
+        /* Matches the 30px from the "ul, ol" selector above */
+		margin-left: 30px;
+	}
+
+    .document {
+    	width: auto;
+    }
+
+    .footer {
+    	width: auto;
+    }
+
+    .bodywrapper {
+    	margin: 0;
+    }
+
+    .footer {
+    	width: auto;
+    }
+
+    .github {
+        display: none;
+    }
+
+
+
+}
+
+
+
+@media screen and (max-width: 875px) {
+
+    body {
+        margin: 0;
+        padding: 20px 30px;
+    }
+
+    div.documentwrapper {
+        float: none;
+        background: #fff;
+    }
+
+    div.sphinxsidebar {
+        display: block;
+        float: none;
+        width: 102.5%;
+        margin: 50px -30px -20px -30px;
+        padding: 10px 20px;
+        background: #333;
+        color: #FFF;
+    }
+
+    div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
+    div.sphinxsidebar h3 a {
+        color: #fff;
+    }
+
+    div.sphinxsidebar a {
+        color: #AAA;
+    }
+
+    div.sphinxsidebar p.logo {
+        display: none;
+    }
+
+    div.document {
+        width: 100%;
+        margin: 0;
+    }
+
+    div.footer {
+        display: none;
+    }
+
+    div.bodywrapper {
+        margin: 0;
+    }
+
+    div.body {
+        min-height: 0;
+        padding: 0;
+    }
+
+    .rtd_doc_footer {
+        display: none;
+    }
+
+    .document {
+        width: auto;
+    }
+
+    .footer {
+        width: auto;
+    }
+
+    .footer {
+        width: auto;
+    }
+
+    .github {
+        display: none;
+    }
+}
+
+
+/* misc. */
+
+.revsys-inline {
+    display: none!important;
+}
+
+/* Make nested-list/multi-paragraph items look better in Releases changelog
+ * pages. Without this, docutils' magical list fuckery causes inconsistent
+ * formatting between different release sub-lists.
+ */
+div#changelog > div.section > ul > li > p:only-child {
+    margin-bottom: 0;
+}
+
+/* Hide fugly table cell borders in ..bibliography:: directive output */
+table.docutils.citation, table.docutils.citation td, table.docutils.citation th {
+  border: none;
+  /* Below needed in some edge cases; if not applied, bottom shadows appear */
+  -moz-box-shadow: none;
+  -webkit-box-shadow: none;
+  box-shadow: none;
+}
+
+
+/* relbar */
+
+.related {
+    line-height: 30px;
+    width: 100%;
+    font-size: 0.9rem;
+}
+
+.related.top {
+    border-bottom: 1px solid #EEE;
+    margin-bottom: 20px;
+}
+
+.related.bottom {
+    border-top: 1px solid #EEE;
+}
+
+.related ul {
+    padding: 0;
+    margin: 0;
+    list-style: none;
+}
+
+.related li {
+    display: inline;
+}
+
+nav#rellinks {
+    float: right;
+}
+
+nav#rellinks li+li:before {
+    content: "|";
+}
+
+nav#breadcrumbs li+li:before {
+    content: "\00BB";
+}
+
+/* Hide certain items when printing */
+@media print {
+    div.related {
+        display: none;
+    }
+}

docs/pylagrit/original/static/autodoc.html

@@ -0,0 +1,130 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Class Documentation &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="PyLaGriT" href="autodoc_pylagrit.html" />
+    <link rel="prev" title="Getting Started" href="gettingstarted.html" />
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <div class="section" id="class-documentation">
+<span id="class-docs"></span><h1>Class Documentation<a class="headerlink" href="#class-documentation" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_pylagrit.html">PyLaGriT Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_pset.html">Point Set Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc_region.html">Region Class</a></li>
+</ul>
+</div>
+</div>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Class Documentation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pylagrit.html">PyLaGriT Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pset.html">Point Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_region.html">Region Class</a></li>
+</ul>
+</li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+      <li>Previous: <a href="gettingstarted.html" title="previous chapter">Getting Started</a></li>
+      <li>Next: <a href="autodoc_pylagrit.html" title="next chapter">PyLaGriT</a></li>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2016, Dylan R. Harp.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      
+      |
+      <a href="sources/autodoc.rst.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>

docs/pylagrit/original/static/autodoc_eltset.html

@@ -0,0 +1,217 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Element Set Object &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Face Set Object" href="autodoc_faceset.html" />
+    <link rel="prev" title="Point Set Object" href="autodoc_pset.html" />
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <div class="section" id="module-pylagrit">
+<span id="element-set-object"></span><h1>Element Set Object<a class="headerlink" href="#module-pylagrit" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="pylagrit.EltSet">
+<em class="property">class </em><code class="descclassname">pylagrit.</code><code class="descname">EltSet</code><span class="sig-paren">(</span><em>name</em>, <em>parent</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet" title="Permalink to this definition">¶</a></dt>
+<dd><p>EltSet class</p>
+<dl class="method">
+<dt id="pylagrit.EltSet.create_faceset">
+<code class="descname">create_faceset</code><span class="sig-paren">(</span><em>filename=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.create_faceset" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.delete">
+<code class="descname">delete</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.delete" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.list">
+<code class="descname">list</code><span class="sig-paren">(</span><em>attname=None, stride=[1, 0, 0]</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.list" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.minmax">
+<code class="descname">minmax</code><span class="sig-paren">(</span><em>attname=None, stride=[1, 0, 0]</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.minmax" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.pset">
+<code class="descname">pset</code><span class="sig-paren">(</span><em>name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.pset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create a pset from the points in an element set
+:arg name: Name of point set to be used within LaGriT
+:type name: str
+:returns: PyLaGriT PSet object</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.refine">
+<code class="descname">refine</code><span class="sig-paren">(</span><em>amr=''</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.refine" title="Permalink to this definition">¶</a></dt>
+<dd><p>Refine elements in the element set</p>
+<dl class="docutils">
+<dt>Example:</dt>
+<dd><div class="first last highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">pylagrit</span> <span class="k">import</span> <span class="n">PyLaGriT</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">numpy</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">sys</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">df</span> <span class="o">=</span> <span class="mf">0.0005</span> <span class="c1"># Fault half aperture</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">lr</span> <span class="o">=</span> <span class="mi">7</span> <span class="c1"># Levels of refinement</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">nx</span> <span class="o">=</span> <span class="mi">4</span> <span class="c1"># Number of base mesh blocks in x direction</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">nz</span> <span class="o">=</span> <span class="mi">20</span> <span class="c1"># Number of base mesh blocks in z direction</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">d_base</span> <span class="o">=</span> <span class="n">df</span><span class="o">*</span><span class="mi">2</span><span class="o">**</span><span class="p">(</span><span class="n">lr</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># Calculated dimension of base block</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">w</span> <span class="o">=</span> <span class="n">d_base</span><span class="o">*</span><span class="n">nx</span> <span class="c1"># Calculated width of model</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">d</span> <span class="o">=</span> <span class="n">d_base</span><span class="o">*</span><span class="n">nz</span> <span class="c1"># Calculated depth of model</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">lg</span> <span class="o">=</span> <span class="n">PyLaGriT</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="c1"># Create discrete fracture mesh</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">dxyz</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">d_base</span><span class="p">,</span><span class="n">d_base</span><span class="p">,</span><span class="mf">0.</span><span class="p">])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mins</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="mf">0.</span><span class="p">,</span><span class="o">-</span><span class="n">d</span><span class="p">,</span><span class="mf">0.</span><span class="p">])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">maxs</span> <span class="o">=</span> <span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">w</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">])</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mqua</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">createpts_dxyz</span><span class="p">(</span><span class="n">dxyz</span><span class="p">,</span><span class="n">mins</span><span class="p">,</span><span class="n">maxs</span><span class="p">,</span><span class="s1">&#39;quad&#39;</span><span class="p">,</span><span class="n">hard_bound</span><span class="o">=</span><span class="p">(</span><span class="s1">&#39;min&#39;</span><span class="p">,</span><span class="s1">&#39;max&#39;</span><span class="p">,</span><span class="s1">&#39;min&#39;</span><span class="p">),</span><span class="n">connect</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">lr</span><span class="p">):</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">prefine</span> <span class="o">=</span> <span class="n">mqua</span><span class="o">.</span><span class="n">pset_geom_xyz</span><span class="p">(</span><span class="n">mins</span><span class="o">-</span><span class="mf">0.1</span><span class="p">,(</span><span class="mf">0.0001</span><span class="p">,</span><span class="mf">0.1</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">erefine</span> <span class="o">=</span> <span class="n">prefine</span><span class="o">.</span><span class="n">eltset</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">erefine</span><span class="o">.</span><span class="n">refine</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">prefine</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">erefine</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span> <span class="o">=</span> <span class="n">mqua</span><span class="o">.</span><span class="n">copypts</span><span class="p">(</span><span class="s1">&#39;triplane&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span><span class="o">.</span><span class="n">connect</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="c1"># Make sure that not nodes are lost during connect</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">if</span> <span class="s1">&#39;The mesh is complete but could not include all points.&#39;</span> <span class="ow">in</span> <span class="n">lg</span><span class="o">.</span><span class="n">before</span><span class="p">:</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="nb">print</span> <span class="s1">&#39;Error: Lost some points during connect, not completing mesh and exiting workflow!&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="nb">print</span> <span class="s1">&#39;&#39;</span>
+<span class="gp">&gt;&gt;&gt; </span>    <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span><span class="o">.</span><span class="n">tri_mesh_output_prep</span><span class="p">()</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span><span class="o">.</span><span class="n">reorder_nodes</span><span class="p">(</span><span class="n">cycle</span><span class="o">=</span><span class="s1">&#39;xic yic zic&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">pfault</span> <span class="o">=</span> <span class="n">mtri</span><span class="o">.</span><span class="n">pset_geom_xyz</span><span class="p">(</span><span class="n">mins</span><span class="o">-</span><span class="mf">0.1</span><span class="p">,(</span><span class="mf">0.0001</span><span class="p">,</span><span class="mf">0.1</span><span class="p">,</span><span class="mi">0</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">psource</span> <span class="o">=</span> <span class="n">mtri</span><span class="o">.</span><span class="n">pset_geom_xyz</span><span class="p">(</span><span class="n">mins</span><span class="o">-</span><span class="mf">0.1</span><span class="p">,</span><span class="n">mins</span><span class="o">+</span><span class="mf">0.0001</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">pfault</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">psource</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">mtri</span><span class="o">.</span><span class="n">paraview</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="s1">&#39;discrete_fracture.inp&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.EltSet.setatt">
+<code class="descname">setatt</code><span class="sig-paren">(</span><em>attname</em>, <em>value</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.EltSet.setatt" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</div>
+
+
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+<li class="toctree-l2 current"><a class="current reference internal" href="#">Element Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
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docs/pylagrit/original/static/autodoc_faceset.html

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+    <link rel="next" title="Region Object" href="autodoc_region.html" />
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+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
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+            
+  <div class="section" id="module-pylagrit">
+<span id="face-set-object"></span><h1>Face Set Object<a class="headerlink" href="#module-pylagrit" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="pylagrit.FaceSet">
+<em class="property">class </em><code class="descclassname">pylagrit.</code><code class="descname">FaceSet</code><span class="sig-paren">(</span><em>filename</em>, <em>parent</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.FaceSet" title="Permalink to this definition">¶</a></dt>
+<dd><p>FaceSet class</p>
+</dd></dl>
+
+</div>
+
+
+          </div>
+          
+        </div>
+      </div>
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+<li class="toctree-l2"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pset.html">Point Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Face Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_region.html">Region Class</a></li>
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+  <li><a href="index.html">Documentation overview</a><ul>
+  <li><a href="autodoc.html">Class Documentation</a><ul>
+      <li>Previous: <a href="autodoc_eltset.html" title="previous chapter">Element Set Object</a></li>
+      <li>Next: <a href="autodoc_region.html" title="next chapter">Region Object</a></li>
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docs/pylagrit/original/static/autodoc_pset.html

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+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Element Set Object" href="autodoc_eltset.html" />
+    <link rel="prev" title="Mesh Object" href="autodoc_mo.html" />
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <div class="section" id="module-pylagrit">
+<span id="point-set-object"></span><h1>Point Set Object<a class="headerlink" href="#module-pylagrit" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="pylagrit.PSet">
+<em class="property">class </em><code class="descclassname">pylagrit.</code><code class="descname">PSet</code><span class="sig-paren">(</span><em>name</em>, <em>parent</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet" title="Permalink to this definition">¶</a></dt>
+<dd><p>Pset class</p>
+<dl class="method">
+<dt id="pylagrit.PSet.delete">
+<code class="descname">delete</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.delete" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.dump">
+<code class="descname">dump</code><span class="sig-paren">(</span><em>filerootname</em>, <em>zonetype='zone'</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.dump" title="Permalink to this definition">¶</a></dt>
+<dd><p>Dump zone file of pset nodes
+:arg filerootname: rootname of files to create, pset name will be added to name
+:type filerootname: string
+:arg zonetype: Type of zone file to dump, ‘zone’ or ‘zonn’
+:tpye zonetype: string</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.eltset">
+<code class="descname">eltset</code><span class="sig-paren">(</span><em>membership='inclusive'</em>, <em>name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.eltset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Create eltset from pset</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>membership</strong> (<em>str</em>) – type of element membership, one of [inclusive,exclusive,face]</li>
+<li><strong>name</strong> (<em>str</em>) – Name of element set to be used within LaGriT</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">PyLaGriT EltSet object</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.expand">
+<code class="descname">expand</code><span class="sig-paren">(</span><em>membership='inclusive'</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.expand" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add points surrounding pset to pset</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>membership</strong> (<em>str</em>) – type of element membership, one of [inclusive,exclusive,face]</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.interpolate">
+<code class="descname">interpolate</code><span class="sig-paren">(</span><em>method</em>, <em>attsink</em>, <em>cmosrc</em>, <em>attsrc</em>, <em>interp_function=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.interpolate" title="Permalink to this definition">¶</a></dt>
+<dd><p>Interpolate values from attribute attsrc from mesh object cmosrc to current mesh object</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.interpolate_continuous">
+<code class="descname">interpolate_continuous</code><span class="sig-paren">(</span><em>attsink</em>, <em>cmosrc</em>, <em>attsrc</em>, <em>interp_function=None</em>, <em>nearest=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.interpolate_continuous" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.interpolate_default">
+<code class="descname">interpolate_default</code><span class="sig-paren">(</span><em>attsink</em>, <em>cmosrc</em>, <em>attsrc</em>, <em>tie_option='tiemax'</em>, <em>flag_option='plus1'</em>, <em>keep_option='delatt'</em>, <em>interp_function=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.interpolate_default" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.interpolate_map">
+<code class="descname">interpolate_map</code><span class="sig-paren">(</span><em>attsink</em>, <em>cmosrc</em>, <em>attsrc</em>, <em>tie_option='tiemax'</em>, <em>flag_option='plus1'</em>, <em>keep_option='delatt'</em>, <em>interp_function=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.interpolate_map" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.interpolate_voronoi">
+<code class="descname">interpolate_voronoi</code><span class="sig-paren">(</span><em>attsink</em>, <em>cmosrc</em>, <em>attsrc</em>, <em>interp_function=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.interpolate_voronoi" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.list">
+<code class="descname">list</code><span class="sig-paren">(</span><em>attname=None, stride=[1, 0, 0]</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.list" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.minmax">
+<code class="descname">minmax</code><span class="sig-paren">(</span><em>attname=None, stride=[1, 0, 0]</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.minmax" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.minmax_xyz">
+<code class="descname">minmax_xyz</code><span class="sig-paren">(</span><em>stride=[1, 0, 0], verbose=True</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.minmax_xyz" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.perturb">
+<code class="descname">perturb</code><span class="sig-paren">(</span><em>xfactor</em>, <em>yfactor</em>, <em>zfactor</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.perturb" title="Permalink to this definition">¶</a></dt>
+<dd><p>This command moves node coordinates in the following manner.</p>
+<p>Three pairs of random numbers between 0 and 1 are generated.
+These pairs refer to the x, y and z coordinates of the nodes respectively.
+The first random number of each pair is multiplied by the factor given in
+the command. The second random number is used to determine
+if the calculated offset is to be added or subtracted from the coordinate.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.pset_attribute">
+<code class="descname">pset_attribute</code><span class="sig-paren">(</span><em>attribute</em>, <em>value</em>, <em>comparison='eq'</em>, <em>name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.pset_attribute" title="Permalink to this definition">¶</a></dt>
+<dd><p>Define PSet from another PSet by attribute</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>attribute</strong> (<em>str</em>) – Nodes defined by attribute ID.</li>
+<li><strong>value</strong> (<em>integer</em>) – attribute ID value.</li>
+<li><strong>comparison</strong> (<em>can use default without specifiy anything</em><em>, or </em><em>list</em><em>[</em><em>lt|le|gt|ge|eq|ne</em><em>]</em>) – attribute comparison, default is eq.</li>
+<li><strong>name</strong> (<em>str</em>) – The name to be assigned to the PSet created.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Returns: PSet object</p>
+<p>Usage: newpset = oldpset.pset_attribute(‘attribute’,’value’,’comparison’)</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.refine">
+<code class="descname">refine</code><span class="sig-paren">(</span><em>refine_type='element', refine_option='constant', interpolation=' ', prange=[-1, 0, 0], field=' ', inclusive_flag='exclusive', prd_choice=None</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.refine" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.scale">
+<code class="descname">scale</code><span class="sig-paren">(</span><em>scale_type='relative', scale_geom='xyz', scale_factor=[1, 1, 1], scale_center=[0, 0, 0]</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.scale" title="Permalink to this definition">¶</a></dt>
+<dd><p>Scale pset nodes by a relative or absolute amount
+:arg scale_type: Scaling type may be ‘relative’ or ‘absolute’
+:type scale_type: string
+:arg scale_geom: May be one of the geometry types ‘xyz’ (Cartesian), ‘rtz’ (cylindrical), or ‘rtp’ (spherical)
+:type scale_geom: string
+:arg scale_factor: If scale_factor is relative, scaling factors are unitless multipliers. If absolute, scaling factors are constants added to existing coordinates.
+:type scale_factor: list
+:arg scale_center: Geometric center to scale from
+:type scale_center: list</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.setatt">
+<code class="descname">setatt</code><span class="sig-paren">(</span><em>attname</em>, <em>value</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.setatt" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.smooth">
+<code class="descname">smooth</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.smooth" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="pylagrit.PSet.trans">
+<code class="descname">trans</code><span class="sig-paren">(</span><em>xold</em>, <em>xnew</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.PSet.trans" title="Permalink to this definition">¶</a></dt>
+<dd><p>Translate points within a pset by the linear translation from (xold, yold, zold) to (xnew, ynew, znew)</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>xold</strong> (<em>tuple</em>) – Tuple containing point (xold, yold, zold) to translate from</li>
+<li><strong>xnew</strong> (<em>tuple</em>) – Tuple containing point (xnew, ynew, znew) to translate to</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.xlength">
+<code class="descname">xlength</code><a class="headerlink" href="#pylagrit.PSet.xlength" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.xmax">
+<code class="descname">xmax</code><a class="headerlink" href="#pylagrit.PSet.xmax" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.xmin">
+<code class="descname">xmin</code><a class="headerlink" href="#pylagrit.PSet.xmin" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.ylength">
+<code class="descname">ylength</code><a class="headerlink" href="#pylagrit.PSet.ylength" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.ymax">
+<code class="descname">ymax</code><a class="headerlink" href="#pylagrit.PSet.ymax" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.ymin">
+<code class="descname">ymin</code><a class="headerlink" href="#pylagrit.PSet.ymin" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.zlength">
+<code class="descname">zlength</code><a class="headerlink" href="#pylagrit.PSet.zlength" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.zmax">
+<code class="descname">zmax</code><a class="headerlink" href="#pylagrit.PSet.zmax" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="pylagrit.PSet.zmin">
+<code class="descname">zmin</code><a class="headerlink" href="#pylagrit.PSet.zmin" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
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+<li class="toctree-l2"><a class="reference internal" href="autodoc_pylagrit.html">PyLaGriT Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Point Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_region.html">Region Class</a></li>
+</ul>
+</li>
+</ul>
+
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+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
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+      <li>Previous: <a href="autodoc_mo.html" title="previous chapter">Mesh Object</a></li>
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docs/pylagrit/original/static/autodoc_region.html

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+
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+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Region Object &#8212; PyLaGriT 0.0.0 documentation</title>
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+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <div class="section" id="module-pylagrit">
+<span id="region-object"></span><h1>Region Object<a class="headerlink" href="#module-pylagrit" title="Permalink to this headline">¶</a></h1>
+<dl class="class">
+<dt id="pylagrit.Region">
+<em class="property">class </em><code class="descclassname">pylagrit.</code><code class="descname">Region</code><span class="sig-paren">(</span><em>name</em>, <em>parent</em><span class="sig-paren">)</span><a class="headerlink" href="#pylagrit.Region" title="Permalink to this definition">¶</a></dt>
+<dd><p>Region class</p>
+</dd></dl>
+
+</div>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
+
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+
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+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="autodoc.html">Class Documentation</a><ul class="current">
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pylagrit.html">PyLaGriT Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pset.html">Point Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">Region Class</a></li>
+</ul>
+</li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+  <li><a href="autodoc.html">Class Documentation</a><ul>
+      <li>Previous: <a href="autodoc_faceset.html" title="previous chapter">Face Set Object</a></li>
+  </ul></li>
+  </ul></li>
+</ul>
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+  <h3>Quick search</h3>
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+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2016, Dylan R. Harp.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      
+      |
+      <a href="sources/autodoc_region.rst.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>

docs/pylagrit/original/static/basic.css

@@ -0,0 +1,676 @@
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+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
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+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
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+
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+
+/* -- relbar ---------------------------------------------------------------- */
+
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+    width: 100%;
+    font-size: 90%;
+}
+
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+    display: none;
+}
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+    margin: 0;
+    padding: 0 0 0 10px;
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+}
+
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+    display: inline;
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+    font-size: 90%;
+    word-wrap: break-word;
+    overflow-wrap : break-word;
+}
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+    margin-bottom: 0;
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+    font-size: 1em;
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+div.sphinxsidebar #searchbox input[type="text"] {
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+    width: 80%;
+    padding: 0.25em;
+    box-sizing: border-box;
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+
+div.sphinxsidebar #searchbox input[type="submit"] {
+    float: left;
+    width: 20%;
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+    padding: 0.25em;
+    box-sizing: border-box;
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+
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+    border: 0;
+    max-width: 100%;
+}
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+    padding: 0;
+}
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+    background-image: url(file.png);
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+}
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+    -ms-hyphens: manual;
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+}
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+    font-size: small;
+}
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+}
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+    margin: -1px -10px;
+    padding: 0 10px;
+}
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+}
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+}
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+    float: right;
+}
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+    left: 0px;
+    z-index: 1;
+}
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+div.math:hover a.headerlink {
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+}
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+/* -- printout stylesheet --------------------------------------------------- */
+
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+        display: none;
+    }
+}

docs/pylagrit/original/static/custom.css

@@ -0,0 +1 @@
+/* This file intentionally left blank. */

docs/pylagrit/original/static/doctools.js

@@ -0,0 +1,315 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+    "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+    "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s === 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node, addItems) {
+    if (node.nodeType === 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 &&
+          !jQuery(node.parentNode).hasClass(className) &&
+          !jQuery(node.parentNode).hasClass("nohighlight")) {
+        var span;
+        var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+        if (isInSVG) {
+          span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+        } else {
+          span = document.createElement("span");
+          span.className = className;
+        }
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+        if (isInSVG) {
+          var bbox = span.getBBox();
+          var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+       	  rect.x.baseVal.value = bbox.x;
+          rect.y.baseVal.value = bbox.y;
+          rect.width.baseVal.value = bbox.width;
+          rect.height.baseVal.value = bbox.height;
+          rect.setAttribute('class', className);
+          var parentOfText = node.parentNode.parentNode;
+          addItems.push({
+              "parent": node.parentNode,
+              "target": rect});
+        }
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this, addItems);
+      });
+    }
+  }
+  var addItems = [];
+  var result = this.each(function() {
+    highlight(this, addItems);
+  });
+  for (var i = 0; i < addItems.length; ++i) {
+    jQuery(addItems[i].parent).before(addItems[i].target);
+  }
+  return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+  jQuery.uaMatch = function(ua) {
+    ua = ua.toLowerCase();
+
+    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+      /(msie) ([\w.]+)/.exec(ua) ||
+      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+      [];
+
+    return {
+      browser: match[ 1 ] || "",
+      version: match[ 2 ] || "0"
+    };
+  };
+  jQuery.browser = {};
+  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initIndexTable();
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated === 'undefined')
+      return string;
+    return (typeof translated === 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated === 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      if (!body.length) {
+        body = $('body');
+      }
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlighted');
+        });
+      }, 10);
+      $('<p class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+          .appendTo($('#searchbox'));
+    }
+  },
+
+  /**
+   * init the domain index toggle buttons
+   */
+  initIndexTable : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      $('tr.cg-' + idnum).toggle();
+      if (src.substr(-9) === 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('#searchbox .highlight-link').fadeOut(300);
+    $('span.highlighted').removeClass('highlighted');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this === '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  },
+
+  initOnKeyListeners: function() {
+    $(document).keyup(function(event) {
+      var activeElementType = document.activeElement.tagName;
+      // don't navigate when in search box or textarea
+      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
+        switch (event.keyCode) {
+          case 37: // left
+            var prevHref = $('link[rel="prev"]').prop('href');
+            if (prevHref) {
+              window.location.href = prevHref;
+              return false;
+            }
+          case 39: // right
+            var nextHref = $('link[rel="next"]').prop('href');
+            if (nextHref) {
+              window.location.href = nextHref;
+              return false;
+            }
+        }
+      }
+    });
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});

docs/pylagrit/original/static/documentation_options.js

@@ -0,0 +1,10 @@
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+    VERSION: '0.0.0',
+    LANGUAGE: 'None',
+    COLLAPSE_INDEX: false,
+    FILE_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+};

docs/pylagrit/original/static/genindex.html

@@ -0,0 +1,841 @@
+
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Index &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="#" />
+    <link rel="search" title="Search" href="search.html" />
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#N"><strong>N</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#Q"><strong>Q</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#X"><strong>X</strong></a>
+ | <a href="#Y"><strong>Y</strong></a>
+ | <a href="#Z"><strong>Z</strong></a>
+ 
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.addatt">addatt() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.addatt_voronoi_volume">addatt_voronoi_volume() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh">addmesh() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_add">addmesh_add() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_amr">addmesh_amr() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_append">addmesh_append() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_delete">addmesh_delete() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_excavate">addmesh_excavate() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_glue">addmesh_glue() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_intersect">addmesh_intersect() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_merge">addmesh_merge() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.addmesh_pyramid">addmesh_pyramid() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="B">B</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.boundary_components">boundary_components() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.cmo_status">cmo_status() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.compute_distance">compute_distance() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.compute_extrapolate">compute_extrapolate() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.connect">connect() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.connect_check_interface">connect_check_interface() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.connect_delaunay">connect_delaunay() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.connect_noadd">connect_noadd() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.convert">convert() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.copy">copy() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.copy">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.copyatt">copyatt() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.copypts">copypts() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create">create() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.create_boundary_facesets">create_boundary_facesets() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.create_faceset">create_faceset() (pylagrit.EltSet method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_hex">create_hex() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_hyb">create_hyb() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_line">create_line() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_pri">create_pri() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_pyr">create_pyr() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_qua">create_qua() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_tet">create_tet() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_tri">create_tri() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.create_triplane">create_triplane() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts">createpts() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_brick">createpts_brick() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_brick_rtp">createpts_brick_rtp() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_brick_rtz">createpts_brick_rtz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_brick_xyz">createpts_brick_xyz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_dxyz">createpts_dxyz() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts_dxyz">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_line">createpts_line() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts_line">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_median">createpts_median() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_rtp">createpts_rtp() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts_rtp">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_rtz">createpts_rtz() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts_rtz">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.createpts_xyz">createpts_xyz() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.createpts_xyz">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.define">define() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.delatt">delatt() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.delete">delete() (pylagrit.EltSet method)</a>
+
+      <ul>
+        <li><a href="autodoc_mo.html#pylagrit.MO.delete">(pylagrit.MO method)</a>
+</li>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.delete">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump">dump() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.dump">(pylagrit.PSet method)</a>
+</li>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.dump">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_ats_xml">dump_ats_xml() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_avs2">dump_avs2() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_exo">dump_exo() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_fehm">dump_fehm() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_gmv">dump_gmv() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_lg">dump_lg() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_pset">dump_pset() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_zone_imt">dump_zone_imt() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.dump_zone_outside">dump_zone_outside() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="E">E</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.elem_type">elem_type (pylagrit.MO attribute)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet">EltSet (class in pylagrit)</a>
+</li>
+      <li><a href="autodoc_pset.html#pylagrit.PSet.eltset">eltset() (pylagrit.PSet method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_attribute">eltset_attribute() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_bool">eltset_bool() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_inter">eltset_inter() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_not">eltset_not() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_object">eltset_object() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_region">eltset_region() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.eltset_union">eltset_union() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pset.html#pylagrit.PSet.expand">expand() (pylagrit.PSet method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.expect">expect() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.extract_surfmesh">extract_surfmesh() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.extract_surfmesh">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.extrude">extrude() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_faceset.html#pylagrit.FaceSet">FaceSet (class in pylagrit)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.filter">filter() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.gmv">gmv() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid">grid2grid() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_hextotet24">grid2grid_hextotet24() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_hextotet5">grid2grid_hextotet5() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_hextotet6">grid2grid_hextotet6() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_prismtotet14">grid2grid_prismtotet14() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_prismtotet18">grid2grid_prismtotet18() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_prismtotet3">grid2grid_prismtotet3() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_pyrtotet4">grid2grid_pyrtotet4() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_quadtotri2">grid2grid_quadtotri2() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_quadtotri4">grid2grid_quadtotri4() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.grid2grid_tree_to_fe">grid2grid_tree_to_fe() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.gridder">gridder() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.information">information() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.interact">interact() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.interpolate">interpolate() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.interpolate">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.interpolate_continuous">interpolate_continuous() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.interpolate_continuous">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.interpolate_default">interpolate_default() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.interpolate_default">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.interpolate_map">interpolate_map() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.interpolate_map">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.interpolate_voronoi">interpolate_voronoi() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.interpolate_voronoi">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.intersect_elements">intersect_elements() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.list">list() (pylagrit.EltSet method)</a>
+
+      <ul>
+        <li><a href="autodoc_mo.html#pylagrit.MO.list">(pylagrit.MO method)</a>
+</li>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.list">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.massage">massage() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.massage2">massage2() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.math">math() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.maxs">maxs (pylagrit.MO attribute)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.merge">merge() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.minmax">minmax() (pylagrit.EltSet method)</a>
+
+      <ul>
+        <li><a href="autodoc_mo.html#pylagrit.MO.minmax">(pylagrit.MO method)</a>
+</li>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.minmax">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.minmax_xyz">minmax_xyz() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.minmax_xyz">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.mins">mins (pylagrit.MO attribute)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO">MO (class in pylagrit)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="N">N</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.ndim_geo">ndim_geo (pylagrit.MO attribute)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.ndim_topo">ndim_topo (pylagrit.MO attribute)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.nelems">nelems (pylagrit.MO attribute)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.nnodes">nnodes (pylagrit.MO attribute)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.paraview">paraview() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.perturb">perturb() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.perturb">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.points">points() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.printatt">printatt() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pset.html#pylagrit.PSet">PSet (class in pylagrit)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.pset">pset() (pylagrit.EltSet method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_attribute">pset_attribute() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.pset_attribute">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_bool">pset_bool() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_geom">pset_geom() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_geom_rtp">pset_geom_rtp() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_geom_rtz">pset_geom_rtz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_geom_xyz">pset_geom_xyz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_inter">pset_inter() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_not">pset_not() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_region">pset_region() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_surface">pset_surface() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.pset_union">pset_union() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT">PyLaGriT (class in pylagrit)</a>
+</li>
+      <li><a href="autodoc_eltset.html#module-pylagrit">pylagrit (module)</a>, <a href="autodoc_faceset.html#module-pylagrit">[1]</a>, <a href="autodoc_mo.html#module-pylagrit">[2]</a>, <a href="autodoc_pset.html#module-pylagrit">[3]</a>, <a href="autodoc_pylagrit.html#module-pylagrit">[4]</a>, <a href="autodoc_region.html#module-pylagrit">[5]</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Q">Q</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quadxy">quadxy() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality">quality() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_angle">quality_angle() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_aspect">quality_aspect() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_edge_max">quality_edge_max() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_edge_min">quality_edge_min() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_edge_ratio">quality_edge_ratio() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.quality_pcc">quality_pcc() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.read">read() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read_att">read_att() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read_fehm">read_fehm() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read_modflow">read_modflow() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read_script">read_script() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.read_sheetij">read_sheetij() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.recon">recon() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.refine">refine() (pylagrit.EltSet method)</a>
+
+      <ul>
+        <li><a href="autodoc_mo.html#pylagrit.MO.refine">(pylagrit.MO method)</a>
+</li>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.refine">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.refine_to_object">refine_to_object() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_region.html#pylagrit.Region">Region (class in pylagrit)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.region_bool">region_bool() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.region_bool">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.reorder_nodes">reorder_nodes() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.resetpts_itp">resetpts_itp() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.rmpoint_compress">rmpoint_compress() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.rmpoint_eltset">rmpoint_eltset() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.rmpoint_pset">rmpoint_pset() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.rotateln">rotateln() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.run_batch">run_batch() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.rzbrick">rzbrick() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_pset.html#pylagrit.PSet.scale">scale() (pylagrit.PSet method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.select">select() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.sendline">sendline() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.sendline">(pylagrit.PyLaGriT method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_eltset.html#pylagrit.EltSet.setatt">setatt() (pylagrit.EltSet method)</a>
+
+      <ul>
+        <li><a href="autodoc_mo.html#pylagrit.MO.setatt">(pylagrit.MO method)</a>
+</li>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.setatt">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets">settets() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_color_points">settets_color_points() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_color_tets">settets_color_tets() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_geometry">settets_geometry() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_newtets">settets_newtets() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_normal">settets_normal() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.settets_parents">settets_parents() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.smooth">smooth() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.smooth">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.stack_fill">stack_fill() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.stack_layers">stack_layers() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.status">status() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.subset">subset() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.subset_rtp">subset_rtp() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.subset_rtz">subset_rtz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.subset_xyz">subset_xyz() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.surface">surface() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.surface_box">surface_box() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.surface_cylinder">surface_cylinder() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.surface_plane">surface_plane() (pylagrit.PyLaGriT method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.trans">trans() (pylagrit.MO method)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.trans">(pylagrit.PSet method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.tri_mesh_output_prep">tri_mesh_output_prep() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_pylagrit.html#pylagrit.PyLaGriT.tri_mo_from_polyline">tri_mo_from_polyline() (pylagrit.PyLaGriT method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.triangulate">triangulate() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale">upscale() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_ariave">upscale_ariave() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_geoave">upscale_geoave() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_harave">upscale_harave() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_max">upscale_max() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_min">upscale_min() (pylagrit.MO method)</a>
+</li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.upscale_sum">upscale_sum() (pylagrit.MO method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
+<h2 id="X">X</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.xlength">xlength (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.xlength">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.xmax">xmax (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.xmax">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.xmin">xmin (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.xmin">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Y">Y</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.ylength">ylength (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.ylength">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.ymax">ymax (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.ymax">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.ymin">ymin (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.ymin">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+</tr></table>
+
+<h2 id="Z">Z</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.zlength">zlength (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.zlength">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+      <li><a href="autodoc_mo.html#pylagrit.MO.zmax">zmax (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.zmax">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autodoc_mo.html#pylagrit.MO.zmin">zmin (pylagrit.MO attribute)</a>
+
+      <ul>
+        <li><a href="autodoc_pset.html#pylagrit.PSet.zmin">(pylagrit.PSet attribute)</a>
+</li>
+      </ul></li>
+  </ul></td>
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+        <div class="bodywrapper">
+          
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+          <div class="body" role="main">
+            
+  <div class="section" id="getting-started">
+<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="installation">
+<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
+<p>The Python module PyLaGriT allows LaGriT to be accessed interactively and in batch mode from Python.
+To install PyLaGriT on your system, change to the PyLaGriT directory and run <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">setup.py</span> <span class="pre">install</span></code>.
+Alternatively, the PyLaGriT folder can be added to your <strong>PYTHONPATH</strong> environment variable.
+Due to the use of the pexpect Python module, PyLaGriT does not work on Windows.
+It has been tested on Mac and Linux operating systems.</p>
+<p>Since PyLaGriT is simply a frontend for LaGriT, you will need a lagrit executable to use PyLaGriT.
+To use the paraview and gmv methods, you will need ParaView (<a class="reference external" href="http://www.paraview.org">http://www.paraview.org</a>) and GMV (<a class="reference external" href="http://www.generalmeshviewer.com">http://www.generalmeshviewer.com</a>) installed, respectively.</p>
+<p>To avoid specifying the LaGriT, ParaView, and GMV executable locations, copy the <strong>pylagritrc_example</strong> file:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># This is an example pylagritrc file. </span>
+<span class="c1"># To use, change its name to pylagritrc or .pylagritrc, uncomment and modify attributes and move to your working directory or your home directory. </span>
+<span class="c1"># The rc file in the working directory will take precedence over the one in your home directory. </span>
+
+<span class="c1">#lagrit_exe : &#39;/lagrit/executable/location/lagrit&#39; </span>
+<span class="c1">#gmv_exe : &#39;/gmv/executable/location/gmv&#39; </span>
+<span class="c1">#paraview_exe : &#39;/paraview/executable/location/paraview&#39; </span>
+</pre></div>
+</div>
+<p>in the PyLaGriT folder to your home directory or working directory changing its name to either <strong>pylagritrc</strong> or <strong>.pylagritrc</strong> and uncomment and change the path locations.</p>
+</div>
+<div class="section" id="simple-example">
+<h2>Simple example<a class="headerlink" href="#simple-example" title="Permalink to this headline">¶</a></h2>
+<p>The following is a PyLaGriT script for creating a simple cube shaped mesh using the <a class="reference internal" href="autodoc_pylagrit.html#pylagrit.PyLaGriT.gridder" title="pylagrit.PyLaGriT.gridder"><code class="xref py py-func docutils literal notranslate"><span class="pre">gridder</span></code></a> and <cite>connect &lt;pylagrit.PyLaGriT.connect&gt;</cite> methods:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Import PyLaGriT class from pylagrit module</span>
+<span class="kn">from</span> <span class="nn">pylagrit</span> <span class="kn">import</span> <span class="n">PyLaGriT</span>
+
+<span class="c1"># Create PyLaGriT object</span>
+<span class="c1"># This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified</span>
+<span class="n">l</span> <span class="o">=</span> <span class="n">PyLaGriT</span><span class="p">()</span>
+
+<span class="c1"># Create x,y,z arrays for location of points</span>
+<span class="n">x</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">5</span><span class="p">)</span>
+<span class="n">y</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">5</span><span class="p">)</span>
+<span class="n">z</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">5</span><span class="p">)</span>
+
+<span class="c1"># Create mesh object using x,y,z arrays</span>
+<span class="n">m</span> <span class="o">=</span> <span class="n">l</span><span class="o">.</span><span class="n">gridder</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">)</span>
+
+<span class="c1"># Connect points</span>
+<span class="n">m</span><span class="o">.</span><span class="n">connect</span><span class="p">()</span>
+
+<span class="c1"># Visualize connected mesh using ParaView</span>
+<span class="c1"># This assumes that pylagritrc is being used so that exe option does not need to be specified</span>
+<span class="n">m</span><span class="o">.</span><span class="n">paraview</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>The script can be pasted line by line into a Python or IPython terminal, or saved in a file (e.g., <code class="docutils literal notranslate"><span class="pre">script.py</span></code>) and run on the command line as <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">script.py</span></code>.</p>
+<p>This will open up ParaView with the mesh loaded:</p>
+<img alt="images/cube.png" src="images/cube.png" />
+</div>
+<div class="section" id="next-steps">
+<h2>Next steps<a class="headerlink" href="#next-steps" title="Permalink to this headline">¶</a></h2>
+<p>Additional example PyLaGriT scripts are provided in the PyLaGriT/examples folder and in the <a class="reference internal" href="autodoc.html#class-docs"><span class="std std-ref">Class Documentation</span></a>.</p>
+<div class="section" id="combining-lagrit-and-python-functionality">
+<h3>Combining LaGriT and Python functionality<a class="headerlink" href="#combining-lagrit-and-python-functionality" title="Permalink to this headline">¶</a></h3>
+<p>An example of using PyLaGriT to facilitate looping over LaGriT functionality is described in the <a class="reference internal" href="autodoc_pylagrit.html#pylagrit.PyLaGriT.merge" title="pylagrit.PyLaGriT.merge"><code class="xref py py-func docutils literal notranslate"><span class="pre">merge</span> <span class="pre">method</span></code></a> documentation, where a mesh is successively copied, translated and merged into a larger mesh.
+Other examples of usage are provided for other methods and more will be added in the future.</p>
+</div>
+<div class="section" id="user-defined-error-checking">
+<h3>User defined error checking<a class="headerlink" href="#user-defined-error-checking" title="Permalink to this headline">¶</a></h3>
+<p>Since PyLaGriT stores the LaGriT terminal output from each command in the PyLaGriT object attribute <code class="docutils literal notranslate"><span class="pre">before</span></code>, user-defined error checking can be easily implemented.
+The example provided with the <a class="reference internal" href="autodoc_eltset.html#pylagrit.EltSet.refine" title="pylagrit.EltSet.refine"><code class="xref py py-func docutils literal notranslate"><span class="pre">refine</span> <span class="pre">method</span></code></a> demonstrates this by checking for the string <cite>The mesh is complete but could not include all points.</cite> in the LaGriT output using <code class="docutils literal notranslate"><span class="pre">lg.before</span></code>.
+In this example, an error message is printed to the screen and the script is aborted.</p>
+</div>
+</div>
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+<h1>PyLaGriT, Python interface for LaGriT<a class="headerlink" href="#pylagrit-python-interface-for-lagrit" title="Permalink to this headline">¶</a></h1>
+<p>PyLaGriT Class</p>
+<ul class="simple">
+<li>The PyLaGriT class provides a python interface to the Los Alamos Grid Toolbox.</li>
+<li>The PyLaGrit class is derived class of the perplex packages spawn class, and its objects contains all of spawn’s functionality.</li>
+<li>Commands can be sent using LaGriT syntax as string arguments to the sendline method.</li>
+<li>Direct access to the LaGriT shell is provided by the interact method.</li>
+<li>Subclasses of the PyLaGrit class include mesh object (MO), surface, and region and can be created using various methods to PyLaGriT objects.</li>
+<li>The mesh object subclass contains subclasses pset and eltset.</li>
+<li>Subclasses are contained in dictionaries in the parent class.</li>
+<li>The mesh object class contains gmv and paraview methods that dump the appropriate files and open them in viewer.</li>
+<li>PyLaGriT can be accessed in Julia using the Julia PyCall package (refer to PyLaGriT/examples/julia folder in the source code)</li>
+</ul>
+<div class="toctree-wrapper compound">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#installation">Installation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#simple-example">Simple example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#next-steps">Next steps</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc.html">Class Documentation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pylagrit.html">PyLaGriT Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_mo.html">Mesh Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_pset.html">Point Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_eltset.html">Element Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_faceset.html">Face Set Class</a></li>
+<li class="toctree-l2"><a class="reference internal" href="autodoc_region.html">Region Class</a></li>
+</ul>
+</li>
+</ul>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
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+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      
+      |
+      <a href="sources/index.rst.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+    
+
+    
+  </body>
+</html>

docs/pylagrit/original/static/language_data.js

@@ -0,0 +1,297 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */ 
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+
+
+var splitChars = (function() {
+    var result = {};
+    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+    var i, j, start, end;
+    for (i = 0; i < singles.length; i++) {
+        result[singles[i]] = true;
+    }
+    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
+         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
+         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
+         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
+         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
+         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
+         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
+         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
+         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
+         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
+         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
+         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
+         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
+         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
+         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
+         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
+         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
+         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
+         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
+         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
+         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
+         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
+         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
+         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
+         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
+         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
+         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
+         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
+         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
+         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
+         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
+         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
+         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
+         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
+         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
+         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
+         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
+         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
+         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
+         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
+         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
+         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
+         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
+         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
+         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+    for (i = 0; i < ranges.length; i++) {
+        start = ranges[i][0];
+        end = ranges[i][1];
+        for (j = start; j <= end; j++) {
+            result[j] = true;
+        }
+    }
+    return result;
+})();
+
+function splitQuery(query) {
+    var result = [];
+    var start = -1;
+    for (var i = 0; i < query.length; i++) {
+        if (splitChars[query.charCodeAt(i)]) {
+            if (start !== -1) {
+                result.push(query.slice(start, i));
+                start = -1;
+            }
+        } else if (start === -1) {
+            start = i;
+        }
+    }
+    if (start !== -1) {
+        result.push(query.slice(start));
+    }
+    return result;
+}
+
+

docs/pylagrit/original/static/py-modindex.html

@@ -0,0 +1,126 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Python Module Index &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+
+    <script type="text/javascript">
+      DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
+    </script>
+
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+
+   <h1>Python Module Index</h1>
+
+   <div class="modindex-jumpbox">
+   <a href="#cap-p"><strong>p</strong></a>
+   </div>
+
+   <table class="indextable modindextable">
+     <tr class="pcap"><td></td><td>&#160;</td><td></td></tr>
+     <tr class="cap" id="cap-p"><td></td><td>
+       <strong>p</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="autodoc_region.html#module-pylagrit"><code class="xref">pylagrit</code></a></td><td>
+       <em></em></td></tr>
+   </table>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc.html">Class Documentation</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2016, Dylan R. Harp.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      
+    </div>
+
+    
+
+    
+  </body>
+</html>

docs/pylagrit/original/static/pygments.css

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+.highlight  { background: #eeffcc; }
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+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
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+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
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+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
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+.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
+.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
+.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
+.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
+.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
+.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
+.highlight .sx { color: #c65d09 } /* Literal.String.Other */
+.highlight .sr { color: #235388 } /* Literal.String.Regex */
+.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
+.highlight .ss { color: #517918 } /* Literal.String.Symbol */
+.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
+.highlight .fm { color: #06287e } /* Name.Function.Magic */
+.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
+.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
+.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
+.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
+.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */

docs/pylagrit/original/static/search.html

@@ -0,0 +1,121 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Search &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <script type="text/javascript" src="static/searchtools.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="#" />
+  <script type="text/javascript">
+    jQuery(function() { Search.loadIndex("searchindex.js"); });
+  </script>
+  
+  <script type="text/javascript" id="searchindexloader"></script>
+  
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <h1 id="search-documentation">Search</h1>
+  <div id="fallback" class="admonition warning">
+  <script type="text/javascript">$('#fallback').hide();</script>
+  <p>
+    Please activate JavaScript to enable the search
+    functionality.
+  </p>
+  </div>
+  <p>
+    From here you can search these documents. Enter your search
+    words into the box below and click "search". Note that the search
+    function will automatically search for all of the words. Pages
+    containing fewer words won't appear in the result list.
+  </p>
+  <form action="" method="get">
+    <input type="text" name="q" value="" />
+    <input type="submit" value="search" />
+    <span id="search-progress" style="padding-left: 10px"></span>
+  </form>
+  
+  <div id="search-results">
+  
+  </div>
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc.html">Class Documentation</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2016, Dylan R. Harp.
+      
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      
+    </div>
+
+    
+
+    
+  </body>
+</html>

docs/pylagrit/original/static/searchtools.js

@@ -0,0 +1,481 @@
+/*
+ * searchtools.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for the full-text search.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+if (!Scorer) {
+  /**
+   * Simple result scoring code.
+   */
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [filename, title, anchor, descr, score]
+    // and returns the new score.
+    /*
+    score: function(result) {
+      return result[4];
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {0:  15,   // used to be importantResults
+              1:  5,   // used to be objectResults
+              2: -5},  // used to be unimportantResults
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    // query found in terms
+    term: 5
+  };
+}
+
+if (!splitQuery) {
+  function splitQuery(query) {
+    return query.split(/\s+/);
+  }
+}
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  loadIndex : function(url) {
+    $.ajax({type: "GET", url: url, data: null,
+            dataType: "script", cache: true,
+            complete: function(jqxhr, textstatus) {
+              if (textstatus != "success") {
+                document.getElementById("searchindexloader").src = url;
+              }
+            }});
+  },
+
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      var i;
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    }
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  query : function(query) {
+    var i;
+
+    // stem the searchterms and add them to the correct list
+    var stemmer = new Stemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = splitQuery(query);
+    var objectterms = [];
+    for (i = 0; i < tmp.length; i++) {
+      if (tmp[i] !== "") {
+          objectterms.push(tmp[i].toLowerCase());
+      }
+
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] === "") {
+        // skip this "word"
+        continue;
+      }
+      // stem the word
+      var word = stemmer.stemWord(tmp[i].toLowerCase());
+      // prevent stemmer from cutting word smaller than two chars
+      if(word.length < 3 && tmp[i].length >= 3) {
+        word = tmp[i];
+      }
+      var toAppend;
+      // select the correct list
+      if (word[0] == '-') {
+        toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$u.contains(toAppend, word))
+        toAppend.push(word);
+    }
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    // console.debug('SEARCH: searching for:');
+    // console.info('required: ', searchterms);
+    // console.info('excluded: ', excluded);
+
+    // prepare search
+    var terms = this._index.terms;
+    var titleterms = this._index.titleterms;
+
+    // array of [filename, title, anchor, descr, score]
+    var results = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    for (i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0, i),
+                             objectterms.slice(i+1, objectterms.length));
+      results = results.concat(this.performObjectSearch(objectterms[i], others));
+    }
+
+    // lookup as search terms in fulltext
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      for (i = 0; i < results.length; i++)
+        results[i][4] = Scorer.score(results[i]);
+    }
+
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort(function(a, b) {
+      var left = a[4];
+      var right = b[4];
+      if (left > right) {
+        return 1;
+      } else if (left < right) {
+        return -1;
+      } else {
+        // same score: sort alphabetically
+        left = a[1].toLowerCase();
+        right = b[1].toLowerCase();
+        return (left > right) ? -1 : ((left < right) ? 1 : 0);
+      }
+    });
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    //console.info('search results:', Search.lastresults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+          // dirhtml builder
+          var dirname = item[0] + '/';
+          if (dirname.match(/\/index\/$/)) {
+            dirname = dirname.substring(0, dirname.length-6);
+          } else if (dirname == 'index/') {
+            dirname = '';
+          }
+          listItem.append($('<a/>').attr('href',
+            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+            highlightstring + item[2]).html(item[1]));
+        } else {
+          // normal html builders
+          listItem.append($('<a/>').attr('href',
+            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+            highlightstring + item[2]).html(item[1]));
+        }
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
+          if (suffix === undefined) {
+            suffix = '.txt';
+          }
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
+                  dataType: "text",
+                  complete: function(jqxhr, textstatus) {
+                    var data = jqxhr.responseText;
+                    if (data !== '' && data !== undefined) {
+                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                    }
+                    Search.output.append(listItem);
+                    listItem.slideDown(5, function() {
+                      displayNextItem();
+                    });
+                  }});
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch : function(object, otherterms) {
+    var filenames = this._index.filenames;
+    var docnames = this._index.docnames;
+    var objects = this._index.objects;
+    var objnames = this._index.objnames;
+    var titles = this._index.titles;
+
+    var i;
+    var results = [];
+
+    for (var prefix in objects) {
+      for (var name in objects[prefix]) {
+        var fullname = (prefix ? prefix + '.' : '') + name;
+        if (fullname.toLowerCase().indexOf(object) > -1) {
+          var score = 0;
+          var parts = fullname.split('.');
+          // check for different match types: exact matches of full name or
+          // "last name" (i.e. last dotted part)
+          if (fullname == object || parts[parts.length - 1] == object) {
+            score += Scorer.objNameMatch;
+          // matches in last name
+          } else if (parts[parts.length - 1].indexOf(object) > -1) {
+            score += Scorer.objPartialMatch;
+          }
+          var match = objects[prefix][name];
+          var objname = objnames[match[1]][2];
+          var title = titles[match[0]];
+          // If more than one term searched for, we require other words to be
+          // found in the name/title/description
+          if (otherterms.length > 0) {
+            var haystack = (prefix + ' ' + name + ' ' +
+                            objname + ' ' + title).toLowerCase();
+            var allfound = true;
+            for (i = 0; i < otherterms.length; i++) {
+              if (haystack.indexOf(otherterms[i]) == -1) {
+                allfound = false;
+                break;
+              }
+            }
+            if (!allfound) {
+              continue;
+            }
+          }
+          var descr = objname + _(', in ') + title;
+
+          var anchor = match[3];
+          if (anchor === '')
+            anchor = fullname;
+          else if (anchor == '-')
+            anchor = objnames[match[1]][1] + '-' + fullname;
+          // add custom score for some objects according to scorer
+          if (Scorer.objPrio.hasOwnProperty(match[2])) {
+            score += Scorer.objPrio[match[2]];
+          } else {
+            score += Scorer.objPrioDefault;
+          }
+          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
+        }
+      }
+    }
+
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+    var docnames = this._index.docnames;
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+
+    var i, j, file;
+    var fileMap = {};
+    var scoreMap = {};
+    var results = [];
+
+    // perform the search on the required terms
+    for (i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      var files = [];
+      var _o = [
+        {files: terms[word], score: Scorer.term},
+        {files: titleterms[word], score: Scorer.title}
+      ];
+
+      // no match but word was a required one
+      if ($u.every(_o, function(o){return o.files === undefined;})) {
+        break;
+      }
+      // found search word in contents
+      $u.each(_o, function(o) {
+        var _files = o.files;
+        if (_files === undefined)
+          return
+
+        if (_files.length === undefined)
+          _files = [_files];
+        files = files.concat(_files);
+
+        // set score for the word in each file to Scorer.term
+        for (j = 0; j < _files.length; j++) {
+          file = _files[j];
+          if (!(file in scoreMap))
+            scoreMap[file] = {}
+          scoreMap[file][word] = o.score;
+        }
+      });
+
+      // create the mapping
+      for (j = 0; j < files.length; j++) {
+        file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+          continue;
+
+      // ensure that none of the excluded terms is in the search result
+      for (i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+            titleterms[excluded[i]] == file ||
+            $u.contains(terms[excluded[i]] || [], file) ||
+            $u.contains(titleterms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it to the result list
+      if (valid) {
+        // select one (max) score for the file.
+        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
+        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
+        results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
+      }
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words, hlwords is the list of normal, unstemmed
+   * words. the first one is used to find the occurrence, the
+   * latter for highlighting it.
+   */
+  makeSearchSummary : function(text, keywords, hlwords) {
+    var textLower = text.toLowerCase();
+    var start = 0;
+    $.each(keywords, function() {
+      var i = textLower.indexOf(this.toLowerCase());
+      if (i > -1)
+        start = i;
+    });
+    start = Math.max(start - 120, 0);
+    var excerpt = ((start > 0) ? '...' : '') +
+      $.trim(text.substr(start, 240)) +
+      ((start + 240 - text.length) ? '...' : '');
+    var rv = $('<div class="context"></div>').text(excerpt);
+    $.each(hlwords, function() {
+      rv = rv.highlightText(this, 'highlighted');
+    });
+    return rv;
+  }
+};
+
+$(document).ready(function() {
+  Search.init();
+});

docs/pylagrit/original/static/sources/autodoc.rst.txt

@@ -0,0 +1,21 @@
+.. _class_docs:
+
+Class Documentation
+-------------------
+
+.. toctree::
+
+    PyLaGriT Class <autodoc_pylagrit.rst>
+
+    Mesh Class <autodoc_mo.rst>
+
+    Point Set Class <autodoc_pset.rst>
+
+    Element Set Class <autodoc_eltset.rst>
+
+    Face Set Class <autodoc_faceset.rst>
+
+    Region Class <autodoc_region.rst>
+
+    
+

docs/pylagrit/original/static/sources/autodoc_eltset.rst.txt

@@ -0,0 +1,8 @@
+Element Set Object
+------------------
+.. automodule:: pylagrit
+
+.. autoclass:: EltSet
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/autodoc_faceset.rst.txt

@@ -0,0 +1,8 @@
+Face Set Object
+---------------
+.. automodule:: pylagrit
+
+.. autoclass:: FaceSet
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/autodoc_mo.rst.txt

@@ -0,0 +1,8 @@
+Mesh Object
+-----------
+.. automodule:: pylagrit
+
+.. autoclass:: MO
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/autodoc_pset.rst.txt

@@ -0,0 +1,8 @@
+Point Set Object
+----------------
+.. automodule:: pylagrit
+
+.. autoclass:: PSet
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/autodoc_pylagrit.rst.txt

@@ -0,0 +1,8 @@
+PyLaGriT
+--------
+.. automodule:: pylagrit
+
+.. autoclass:: PyLaGriT
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/autodoc_region.rst.txt

@@ -0,0 +1,8 @@
+Region Object
+-------------
+.. automodule:: pylagrit
+
+.. autoclass:: Region
+   :members:
+   :undoc-members:
+

docs/pylagrit/original/static/sources/gettingstarted.rst.txt

@@ -0,0 +1,73 @@
+Getting Started
+===============
+
+Installation
+------------
+
+The Python module PyLaGriT allows LaGriT to be accessed interactively and in batch mode from Python. 
+To install PyLaGriT on your system, change to the PyLaGriT directory and run ``python setup.py install``. 
+Alternatively, the PyLaGriT folder can be added to your **PYTHONPATH** environment variable. 
+Due to the use of the pexpect Python module, PyLaGriT does not work on Windows. 
+It has been tested on Mac and Linux operating systems. 
+
+Since PyLaGriT is simply a frontend for LaGriT, you will need a lagrit executable to use PyLaGriT.
+To use the paraview and gmv methods, you will need ParaView (http://www.paraview.org) and GMV (http://www.generalmeshviewer.com) installed, respectively.
+
+To avoid specifying the LaGriT, ParaView, and GMV executable locations, copy the **pylagritrc_example** file:
+
+.. literalinclude:: ../../pylagritrc_example
+
+in the PyLaGriT folder to your home directory or working directory changing its name to either **pylagritrc** or **.pylagritrc** and uncomment and change the path locations.
+
+Simple example
+--------------
+
+The following is a PyLaGriT script for creating a simple cube shaped mesh using the :func:`gridder <pylagrit.PyLaGriT.gridder>` and `connect <pylagrit.PyLaGriT.connect>` methods:
+
+.. code-block:: python
+
+    # Import PyLaGriT class from pylagrit module
+    from pylagrit import PyLaGriT
+    
+    # Create PyLaGriT object
+    # This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified
+    l = PyLaGriT()
+
+    # Create x,y,z arrays for location of points
+    x = range(1,5)
+    y = range(1,5)
+    z = range(1,5)
+
+    # Create mesh object using x,y,z arrays
+    m = l.gridder(x,y,z)
+
+    # Connect points
+    m.connect()
+
+    # Visualize connected mesh using ParaView
+    # This assumes that pylagritrc is being used so that exe option does not need to be specified
+    m.paraview()
+
+The script can be pasted line by line into a Python or IPython terminal, or saved in a file (e.g., ``script.py``) and run on the command line as ``python script.py``.
+
+This will open up ParaView with the mesh loaded:
+
+.. image:: cube.png
+
+Next steps
+----------
+
+Additional example PyLaGriT scripts are provided in the PyLaGriT/examples folder and in the :ref:`class_docs`. 
+
+Combining LaGriT and Python functionality
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+An example of using PyLaGriT to facilitate looping over LaGriT functionality is described in the :func:`merge method <pylagrit.PyLaGriT.merge>` documentation, where a mesh is successively copied, translated and merged into a larger mesh.
+Other examples of usage are provided for other methods and more will be added in the future.
+
+User defined error checking
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Since PyLaGriT stores the LaGriT terminal output from each command in the PyLaGriT object attribute ``before``, user-defined error checking can be easily implemented.
+The example provided with the :func:`refine method <pylagrit.EltSet.refine>` demonstrates this by checking for the string `The mesh is complete but could not include all points.` in the LaGriT output using ``lg.before``. 
+In this example, an error message is printed to the screen and the script is aborted.

docs/pylagrit/original/static/sources/index.rst.txt

@@ -0,0 +1,24 @@
+.. PyLaGriT documentation master file, created by
+   sphinx-quickstart on Tue Oct  4 10:10:46 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+PyLaGriT, Python interface for LaGriT
+=====================================
+
+.. include:: ../../README
+
+.. toctree::
+   :maxdepth: 2
+
+   Getting Started <gettingstarted.rst>    
+
+   Class Documentation <autodoc.rst>
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/pylagrit/original/static/sources/stratigraphic.rst.txt

@@ -0,0 +1,11 @@
+Stratigraphic Hex Mesh Tutorial
+===============================
+Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). 
+The associated LaGriT tutorial is `here <https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html>`_.
+
+
+.. literalinclude:: ../../examples/stratigraphic_hex_mesh_tutorial.py
+
+The final result:
+
+.. image:: stratigraphy.png

docs/pylagrit/original/static/static/alabaster.css

@@ -0,0 +1,701 @@
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docs/pylagrit/original/static/static/basic.css

@@ -0,0 +1,676 @@
+/*
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+    margin-right: auto;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+    width: 100%;
+}
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable ul {
+    margin-top: 0;
+    margin-bottom: 0;
+    list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+    padding-left: 0em;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+div.modindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+    padding: 2px;
+    border-collapse: collapse;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+div.body {
+    min-width: 450px;
+    max-width: 800px;
+}
+
+div.body p, div.body dd, div.body li, div.body blockquote {
+    -moz-hyphens: auto;
+    -ms-hyphens: auto;
+    -webkit-hyphens: auto;
+    hyphens: auto;
+}
+
+a.headerlink {
+    visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px 7px 0 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px 7px 0 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+div.admonition dl {
+    margin-bottom: 0;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.align-center {
+    margin-left: auto;
+    margin-right: auto;
+}
+
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+table.footnote td, table.footnote th {
+    border: 0 !important;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+
+/* -- figures --------------------------------------------------------------- */
+
+div.figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text {
+}
+
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.field-name {
+    -moz-hyphens: manual;
+    -ms-hyphens: manual;
+    -webkit-hyphens: manual;
+    hyphens: manual;
+}
+
+/* -- hlist styles ---------------------------------------------------------- */
+
+table.hlist td {
+    vertical-align: top;
+}
+
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+    list-style: decimal;
+}
+
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
+ol.upperalpha {
+    list-style: upper-alpha;
+}
+
+ol.lowerroman {
+    list-style: lower-roman;
+}
+
+ol.upperroman {
+    list-style: upper-roman;
+}
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd p {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+dt:target, span.highlighted {
+    background-color: #fbe54e;
+}
+
+rect.highlighted {
+    fill: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.sig-paren {
+    font-size: larger;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+    font-family: sans-serif;
+}
+
+.accelerator {
+    text-decoration: underline;
+}
+
+.classifier {
+    font-style: oblique;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+}
+
+td.linenos pre {
+    padding: 5px 0px;
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    margin-left: 0.5em;
+}
+
+table.highlighttable td {
+    padding: 0 0.5em 0 0.5em;
+}
+
+div.code-block-caption {
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+div.code-block-caption + div > div.highlight > pre {
+    margin-top: 0;
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    padding: 1em 1em 0;
+}
+
+div.literal-block-wrapper div.highlight {
+    margin: 0;
+}
+
+code.descname {
+    background-color: transparent;
+    font-weight: bold;
+    font-size: 1.2em;
+}
+
+code.descclassname {
+    background-color: transparent;
+}
+
+code.xref, a code {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
+    background-color: transparent;
+}
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+span.eqno a.headerlink {
+    position: relative;
+    left: 0px;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}

docs/pylagrit/original/static/static/custom.css

@@ -0,0 +1 @@
+/* This file intentionally left blank. */

docs/pylagrit/original/static/static/doctools.js

@@ -0,0 +1,315 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+    "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+    "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s === 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node, addItems) {
+    if (node.nodeType === 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 &&
+          !jQuery(node.parentNode).hasClass(className) &&
+          !jQuery(node.parentNode).hasClass("nohighlight")) {
+        var span;
+        var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+        if (isInSVG) {
+          span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+        } else {
+          span = document.createElement("span");
+          span.className = className;
+        }
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+        if (isInSVG) {
+          var bbox = span.getBBox();
+          var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+       	  rect.x.baseVal.value = bbox.x;
+          rect.y.baseVal.value = bbox.y;
+          rect.width.baseVal.value = bbox.width;
+          rect.height.baseVal.value = bbox.height;
+          rect.setAttribute('class', className);
+          var parentOfText = node.parentNode.parentNode;
+          addItems.push({
+              "parent": node.parentNode,
+              "target": rect});
+        }
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this, addItems);
+      });
+    }
+  }
+  var addItems = [];
+  var result = this.each(function() {
+    highlight(this, addItems);
+  });
+  for (var i = 0; i < addItems.length; ++i) {
+    jQuery(addItems[i].parent).before(addItems[i].target);
+  }
+  return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+  jQuery.uaMatch = function(ua) {
+    ua = ua.toLowerCase();
+
+    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+      /(msie) ([\w.]+)/.exec(ua) ||
+      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+      [];
+
+    return {
+      browser: match[ 1 ] || "",
+      version: match[ 2 ] || "0"
+    };
+  };
+  jQuery.browser = {};
+  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initIndexTable();
+    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
+      this.initOnKeyListeners();
+    }
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated === 'undefined')
+      return string;
+    return (typeof translated === 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated === 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      if (!body.length) {
+        body = $('body');
+      }
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlighted');
+        });
+      }, 10);
+      $('<p class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+          .appendTo($('#searchbox'));
+    }
+  },
+
+  /**
+   * init the domain index toggle buttons
+   */
+  initIndexTable : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      $('tr.cg-' + idnum).toggle();
+      if (src.substr(-9) === 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('#searchbox .highlight-link').fadeOut(300);
+    $('span.highlighted').removeClass('highlighted');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this === '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  },
+
+  initOnKeyListeners: function() {
+    $(document).keyup(function(event) {
+      var activeElementType = document.activeElement.tagName;
+      // don't navigate when in search box or textarea
+      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
+        switch (event.keyCode) {
+          case 37: // left
+            var prevHref = $('link[rel="prev"]').prop('href');
+            if (prevHref) {
+              window.location.href = prevHref;
+              return false;
+            }
+          case 39: // right
+            var nextHref = $('link[rel="next"]').prop('href');
+            if (nextHref) {
+              window.location.href = nextHref;
+              return false;
+            }
+        }
+      }
+    });
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});

docs/pylagrit/original/static/static/documentation_options.js

@@ -0,0 +1,10 @@
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+    VERSION: '0.0.0',
+    LANGUAGE: 'None',
+    COLLAPSE_INDEX: false,
+    FILE_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false,
+};

docs/pylagrit/original/static/static/language_data.js

@@ -0,0 +1,297 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */ 
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+
+
+var splitChars = (function() {
+    var result = {};
+    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+    var i, j, start, end;
+    for (i = 0; i < singles.length; i++) {
+        result[singles[i]] = true;
+    }
+    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
+         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
+         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
+         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
+         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
+         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
+         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
+         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
+         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
+         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
+         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
+         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
+         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
+         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
+         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
+         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
+         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
+         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
+         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
+         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
+         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
+         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
+         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
+         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
+         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
+         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
+         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
+         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
+         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
+         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
+         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
+         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
+         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
+         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
+         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
+         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
+         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
+         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
+         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
+         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
+         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
+         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
+         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
+         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
+         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+    for (i = 0; i < ranges.length; i++) {
+        start = ranges[i][0];
+        end = ranges[i][1];
+        for (j = start; j <= end; j++) {
+            result[j] = true;
+        }
+    }
+    return result;
+})();
+
+function splitQuery(query) {
+    var result = [];
+    var start = -1;
+    for (var i = 0; i < query.length; i++) {
+        if (splitChars[query.charCodeAt(i)]) {
+            if (start !== -1) {
+                result.push(query.slice(start, i));
+                start = -1;
+            }
+        } else if (start === -1) {
+            start = i;
+        }
+    }
+    if (start !== -1) {
+        result.push(query.slice(start));
+    }
+    return result;
+}
+
+

docs/pylagrit/original/static/static/pygments.css

@@ -0,0 +1,69 @@
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+.highlight  { background: #eeffcc; }
+.highlight .c { color: #408090; font-style: italic } /* Comment */
+.highlight .err { border: 1px solid #FF0000 } /* Error */
+.highlight .k { color: #007020; font-weight: bold } /* Keyword */
+.highlight .o { color: #666666 } /* Operator */
+.highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
+.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
+.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
+.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
+.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
+.highlight .gd { color: #A00000 } /* Generic.Deleted */
+.highlight .ge { font-style: italic } /* Generic.Emph */
+.highlight .gr { color: #FF0000 } /* Generic.Error */
+.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
+.highlight .gi { color: #00A000 } /* Generic.Inserted */
+.highlight .go { color: #333333 } /* Generic.Output */
+.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
+.highlight .gs { font-weight: bold } /* Generic.Strong */
+.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
+.highlight .gt { color: #0044DD } /* Generic.Traceback */
+.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
+.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
+.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
+.highlight .kp { color: #007020 } /* Keyword.Pseudo */
+.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
+.highlight .kt { color: #902000 } /* Keyword.Type */
+.highlight .m { color: #208050 } /* Literal.Number */
+.highlight .s { color: #4070a0 } /* Literal.String */
+.highlight .na { color: #4070a0 } /* Name.Attribute */
+.highlight .nb { color: #007020 } /* Name.Builtin */
+.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
+.highlight .no { color: #60add5 } /* Name.Constant */
+.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
+.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
+.highlight .ne { color: #007020 } /* Name.Exception */
+.highlight .nf { color: #06287e } /* Name.Function */
+.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
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+.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
+.highlight .w { color: #bbbbbb } /* Text.Whitespace */
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+.highlight .mf { color: #208050 } /* Literal.Number.Float */
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+.highlight .mo { color: #208050 } /* Literal.Number.Oct */
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+.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
+.highlight .sc { color: #4070a0 } /* Literal.String.Char */
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docs/pylagrit/original/static/static/searchtools.js

@@ -0,0 +1,481 @@
+/*
+ * searchtools.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for the full-text search.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+if (!Scorer) {
+  /**
+   * Simple result scoring code.
+   */
+  var Scorer = {
+    // Implement the following function to further tweak the score for each result
+    // The function takes a result array [filename, title, anchor, descr, score]
+    // and returns the new score.
+    /*
+    score: function(result) {
+      return result[4];
+    },
+    */
+
+    // query matches the full name of an object
+    objNameMatch: 11,
+    // or matches in the last dotted part of the object name
+    objPartialMatch: 6,
+    // Additive scores depending on the priority of the object
+    objPrio: {0:  15,   // used to be importantResults
+              1:  5,   // used to be objectResults
+              2: -5},  // used to be unimportantResults
+    //  Used when the priority is not in the mapping.
+    objPrioDefault: 0,
+
+    // query found in title
+    title: 15,
+    // query found in terms
+    term: 5
+  };
+}
+
+if (!splitQuery) {
+  function splitQuery(query) {
+    return query.split(/\s+/);
+  }
+}
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  loadIndex : function(url) {
+    $.ajax({type: "GET", url: url, data: null,
+            dataType: "script", cache: true,
+            complete: function(jqxhr, textstatus) {
+              if (textstatus != "success") {
+                document.getElementById("searchindexloader").src = url;
+              }
+            }});
+  },
+
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      var i;
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    }
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  query : function(query) {
+    var i;
+
+    // stem the searchterms and add them to the correct list
+    var stemmer = new Stemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = splitQuery(query);
+    var objectterms = [];
+    for (i = 0; i < tmp.length; i++) {
+      if (tmp[i] !== "") {
+          objectterms.push(tmp[i].toLowerCase());
+      }
+
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] === "") {
+        // skip this "word"
+        continue;
+      }
+      // stem the word
+      var word = stemmer.stemWord(tmp[i].toLowerCase());
+      // prevent stemmer from cutting word smaller than two chars
+      if(word.length < 3 && tmp[i].length >= 3) {
+        word = tmp[i];
+      }
+      var toAppend;
+      // select the correct list
+      if (word[0] == '-') {
+        toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$u.contains(toAppend, word))
+        toAppend.push(word);
+    }
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    // console.debug('SEARCH: searching for:');
+    // console.info('required: ', searchterms);
+    // console.info('excluded: ', excluded);
+
+    // prepare search
+    var terms = this._index.terms;
+    var titleterms = this._index.titleterms;
+
+    // array of [filename, title, anchor, descr, score]
+    var results = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    for (i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0, i),
+                             objectterms.slice(i+1, objectterms.length));
+      results = results.concat(this.performObjectSearch(objectterms[i], others));
+    }
+
+    // lookup as search terms in fulltext
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      for (i = 0; i < results.length; i++)
+        results[i][4] = Scorer.score(results[i]);
+    }
+
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort(function(a, b) {
+      var left = a[4];
+      var right = b[4];
+      if (left > right) {
+        return 1;
+      } else if (left < right) {
+        return -1;
+      } else {
+        // same score: sort alphabetically
+        left = a[1].toLowerCase();
+        right = b[1].toLowerCase();
+        return (left > right) ? -1 : ((left < right) ? 1 : 0);
+      }
+    });
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    //console.info('search results:', Search.lastresults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+          // dirhtml builder
+          var dirname = item[0] + '/';
+          if (dirname.match(/\/index\/$/)) {
+            dirname = dirname.substring(0, dirname.length-6);
+          } else if (dirname == 'index/') {
+            dirname = '';
+          }
+          listItem.append($('<a/>').attr('href',
+            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+            highlightstring + item[2]).html(item[1]));
+        } else {
+          // normal html builders
+          listItem.append($('<a/>').attr('href',
+            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+            highlightstring + item[2]).html(item[1]));
+        }
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
+          if (suffix === undefined) {
+            suffix = '.txt';
+          }
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
+                  dataType: "text",
+                  complete: function(jqxhr, textstatus) {
+                    var data = jqxhr.responseText;
+                    if (data !== '' && data !== undefined) {
+                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                    }
+                    Search.output.append(listItem);
+                    listItem.slideDown(5, function() {
+                      displayNextItem();
+                    });
+                  }});
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch : function(object, otherterms) {
+    var filenames = this._index.filenames;
+    var docnames = this._index.docnames;
+    var objects = this._index.objects;
+    var objnames = this._index.objnames;
+    var titles = this._index.titles;
+
+    var i;
+    var results = [];
+
+    for (var prefix in objects) {
+      for (var name in objects[prefix]) {
+        var fullname = (prefix ? prefix + '.' : '') + name;
+        if (fullname.toLowerCase().indexOf(object) > -1) {
+          var score = 0;
+          var parts = fullname.split('.');
+          // check for different match types: exact matches of full name or
+          // "last name" (i.e. last dotted part)
+          if (fullname == object || parts[parts.length - 1] == object) {
+            score += Scorer.objNameMatch;
+          // matches in last name
+          } else if (parts[parts.length - 1].indexOf(object) > -1) {
+            score += Scorer.objPartialMatch;
+          }
+          var match = objects[prefix][name];
+          var objname = objnames[match[1]][2];
+          var title = titles[match[0]];
+          // If more than one term searched for, we require other words to be
+          // found in the name/title/description
+          if (otherterms.length > 0) {
+            var haystack = (prefix + ' ' + name + ' ' +
+                            objname + ' ' + title).toLowerCase();
+            var allfound = true;
+            for (i = 0; i < otherterms.length; i++) {
+              if (haystack.indexOf(otherterms[i]) == -1) {
+                allfound = false;
+                break;
+              }
+            }
+            if (!allfound) {
+              continue;
+            }
+          }
+          var descr = objname + _(', in ') + title;
+
+          var anchor = match[3];
+          if (anchor === '')
+            anchor = fullname;
+          else if (anchor == '-')
+            anchor = objnames[match[1]][1] + '-' + fullname;
+          // add custom score for some objects according to scorer
+          if (Scorer.objPrio.hasOwnProperty(match[2])) {
+            score += Scorer.objPrio[match[2]];
+          } else {
+            score += Scorer.objPrioDefault;
+          }
+          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
+        }
+      }
+    }
+
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+    var docnames = this._index.docnames;
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+
+    var i, j, file;
+    var fileMap = {};
+    var scoreMap = {};
+    var results = [];
+
+    // perform the search on the required terms
+    for (i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      var files = [];
+      var _o = [
+        {files: terms[word], score: Scorer.term},
+        {files: titleterms[word], score: Scorer.title}
+      ];
+
+      // no match but word was a required one
+      if ($u.every(_o, function(o){return o.files === undefined;})) {
+        break;
+      }
+      // found search word in contents
+      $u.each(_o, function(o) {
+        var _files = o.files;
+        if (_files === undefined)
+          return
+
+        if (_files.length === undefined)
+          _files = [_files];
+        files = files.concat(_files);
+
+        // set score for the word in each file to Scorer.term
+        for (j = 0; j < _files.length; j++) {
+          file = _files[j];
+          if (!(file in scoreMap))
+            scoreMap[file] = {}
+          scoreMap[file][word] = o.score;
+        }
+      });
+
+      // create the mapping
+      for (j = 0; j < files.length; j++) {
+        file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+          continue;
+
+      // ensure that none of the excluded terms is in the search result
+      for (i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+            titleterms[excluded[i]] == file ||
+            $u.contains(terms[excluded[i]] || [], file) ||
+            $u.contains(titleterms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it to the result list
+      if (valid) {
+        // select one (max) score for the file.
+        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
+        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
+        results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
+      }
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words, hlwords is the list of normal, unstemmed
+   * words. the first one is used to find the occurrence, the
+   * latter for highlighting it.
+   */
+  makeSearchSummary : function(text, keywords, hlwords) {
+    var textLower = text.toLowerCase();
+    var start = 0;
+    $.each(keywords, function() {
+      var i = textLower.indexOf(this.toLowerCase());
+      if (i > -1)
+        start = i;
+    });
+    start = Math.max(start - 120, 0);
+    var excerpt = ((start > 0) ? '...' : '') +
+      $.trim(text.substr(start, 240)) +
+      ((start + 240 - text.length) ? '...' : '');
+    var rv = $('<div class="context"></div>').text(excerpt);
+    $.each(hlwords, function() {
+      rv = rv.highlightText(this, 'highlighted');
+    });
+    return rv;
+  }
+};
+
+$(document).ready(function() {
+  Search.init();
+});

docs/pylagrit/original/static/static/underscore-1.3.1.js

@@ -0,0 +1,999 @@
+//     Underscore.js 1.3.1
+//     (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+//     Underscore is freely distributable under the MIT license.
+//     Portions of Underscore are inspired or borrowed from Prototype,
+//     Oliver Steele's Functional, and John Resig's Micro-Templating.
+//     For all details and documentation:
+//     http://documentcloud.github.com/underscore
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `global` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Establish the object that gets returned to break out of a loop iteration.
+  var breaker = {};
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var slice            = ArrayProto.slice,
+      unshift          = ArrayProto.unshift,
+      toString         = ObjProto.toString,
+      hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeForEach      = ArrayProto.forEach,
+    nativeMap          = ArrayProto.map,
+    nativeReduce       = ArrayProto.reduce,
+    nativeReduceRight  = ArrayProto.reduceRight,
+    nativeFilter       = ArrayProto.filter,
+    nativeEvery        = ArrayProto.every,
+    nativeSome         = ArrayProto.some,
+    nativeIndexOf      = ArrayProto.indexOf,
+    nativeLastIndexOf  = ArrayProto.lastIndexOf,
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind;
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) { return new wrapper(obj); };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object via a string identifier,
+  // for Closure Compiler "advanced" mode.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root['_'] = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.3.1';
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles objects with the built-in `forEach`, arrays, and raw objects.
+  // Delegates to **ECMAScript 5**'s native `forEach` if available.
+  var each = _.each = _.forEach = function(obj, iterator, context) {
+    if (obj == null) return;
+    if (nativeForEach && obj.forEach === nativeForEach) {
+      obj.forEach(iterator, context);
+    } else if (obj.length === +obj.length) {
+      for (var i = 0, l = obj.length; i < l; i++) {
+        if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
+      }
+    } else {
+      for (var key in obj) {
+        if (_.has(obj, key)) {
+          if (iterator.call(context, obj[key], key, obj) === breaker) return;
+        }
+      }
+    }
+  };
+
+  // Return the results of applying the iterator to each element.
+  // Delegates to **ECMAScript 5**'s native `map` if available.
+  _.map = _.collect = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
+    each(obj, function(value, index, list) {
+      results[results.length] = iterator.call(context, value, index, list);
+    });
+    if (obj.length === +obj.length) results.length = obj.length;
+    return results;
+  };
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
+  _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduce && obj.reduce === nativeReduce) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
+    }
+    each(obj, function(value, index, list) {
+      if (!initial) {
+        memo = value;
+        initial = true;
+      } else {
+        memo = iterator.call(context, memo, value, index, list);
+      }
+    });
+    if (!initial) throw new TypeError('Reduce of empty array with no initial value');
+    return memo;
+  };
+
+  // The right-associative version of reduce, also known as `foldr`.
+  // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
+  _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
+    }
+    var reversed = _.toArray(obj).reverse();
+    if (context && !initial) iterator = _.bind(iterator, context);
+    return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
+  };
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, iterator, context) {
+    var result;
+    any(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) {
+        result = value;
+        return true;
+      }
+    });
+    return result;
+  };
+
+  // Return all the elements that pass a truth test.
+  // Delegates to **ECMAScript 5**'s native `filter` if available.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
+    each(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    each(obj, function(value, index, list) {
+      if (!iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Delegates to **ECMAScript 5**'s native `every` if available.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, iterator, context) {
+    var result = true;
+    if (obj == null) return result;
+    if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
+    each(obj, function(value, index, list) {
+      if (!(result = result && iterator.call(context, value, index, list))) return breaker;
+    });
+    return result;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Delegates to **ECMAScript 5**'s native `some` if available.
+  // Aliased as `any`.
+  var any = _.some = _.any = function(obj, iterator, context) {
+    iterator || (iterator = _.identity);
+    var result = false;
+    if (obj == null) return result;
+    if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
+    each(obj, function(value, index, list) {
+      if (result || (result = iterator.call(context, value, index, list))) return breaker;
+    });
+    return !!result;
+  };
+
+  // Determine if a given value is included in the array or object using `===`.
+  // Aliased as `contains`.
+  _.include = _.contains = function(obj, target) {
+    var found = false;
+    if (obj == null) return found;
+    if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
+    found = any(obj, function(value) {
+      return value === target;
+    });
+    return found;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    return _.map(obj, function(value) {
+      return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, function(value){ return value[key]; });
+  };
+
+  // Return the maximum element or (element-based computation).
+  _.max = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return -Infinity;
+    var result = {computed : -Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed >= result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return Infinity;
+    var result = {computed : Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed < result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Shuffle an array.
+  _.shuffle = function(obj) {
+    var shuffled = [], rand;
+    each(obj, function(value, index, list) {
+      if (index == 0) {
+        shuffled[0] = value;
+      } else {
+        rand = Math.floor(Math.random() * (index + 1));
+        shuffled[index] = shuffled[rand];
+        shuffled[rand] = value;
+      }
+    });
+    return shuffled;
+  };
+
+  // Sort the object's values by a criterion produced by an iterator.
+  _.sortBy = function(obj, iterator, context) {
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value : value,
+        criteria : iterator.call(context, value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria, b = right.criteria;
+      return a < b ? -1 : a > b ? 1 : 0;
+    }), 'value');
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = function(obj, val) {
+    var result = {};
+    var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
+    each(obj, function(value, index) {
+      var key = iterator(value, index);
+      (result[key] || (result[key] = [])).push(value);
+    });
+    return result;
+  };
+
+  // Use a comparator function to figure out at what index an object should
+  // be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iterator) {
+    iterator || (iterator = _.identity);
+    var low = 0, high = array.length;
+    while (low < high) {
+      var mid = (low + high) >> 1;
+      iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
+    }
+    return low;
+  };
+
+  // Safely convert anything iterable into a real, live array.
+  _.toArray = function(iterable) {
+    if (!iterable)                return [];
+    if (iterable.toArray)         return iterable.toArray();
+    if (_.isArray(iterable))      return slice.call(iterable);
+    if (_.isArguments(iterable))  return slice.call(iterable);
+    return _.values(iterable);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    return _.toArray(obj).length;
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head`. The **guard** check allows it to work
+  // with `_.map`.
+  _.first = _.head = function(array, n, guard) {
+    return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
+  };
+
+  // Returns everything but the last entry of the array. Especcialy useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N. The **guard** check allows it to work with
+  // `_.map`.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array. The **guard** check allows it to work with `_.map`.
+  _.last = function(array, n, guard) {
+    if ((n != null) && !guard) {
+      return slice.call(array, Math.max(array.length - n, 0));
+    } else {
+      return array[array.length - 1];
+    }
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail`.
+  // Especially useful on the arguments object. Passing an **index** will return
+  // the rest of the values in the array from that index onward. The **guard**
+  // check allows it to work with `_.map`.
+  _.rest = _.tail = function(array, index, guard) {
+    return slice.call(array, (index == null) || guard ? 1 : index);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, function(value){ return !!value; });
+  };
+
+  // Return a completely flattened version of an array.
+  _.flatten = function(array, shallow) {
+    return _.reduce(array, function(memo, value) {
+      if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
+      memo[memo.length] = value;
+      return memo;
+    }, []);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iterator) {
+    var initial = iterator ? _.map(array, iterator) : array;
+    var result = [];
+    _.reduce(initial, function(memo, el, i) {
+      if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
+        memo[memo.length] = el;
+        result[result.length] = array[i];
+      }
+      return memo;
+    }, []);
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(_.flatten(arguments, true));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays. (Aliased as "intersect" for back-compat.)
+  _.intersection = _.intersect = function(array) {
+    var rest = slice.call(arguments, 1);
+    return _.filter(_.uniq(array), function(item) {
+      return _.every(rest, function(other) {
+        return _.indexOf(other, item) >= 0;
+      });
+    });
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = _.flatten(slice.call(arguments, 1));
+    return _.filter(array, function(value){ return !_.include(rest, value); });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function() {
+    var args = slice.call(arguments);
+    var length = _.max(_.pluck(args, 'length'));
+    var results = new Array(length);
+    for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
+    return results;
+  };
+
+  // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
+  // we need this function. Return the position of the first occurrence of an
+  // item in an array, or -1 if the item is not included in the array.
+  // Delegates to **ECMAScript 5**'s native `indexOf` if available.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = function(array, item, isSorted) {
+    if (array == null) return -1;
+    var i, l;
+    if (isSorted) {
+      i = _.sortedIndex(array, item);
+      return array[i] === item ? i : -1;
+    }
+    if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
+    for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
+  _.lastIndexOf = function(array, item) {
+    if (array == null) return -1;
+    if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
+    var i = array.length;
+    while (i--) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (arguments.length <= 1) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = arguments[2] || 1;
+
+    var len = Math.max(Math.ceil((stop - start) / step), 0);
+    var idx = 0;
+    var range = new Array(len);
+
+    while(idx < len) {
+      range[idx++] = start;
+      start += step;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Reusable constructor function for prototype setting.
+  var ctor = function(){};
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Binding with arguments is also known as `curry`.
+  // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
+  // We check for `func.bind` first, to fail fast when `func` is undefined.
+  _.bind = function bind(func, context) {
+    var bound, args;
+    if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError;
+    args = slice.call(arguments, 2);
+    return bound = function() {
+      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
+      ctor.prototype = func.prototype;
+      var self = new ctor;
+      var result = func.apply(self, args.concat(slice.call(arguments)));
+      if (Object(result) === result) return result;
+      return self;
+    };
+  };
+
+  // Bind all of an object's methods to that object. Useful for ensuring that
+  // all callbacks defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var funcs = slice.call(arguments, 1);
+    if (funcs.length == 0) funcs = _.functions(obj);
+    each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memo = {};
+    hasher || (hasher = _.identity);
+    return function() {
+      var key = hasher.apply(this, arguments);
+      return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
+    };
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){ return func.apply(func, args); }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = function(func) {
+    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
+  };
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time.
+  _.throttle = function(func, wait) {
+    var context, args, timeout, throttling, more;
+    var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
+    return function() {
+      context = this; args = arguments;
+      var later = function() {
+        timeout = null;
+        if (more) func.apply(context, args);
+        whenDone();
+      };
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (throttling) {
+        more = true;
+      } else {
+        func.apply(context, args);
+      }
+      whenDone();
+      throttling = true;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds.
+  _.debounce = function(func, wait) {
+    var timeout;
+    return function() {
+      var context = this, args = arguments;
+      var later = function() {
+        timeout = null;
+        func.apply(context, args);
+      };
+      clearTimeout(timeout);
+      timeout = setTimeout(later, wait);
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = function(func) {
+    var ran = false, memo;
+    return function() {
+      if (ran) return memo;
+      ran = true;
+      return memo = func.apply(this, arguments);
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return function() {
+      var args = [func].concat(slice.call(arguments, 0));
+      return wrapper.apply(this, args);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var funcs = arguments;
+    return function() {
+      var args = arguments;
+      for (var i = funcs.length - 1; i >= 0; i--) {
+        args = [funcs[i].apply(this, args)];
+      }
+      return args[0];
+    };
+  };
+
+  // Returns a function that will only be executed after being called N times.
+  _.after = function(times, func) {
+    if (times <= 0) return func();
+    return function() {
+      if (--times < 1) { return func.apply(this, arguments); }
+    };
+  };
+
+  // Object Functions
+  // ----------------
+
+  // Retrieve the names of an object's properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = nativeKeys || function(obj) {
+    if (obj !== Object(obj)) throw new TypeError('Invalid object');
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    return _.map(obj, _.identity);
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        if (obj[prop] == null) obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Internal recursive comparison function.
+  function eq(a, b, stack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
+    if (a === b) return a !== 0 || 1 / a == 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a._chain) a = a._wrapped;
+    if (b._chain) b = b._wrapped;
+    // Invoke a custom `isEqual` method if one is provided.
+    if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
+    if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className != toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, dates, and booleans are compared by value.
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return a == String(b);
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
+        // other numeric values.
+        return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a == +b;
+      // RegExps are compared by their source patterns and flags.
+      case '[object RegExp]':
+        return a.source == b.source &&
+               a.global == b.global &&
+               a.multiline == b.multiline &&
+               a.ignoreCase == b.ignoreCase;
+    }
+    if (typeof a != 'object' || typeof b != 'object') return false;
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+    var length = stack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (stack[length] == a) return true;
+    }
+    // Add the first object to the stack of traversed objects.
+    stack.push(a);
+    var size = 0, result = true;
+    // Recursively compare objects and arrays.
+    if (className == '[object Array]') {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      size = a.length;
+      result = size == b.length;
+      if (result) {
+        // Deep compare the contents, ignoring non-numeric properties.
+        while (size--) {
+          // Ensure commutative equality for sparse arrays.
+          if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
+        }
+      }
+    } else {
+      // Objects with different constructors are not equivalent.
+      if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
+      // Deep compare objects.
+      for (var key in a) {
+        if (_.has(a, key)) {
+          // Count the expected number of properties.
+          size++;
+          // Deep compare each member.
+          if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
+        }
+      }
+      // Ensure that both objects contain the same number of properties.
+      if (result) {
+        for (key in b) {
+          if (_.has(b, key) && !(size--)) break;
+        }
+        result = !size;
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    stack.pop();
+    return result;
+  }
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b, []);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
+    for (var key in obj) if (_.has(obj, key)) return false;
+    return true;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType == 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) == '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    return obj === Object(obj);
+  };
+
+  // Is a given variable an arguments object?
+  _.isArguments = function(obj) {
+    return toString.call(obj) == '[object Arguments]';
+  };
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return !!(obj && _.has(obj, 'callee'));
+    };
+  }
+
+  // Is a given value a function?
+  _.isFunction = function(obj) {
+    return toString.call(obj) == '[object Function]';
+  };
+
+  // Is a given value a string?
+  _.isString = function(obj) {
+    return toString.call(obj) == '[object String]';
+  };
+
+  // Is a given value a number?
+  _.isNumber = function(obj) {
+    return toString.call(obj) == '[object Number]';
+  };
+
+  // Is the given value `NaN`?
+  _.isNaN = function(obj) {
+    // `NaN` is the only value for which `===` is not reflexive.
+    return obj !== obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
+  };
+
+  // Is a given value a date?
+  _.isDate = function(obj) {
+    return toString.call(obj) == '[object Date]';
+  };
+
+  // Is the given value a regular expression?
+  _.isRegExp = function(obj) {
+    return toString.call(obj) == '[object RegExp]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Has own property?
+  _.has = function(obj, key) {
+    return hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iterators.
+  _.identity = function(value) {
+    return value;
+  };
+
+  // Run a function **n** times.
+  _.times = function (n, iterator, context) {
+    for (var i = 0; i < n; i++) iterator.call(context, i);
+  };
+
+  // Escape a string for HTML interpolation.
+  _.escape = function(string) {
+    return (''+string).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;').replace(/'/g, '&#x27;').replace(/\//g,'&#x2F;');
+  };
+
+  // Add your own custom functions to the Underscore object, ensuring that
+  // they're correctly added to the OOP wrapper as well.
+  _.mixin = function(obj) {
+    each(_.functions(obj), function(name){
+      addToWrapper(name, _[name] = obj[name]);
+    });
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = idCounter++;
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /.^/;
+
+  // Within an interpolation, evaluation, or escaping, remove HTML escaping
+  // that had been previously added.
+  var unescape = function(code) {
+    return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  _.template = function(str, data) {
+    var c  = _.templateSettings;
+    var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
+      'with(obj||{}){__p.push(\'' +
+      str.replace(/\\/g, '\\\\')
+         .replace(/'/g, "\\'")
+         .replace(c.escape || noMatch, function(match, code) {
+           return "',_.escape(" + unescape(code) + "),'";
+         })
+         .replace(c.interpolate || noMatch, function(match, code) {
+           return "'," + unescape(code) + ",'";
+         })
+         .replace(c.evaluate || noMatch, function(match, code) {
+           return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
+         })
+         .replace(/\r/g, '\\r')
+         .replace(/\n/g, '\\n')
+         .replace(/\t/g, '\\t')
+         + "');}return __p.join('');";
+    var func = new Function('obj', '_', tmpl);
+    if (data) return func(data, _);
+    return function(data) {
+      return func.call(this, data, _);
+    };
+  };
+
+  // Add a "chain" function, which will delegate to the wrapper.
+  _.chain = function(obj) {
+    return _(obj).chain();
+  };
+
+  // The OOP Wrapper
+  // ---------------
+
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+  var wrapper = function(obj) { this._wrapped = obj; };
+
+  // Expose `wrapper.prototype` as `_.prototype`
+  _.prototype = wrapper.prototype;
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(obj, chain) {
+    return chain ? _(obj).chain() : obj;
+  };
+
+  // A method to easily add functions to the OOP wrapper.
+  var addToWrapper = function(name, func) {
+    wrapper.prototype[name] = function() {
+      var args = slice.call(arguments);
+      unshift.call(args, this._wrapped);
+      return result(func.apply(_, args), this._chain);
+    };
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      var wrapped = this._wrapped;
+      method.apply(wrapped, arguments);
+      var length = wrapped.length;
+      if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
+      return result(wrapped, this._chain);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      return result(method.apply(this._wrapped, arguments), this._chain);
+    };
+  });
+
+  // Start chaining a wrapped Underscore object.
+  wrapper.prototype.chain = function() {
+    this._chain = true;
+    return this;
+  };
+
+  // Extracts the result from a wrapped and chained object.
+  wrapper.prototype.value = function() {
+    return this._wrapped;
+  };
+
+}).call(this);

docs/pylagrit/original/static/static/underscore.js

@@ -0,0 +1,31 @@
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
+c.source&&a.global==c.global&&a.multiline==c.multiline&&a.ignoreCase==c.ignoreCase}if(typeof a!="object"||typeof c!="object")return false;for(var f=d.length;f--;)if(d[f]==a)return true;d.push(a);var f=0,g=true;if(e=="[object Array]"){if(f=a.length,g=f==c.length)for(;f--;)if(!(g=f in a==f in c&&q(a[f],c[f],d)))break}else{if("constructor"in a!="constructor"in c||a.constructor!=c.constructor)return false;for(var h in a)if(b.has(a,h)&&(f++,!(g=b.has(c,h)&&q(a[h],c[h],d))))break;if(g){for(h in c)if(b.has(c,
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+null&&(a=[]);if(y&&a.reduce===y)return e&&(c=b.bind(c,e)),f?a.reduce(c,d):a.reduce(c);j(a,function(a,b,i){f?d=c.call(e,d,a,b,i):(d=a,f=true)});if(!f)throw new TypeError("Reduce of empty array with no initial value");return d};b.reduceRight=b.foldr=function(a,c,d,e){var f=arguments.length>2;a==null&&(a=[]);if(z&&a.reduceRight===z)return e&&(c=b.bind(c,e)),f?a.reduceRight(c,d):a.reduceRight(c);var g=b.toArray(a).reverse();e&&!f&&(c=b.bind(c,e));return f?b.reduce(g,c,d,e):b.reduce(g,c)};b.find=b.detect=
+function(a,c,b){var e;E(a,function(a,g,h){if(c.call(b,a,g,h))return e=a,true});return e};b.filter=b.select=function(a,c,b){var e=[];if(a==null)return e;if(A&&a.filter===A)return a.filter(c,b);j(a,function(a,g,h){c.call(b,a,g,h)&&(e[e.length]=a)});return e};b.reject=function(a,c,b){var e=[];if(a==null)return e;j(a,function(a,g,h){c.call(b,a,g,h)||(e[e.length]=a)});return e};b.every=b.all=function(a,c,b){var e=true;if(a==null)return e;if(B&&a.every===B)return a.every(c,b);j(a,function(a,g,h){if(!(e=
+e&&c.call(b,a,g,h)))return n});return e};var E=b.some=b.any=function(a,c,d){c||(c=b.identity);var e=false;if(a==null)return e;if(C&&a.some===C)return a.some(c,d);j(a,function(a,b,h){if(e||(e=c.call(d,a,b,h)))return n});return!!e};b.include=b.contains=function(a,c){var b=false;if(a==null)return b;return p&&a.indexOf===p?a.indexOf(c)!=-1:b=E(a,function(a){return a===c})};b.invoke=function(a,c){var d=i.call(arguments,2);return b.map(a,function(a){return(b.isFunction(c)?c||a:a[c]).apply(a,d)})};b.pluck=
+function(a,c){return b.map(a,function(a){return a[c]})};b.max=function(a,c,d){if(!c&&b.isArray(a))return Math.max.apply(Math,a);if(!c&&b.isEmpty(a))return-Infinity;var e={computed:-Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b>=e.computed&&(e={value:a,computed:b})});return e.value};b.min=function(a,c,d){if(!c&&b.isArray(a))return Math.min.apply(Math,a);if(!c&&b.isEmpty(a))return Infinity;var e={computed:Infinity};j(a,function(a,b,h){b=c?c.call(d,a,b,h):a;b<e.computed&&(e={value:a,computed:b})});
+return e.value};b.shuffle=function(a){var b=[],d;j(a,function(a,f){f==0?b[0]=a:(d=Math.floor(Math.random()*(f+1)),b[f]=b[d],b[d]=a)});return b};b.sortBy=function(a,c,d){return b.pluck(b.map(a,function(a,b,g){return{value:a,criteria:c.call(d,a,b,g)}}).sort(function(a,b){var c=a.criteria,d=b.criteria;return c<d?-1:c>d?1:0}),"value")};b.groupBy=function(a,c){var d={},e=b.isFunction(c)?c:function(a){return a[c]};j(a,function(a,b){var c=e(a,b);(d[c]||(d[c]=[])).push(a)});return d};b.sortedIndex=function(a,
+c,d){d||(d=b.identity);for(var e=0,f=a.length;e<f;){var g=e+f>>1;d(a[g])<d(c)?e=g+1:f=g}return e};b.toArray=function(a){return!a?[]:a.toArray?a.toArray():b.isArray(a)?i.call(a):b.isArguments(a)?i.call(a):b.values(a)};b.size=function(a){return b.toArray(a).length};b.first=b.head=function(a,b,d){return b!=null&&!d?i.call(a,0,b):a[0]};b.initial=function(a,b,d){return i.call(a,0,a.length-(b==null||d?1:b))};b.last=function(a,b,d){return b!=null&&!d?i.call(a,Math.max(a.length-b,0)):a[a.length-1]};b.rest=
+b.tail=function(a,b,d){return i.call(a,b==null||d?1:b)};b.compact=function(a){return b.filter(a,function(a){return!!a})};b.flatten=function(a,c){return b.reduce(a,function(a,e){if(b.isArray(e))return a.concat(c?e:b.flatten(e));a[a.length]=e;return a},[])};b.without=function(a){return b.difference(a,i.call(arguments,1))};b.uniq=b.unique=function(a,c,d){var d=d?b.map(a,d):a,e=[];b.reduce(d,function(d,g,h){if(0==h||(c===true?b.last(d)!=g:!b.include(d,g)))d[d.length]=g,e[e.length]=a[h];return d},[]);
+return e};b.union=function(){return b.uniq(b.flatten(arguments,true))};b.intersection=b.intersect=function(a){var c=i.call(arguments,1);return b.filter(b.uniq(a),function(a){return b.every(c,function(c){return b.indexOf(c,a)>=0})})};b.difference=function(a){var c=b.flatten(i.call(arguments,1));return b.filter(a,function(a){return!b.include(c,a)})};b.zip=function(){for(var a=i.call(arguments),c=b.max(b.pluck(a,"length")),d=Array(c),e=0;e<c;e++)d[e]=b.pluck(a,""+e);return d};b.indexOf=function(a,c,
+d){if(a==null)return-1;var e;if(d)return d=b.sortedIndex(a,c),a[d]===c?d:-1;if(p&&a.indexOf===p)return a.indexOf(c);for(d=0,e=a.length;d<e;d++)if(d in a&&a[d]===c)return d;return-1};b.lastIndexOf=function(a,b){if(a==null)return-1;if(D&&a.lastIndexOf===D)return a.lastIndexOf(b);for(var d=a.length;d--;)if(d in a&&a[d]===b)return d;return-1};b.range=function(a,b,d){arguments.length<=1&&(b=a||0,a=0);for(var d=arguments[2]||1,e=Math.max(Math.ceil((b-a)/d),0),f=0,g=Array(e);f<e;)g[f++]=a,a+=d;return g};
+var F=function(){};b.bind=function(a,c){var d,e;if(a.bind===s&&s)return s.apply(a,i.call(arguments,1));if(!b.isFunction(a))throw new TypeError;e=i.call(arguments,2);return d=function(){if(!(this instanceof d))return a.apply(c,e.concat(i.call(arguments)));F.prototype=a.prototype;var b=new F,g=a.apply(b,e.concat(i.call(arguments)));return Object(g)===g?g:b}};b.bindAll=function(a){var c=i.call(arguments,1);c.length==0&&(c=b.functions(a));j(c,function(c){a[c]=b.bind(a[c],a)});return a};b.memoize=function(a,
+c){var d={};c||(c=b.identity);return function(){var e=c.apply(this,arguments);return b.has(d,e)?d[e]:d[e]=a.apply(this,arguments)}};b.delay=function(a,b){var d=i.call(arguments,2);return setTimeout(function(){return a.apply(a,d)},b)};b.defer=function(a){return b.delay.apply(b,[a,1].concat(i.call(arguments,1)))};b.throttle=function(a,c){var d,e,f,g,h,i=b.debounce(function(){h=g=false},c);return function(){d=this;e=arguments;var b;f||(f=setTimeout(function(){f=null;h&&a.apply(d,e);i()},c));g?h=true:
+a.apply(d,e);i();g=true}};b.debounce=function(a,b){var d;return function(){var e=this,f=arguments;clearTimeout(d);d=setTimeout(function(){d=null;a.apply(e,f)},b)}};b.once=function(a){var b=false,d;return function(){if(b)return d;b=true;return d=a.apply(this,arguments)}};b.wrap=function(a,b){return function(){var d=[a].concat(i.call(arguments,0));return b.apply(this,d)}};b.compose=function(){var a=arguments;return function(){for(var b=arguments,d=a.length-1;d>=0;d--)b=[a[d].apply(this,b)];return b[0]}};
+b.after=function(a,b){return a<=0?b():function(){if(--a<1)return b.apply(this,arguments)}};b.keys=J||function(a){if(a!==Object(a))throw new TypeError("Invalid object");var c=[],d;for(d in a)b.has(a,d)&&(c[c.length]=d);return c};b.values=function(a){return b.map(a,b.identity)};b.functions=b.methods=function(a){var c=[],d;for(d in a)b.isFunction(a[d])&&c.push(d);return c.sort()};b.extend=function(a){j(i.call(arguments,1),function(b){for(var d in b)a[d]=b[d]});return a};b.defaults=function(a){j(i.call(arguments,
+1),function(b){for(var d in b)a[d]==null&&(a[d]=b[d])});return a};b.clone=function(a){return!b.isObject(a)?a:b.isArray(a)?a.slice():b.extend({},a)};b.tap=function(a,b){b(a);return a};b.isEqual=function(a,b){return q(a,b,[])};b.isEmpty=function(a){if(b.isArray(a)||b.isString(a))return a.length===0;for(var c in a)if(b.has(a,c))return false;return true};b.isElement=function(a){return!!(a&&a.nodeType==1)};b.isArray=o||function(a){return l.call(a)=="[object Array]"};b.isObject=function(a){return a===Object(a)};
+b.isArguments=function(a){return l.call(a)=="[object Arguments]"};if(!b.isArguments(arguments))b.isArguments=function(a){return!(!a||!b.has(a,"callee"))};b.isFunction=function(a){return l.call(a)=="[object Function]"};b.isString=function(a){return l.call(a)=="[object String]"};b.isNumber=function(a){return l.call(a)=="[object Number]"};b.isNaN=function(a){return a!==a};b.isBoolean=function(a){return a===true||a===false||l.call(a)=="[object Boolean]"};b.isDate=function(a){return l.call(a)=="[object Date]"};
+b.isRegExp=function(a){return l.call(a)=="[object RegExp]"};b.isNull=function(a){return a===null};b.isUndefined=function(a){return a===void 0};b.has=function(a,b){return I.call(a,b)};b.noConflict=function(){r._=G;return this};b.identity=function(a){return a};b.times=function(a,b,d){for(var e=0;e<a;e++)b.call(d,e)};b.escape=function(a){return(""+a).replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/>/g,"&gt;").replace(/"/g,"&quot;").replace(/'/g,"&#x27;").replace(/\//g,"&#x2F;")};b.mixin=function(a){j(b.functions(a),
+function(c){K(c,b[c]=a[c])})};var L=0;b.uniqueId=function(a){var b=L++;return a?a+b:b};b.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var t=/.^/,u=function(a){return a.replace(/\\\\/g,"\\").replace(/\\'/g,"'")};b.template=function(a,c){var d=b.templateSettings,d="var __p=[],print=function(){__p.push.apply(__p,arguments);};with(obj||{}){__p.push('"+a.replace(/\\/g,"\\\\").replace(/'/g,"\\'").replace(d.escape||t,function(a,b){return"',_.escape("+
+u(b)+"),'"}).replace(d.interpolate||t,function(a,b){return"',"+u(b)+",'"}).replace(d.evaluate||t,function(a,b){return"');"+u(b).replace(/[\r\n\t]/g," ")+";__p.push('"}).replace(/\r/g,"\\r").replace(/\n/g,"\\n").replace(/\t/g,"\\t")+"');}return __p.join('');",e=new Function("obj","_",d);return c?e(c,b):function(a){return e.call(this,a,b)}};b.chain=function(a){return b(a).chain()};var m=function(a){this._wrapped=a};b.prototype=m.prototype;var v=function(a,c){return c?b(a).chain():a},K=function(a,c){m.prototype[a]=
+function(){var a=i.call(arguments);H.call(a,this._wrapped);return v(c.apply(b,a),this._chain)}};b.mixin(b);j("pop,push,reverse,shift,sort,splice,unshift".split(","),function(a){var b=k[a];m.prototype[a]=function(){var d=this._wrapped;b.apply(d,arguments);var e=d.length;(a=="shift"||a=="splice")&&e===0&&delete d[0];return v(d,this._chain)}});j(["concat","join","slice"],function(a){var b=k[a];m.prototype[a]=function(){return v(b.apply(this._wrapped,arguments),this._chain)}});m.prototype.chain=function(){this._chain=
+true;return this};m.prototype.value=function(){return this._wrapped}}).call(this);

docs/pylagrit/original/static/static/websupport.js

@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+  $.fn.autogrow = function() {
+    return this.each(function() {
+    var textarea = this;
+
+    $.fn.autogrow.resize(textarea);
+
+    $(textarea)
+      .focus(function() {
+        textarea.interval = setInterval(function() {
+          $.fn.autogrow.resize(textarea);
+        }, 500);
+      })
+      .blur(function() {
+        clearInterval(textarea.interval);
+      });
+    });
+  };
+
+  $.fn.autogrow.resize = function(textarea) {
+    var lineHeight = parseInt($(textarea).css('line-height'), 10);
+    var lines = textarea.value.split('\n');
+    var columns = textarea.cols;
+    var lineCount = 0;
+    $.each(lines, function() {
+      lineCount += Math.ceil(this.length / columns) || 1;
+    });
+    var height = lineHeight * (lineCount + 1);
+    $(textarea).css('height', height);
+  };
+})(jQuery);
+
+(function($) {
+  var comp, by;
+
+  function init() {
+    initEvents();
+    initComparator();
+  }
+
+  function initEvents() {
+    $(document).on("click", 'a.comment-close', function(event) {
+      event.preventDefault();
+      hide($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.vote', function(event) {
+      event.preventDefault();
+      handleVote($(this));
+    });
+    $(document).on("click", 'a.reply', function(event) {
+      event.preventDefault();
+      openReply($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.close-reply', function(event) {
+      event.preventDefault();
+      closeReply($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.sort-option', function(event) {
+      event.preventDefault();
+      handleReSort($(this));
+    });
+    $(document).on("click", 'a.show-proposal', function(event) {
+      event.preventDefault();
+      showProposal($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.hide-proposal', function(event) {
+      event.preventDefault();
+      hideProposal($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.show-propose-change', function(event) {
+      event.preventDefault();
+      showProposeChange($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.hide-propose-change', function(event) {
+      event.preventDefault();
+      hideProposeChange($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.accept-comment', function(event) {
+      event.preventDefault();
+      acceptComment($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.delete-comment', function(event) {
+      event.preventDefault();
+      deleteComment($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.comment-markup', function(event) {
+      event.preventDefault();
+      toggleCommentMarkupBox($(this).attr('id').substring(2));
+    });
+  }
+
+  /**
+   * Set comp, which is a comparator function used for sorting and
+   * inserting comments into the list.
+   */
+  function setComparator() {
+    // If the first three letters are "asc", sort in ascending order
+    // and remove the prefix.
+    if (by.substring(0,3) == 'asc') {
+      var i = by.substring(3);
+      comp = function(a, b) { return a[i] - b[i]; };
+    } else {
+      // Otherwise sort in descending order.
+      comp = function(a, b) { return b[by] - a[by]; };
+    }
+
+    // Reset link styles and format the selected sort option.
+    $('a.sel').attr('href', '#').removeClass('sel');
+    $('a.by' + by).removeAttr('href').addClass('sel');
+  }
+
+  /**
+   * Create a comp function. If the user has preferences stored in
+   * the sortBy cookie, use those, otherwise use the default.
+   */
+  function initComparator() {
+    by = 'rating'; // Default to sort by rating.
+    // If the sortBy cookie is set, use that instead.
+    if (document.cookie.length > 0) {
+      var start = document.cookie.indexOf('sortBy=');
+      if (start != -1) {
+        start = start + 7;
+        var end = document.cookie.indexOf(";", start);
+        if (end == -1) {
+          end = document.cookie.length;
+          by = unescape(document.cookie.substring(start, end));
+        }
+      }
+    }
+    setComparator();
+  }
+
+  /**
+   * Show a comment div.
+   */
+  function show(id) {
+    $('#ao' + id).hide();
+    $('#ah' + id).show();
+    var context = $.extend({id: id}, opts);
+    var popup = $(renderTemplate(popupTemplate, context)).hide();
+    popup.find('textarea[name="proposal"]').hide();
+    popup.find('a.by' + by).addClass('sel');
+    var form = popup.find('#cf' + id);
+    form.submit(function(event) {
+      event.preventDefault();
+      addComment(form);
+    });
+    $('#s' + id).after(popup);
+    popup.slideDown('fast', function() {
+      getComments(id);
+    });
+  }
+
+  /**
+   * Hide a comment div.
+   */
+  function hide(id) {
+    $('#ah' + id).hide();
+    $('#ao' + id).show();
+    var div = $('#sc' + id);
+    div.slideUp('fast', function() {
+      div.remove();
+    });
+  }
+
+  /**
+   * Perform an ajax request to get comments for a node
+   * and insert the comments into the comments tree.
+   */
+  function getComments(id) {
+    $.ajax({
+     type: 'GET',
+     url: opts.getCommentsURL,
+     data: {node: id},
+     success: function(data, textStatus, request) {
+       var ul = $('#cl' + id);
+       var speed = 100;
+       $('#cf' + id)
+         .find('textarea[name="proposal"]')
+         .data('source', data.source);
+
+       if (data.comments.length === 0) {
+         ul.html('<li>No comments yet.</li>');
+         ul.data('empty', true);
+       } else {
+         // If there are comments, sort them and put them in the list.
+         var comments = sortComments(data.comments);
+         speed = data.comments.length * 100;
+         appendComments(comments, ul);
+         ul.data('empty', false);
+       }
+       $('#cn' + id).slideUp(speed + 200);
+       ul.slideDown(speed);
+     },
+     error: function(request, textStatus, error) {
+       showError('Oops, there was a problem retrieving the comments.');
+     },
+     dataType: 'json'
+    });
+  }
+
+  /**
+   * Add a comment via ajax and insert the comment into the comment tree.
+   */
+  function addComment(form) {
+    var node_id = form.find('input[name="node"]').val();
+    var parent_id = form.find('input[name="parent"]').val();
+    var text = form.find('textarea[name="comment"]').val();
+    var proposal = form.find('textarea[name="proposal"]').val();
+
+    if (text == '') {
+      showError('Please enter a comment.');
+      return;
+    }
+
+    // Disable the form that is being submitted.
+    form.find('textarea,input').attr('disabled', 'disabled');
+
+    // Send the comment to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.addCommentURL,
+      dataType: 'json',
+      data: {
+        node: node_id,
+        parent: parent_id,
+        text: text,
+        proposal: proposal
+      },
+      success: function(data, textStatus, error) {
+        // Reset the form.
+        if (node_id) {
+          hideProposeChange(node_id);
+        }
+        form.find('textarea')
+          .val('')
+          .add(form.find('input'))
+          .removeAttr('disabled');
+	var ul = $('#cl' + (node_id || parent_id));
+        if (ul.data('empty')) {
+          $(ul).empty();
+          ul.data('empty', false);
+        }
+        insertComment(data.comment);
+        var ao = $('#ao' + node_id);
+        ao.find('img').attr({'src': opts.commentBrightImage});
+        if (node_id) {
+          // if this was a "root" comment, remove the commenting box
+          // (the user can get it back by reopening the comment popup)
+          $('#ca' + node_id).slideUp();
+        }
+      },
+      error: function(request, textStatus, error) {
+        form.find('textarea,input').removeAttr('disabled');
+        showError('Oops, there was a problem adding the comment.');
+      }
+    });
+  }
+
+  /**
+   * Recursively append comments to the main comment list and children
+   * lists, creating the comment tree.
+   */
+  function appendComments(comments, ul) {
+    $.each(comments, function() {
+      var div = createCommentDiv(this);
+      ul.append($(document.createElement('li')).html(div));
+      appendComments(this.children, div.find('ul.comment-children'));
+      // To avoid stagnating data, don't store the comments children in data.
+      this.children = null;
+      div.data('comment', this);
+    });
+  }
+
+  /**
+   * After adding a new comment, it must be inserted in the correct
+   * location in the comment tree.
+   */
+  function insertComment(comment) {
+    var div = createCommentDiv(comment);
+
+    // To avoid stagnating data, don't store the comments children in data.
+    comment.children = null;
+    div.data('comment', comment);
+
+    var ul = $('#cl' + (comment.node || comment.parent));
+    var siblings = getChildren(ul);
+
+    var li = $(document.createElement('li'));
+    li.hide();
+
+    // Determine where in the parents children list to insert this comment.
+    for(var i=0; i < siblings.length; i++) {
+      if (comp(comment, siblings[i]) <= 0) {
+        $('#cd' + siblings[i].id)
+          .parent()
+          .before(li.html(div));
+        li.slideDown('fast');
+        return;
+      }
+    }
+
+    // If we get here, this comment rates lower than all the others,
+    // or it is the only comment in the list.
+    ul.append(li.html(div));
+    li.slideDown('fast');
+  }
+
+  function acceptComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.acceptCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        $('#cm' + id).fadeOut('fast');
+        $('#cd' + id).removeClass('moderate');
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem accepting the comment.');
+      }
+    });
+  }
+
+  function deleteComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.deleteCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        var div = $('#cd' + id);
+        if (data == 'delete') {
+          // Moderator mode: remove the comment and all children immediately
+          div.slideUp('fast', function() {
+            div.remove();
+          });
+          return;
+        }
+        // User mode: only mark the comment as deleted
+        div
+          .find('span.user-id:first')
+          .text('[deleted]').end()
+          .find('div.comment-text:first')
+          .text('[deleted]').end()
+          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+          .remove();
+        var comment = div.data('comment');
+        comment.username = '[deleted]';
+        comment.text = '[deleted]';
+        div.data('comment', comment);
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem deleting the comment.');
+      }
+    });
+  }
+
+  function showProposal(id) {
+    $('#sp' + id).hide();
+    $('#hp' + id).show();
+    $('#pr' + id).slideDown('fast');
+  }
+
+  function hideProposal(id) {
+    $('#hp' + id).hide();
+    $('#sp' + id).show();
+    $('#pr' + id).slideUp('fast');
+  }
+
+  function showProposeChange(id) {
+    $('#pc' + id).hide();
+    $('#hc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val(textarea.data('source'));
+    $.fn.autogrow.resize(textarea[0]);
+    textarea.slideDown('fast');
+  }
+
+  function hideProposeChange(id) {
+    $('#hc' + id).hide();
+    $('#pc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val('').removeAttr('disabled');
+    textarea.slideUp('fast');
+  }
+
+  function toggleCommentMarkupBox(id) {
+    $('#mb' + id).toggle();
+  }
+
+  /** Handle when the user clicks on a sort by link. */
+  function handleReSort(link) {
+    var classes = link.attr('class').split(/\s+/);
+    for (var i=0; i<classes.length; i++) {
+      if (classes[i] != 'sort-option') {
+	by = classes[i].substring(2);
+      }
+    }
+    setComparator();
+    // Save/update the sortBy cookie.
+    var expiration = new Date();
+    expiration.setDate(expiration.getDate() + 365);
+    document.cookie= 'sortBy=' + escape(by) +
+                     ';expires=' + expiration.toUTCString();
+    $('ul.comment-ul').each(function(index, ul) {
+      var comments = getChildren($(ul), true);
+      comments = sortComments(comments);
+      appendComments(comments, $(ul).empty());
+    });
+  }
+
+  /**
+   * Function to process a vote when a user clicks an arrow.
+   */
+  function handleVote(link) {
+    if (!opts.voting) {
+      showError("You'll need to login to vote.");
+      return;
+    }
+
+    var id = link.attr('id');
+    if (!id) {
+      // Didn't click on one of the voting arrows.
+      return;
+    }
+    // If it is an unvote, the new vote value is 0,
+    // Otherwise it's 1 for an upvote, or -1 for a downvote.
+    var value = 0;
+    if (id.charAt(1) != 'u') {
+      value = id.charAt(0) == 'u' ? 1 : -1;
+    }
+    // The data to be sent to the server.
+    var d = {
+      comment_id: id.substring(2),
+      value: value
+    };
+
+    // Swap the vote and unvote links.
+    link.hide();
+    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+      .show();
+
+    // The div the comment is displayed in.
+    var div = $('div#cd' + d.comment_id);
+    var data = div.data('comment');
+
+    // If this is not an unvote, and the other vote arrow has
+    // already been pressed, unpress it.
+    if ((d.value !== 0) && (data.vote === d.value * -1)) {
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+    }
+
+    // Update the comments rating in the local data.
+    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+    data.vote = d.value;
+    div.data('comment', data);
+
+    // Change the rating text.
+    div.find('.rating:first')
+      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+    // Send the vote information to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.processVoteURL,
+      data: d,
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem casting that vote.');
+      }
+    });
+  }
+
+  /**
+   * Open a reply form used to reply to an existing comment.
+   */
+  function openReply(id) {
+    // Swap out the reply link for the hide link
+    $('#rl' + id).hide();
+    $('#cr' + id).show();
+
+    // Add the reply li to the children ul.
+    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+    $('#cl' + id)
+      .prepend(div)
+      // Setup the submit handler for the reply form.
+      .find('#rf' + id)
+      .submit(function(event) {
+        event.preventDefault();
+        addComment($('#rf' + id));
+        closeReply(id);
+      })
+      .find('input[type=button]')
+      .click(function() {
+        closeReply(id);
+      });
+    div.slideDown('fast', function() {
+      $('#rf' + id).find('textarea').focus();
+    });
+  }
+
+  /**
+   * Close the reply form opened with openReply.
+   */
+  function closeReply(id) {
+    // Remove the reply div from the DOM.
+    $('#rd' + id).slideUp('fast', function() {
+      $(this).remove();
+    });
+
+    // Swap out the hide link for the reply link
+    $('#cr' + id).hide();
+    $('#rl' + id).show();
+  }
+
+  /**
+   * Recursively sort a tree of comments using the comp comparator.
+   */
+  function sortComments(comments) {
+    comments.sort(comp);
+    $.each(comments, function() {
+      this.children = sortComments(this.children);
+    });
+    return comments;
+  }
+
+  /**
+   * Get the children comments from a ul. If recursive is true,
+   * recursively include childrens' children.
+   */
+  function getChildren(ul, recursive) {
+    var children = [];
+    ul.children().children("[id^='cd']")
+      .each(function() {
+        var comment = $(this).data('comment');
+        if (recursive)
+          comment.children = getChildren($(this).find('#cl' + comment.id), true);
+        children.push(comment);
+      });
+    return children;
+  }
+
+  /** Create a div to display a comment in. */
+  function createCommentDiv(comment) {
+    if (!comment.displayed && !opts.moderator) {
+      return $('<div class="moderate">Thank you!  Your comment will show up '
+               + 'once it is has been approved by a moderator.</div>');
+    }
+    // Prettify the comment rating.
+    comment.pretty_rating = comment.rating + ' point' +
+      (comment.rating == 1 ? '' : 's');
+    // Make a class (for displaying not yet moderated comments differently)
+    comment.css_class = comment.displayed ? '' : ' moderate';
+    // Create a div for this comment.
+    var context = $.extend({}, opts, comment);
+    var div = $(renderTemplate(commentTemplate, context));
+
+    // If the user has voted on this comment, highlight the correct arrow.
+    if (comment.vote) {
+      var direction = (comment.vote == 1) ? 'u' : 'd';
+      div.find('#' + direction + 'v' + comment.id).hide();
+      div.find('#' + direction + 'u' + comment.id).show();
+    }
+
+    if (opts.moderator || comment.text != '[deleted]') {
+      div.find('a.reply').show();
+      if (comment.proposal_diff)
+        div.find('#sp' + comment.id).show();
+      if (opts.moderator && !comment.displayed)
+        div.find('#cm' + comment.id).show();
+      if (opts.moderator || (opts.username == comment.username))
+        div.find('#dc' + comment.id).show();
+    }
+    return div;
+  }
+
+  /**
+   * A simple template renderer. Placeholders such as <%id%> are replaced
+   * by context['id'] with items being escaped. Placeholders such as <#id#>
+   * are not escaped.
+   */
+  function renderTemplate(template, context) {
+    var esc = $(document.createElement('div'));
+
+    function handle(ph, escape) {
+      var cur = context;
+      $.each(ph.split('.'), function() {
+        cur = cur[this];
+      });
+      return escape ? esc.text(cur || "").html() : cur;
+    }
+
+    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+      return handle(arguments[2], arguments[1] == '%' ? true : false);
+    });
+  }
+
+  /** Flash an error message briefly. */
+  function showError(message) {
+    $(document.createElement('div')).attr({'class': 'popup-error'})
+      .append($(document.createElement('div'))
+               .attr({'class': 'error-message'}).text(message))
+      .appendTo('body')
+      .fadeIn("slow")
+      .delay(2000)
+      .fadeOut("slow");
+  }
+
+  /** Add a link the user uses to open the comments popup. */
+  $.fn.comment = function() {
+    return this.each(function() {
+      var id = $(this).attr('id').substring(1);
+      var count = COMMENT_METADATA[id];
+      var title = count + ' comment' + (count == 1 ? '' : 's');
+      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+      var addcls = count == 0 ? ' nocomment' : '';
+      $(this)
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-open' + addcls,
+            id: 'ao' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: image,
+              alt: 'comment',
+              title: title
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              show($(this).attr('id').substring(2));
+            })
+        )
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-close hidden',
+            id: 'ah' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: opts.closeCommentImage,
+              alt: 'close',
+              title: 'close'
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              hide($(this).attr('id').substring(2));
+            })
+        );
+    });
+  };
+
+  var opts = {
+    processVoteURL: '/_process_vote',
+    addCommentURL: '/_add_comment',
+    getCommentsURL: '/_get_comments',
+    acceptCommentURL: '/_accept_comment',
+    deleteCommentURL: '/_delete_comment',
+    commentImage: '/static/_static/comment.png',
+    closeCommentImage: '/static/_static/comment-close.png',
+    loadingImage: '/static/_static/ajax-loader.gif',
+    commentBrightImage: '/static/_static/comment-bright.png',
+    upArrow: '/static/_static/up.png',
+    downArrow: '/static/_static/down.png',
+    upArrowPressed: '/static/_static/up-pressed.png',
+    downArrowPressed: '/static/_static/down-pressed.png',
+    voting: false,
+    moderator: false
+  };
+
+  if (typeof COMMENT_OPTIONS != "undefined") {
+    opts = jQuery.extend(opts, COMMENT_OPTIONS);
+  }
+
+  var popupTemplate = '\
+    <div class="sphinx-comments" id="sc<%id%>">\
+      <p class="sort-options">\
+        Sort by:\
+        <a href="#" class="sort-option byrating">best rated</a>\
+        <a href="#" class="sort-option byascage">newest</a>\
+        <a href="#" class="sort-option byage">oldest</a>\
+      </p>\
+      <div class="comment-header">Comments</div>\
+      <div class="comment-loading" id="cn<%id%>">\
+        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+      <ul id="cl<%id%>" class="comment-ul"></ul>\
+      <div id="ca<%id%>">\
+      <p class="add-a-comment">Add a comment\
+        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+      <div class="comment-markup-box" id="mb<%id%>">\
+        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+        <code>``code``</code>, \
+        code blocks: <code>::</code> and an indented block after blank line</div>\
+      <form method="post" id="cf<%id%>" class="comment-form" action="">\
+        <textarea name="comment" cols="80"></textarea>\
+        <p class="propose-button">\
+          <a href="#" id="pc<%id%>" class="show-propose-change">\
+            Propose a change &#9657;\
+          </a>\
+          <a href="#" id="hc<%id%>" class="hide-propose-change">\
+            Propose a change &#9663;\
+          </a>\
+        </p>\
+        <textarea name="proposal" id="pt<%id%>" cols="80"\
+                  spellcheck="false"></textarea>\
+        <input type="submit" value="Add comment" />\
+        <input type="hidden" name="node" value="<%id%>" />\
+        <input type="hidden" name="parent" value="" />\
+      </form>\
+      </div>\
+    </div>';
+
+  var commentTemplate = '\
+    <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+      <div class="vote">\
+        <div class="arrow">\
+          <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+            <img src="<%upArrow%>" />\
+          </a>\
+          <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+            <img src="<%upArrowPressed%>" />\
+          </a>\
+        </div>\
+        <div class="arrow">\
+          <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+            <img src="<%downArrow%>" id="da<%id%>" />\
+          </a>\
+          <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+            <img src="<%downArrowPressed%>" />\
+          </a>\
+        </div>\
+      </div>\
+      <div class="comment-content">\
+        <p class="tagline comment">\
+          <span class="user-id"><%username%></span>\
+          <span class="rating"><%pretty_rating%></span>\
+          <span class="delta"><%time.delta%></span>\
+        </p>\
+        <div class="comment-text comment"><#text#></div>\
+        <p class="comment-opts comment">\
+          <a href="#" class="reply hidden" id="rl<%id%>">reply &#9657;</a>\
+          <a href="#" class="close-reply" id="cr<%id%>">reply &#9663;</a>\
+          <a href="#" id="sp<%id%>" class="show-proposal">proposal &#9657;</a>\
+          <a href="#" id="hp<%id%>" class="hide-proposal">proposal &#9663;</a>\
+          <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+          <span id="cm<%id%>" class="moderation hidden">\
+            <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+          </span>\
+        </p>\
+        <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+        </pre>\
+          <ul class="comment-children" id="cl<%id%>"></ul>\
+        </div>\
+        <div class="clearleft"></div>\
+      </div>\
+    </div>';
+
+  var replyTemplate = '\
+    <li>\
+      <div class="reply-div" id="rd<%id%>">\
+        <form id="rf<%id%>">\
+          <textarea name="comment" cols="80"></textarea>\
+          <input type="submit" value="Add reply" />\
+          <input type="button" value="Cancel" />\
+          <input type="hidden" name="parent" value="<%id%>" />\
+          <input type="hidden" name="node" value="" />\
+        </form>\
+      </div>\
+    </li>';
+
+  $(document).ready(function() {
+    init();
+  });
+})(jQuery);
+
+$(document).ready(function() {
+  // add comment anchors for all paragraphs that are commentable
+  $('.sphinx-has-comment').comment();
+
+  // highlight search words in search results
+  $("div.context").each(function() {
+    var params = $.getQueryParameters();
+    var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+    var result = $(this);
+    $.each(terms, function() {
+      result.highlightText(this.toLowerCase(), 'highlighted');
+    });
+  });
+
+  // directly open comment window if requested
+  var anchor = document.location.hash;
+  if (anchor.substring(0, 9) == '#comment-') {
+    $('#ao' + anchor.substring(9)).click();
+    document.location.hash = '#s' + anchor.substring(9);
+  }
+});

docs/pylagrit/original/static/stratigraphic.html

@@ -0,0 +1,598 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Stratigraphic Hex Mesh Tutorial &#8212; PyLaGriT 0.0.0 documentation</title>
+    <link rel="stylesheet" href="static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="static/documentation_options.js"></script>
+    <script type="text/javascript" src="static/jquery.js"></script>
+    <script type="text/javascript" src="static/underscore.js"></script>
+    <script type="text/javascript" src="static/doctools.js"></script>
+    <script type="text/javascript" src="static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="Class Documentation" href="autodoc.html" />
+    <link rel="prev" title="Getting Started" href="gettingstarted.html" />
+   
+  <link rel="stylesheet" href="static/custom.css" type="text/css" />
+  
+  
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          
+
+          <div class="body" role="main">
+            
+  <div class="section" id="stratigraphic-hex-mesh-tutorial">
+<h1>Stratigraphic Hex Mesh Tutorial<a class="headerlink" href="#stratigraphic-hex-mesh-tutorial" title="Permalink to this headline">¶</a></h1>
+<p>Written by Guoyan Jiang (<a class="reference external" href="mailto:gyjiang&#37;&#52;&#48;whu&#46;edu&#46;cn">gyjiang<span>&#64;</span>whu<span>&#46;</span>edu<span>&#46;</span>cn</a>) with technical support from Dylan Harp (<a class="reference external" href="mailto:dharp&#37;&#52;&#48;lanl&#46;gov">dharp<span>&#64;</span>lanl<span>&#46;</span>gov</a>) and Terry Miller (<a class="reference external" href="mailto:tamiller&#37;&#52;&#48;lanl&#46;gov">tamiller<span>&#64;</span>lanl<span>&#46;</span>gov</a>).
+The associated LaGriT tutorial is <a class="reference external" href="https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html">here</a>.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># -*- coding: utf-8</span>
+<span class="c1"># This script is the PyLaGriT version of LaGriT tutorial example at</span>
+<span class="c1"># https://lanl.github.io/LaGriT/pages/tutorial/stratigraphy/index.html.</span>
+<span class="c1"># Written by Guoyan Jiang (gyjiang@whu.edu.cn) with technical support</span>
+<span class="c1"># from Dylan Harp (dharp@lanl.gov) and Terry Miller (tamiller@lanl.gov). </span>
+
+<span class="c1"># Import PyLaGriT class from pylagrit module</span>
+<span class="kn">from</span> <span class="nn">pylagrit</span> <span class="k">import</span> <span class="n">PyLaGriT</span>
+<span class="kn">import</span> <span class="nn">numpy</span>
+
+<span class="c1"># Variables</span>
+<span class="n">maxX</span>  <span class="o">=</span> <span class="mi">4000</span>              <span class="c1"># Max value in x direction</span>
+<span class="n">maxY</span>  <span class="o">=</span> <span class="mi">4000</span>              <span class="c1"># Max value in y direction</span>
+<span class="n">maxZ</span>  <span class="o">=</span> <span class="mi">3000</span>              <span class="c1"># Max value in z direction</span>
+<span class="n">numX</span> <span class="o">=</span> <span class="mi">51</span>                 <span class="c1"># Number of points in x direction</span>
+<span class="n">numY</span> <span class="o">=</span> <span class="mi">51</span>                 <span class="c1"># Number of points in y direction</span>
+<span class="n">numZ</span> <span class="o">=</span> <span class="mi">26</span>                 <span class="c1"># Number of points in z direction</span>
+
+<span class="c1"># Create PyLaGriT object</span>
+<span class="c1"># This assumes that pylagritrc is being used so that lagrit_exe option does not need to be specified</span>
+<span class="n">lg</span> <span class="o">=</span> <span class="n">PyLaGriT</span><span class="p">()</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 01 Built HEX Mesh</span>
+<span class="c1">#********************************************</span>
+<span class="c1"># Create mesh object </span>
+<span class="n">mo</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_hex</span><span class="p">()</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">createpts_brick_xyz</span><span class="p">((</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="n">numZ</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="n">maxX</span><span class="p">,</span> <span class="n">maxY</span><span class="p">,</span> <span class="n">maxZ</span><span class="p">))</span>
+
+<span class="c1"># Save the mesh object</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_hex_01.inp&#39;</span><span class="p">)</span>
+
+<span class="c1"># Set vertices (imt) and cells (itetlcr) to 1</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+<span class="c1"># Set node type from connectivity of mesh</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 02 Use pset’s to identify (for setting boundary conditions, </span>
+<span class="c1"># initial conditions, etc.) a set of vertices on the top </span>
+<span class="c1"># surface of the mesh</span>
+<span class="c1">#********************************************</span>
+<span class="c1"># Create a pset named p_top, which contains all nodes (stride = 1 0 0) </span>
+<span class="c1"># where the node’s Z value (zic) is greater than or equal to (ge) the top of the mesh (maxZ) </span>
+<span class="n">pset0</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;zic&#39;</span><span class="p">,</span> <span class="n">maxZ</span><span class="p">,</span> <span class="s1">&#39;ge&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;p_top&#39;</span><span class="p">)</span>
+
+<span class="c1"># Define three cylindrical objects</span>
+<span class="n">pset1</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_geom</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="p">(</span><span class="mi">1100</span><span class="p">,</span><span class="mi">360</span><span class="p">,</span><span class="mi">10000</span><span class="p">),</span> <span class="p">(</span><span class="mi">1500</span><span class="p">,</span><span class="mi">1500</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;rtz&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;p_circle1&#39;</span><span class="p">)</span>
+<span class="n">pset2</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_geom</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="p">(</span><span class="mi">1100</span><span class="p">,</span><span class="mi">360</span><span class="p">,</span><span class="mi">10000</span><span class="p">),</span> <span class="p">(</span><span class="mi">2500</span><span class="p">,</span><span class="mi">2500</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;rtz&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;p_circle2&#39;</span><span class="p">)</span>
+<span class="n">pset3</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_geom</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">),</span> <span class="p">(</span><span class="mi">1100</span><span class="p">,</span><span class="mi">360</span><span class="p">,</span><span class="mi">10000</span><span class="p">),</span> <span class="p">(</span><span class="mi">2500</span><span class="p">,</span><span class="mi">1500</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;rtz&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;p_circle3&#39;</span><span class="p">)</span>
+
+<span class="c1"># Intersect four psets, points belonging to the union of all given sets are preserved into the pset p_region</span>
+<span class="n">pset4</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_inter</span><span class="p">([</span><span class="n">pset0</span><span class="p">,</span> <span class="n">pset1</span><span class="p">,</span> <span class="n">pset2</span><span class="p">,</span> <span class="n">pset3</span><span class="p">],</span> <span class="s1">&#39;p_region&#39;</span><span class="p">)</span>
+
+<span class="c1"># Map psets to an attribute</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">addatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="n">vtype</span><span class="o">=</span><span class="s1">&#39;vint&#39;</span><span class="p">,</span> <span class="n">rank</span><span class="o">=</span><span class="s1">&#39;scalar&#39;</span><span class="p">)</span>     <span class="c1"># Creat a node-based attribute id_top_region within the mesh object</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>              <span class="c1">#Fill the entire attribute with 1</span>
+<span class="n">pset1</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>           <span class="c1">#Color all nodes in the pset p_circle1 with the value 2</span>
+<span class="n">pset2</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="n">pset3</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
+<span class="n">pset4</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_top_region&#39;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+
+<span class="c1"># Release the psets from memory</span>
+<span class="n">pset0</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">pset1</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">pset2</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">pset3</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">pset4</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 03 Build some surfaces to define stratigraphy.</span>
+<span class="c1"># In a real model, the surfaces would come from some geologic framework model</span>
+<span class="c1"># and would define geologic or hydro-geologic horizons and topography.</span>
+<span class="c1">#********************************************</span>
+<span class="n">mosurf1</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>       <span class="c1"># Create the top surface</span>
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1500</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">2500</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf1</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf1.paraview()</span>
+<span class="n">mosurf1</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf1</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_surf1_quad.inp&#39;</span><span class="p">)</span>
+
+<span class="n">mosurf2</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>       <span class="c1"># Create the bottom surface</span>
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1800</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">2100</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">2800</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">800</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf2</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf2.paraview()</span>
+<span class="n">mosurf2</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf2</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_surf2_quad.inp&#39;</span><span class="p">)</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 04 Use the surfaces to define regions and set</span>
+<span class="c1"># vertex and cell ids</span>
+<span class="c1">#********************************************</span>
+<span class="c1"># Define Regions</span>
+<span class="n">sf1</span> <span class="o">=</span> <span class="n">mosurf1</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf1&#39;</span><span class="p">)</span>
+<span class="n">sf2</span> <span class="o">=</span> <span class="n">mosurf2</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf2&#39;</span><span class="p">)</span>
+
+<span class="n">r1</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1</span><span class="p">))</span>
+<span class="n">r2</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2</span><span class="p">))</span>
+<span class="n">r3</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2</span><span class="p">))</span>
+
+<span class="n">mosurf1</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mosurf2</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+
+<span class="c1"># Create Eltsets and PSets from Regions</span>
+<span class="n">pset1</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r1</span><span class="p">)</span>
+<span class="n">pset2</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r2</span><span class="p">)</span>
+<span class="n">pset3</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r3</span><span class="p">)</span>
+
+<span class="n">eltset1</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r1</span><span class="p">)</span>
+<span class="n">eltset2</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r2</span><span class="p">)</span>
+<span class="n">eltset3</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r3</span><span class="p">)</span>
+
+<span class="c1">#Set Attributes from Eltsets and PSets</span>
+<span class="n">pset1</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">pset2</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="n">pset3</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+
+<span class="n">eltset1</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">eltset2</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="n">eltset3</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 05 Build a fault surface and define stratigraphy </span>
+<span class="c1"># on each side of the fault</span>
+<span class="c1">#********************************************</span>
+<span class="c1"># Create fault surface and surfaces to either side of fault</span>
+<span class="n">mosurf1_fminus</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>       
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1500</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">2500</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf1_fminus</span> <span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf1_fminus .paraview()</span>
+<span class="n">mosurf1_fminus</span> <span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf1_fminus</span> <span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_s1_fm.inp&#39;</span><span class="p">)</span>
+
+<span class="n">mosurf2_fminus</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>      
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1800</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">2100</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">2800</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">800</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf2_fminus</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf2_fminus.paraview()</span>
+<span class="n">mosurf2_fminus</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf2_fminus</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_s2_fm.inp&#39;</span><span class="p">)</span>
+
+<span class="n">mosurf1_fplus</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>      
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1400</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">1900</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">2900</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">900</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf1_fplus</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf1_fplus.paraview()</span>
+<span class="n">mosurf1_fplus</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf1_fplus</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;mosurf1_fplus.inp&#39;</span><span class="p">)</span>
+
+<span class="n">mosurf2_fplus</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>      
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">2200</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">2500</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">3200</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mi">1200</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf2_fplus</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf2_fplus.paraview()</span>
+<span class="n">mosurf2_fplus</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf2_fplus</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;mosurf2_fplus.inp&#39;</span><span class="p">)</span>
+
+<span class="n">mosurf_fault</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_qua</span><span class="p">()</span>      
+<span class="n">p1</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.e4</span><span class="p">)</span>
+<span class="n">p2</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.e4</span><span class="p">)</span>
+<span class="n">p3</span> <span class="o">=</span> <span class="p">(</span><span class="mi">4020</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mf">1.e4</span><span class="p">)</span>
+<span class="n">p4</span> <span class="o">=</span> <span class="p">(</span><span class="o">-</span><span class="mi">20</span><span class="p">,</span> <span class="mi">4020</span><span class="p">,</span> <span class="mf">1.e4</span><span class="p">)</span>
+<span class="n">pts</span> <span class="o">=</span> <span class="p">[</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">,</span> <span class="n">p3</span><span class="p">,</span> <span class="n">p4</span><span class="p">]</span>
+<span class="n">nnodes</span> <span class="o">=</span> <span class="p">(</span><span class="n">numX</span><span class="p">,</span> <span class="n">numY</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">mosurf_fault</span><span class="o">.</span><span class="n">quadxy</span><span class="p">(</span><span class="n">nnodes</span><span class="p">,</span> <span class="n">pts</span><span class="p">)</span>
+<span class="c1">#mosurf_fault.paraview()</span>
+<span class="n">mosurf_fault</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mosurf_fault</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;mosurf_fault.inp&#39;</span><span class="p">)</span>
+
+<span class="c1"># Define geometry of hydrostratigraphic model</span>
+<span class="n">sf1_fm</span> <span class="o">=</span> <span class="n">mosurf1_fminus</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf1_fm&#39;</span><span class="p">)</span>
+<span class="n">sf2_fm</span> <span class="o">=</span> <span class="n">mosurf2_fminus</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf2_fm&#39;</span><span class="p">)</span>
+<span class="n">sf1_fp</span> <span class="o">=</span> <span class="n">mosurf1_fplus</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf1_fp&#39;</span><span class="p">)</span>
+<span class="n">sf2_fp</span> <span class="o">=</span> <span class="n">mosurf2_fplus</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf2_fp&#39;</span><span class="p">)</span>
+<span class="n">sf_f</span> <span class="o">=</span> <span class="n">mosurf_fault</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf_f&#39;</span><span class="p">)</span>
+
+<span class="n">r1_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1_fm</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+<span class="n">r2_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1_fm</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2_fm</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+<span class="n">r3_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2_fm</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+<span class="n">r1_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1_fp</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+<span class="n">r2_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf1_fp</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;le &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2_fp</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+<span class="n">r3_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf2_fp</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39; and &#39;</span> <span class="o">+</span> <span class="s1">&#39;gt &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_f</span><span class="p">))</span>
+
+<span class="n">mosurf1_fminus</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mosurf2_fminus</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mosurf1_fplus</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mosurf2_fplus</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mosurf_fault</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+
+<span class="c1"># Set fault node and element materials</span>
+<span class="n">pset1_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r1_fm</span><span class="p">)</span>
+<span class="n">pset2_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r2_fm</span><span class="p">)</span>
+<span class="n">pset3_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r3_fm</span><span class="p">)</span>
+<span class="n">pset1_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r1_fp</span><span class="p">)</span>
+<span class="n">pset2_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r2_fp</span><span class="p">)</span>
+<span class="n">pset3_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r3_fp</span><span class="p">)</span>
+
+<span class="n">eltset1_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r1_fm</span><span class="p">)</span>
+<span class="n">eltset2_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r2_fm</span><span class="p">)</span>
+<span class="n">eltset3_fm</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r3_fm</span><span class="p">)</span>
+<span class="n">eltset1_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r1_fp</span><span class="p">)</span>
+<span class="n">eltset2_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r2_fp</span><span class="p">)</span>
+<span class="n">eltset3_fp</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r3_fp</span><span class="p">)</span>
+
+<span class="c1">#Set Attributes from Eltsets and PSets</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
+
+<span class="n">pset1_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">pset2_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="n">pset3_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="n">pset1_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
+<span class="n">pset2_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+<span class="n">pset3_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span>
+
+<span class="n">eltset1_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">eltset2_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="n">eltset3_fm</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
+<span class="n">eltset1_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>
+<span class="n">eltset2_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+<span class="n">eltset3_fp</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">6</span><span class="p">)</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 06 Define a polyline and truncate the exterior boundary of the mesh with the polyline</span>
+<span class="c1">#********************************************</span>
+<span class="c1"># Read boundary polygon file</span>
+<span class="n">mobndry</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">read</span><span class="p">(</span><span class="s1">&#39;basin_bnd_ply_rescale.inp&#39;</span><span class="p">)</span>
+
+<span class="c1"># Extrude the polyline into a vertical surface</span>
+<span class="n">mofence</span> <span class="o">=</span> <span class="n">mobndry</span><span class="o">.</span><span class="n">extrude</span><span class="p">(</span><span class="mi">3200</span><span class="p">,</span> <span class="s1">&#39;const&#39;</span><span class="p">,</span> <span class="s1">&#39;volume&#39;</span><span class="p">,</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">1</span><span class="p">])</span>
+
+<span class="n">mobndry</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="n">mofence</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+
+<span class="c1"># Translate the extrusion to make it cover the vertical extent of the hex mesh</span>
+<span class="n">mofence</span><span class="o">.</span><span class="n">trans</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="o">-</span><span class="mi">3100</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span> <span class="p">,</span><span class="mi">0</span><span class="p">))</span>
+
+<span class="n">mofence</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="c1">#mofence.paraview()</span>
+<span class="c1">#mofence.dump(&#39;3D_vertical_surface.inp&#39;)</span>
+<span class="c1">#mo.dump(&#39;cube.inp&#39;)</span>
+
+<span class="c1"># Truncate mesh</span>
+<span class="n">sf_bndry</span> <span class="o">=</span> <span class="n">mofence</span><span class="o">.</span><span class="n">surface</span><span class="p">(</span><span class="s1">&#39;sf_bndry&#39;</span><span class="p">)</span>
+<span class="n">r_bndry</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">region</span><span class="p">(</span><span class="s1">&#39;ge &#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">sf_bndry</span><span class="p">))</span>
+<span class="n">pset_bndry</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_region</span><span class="p">(</span><span class="n">r_bndry</span><span class="p">)</span>
+
+<span class="n">mobndry</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mofence</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+
+<span class="c1"># Method 1: Only remove a cell if ALL vertices are outside</span>
+<span class="n">e_delete1</span> <span class="o">=</span> <span class="n">pset_bndry</span><span class="o">.</span><span class="n">eltset</span><span class="p">(</span><span class="s1">&#39;exclusive&#39;</span><span class="p">)</span>
+
+<span class="c1"># Method 2: Remove a cell if the centroid (average of all vertices) is outside</span>
+<span class="n">e_delete2</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_region</span><span class="p">(</span><span class="n">r_bndry</span><span class="p">)</span>
+
+<span class="c1"># Method 3: Remove a cell if one or more vertices are outside</span>
+<span class="n">e_delete3</span> <span class="o">=</span> <span class="n">pset_bndry</span><span class="o">.</span><span class="n">eltset</span><span class="p">(</span><span class="s1">&#39;inclusive&#39;</span><span class="p">)</span>
+
+<span class="c1">#mo.addatt(&#39;id_in_out_bndry&#39;, vtype=&#39;vint&#39;, rank=&#39;scalar&#39;, length=&#39;nelements&#39;)</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">add_element_attribute</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="n">vtype</span><span class="o">=</span><span class="s1">&#39;vint&#39;</span><span class="p">)</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>              <span class="c1">#Fill the entire attribute with 4</span>
+<span class="n">e_delete3</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>          
+<span class="n">e_delete2</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="n">e_delete1</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+<span class="n">eltset4</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_attribute</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">4</span><span class="p">,</span> <span class="s1">&#39;eq&#39;</span><span class="p">)</span>
+<span class="n">eltset3</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_attribute</span><span class="p">(</span><span class="s1">&#39;id_in_out_bndry&#39;</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="s1">&#39;eq&#39;</span><span class="p">)</span>
+<span class="c1">#eltset2 = mo.eltset_attribute(&#39;id_in_out_bndry&#39;, 2, &#39;eq&#39;)</span>
+<span class="c1">#eltset1 = mo.eltset_attribute(&#39;id_in_out_bndry&#39;, 1, &#39;eq&#39;)</span>
+
+<span class="n">mo</span><span class="o">.</span><span class="n">rmpoint_eltset</span><span class="p">(</span><span class="n">eltset4</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="kc">False</span><span class="p">)</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">rmpoint_eltset</span><span class="p">(</span><span class="n">eltset3</span><span class="p">,</span> <span class="kc">True</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 07 Refine the mesh around the fault</span>
+<span class="c1">#********************************************</span>
+<span class="n">f_zone</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">intersect_elements</span><span class="p">(</span><span class="n">sf_f</span><span class="p">,</span> <span class="s1">&#39;f_zone&#39;</span><span class="p">)</span>
+<span class="n">fz_i</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_attribute</span><span class="p">(</span><span class="s1">&#39;f_zone&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="s1">&#39;gt&#39;</span><span class="p">)</span>     <span class="c1">#Non-zero indicates intersection</span>
+<span class="n">fz_i</span><span class="o">.</span><span class="n">refine</span><span class="p">()</span>
+
+<span class="n">mo</span><span class="o">.</span><span class="n">delatt</span><span class="p">(</span><span class="s1">&#39;f_zone&#39;</span><span class="p">)</span>
+
+<span class="n">mo</span><span class="o">.</span><span class="n">status</span> <span class="p">(</span><span class="n">brief</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+<span class="c1">#sf_f.delete()</span>
+<span class="c1">#sf1_fm.delete()</span>
+<span class="c1">#sf2_fm.delete()</span>
+<span class="c1">#sf1_fp.delete()</span>
+<span class="c1">#sf1_fp.delete()</span>
+<span class="c1">#sf_bndry.delete()</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 08 Insert a couple of &#39;wells&#39; by refining the mesh and identifying a line of nodes</span>
+<span class="c1"># that will be the well source/sink for boundary conditions.</span>
+<span class="c1">#********************************************</span>
+<span class="n">Well1X</span> <span class="o">=</span> <span class="mf">1234.56</span>
+<span class="n">Well1Y</span> <span class="o">=</span> <span class="mf">1987.65</span>
+<span class="n">Well2X</span> <span class="o">=</span> <span class="mf">2243.21</span>
+<span class="n">Well2Y</span> <span class="o">=</span> <span class="mf">1212.34</span>
+<span class="n">Radius</span> <span class="o">=</span> <span class="mi">25</span>
+<span class="n">NRadius</span> <span class="o">=</span> <span class="mi">2</span>
+
+<span class="c1">#Well 1</span>
+<span class="n">mowell1</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_tet</span><span class="p">()</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">createpts_rtz</span><span class="p">((</span><span class="n">NRadius</span><span class="p">,</span> <span class="mi">9</span><span class="p">,</span> <span class="n">numZ</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">3100</span><span class="p">),</span> <span class="p">(</span><span class="n">Radius</span><span class="p">,</span> <span class="mi">360</span><span class="p">,</span> <span class="mi">1500</span><span class="p">))</span>   <span class="c1">#Create a cylindrical point cloud </span>
+
+<span class="n">mowell1</span><span class="o">.</span><span class="n">filter</span><span class="p">()</span>              <span class="c1"># Filter (delete) points that are too close ( default distance &lt;=1.e-16) or duplicate points</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">rmpoint_compress</span><span class="p">()</span>    <span class="c1"># Remove all marked nodes and correct the itet array</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+<span class="n">mowell1</span><span class="o">.</span><span class="n">connect</span><span class="p">()</span>             <span class="c1"># Connect the point cloud</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+
+<span class="n">mowell1</span><span class="o">.</span><span class="n">trans</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="n">Well1X</span><span class="p">,</span> <span class="n">Well1Y</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="c1">#mowell1.paraview()</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_well1.inp&#39;</span><span class="p">)</span>
+
+<span class="c1">#Well 2</span>
+<span class="n">mowell2</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create_tet</span><span class="p">()</span>
+<span class="n">mowell2</span><span class="o">.</span><span class="n">createpts_rtz</span><span class="p">((</span><span class="n">NRadius</span><span class="p">,</span> <span class="mi">9</span><span class="p">,</span> <span class="n">numZ</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">3100</span><span class="p">),</span> <span class="p">(</span><span class="n">Radius</span><span class="p">,</span> <span class="mi">360</span><span class="p">,</span> <span class="mi">2200</span><span class="p">))</span>   
+
+<span class="n">mowell2</span><span class="o">.</span><span class="n">filter</span><span class="p">()</span>              
+<span class="n">mowell2</span><span class="o">.</span><span class="n">rmpoint_compress</span><span class="p">()</span>    
+<span class="n">mowell2</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+<span class="n">mowell2</span><span class="o">.</span><span class="n">connect</span><span class="p">()</span>             
+<span class="n">mowell2</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+<span class="n">mowell2</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+
+<span class="n">mowell2</span><span class="o">.</span><span class="n">trans</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="n">Well2X</span><span class="p">,</span> <span class="n">Well2Y</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+<span class="n">mowell2</span><span class="o">.</span><span class="n">minmax_xyz</span><span class="p">()</span>
+<span class="c1">#mowell2.paraview()</span>
+<span class="n">mowell2</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_well2.inp&#39;</span><span class="p">)</span>
+
+<span class="c1"># Join the two distinct wells into a single mesh object </span>
+<span class="n">mowells</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">merge</span><span class="p">([</span><span class="n">mowell1</span><span class="p">,</span> <span class="n">mowell2</span><span class="p">])</span>
+<span class="n">mowells</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;tmp_wells.inp&#39;</span><span class="p">)</span> 
+<span class="c1">#mowells.paraview()</span>
+
+<span class="c1"># Refine the mo around the wells</span>
+<span class="c1"># First pass refinement</span>
+<span class="n">w_zone</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">intersect_elements</span><span class="p">(</span><span class="n">mowells</span><span class="p">,</span> <span class="s1">&#39;w_zone&#39;</span><span class="p">)</span>
+<span class="n">wz_i</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_attribute</span><span class="p">(</span><span class="s1">&#39;w_zone&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="s1">&#39;gt&#39;</span><span class="p">)</span>     <span class="c1">#Non-zero indicates intersection</span>
+<span class="n">wz_i</span><span class="o">.</span><span class="n">refine</span><span class="p">()</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;w_zone&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+<span class="c1">#wz_i.delete()</span>
+
+<span class="c1"># Second pass refinement</span>
+<span class="n">w_zone</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">intersect_elements</span><span class="p">(</span><span class="n">mowells</span><span class="p">,</span> <span class="s1">&#39;w_zone&#39;</span><span class="p">)</span>
+<span class="n">wz_i</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">eltset_attribute</span><span class="p">(</span><span class="s1">&#39;w_zone&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="s1">&#39;gt&#39;</span><span class="p">)</span>     <span class="c1">#Non-zero indicates intersection</span>
+<span class="n">wz_i</span><span class="o">.</span><span class="n">refine</span><span class="p">()</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;w_zone&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+<span class="c1">#wz_i.delete()</span>
+
+<span class="n">mohex</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">grid2grid_tree_to_fe</span><span class="p">()</span>                         <span class="c1">#Quadtree or octree grid to grid</span>
+
+<span class="c1">#mo.status (brief=True)</span>
+
+<span class="c1"># Identify the column of vertices closest to the well center.</span>
+<span class="c1">#Well1</span>
+<span class="n">mo_pts1</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create</span><span class="p">()</span>
+<span class="n">mo_pts1</span><span class="o">.</span><span class="n">createpts_rtz</span><span class="p">((</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1000</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">3100</span><span class="p">),</span> <span class="p">(</span><span class="n">Radius</span><span class="p">,</span> <span class="mi">360</span><span class="p">,</span> <span class="mi">2200</span><span class="p">))</span>   
+<span class="n">mo_pts1</span><span class="o">.</span><span class="n">trans</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="n">Well1X</span><span class="p">,</span> <span class="n">Well1Y</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+
+<span class="c1">#Well2</span>
+<span class="n">mo_pts2</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">create</span><span class="p">()</span>
+<span class="n">mo_pts2</span><span class="o">.</span><span class="n">createpts_rtz</span><span class="p">((</span><span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">1000</span><span class="p">),</span> <span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">3100</span><span class="p">),</span> <span class="p">(</span><span class="n">Radius</span><span class="p">,</span> <span class="mi">360</span><span class="p">,</span> <span class="mi">2200</span><span class="p">))</span>   
+<span class="n">mo_pts2</span><span class="o">.</span><span class="n">trans</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">),</span> <span class="p">(</span><span class="n">Well2X</span><span class="p">,</span> <span class="n">Well2Y</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
+
+<span class="n">mo_pts</span> <span class="o">=</span> <span class="n">lg</span><span class="o">.</span><span class="n">merge</span><span class="p">([</span><span class="n">mo_pts1</span><span class="p">,</span> <span class="n">mo_pts2</span><span class="p">])</span>
+<span class="n">mo_pts</span><span class="o">.</span><span class="n">filter</span><span class="p">()</span>              
+<span class="n">mo_pts</span><span class="o">.</span><span class="n">rmpoint_compress</span><span class="p">()</span>   
+
+<span class="c1"># Compute a distance field attribute</span>
+<span class="n">mo</span><span class="o">.</span><span class="n">compute_distance</span><span class="p">(</span><span class="n">mo_pts</span><span class="p">,</span> <span class="n">option</span><span class="o">=</span><span class="s1">&#39;distance_field&#39;</span><span class="p">,</span> <span class="n">attname</span><span class="o">=</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">)</span>
+
+<span class="n">mo_pts1</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mo_pts2</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mo_pts</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mowell1</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mowell2</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+<span class="n">mowells</span><span class="o">.</span><span class="n">delete</span><span class="p">()</span>
+
+<span class="c1"># Describe all nodes within 32, 16, 8, 4, 2 and 1 meters of the wells.</span>
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell1&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_01.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">2.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell2&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_02.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">4.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell4&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_04.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">8.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell8&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_08.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">16.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell16&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_16.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">pwell</span> <span class="o">=</span> <span class="n">mo</span><span class="o">.</span><span class="n">pset_attribute</span><span class="p">(</span><span class="s1">&#39;dfield_well&#39;</span><span class="p">,</span> <span class="mf">32.0</span><span class="p">,</span> <span class="s1">&#39;le&#39;</span><span class="p">,</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">),</span> <span class="s1">&#39;pwell32&#39;</span><span class="p">)</span>
+<span class="n">pwell</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;zone_radius_32.0.zone&#39;</span><span class="p">)</span>
+
+<span class="n">mo</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;Hex_mesh.inp&#39;</span><span class="p">)</span> 
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 09 Convert hex mesh to tet mesh</span>
+<span class="c1">#********************************************</span>
+<span class="n">motet</span> <span class="o">=</span> <span class="n">mohex</span><span class="o">.</span><span class="n">copypts</span><span class="p">()</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itp&#39;</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">option1</span><span class="o">=</span><span class="s1">&#39;check_interface&#39;</span><span class="p">)</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+
+<span class="n">motet</span><span class="o">.</span><span class="n">interpolate_voronoi</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">,</span> <span class="n">mohex</span><span class="p">,</span> <span class="s1">&#39;imt&#39;</span><span class="p">)</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">interpolate_map</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="n">mohex</span><span class="p">,</span> <span class="s1">&#39;itetclr&#39;</span><span class="p">)</span>
+
+<span class="c1">#Remove all nodes and elements with imt and itetclr values of 7</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">rmmat</span><span class="p">(</span><span class="mi">7</span><span class="p">)</span>
+<span class="c1">#pset7 = motet.pset_attribute(&#39;imt&#39;, 7, &#39;eq&#39;, (1,0,0), &#39;pset7&#39;)</span>
+<span class="c1">#motet.rmpoint_pset(pset7)</span>
+<span class="c1">#eltset7 = motet.eltset_attribute(&#39;itetclr&#39;, 7, &#39;eq&#39;)</span>
+<span class="c1">#motet.rmpoint_eltset(eltset7, True, True)</span>
+
+<span class="n">motet</span><span class="o">.</span><span class="n">rmpoint_compress</span><span class="p">()</span> 
+<span class="n">motet</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+
+<span class="c1"># Visualize connected mesh using ParaView</span>
+<span class="c1"># This assumes that pylagritrc is being used so that exe option does not need to be specified</span>
+<span class="c1">#motet.paraview()</span>
+
+<span class="n">motet</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="s1">&#39;Tet_mesh.inp&#39;</span><span class="p">)</span>
+
+<span class="c1">#********************************************</span>
+<span class="c1"># 10 Write tet mesh files for FEHM</span>
+<span class="c1"># FEHM uses node based materials and properties</span>
+<span class="c1">#********************************************</span>
+<span class="c1">#motet.resetpts_parent()</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">filter</span><span class="p">()</span> 
+<span class="n">motet</span><span class="o">.</span><span class="n">rmpoint_compress</span><span class="p">()</span> 
+<span class="n">motet</span><span class="o">.</span><span class="n">resetpts_itp</span><span class="p">()</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">minmax</span><span class="p">(</span><span class="s1">&#39;imt&#39;</span><span class="p">)</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">setatt</span><span class="p">(</span><span class="s1">&#39;itetclr&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="c1">#motet. tri_mesh_output_prep()</span>
+<span class="n">motet</span><span class="o">.</span><span class="n">dump_fehm</span><span class="p">(</span><span class="s1">&#39;Example3&#39;</span><span class="p">)</span>
+
+
+
+</pre></div>
+</div>
+<p>The final result:</p>
+<img alt="images/stratigraphy.png" src="images/stratigraphy.png" />
+</div>
+
+
+          </div>
+          
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="index.html">PyLaGriT</a></h1>
+
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+<h3>Navigation</h3>
+<ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Stratigraphic Hex Mesh Tutorial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="autodoc.html">Class Documentation</a></li>
+</ul>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="index.html">Documentation overview</a><ul>
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+    
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+</html>

docs/pylagrit/original/static/underscore-1.3.1.js

@@ -0,0 +1,999 @@
+//     Underscore.js 1.3.1
+//     (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+//     Underscore is freely distributable under the MIT license.
+//     Portions of Underscore are inspired or borrowed from Prototype,
+//     Oliver Steele's Functional, and John Resig's Micro-Templating.
+//     For all details and documentation:
+//     http://documentcloud.github.com/underscore
+
+(function() {
+
+  // Baseline setup
+  // --------------
+
+  // Establish the root object, `window` in the browser, or `global` on the server.
+  var root = this;
+
+  // Save the previous value of the `_` variable.
+  var previousUnderscore = root._;
+
+  // Establish the object that gets returned to break out of a loop iteration.
+  var breaker = {};
+
+  // Save bytes in the minified (but not gzipped) version:
+  var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
+
+  // Create quick reference variables for speed access to core prototypes.
+  var slice            = ArrayProto.slice,
+      unshift          = ArrayProto.unshift,
+      toString         = ObjProto.toString,
+      hasOwnProperty   = ObjProto.hasOwnProperty;
+
+  // All **ECMAScript 5** native function implementations that we hope to use
+  // are declared here.
+  var
+    nativeForEach      = ArrayProto.forEach,
+    nativeMap          = ArrayProto.map,
+    nativeReduce       = ArrayProto.reduce,
+    nativeReduceRight  = ArrayProto.reduceRight,
+    nativeFilter       = ArrayProto.filter,
+    nativeEvery        = ArrayProto.every,
+    nativeSome         = ArrayProto.some,
+    nativeIndexOf      = ArrayProto.indexOf,
+    nativeLastIndexOf  = ArrayProto.lastIndexOf,
+    nativeIsArray      = Array.isArray,
+    nativeKeys         = Object.keys,
+    nativeBind         = FuncProto.bind;
+
+  // Create a safe reference to the Underscore object for use below.
+  var _ = function(obj) { return new wrapper(obj); };
+
+  // Export the Underscore object for **Node.js**, with
+  // backwards-compatibility for the old `require()` API. If we're in
+  // the browser, add `_` as a global object via a string identifier,
+  // for Closure Compiler "advanced" mode.
+  if (typeof exports !== 'undefined') {
+    if (typeof module !== 'undefined' && module.exports) {
+      exports = module.exports = _;
+    }
+    exports._ = _;
+  } else {
+    root['_'] = _;
+  }
+
+  // Current version.
+  _.VERSION = '1.3.1';
+
+  // Collection Functions
+  // --------------------
+
+  // The cornerstone, an `each` implementation, aka `forEach`.
+  // Handles objects with the built-in `forEach`, arrays, and raw objects.
+  // Delegates to **ECMAScript 5**'s native `forEach` if available.
+  var each = _.each = _.forEach = function(obj, iterator, context) {
+    if (obj == null) return;
+    if (nativeForEach && obj.forEach === nativeForEach) {
+      obj.forEach(iterator, context);
+    } else if (obj.length === +obj.length) {
+      for (var i = 0, l = obj.length; i < l; i++) {
+        if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
+      }
+    } else {
+      for (var key in obj) {
+        if (_.has(obj, key)) {
+          if (iterator.call(context, obj[key], key, obj) === breaker) return;
+        }
+      }
+    }
+  };
+
+  // Return the results of applying the iterator to each element.
+  // Delegates to **ECMAScript 5**'s native `map` if available.
+  _.map = _.collect = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
+    each(obj, function(value, index, list) {
+      results[results.length] = iterator.call(context, value, index, list);
+    });
+    if (obj.length === +obj.length) results.length = obj.length;
+    return results;
+  };
+
+  // **Reduce** builds up a single result from a list of values, aka `inject`,
+  // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
+  _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduce && obj.reduce === nativeReduce) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
+    }
+    each(obj, function(value, index, list) {
+      if (!initial) {
+        memo = value;
+        initial = true;
+      } else {
+        memo = iterator.call(context, memo, value, index, list);
+      }
+    });
+    if (!initial) throw new TypeError('Reduce of empty array with no initial value');
+    return memo;
+  };
+
+  // The right-associative version of reduce, also known as `foldr`.
+  // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
+  _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
+    var initial = arguments.length > 2;
+    if (obj == null) obj = [];
+    if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
+      if (context) iterator = _.bind(iterator, context);
+      return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
+    }
+    var reversed = _.toArray(obj).reverse();
+    if (context && !initial) iterator = _.bind(iterator, context);
+    return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
+  };
+
+  // Return the first value which passes a truth test. Aliased as `detect`.
+  _.find = _.detect = function(obj, iterator, context) {
+    var result;
+    any(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) {
+        result = value;
+        return true;
+      }
+    });
+    return result;
+  };
+
+  // Return all the elements that pass a truth test.
+  // Delegates to **ECMAScript 5**'s native `filter` if available.
+  // Aliased as `select`.
+  _.filter = _.select = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
+    each(obj, function(value, index, list) {
+      if (iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Return all the elements for which a truth test fails.
+  _.reject = function(obj, iterator, context) {
+    var results = [];
+    if (obj == null) return results;
+    each(obj, function(value, index, list) {
+      if (!iterator.call(context, value, index, list)) results[results.length] = value;
+    });
+    return results;
+  };
+
+  // Determine whether all of the elements match a truth test.
+  // Delegates to **ECMAScript 5**'s native `every` if available.
+  // Aliased as `all`.
+  _.every = _.all = function(obj, iterator, context) {
+    var result = true;
+    if (obj == null) return result;
+    if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
+    each(obj, function(value, index, list) {
+      if (!(result = result && iterator.call(context, value, index, list))) return breaker;
+    });
+    return result;
+  };
+
+  // Determine if at least one element in the object matches a truth test.
+  // Delegates to **ECMAScript 5**'s native `some` if available.
+  // Aliased as `any`.
+  var any = _.some = _.any = function(obj, iterator, context) {
+    iterator || (iterator = _.identity);
+    var result = false;
+    if (obj == null) return result;
+    if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
+    each(obj, function(value, index, list) {
+      if (result || (result = iterator.call(context, value, index, list))) return breaker;
+    });
+    return !!result;
+  };
+
+  // Determine if a given value is included in the array or object using `===`.
+  // Aliased as `contains`.
+  _.include = _.contains = function(obj, target) {
+    var found = false;
+    if (obj == null) return found;
+    if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
+    found = any(obj, function(value) {
+      return value === target;
+    });
+    return found;
+  };
+
+  // Invoke a method (with arguments) on every item in a collection.
+  _.invoke = function(obj, method) {
+    var args = slice.call(arguments, 2);
+    return _.map(obj, function(value) {
+      return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
+    });
+  };
+
+  // Convenience version of a common use case of `map`: fetching a property.
+  _.pluck = function(obj, key) {
+    return _.map(obj, function(value){ return value[key]; });
+  };
+
+  // Return the maximum element or (element-based computation).
+  _.max = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return -Infinity;
+    var result = {computed : -Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed >= result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Return the minimum element (or element-based computation).
+  _.min = function(obj, iterator, context) {
+    if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
+    if (!iterator && _.isEmpty(obj)) return Infinity;
+    var result = {computed : Infinity};
+    each(obj, function(value, index, list) {
+      var computed = iterator ? iterator.call(context, value, index, list) : value;
+      computed < result.computed && (result = {value : value, computed : computed});
+    });
+    return result.value;
+  };
+
+  // Shuffle an array.
+  _.shuffle = function(obj) {
+    var shuffled = [], rand;
+    each(obj, function(value, index, list) {
+      if (index == 0) {
+        shuffled[0] = value;
+      } else {
+        rand = Math.floor(Math.random() * (index + 1));
+        shuffled[index] = shuffled[rand];
+        shuffled[rand] = value;
+      }
+    });
+    return shuffled;
+  };
+
+  // Sort the object's values by a criterion produced by an iterator.
+  _.sortBy = function(obj, iterator, context) {
+    return _.pluck(_.map(obj, function(value, index, list) {
+      return {
+        value : value,
+        criteria : iterator.call(context, value, index, list)
+      };
+    }).sort(function(left, right) {
+      var a = left.criteria, b = right.criteria;
+      return a < b ? -1 : a > b ? 1 : 0;
+    }), 'value');
+  };
+
+  // Groups the object's values by a criterion. Pass either a string attribute
+  // to group by, or a function that returns the criterion.
+  _.groupBy = function(obj, val) {
+    var result = {};
+    var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
+    each(obj, function(value, index) {
+      var key = iterator(value, index);
+      (result[key] || (result[key] = [])).push(value);
+    });
+    return result;
+  };
+
+  // Use a comparator function to figure out at what index an object should
+  // be inserted so as to maintain order. Uses binary search.
+  _.sortedIndex = function(array, obj, iterator) {
+    iterator || (iterator = _.identity);
+    var low = 0, high = array.length;
+    while (low < high) {
+      var mid = (low + high) >> 1;
+      iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
+    }
+    return low;
+  };
+
+  // Safely convert anything iterable into a real, live array.
+  _.toArray = function(iterable) {
+    if (!iterable)                return [];
+    if (iterable.toArray)         return iterable.toArray();
+    if (_.isArray(iterable))      return slice.call(iterable);
+    if (_.isArguments(iterable))  return slice.call(iterable);
+    return _.values(iterable);
+  };
+
+  // Return the number of elements in an object.
+  _.size = function(obj) {
+    return _.toArray(obj).length;
+  };
+
+  // Array Functions
+  // ---------------
+
+  // Get the first element of an array. Passing **n** will return the first N
+  // values in the array. Aliased as `head`. The **guard** check allows it to work
+  // with `_.map`.
+  _.first = _.head = function(array, n, guard) {
+    return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
+  };
+
+  // Returns everything but the last entry of the array. Especcialy useful on
+  // the arguments object. Passing **n** will return all the values in
+  // the array, excluding the last N. The **guard** check allows it to work with
+  // `_.map`.
+  _.initial = function(array, n, guard) {
+    return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
+  };
+
+  // Get the last element of an array. Passing **n** will return the last N
+  // values in the array. The **guard** check allows it to work with `_.map`.
+  _.last = function(array, n, guard) {
+    if ((n != null) && !guard) {
+      return slice.call(array, Math.max(array.length - n, 0));
+    } else {
+      return array[array.length - 1];
+    }
+  };
+
+  // Returns everything but the first entry of the array. Aliased as `tail`.
+  // Especially useful on the arguments object. Passing an **index** will return
+  // the rest of the values in the array from that index onward. The **guard**
+  // check allows it to work with `_.map`.
+  _.rest = _.tail = function(array, index, guard) {
+    return slice.call(array, (index == null) || guard ? 1 : index);
+  };
+
+  // Trim out all falsy values from an array.
+  _.compact = function(array) {
+    return _.filter(array, function(value){ return !!value; });
+  };
+
+  // Return a completely flattened version of an array.
+  _.flatten = function(array, shallow) {
+    return _.reduce(array, function(memo, value) {
+      if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
+      memo[memo.length] = value;
+      return memo;
+    }, []);
+  };
+
+  // Return a version of the array that does not contain the specified value(s).
+  _.without = function(array) {
+    return _.difference(array, slice.call(arguments, 1));
+  };
+
+  // Produce a duplicate-free version of the array. If the array has already
+  // been sorted, you have the option of using a faster algorithm.
+  // Aliased as `unique`.
+  _.uniq = _.unique = function(array, isSorted, iterator) {
+    var initial = iterator ? _.map(array, iterator) : array;
+    var result = [];
+    _.reduce(initial, function(memo, el, i) {
+      if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
+        memo[memo.length] = el;
+        result[result.length] = array[i];
+      }
+      return memo;
+    }, []);
+    return result;
+  };
+
+  // Produce an array that contains the union: each distinct element from all of
+  // the passed-in arrays.
+  _.union = function() {
+    return _.uniq(_.flatten(arguments, true));
+  };
+
+  // Produce an array that contains every item shared between all the
+  // passed-in arrays. (Aliased as "intersect" for back-compat.)
+  _.intersection = _.intersect = function(array) {
+    var rest = slice.call(arguments, 1);
+    return _.filter(_.uniq(array), function(item) {
+      return _.every(rest, function(other) {
+        return _.indexOf(other, item) >= 0;
+      });
+    });
+  };
+
+  // Take the difference between one array and a number of other arrays.
+  // Only the elements present in just the first array will remain.
+  _.difference = function(array) {
+    var rest = _.flatten(slice.call(arguments, 1));
+    return _.filter(array, function(value){ return !_.include(rest, value); });
+  };
+
+  // Zip together multiple lists into a single array -- elements that share
+  // an index go together.
+  _.zip = function() {
+    var args = slice.call(arguments);
+    var length = _.max(_.pluck(args, 'length'));
+    var results = new Array(length);
+    for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
+    return results;
+  };
+
+  // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
+  // we need this function. Return the position of the first occurrence of an
+  // item in an array, or -1 if the item is not included in the array.
+  // Delegates to **ECMAScript 5**'s native `indexOf` if available.
+  // If the array is large and already in sort order, pass `true`
+  // for **isSorted** to use binary search.
+  _.indexOf = function(array, item, isSorted) {
+    if (array == null) return -1;
+    var i, l;
+    if (isSorted) {
+      i = _.sortedIndex(array, item);
+      return array[i] === item ? i : -1;
+    }
+    if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
+    for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
+  _.lastIndexOf = function(array, item) {
+    if (array == null) return -1;
+    if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
+    var i = array.length;
+    while (i--) if (i in array && array[i] === item) return i;
+    return -1;
+  };
+
+  // Generate an integer Array containing an arithmetic progression. A port of
+  // the native Python `range()` function. See
+  // [the Python documentation](http://docs.python.org/library/functions.html#range).
+  _.range = function(start, stop, step) {
+    if (arguments.length <= 1) {
+      stop = start || 0;
+      start = 0;
+    }
+    step = arguments[2] || 1;
+
+    var len = Math.max(Math.ceil((stop - start) / step), 0);
+    var idx = 0;
+    var range = new Array(len);
+
+    while(idx < len) {
+      range[idx++] = start;
+      start += step;
+    }
+
+    return range;
+  };
+
+  // Function (ahem) Functions
+  // ------------------
+
+  // Reusable constructor function for prototype setting.
+  var ctor = function(){};
+
+  // Create a function bound to a given object (assigning `this`, and arguments,
+  // optionally). Binding with arguments is also known as `curry`.
+  // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
+  // We check for `func.bind` first, to fail fast when `func` is undefined.
+  _.bind = function bind(func, context) {
+    var bound, args;
+    if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
+    if (!_.isFunction(func)) throw new TypeError;
+    args = slice.call(arguments, 2);
+    return bound = function() {
+      if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
+      ctor.prototype = func.prototype;
+      var self = new ctor;
+      var result = func.apply(self, args.concat(slice.call(arguments)));
+      if (Object(result) === result) return result;
+      return self;
+    };
+  };
+
+  // Bind all of an object's methods to that object. Useful for ensuring that
+  // all callbacks defined on an object belong to it.
+  _.bindAll = function(obj) {
+    var funcs = slice.call(arguments, 1);
+    if (funcs.length == 0) funcs = _.functions(obj);
+    each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
+    return obj;
+  };
+
+  // Memoize an expensive function by storing its results.
+  _.memoize = function(func, hasher) {
+    var memo = {};
+    hasher || (hasher = _.identity);
+    return function() {
+      var key = hasher.apply(this, arguments);
+      return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
+    };
+  };
+
+  // Delays a function for the given number of milliseconds, and then calls
+  // it with the arguments supplied.
+  _.delay = function(func, wait) {
+    var args = slice.call(arguments, 2);
+    return setTimeout(function(){ return func.apply(func, args); }, wait);
+  };
+
+  // Defers a function, scheduling it to run after the current call stack has
+  // cleared.
+  _.defer = function(func) {
+    return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
+  };
+
+  // Returns a function, that, when invoked, will only be triggered at most once
+  // during a given window of time.
+  _.throttle = function(func, wait) {
+    var context, args, timeout, throttling, more;
+    var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
+    return function() {
+      context = this; args = arguments;
+      var later = function() {
+        timeout = null;
+        if (more) func.apply(context, args);
+        whenDone();
+      };
+      if (!timeout) timeout = setTimeout(later, wait);
+      if (throttling) {
+        more = true;
+      } else {
+        func.apply(context, args);
+      }
+      whenDone();
+      throttling = true;
+    };
+  };
+
+  // Returns a function, that, as long as it continues to be invoked, will not
+  // be triggered. The function will be called after it stops being called for
+  // N milliseconds.
+  _.debounce = function(func, wait) {
+    var timeout;
+    return function() {
+      var context = this, args = arguments;
+      var later = function() {
+        timeout = null;
+        func.apply(context, args);
+      };
+      clearTimeout(timeout);
+      timeout = setTimeout(later, wait);
+    };
+  };
+
+  // Returns a function that will be executed at most one time, no matter how
+  // often you call it. Useful for lazy initialization.
+  _.once = function(func) {
+    var ran = false, memo;
+    return function() {
+      if (ran) return memo;
+      ran = true;
+      return memo = func.apply(this, arguments);
+    };
+  };
+
+  // Returns the first function passed as an argument to the second,
+  // allowing you to adjust arguments, run code before and after, and
+  // conditionally execute the original function.
+  _.wrap = function(func, wrapper) {
+    return function() {
+      var args = [func].concat(slice.call(arguments, 0));
+      return wrapper.apply(this, args);
+    };
+  };
+
+  // Returns a function that is the composition of a list of functions, each
+  // consuming the return value of the function that follows.
+  _.compose = function() {
+    var funcs = arguments;
+    return function() {
+      var args = arguments;
+      for (var i = funcs.length - 1; i >= 0; i--) {
+        args = [funcs[i].apply(this, args)];
+      }
+      return args[0];
+    };
+  };
+
+  // Returns a function that will only be executed after being called N times.
+  _.after = function(times, func) {
+    if (times <= 0) return func();
+    return function() {
+      if (--times < 1) { return func.apply(this, arguments); }
+    };
+  };
+
+  // Object Functions
+  // ----------------
+
+  // Retrieve the names of an object's properties.
+  // Delegates to **ECMAScript 5**'s native `Object.keys`
+  _.keys = nativeKeys || function(obj) {
+    if (obj !== Object(obj)) throw new TypeError('Invalid object');
+    var keys = [];
+    for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
+    return keys;
+  };
+
+  // Retrieve the values of an object's properties.
+  _.values = function(obj) {
+    return _.map(obj, _.identity);
+  };
+
+  // Return a sorted list of the function names available on the object.
+  // Aliased as `methods`
+  _.functions = _.methods = function(obj) {
+    var names = [];
+    for (var key in obj) {
+      if (_.isFunction(obj[key])) names.push(key);
+    }
+    return names.sort();
+  };
+
+  // Extend a given object with all the properties in passed-in object(s).
+  _.extend = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Fill in a given object with default properties.
+  _.defaults = function(obj) {
+    each(slice.call(arguments, 1), function(source) {
+      for (var prop in source) {
+        if (obj[prop] == null) obj[prop] = source[prop];
+      }
+    });
+    return obj;
+  };
+
+  // Create a (shallow-cloned) duplicate of an object.
+  _.clone = function(obj) {
+    if (!_.isObject(obj)) return obj;
+    return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+  };
+
+  // Invokes interceptor with the obj, and then returns obj.
+  // The primary purpose of this method is to "tap into" a method chain, in
+  // order to perform operations on intermediate results within the chain.
+  _.tap = function(obj, interceptor) {
+    interceptor(obj);
+    return obj;
+  };
+
+  // Internal recursive comparison function.
+  function eq(a, b, stack) {
+    // Identical objects are equal. `0 === -0`, but they aren't identical.
+    // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
+    if (a === b) return a !== 0 || 1 / a == 1 / b;
+    // A strict comparison is necessary because `null == undefined`.
+    if (a == null || b == null) return a === b;
+    // Unwrap any wrapped objects.
+    if (a._chain) a = a._wrapped;
+    if (b._chain) b = b._wrapped;
+    // Invoke a custom `isEqual` method if one is provided.
+    if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
+    if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
+    // Compare `[[Class]]` names.
+    var className = toString.call(a);
+    if (className != toString.call(b)) return false;
+    switch (className) {
+      // Strings, numbers, dates, and booleans are compared by value.
+      case '[object String]':
+        // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+        // equivalent to `new String("5")`.
+        return a == String(b);
+      case '[object Number]':
+        // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
+        // other numeric values.
+        return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
+      case '[object Date]':
+      case '[object Boolean]':
+        // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+        // millisecond representations. Note that invalid dates with millisecond representations
+        // of `NaN` are not equivalent.
+        return +a == +b;
+      // RegExps are compared by their source patterns and flags.
+      case '[object RegExp]':
+        return a.source == b.source &&
+               a.global == b.global &&
+               a.multiline == b.multiline &&
+               a.ignoreCase == b.ignoreCase;
+    }
+    if (typeof a != 'object' || typeof b != 'object') return false;
+    // Assume equality for cyclic structures. The algorithm for detecting cyclic
+    // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+    var length = stack.length;
+    while (length--) {
+      // Linear search. Performance is inversely proportional to the number of
+      // unique nested structures.
+      if (stack[length] == a) return true;
+    }
+    // Add the first object to the stack of traversed objects.
+    stack.push(a);
+    var size = 0, result = true;
+    // Recursively compare objects and arrays.
+    if (className == '[object Array]') {
+      // Compare array lengths to determine if a deep comparison is necessary.
+      size = a.length;
+      result = size == b.length;
+      if (result) {
+        // Deep compare the contents, ignoring non-numeric properties.
+        while (size--) {
+          // Ensure commutative equality for sparse arrays.
+          if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
+        }
+      }
+    } else {
+      // Objects with different constructors are not equivalent.
+      if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
+      // Deep compare objects.
+      for (var key in a) {
+        if (_.has(a, key)) {
+          // Count the expected number of properties.
+          size++;
+          // Deep compare each member.
+          if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
+        }
+      }
+      // Ensure that both objects contain the same number of properties.
+      if (result) {
+        for (key in b) {
+          if (_.has(b, key) && !(size--)) break;
+        }
+        result = !size;
+      }
+    }
+    // Remove the first object from the stack of traversed objects.
+    stack.pop();
+    return result;
+  }
+
+  // Perform a deep comparison to check if two objects are equal.
+  _.isEqual = function(a, b) {
+    return eq(a, b, []);
+  };
+
+  // Is a given array, string, or object empty?
+  // An "empty" object has no enumerable own-properties.
+  _.isEmpty = function(obj) {
+    if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
+    for (var key in obj) if (_.has(obj, key)) return false;
+    return true;
+  };
+
+  // Is a given value a DOM element?
+  _.isElement = function(obj) {
+    return !!(obj && obj.nodeType == 1);
+  };
+
+  // Is a given value an array?
+  // Delegates to ECMA5's native Array.isArray
+  _.isArray = nativeIsArray || function(obj) {
+    return toString.call(obj) == '[object Array]';
+  };
+
+  // Is a given variable an object?
+  _.isObject = function(obj) {
+    return obj === Object(obj);
+  };
+
+  // Is a given variable an arguments object?
+  _.isArguments = function(obj) {
+    return toString.call(obj) == '[object Arguments]';
+  };
+  if (!_.isArguments(arguments)) {
+    _.isArguments = function(obj) {
+      return !!(obj && _.has(obj, 'callee'));
+    };
+  }
+
+  // Is a given value a function?
+  _.isFunction = function(obj) {
+    return toString.call(obj) == '[object Function]';
+  };
+
+  // Is a given value a string?
+  _.isString = function(obj) {
+    return toString.call(obj) == '[object String]';
+  };
+
+  // Is a given value a number?
+  _.isNumber = function(obj) {
+    return toString.call(obj) == '[object Number]';
+  };
+
+  // Is the given value `NaN`?
+  _.isNaN = function(obj) {
+    // `NaN` is the only value for which `===` is not reflexive.
+    return obj !== obj;
+  };
+
+  // Is a given value a boolean?
+  _.isBoolean = function(obj) {
+    return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
+  };
+
+  // Is a given value a date?
+  _.isDate = function(obj) {
+    return toString.call(obj) == '[object Date]';
+  };
+
+  // Is the given value a regular expression?
+  _.isRegExp = function(obj) {
+    return toString.call(obj) == '[object RegExp]';
+  };
+
+  // Is a given value equal to null?
+  _.isNull = function(obj) {
+    return obj === null;
+  };
+
+  // Is a given variable undefined?
+  _.isUndefined = function(obj) {
+    return obj === void 0;
+  };
+
+  // Has own property?
+  _.has = function(obj, key) {
+    return hasOwnProperty.call(obj, key);
+  };
+
+  // Utility Functions
+  // -----------------
+
+  // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+  // previous owner. Returns a reference to the Underscore object.
+  _.noConflict = function() {
+    root._ = previousUnderscore;
+    return this;
+  };
+
+  // Keep the identity function around for default iterators.
+  _.identity = function(value) {
+    return value;
+  };
+
+  // Run a function **n** times.
+  _.times = function (n, iterator, context) {
+    for (var i = 0; i < n; i++) iterator.call(context, i);
+  };
+
+  // Escape a string for HTML interpolation.
+  _.escape = function(string) {
+    return (''+string).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;').replace(/'/g, '&#x27;').replace(/\//g,'&#x2F;');
+  };
+
+  // Add your own custom functions to the Underscore object, ensuring that
+  // they're correctly added to the OOP wrapper as well.
+  _.mixin = function(obj) {
+    each(_.functions(obj), function(name){
+      addToWrapper(name, _[name] = obj[name]);
+    });
+  };
+
+  // Generate a unique integer id (unique within the entire client session).
+  // Useful for temporary DOM ids.
+  var idCounter = 0;
+  _.uniqueId = function(prefix) {
+    var id = idCounter++;
+    return prefix ? prefix + id : id;
+  };
+
+  // By default, Underscore uses ERB-style template delimiters, change the
+  // following template settings to use alternative delimiters.
+  _.templateSettings = {
+    evaluate    : /<%([\s\S]+?)%>/g,
+    interpolate : /<%=([\s\S]+?)%>/g,
+    escape      : /<%-([\s\S]+?)%>/g
+  };
+
+  // When customizing `templateSettings`, if you don't want to define an
+  // interpolation, evaluation or escaping regex, we need one that is
+  // guaranteed not to match.
+  var noMatch = /.^/;
+
+  // Within an interpolation, evaluation, or escaping, remove HTML escaping
+  // that had been previously added.
+  var unescape = function(code) {
+    return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
+  };
+
+  // JavaScript micro-templating, similar to John Resig's implementation.
+  // Underscore templating handles arbitrary delimiters, preserves whitespace,
+  // and correctly escapes quotes within interpolated code.
+  _.template = function(str, data) {
+    var c  = _.templateSettings;
+    var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
+      'with(obj||{}){__p.push(\'' +
+      str.replace(/\\/g, '\\\\')
+         .replace(/'/g, "\\'")
+         .replace(c.escape || noMatch, function(match, code) {
+           return "',_.escape(" + unescape(code) + "),'";
+         })
+         .replace(c.interpolate || noMatch, function(match, code) {
+           return "'," + unescape(code) + ",'";
+         })
+         .replace(c.evaluate || noMatch, function(match, code) {
+           return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
+         })
+         .replace(/\r/g, '\\r')
+         .replace(/\n/g, '\\n')
+         .replace(/\t/g, '\\t')
+         + "');}return __p.join('');";
+    var func = new Function('obj', '_', tmpl);
+    if (data) return func(data, _);
+    return function(data) {
+      return func.call(this, data, _);
+    };
+  };
+
+  // Add a "chain" function, which will delegate to the wrapper.
+  _.chain = function(obj) {
+    return _(obj).chain();
+  };
+
+  // The OOP Wrapper
+  // ---------------
+
+  // If Underscore is called as a function, it returns a wrapped object that
+  // can be used OO-style. This wrapper holds altered versions of all the
+  // underscore functions. Wrapped objects may be chained.
+  var wrapper = function(obj) { this._wrapped = obj; };
+
+  // Expose `wrapper.prototype` as `_.prototype`
+  _.prototype = wrapper.prototype;
+
+  // Helper function to continue chaining intermediate results.
+  var result = function(obj, chain) {
+    return chain ? _(obj).chain() : obj;
+  };
+
+  // A method to easily add functions to the OOP wrapper.
+  var addToWrapper = function(name, func) {
+    wrapper.prototype[name] = function() {
+      var args = slice.call(arguments);
+      unshift.call(args, this._wrapped);
+      return result(func.apply(_, args), this._chain);
+    };
+  };
+
+  // Add all of the Underscore functions to the wrapper object.
+  _.mixin(_);
+
+  // Add all mutator Array functions to the wrapper.
+  each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      var wrapped = this._wrapped;
+      method.apply(wrapped, arguments);
+      var length = wrapped.length;
+      if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
+      return result(wrapped, this._chain);
+    };
+  });
+
+  // Add all accessor Array functions to the wrapper.
+  each(['concat', 'join', 'slice'], function(name) {
+    var method = ArrayProto[name];
+    wrapper.prototype[name] = function() {
+      return result(method.apply(this._wrapped, arguments), this._chain);
+    };
+  });
+
+  // Start chaining a wrapped Underscore object.
+  wrapper.prototype.chain = function() {
+    this._chain = true;
+    return this;
+  };
+
+  // Extracts the result from a wrapped and chained object.
+  wrapper.prototype.value = function() {
+    return this._wrapped;
+  };
+
+}).call(this);

docs/pylagrit/original/static/underscore.js

@@ -0,0 +1,31 @@
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
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+return e.value};b.shuffle=function(a){var b=[],d;j(a,function(a,f){f==0?b[0]=a:(d=Math.floor(Math.random()*(f+1)),b[f]=b[d],b[d]=a)});return b};b.sortBy=function(a,c,d){return b.pluck(b.map(a,function(a,b,g){return{value:a,criteria:c.call(d,a,b,g)}}).sort(function(a,b){var c=a.criteria,d=b.criteria;return c<d?-1:c>d?1:0}),"value")};b.groupBy=function(a,c){var d={},e=b.isFunction(c)?c:function(a){return a[c]};j(a,function(a,b){var c=e(a,b);(d[c]||(d[c]=[])).push(a)});return d};b.sortedIndex=function(a,
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+b.tail=function(a,b,d){return i.call(a,b==null||d?1:b)};b.compact=function(a){return b.filter(a,function(a){return!!a})};b.flatten=function(a,c){return b.reduce(a,function(a,e){if(b.isArray(e))return a.concat(c?e:b.flatten(e));a[a.length]=e;return a},[])};b.without=function(a){return b.difference(a,i.call(arguments,1))};b.uniq=b.unique=function(a,c,d){var d=d?b.map(a,d):a,e=[];b.reduce(d,function(d,g,h){if(0==h||(c===true?b.last(d)!=g:!b.include(d,g)))d[d.length]=g,e[e.length]=a[h];return d},[]);
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+var F=function(){};b.bind=function(a,c){var d,e;if(a.bind===s&&s)return s.apply(a,i.call(arguments,1));if(!b.isFunction(a))throw new TypeError;e=i.call(arguments,2);return d=function(){if(!(this instanceof d))return a.apply(c,e.concat(i.call(arguments)));F.prototype=a.prototype;var b=new F,g=a.apply(b,e.concat(i.call(arguments)));return Object(g)===g?g:b}};b.bindAll=function(a){var c=i.call(arguments,1);c.length==0&&(c=b.functions(a));j(c,function(c){a[c]=b.bind(a[c],a)});return a};b.memoize=function(a,
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+b.isArguments=function(a){return l.call(a)=="[object Arguments]"};if(!b.isArguments(arguments))b.isArguments=function(a){return!(!a||!b.has(a,"callee"))};b.isFunction=function(a){return l.call(a)=="[object Function]"};b.isString=function(a){return l.call(a)=="[object String]"};b.isNumber=function(a){return l.call(a)=="[object Number]"};b.isNaN=function(a){return a!==a};b.isBoolean=function(a){return a===true||a===false||l.call(a)=="[object Boolean]"};b.isDate=function(a){return l.call(a)=="[object Date]"};
+b.isRegExp=function(a){return l.call(a)=="[object RegExp]"};b.isNull=function(a){return a===null};b.isUndefined=function(a){return a===void 0};b.has=function(a,b){return I.call(a,b)};b.noConflict=function(){r._=G;return this};b.identity=function(a){return a};b.times=function(a,b,d){for(var e=0;e<a;e++)b.call(d,e)};b.escape=function(a){return(""+a).replace(/&/g,"&amp;").replace(/</g,"&lt;").replace(/>/g,"&gt;").replace(/"/g,"&quot;").replace(/'/g,"&#x27;").replace(/\//g,"&#x2F;")};b.mixin=function(a){j(b.functions(a),
+function(c){K(c,b[c]=a[c])})};var L=0;b.uniqueId=function(a){var b=L++;return a?a+b:b};b.templateSettings={evaluate:/<%([\s\S]+?)%>/g,interpolate:/<%=([\s\S]+?)%>/g,escape:/<%-([\s\S]+?)%>/g};var t=/.^/,u=function(a){return a.replace(/\\\\/g,"\\").replace(/\\'/g,"'")};b.template=function(a,c){var d=b.templateSettings,d="var __p=[],print=function(){__p.push.apply(__p,arguments);};with(obj||{}){__p.push('"+a.replace(/\\/g,"\\\\").replace(/'/g,"\\'").replace(d.escape||t,function(a,b){return"',_.escape("+
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docs/pylagrit/original/static/websupport.js

@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+  $.fn.autogrow = function() {
+    return this.each(function() {
+    var textarea = this;
+
+    $.fn.autogrow.resize(textarea);
+
+    $(textarea)
+      .focus(function() {
+        textarea.interval = setInterval(function() {
+          $.fn.autogrow.resize(textarea);
+        }, 500);
+      })
+      .blur(function() {
+        clearInterval(textarea.interval);
+      });
+    });
+  };
+
+  $.fn.autogrow.resize = function(textarea) {
+    var lineHeight = parseInt($(textarea).css('line-height'), 10);
+    var lines = textarea.value.split('\n');
+    var columns = textarea.cols;
+    var lineCount = 0;
+    $.each(lines, function() {
+      lineCount += Math.ceil(this.length / columns) || 1;
+    });
+    var height = lineHeight * (lineCount + 1);
+    $(textarea).css('height', height);
+  };
+})(jQuery);
+
+(function($) {
+  var comp, by;
+
+  function init() {
+    initEvents();
+    initComparator();
+  }
+
+  function initEvents() {
+    $(document).on("click", 'a.comment-close', function(event) {
+      event.preventDefault();
+      hide($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.vote', function(event) {
+      event.preventDefault();
+      handleVote($(this));
+    });
+    $(document).on("click", 'a.reply', function(event) {
+      event.preventDefault();
+      openReply($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.close-reply', function(event) {
+      event.preventDefault();
+      closeReply($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.sort-option', function(event) {
+      event.preventDefault();
+      handleReSort($(this));
+    });
+    $(document).on("click", 'a.show-proposal', function(event) {
+      event.preventDefault();
+      showProposal($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.hide-proposal', function(event) {
+      event.preventDefault();
+      hideProposal($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.show-propose-change', function(event) {
+      event.preventDefault();
+      showProposeChange($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.hide-propose-change', function(event) {
+      event.preventDefault();
+      hideProposeChange($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.accept-comment', function(event) {
+      event.preventDefault();
+      acceptComment($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.delete-comment', function(event) {
+      event.preventDefault();
+      deleteComment($(this).attr('id').substring(2));
+    });
+    $(document).on("click", 'a.comment-markup', function(event) {
+      event.preventDefault();
+      toggleCommentMarkupBox($(this).attr('id').substring(2));
+    });
+  }
+
+  /**
+   * Set comp, which is a comparator function used for sorting and
+   * inserting comments into the list.
+   */
+  function setComparator() {
+    // If the first three letters are "asc", sort in ascending order
+    // and remove the prefix.
+    if (by.substring(0,3) == 'asc') {
+      var i = by.substring(3);
+      comp = function(a, b) { return a[i] - b[i]; };
+    } else {
+      // Otherwise sort in descending order.
+      comp = function(a, b) { return b[by] - a[by]; };
+    }
+
+    // Reset link styles and format the selected sort option.
+    $('a.sel').attr('href', '#').removeClass('sel');
+    $('a.by' + by).removeAttr('href').addClass('sel');
+  }
+
+  /**
+   * Create a comp function. If the user has preferences stored in
+   * the sortBy cookie, use those, otherwise use the default.
+   */
+  function initComparator() {
+    by = 'rating'; // Default to sort by rating.
+    // If the sortBy cookie is set, use that instead.
+    if (document.cookie.length > 0) {
+      var start = document.cookie.indexOf('sortBy=');
+      if (start != -1) {
+        start = start + 7;
+        var end = document.cookie.indexOf(";", start);
+        if (end == -1) {
+          end = document.cookie.length;
+          by = unescape(document.cookie.substring(start, end));
+        }
+      }
+    }
+    setComparator();
+  }
+
+  /**
+   * Show a comment div.
+   */
+  function show(id) {
+    $('#ao' + id).hide();
+    $('#ah' + id).show();
+    var context = $.extend({id: id}, opts);
+    var popup = $(renderTemplate(popupTemplate, context)).hide();
+    popup.find('textarea[name="proposal"]').hide();
+    popup.find('a.by' + by).addClass('sel');
+    var form = popup.find('#cf' + id);
+    form.submit(function(event) {
+      event.preventDefault();
+      addComment(form);
+    });
+    $('#s' + id).after(popup);
+    popup.slideDown('fast', function() {
+      getComments(id);
+    });
+  }
+
+  /**
+   * Hide a comment div.
+   */
+  function hide(id) {
+    $('#ah' + id).hide();
+    $('#ao' + id).show();
+    var div = $('#sc' + id);
+    div.slideUp('fast', function() {
+      div.remove();
+    });
+  }
+
+  /**
+   * Perform an ajax request to get comments for a node
+   * and insert the comments into the comments tree.
+   */
+  function getComments(id) {
+    $.ajax({
+     type: 'GET',
+     url: opts.getCommentsURL,
+     data: {node: id},
+     success: function(data, textStatus, request) {
+       var ul = $('#cl' + id);
+       var speed = 100;
+       $('#cf' + id)
+         .find('textarea[name="proposal"]')
+         .data('source', data.source);
+
+       if (data.comments.length === 0) {
+         ul.html('<li>No comments yet.</li>');
+         ul.data('empty', true);
+       } else {
+         // If there are comments, sort them and put them in the list.
+         var comments = sortComments(data.comments);
+         speed = data.comments.length * 100;
+         appendComments(comments, ul);
+         ul.data('empty', false);
+       }
+       $('#cn' + id).slideUp(speed + 200);
+       ul.slideDown(speed);
+     },
+     error: function(request, textStatus, error) {
+       showError('Oops, there was a problem retrieving the comments.');
+     },
+     dataType: 'json'
+    });
+  }
+
+  /**
+   * Add a comment via ajax and insert the comment into the comment tree.
+   */
+  function addComment(form) {
+    var node_id = form.find('input[name="node"]').val();
+    var parent_id = form.find('input[name="parent"]').val();
+    var text = form.find('textarea[name="comment"]').val();
+    var proposal = form.find('textarea[name="proposal"]').val();
+
+    if (text == '') {
+      showError('Please enter a comment.');
+      return;
+    }
+
+    // Disable the form that is being submitted.
+    form.find('textarea,input').attr('disabled', 'disabled');
+
+    // Send the comment to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.addCommentURL,
+      dataType: 'json',
+      data: {
+        node: node_id,
+        parent: parent_id,
+        text: text,
+        proposal: proposal
+      },
+      success: function(data, textStatus, error) {
+        // Reset the form.
+        if (node_id) {
+          hideProposeChange(node_id);
+        }
+        form.find('textarea')
+          .val('')
+          .add(form.find('input'))
+          .removeAttr('disabled');
+	var ul = $('#cl' + (node_id || parent_id));
+        if (ul.data('empty')) {
+          $(ul).empty();
+          ul.data('empty', false);
+        }
+        insertComment(data.comment);
+        var ao = $('#ao' + node_id);
+        ao.find('img').attr({'src': opts.commentBrightImage});
+        if (node_id) {
+          // if this was a "root" comment, remove the commenting box
+          // (the user can get it back by reopening the comment popup)
+          $('#ca' + node_id).slideUp();
+        }
+      },
+      error: function(request, textStatus, error) {
+        form.find('textarea,input').removeAttr('disabled');
+        showError('Oops, there was a problem adding the comment.');
+      }
+    });
+  }
+
+  /**
+   * Recursively append comments to the main comment list and children
+   * lists, creating the comment tree.
+   */
+  function appendComments(comments, ul) {
+    $.each(comments, function() {
+      var div = createCommentDiv(this);
+      ul.append($(document.createElement('li')).html(div));
+      appendComments(this.children, div.find('ul.comment-children'));
+      // To avoid stagnating data, don't store the comments children in data.
+      this.children = null;
+      div.data('comment', this);
+    });
+  }
+
+  /**
+   * After adding a new comment, it must be inserted in the correct
+   * location in the comment tree.
+   */
+  function insertComment(comment) {
+    var div = createCommentDiv(comment);
+
+    // To avoid stagnating data, don't store the comments children in data.
+    comment.children = null;
+    div.data('comment', comment);
+
+    var ul = $('#cl' + (comment.node || comment.parent));
+    var siblings = getChildren(ul);
+
+    var li = $(document.createElement('li'));
+    li.hide();
+
+    // Determine where in the parents children list to insert this comment.
+    for(var i=0; i < siblings.length; i++) {
+      if (comp(comment, siblings[i]) <= 0) {
+        $('#cd' + siblings[i].id)
+          .parent()
+          .before(li.html(div));
+        li.slideDown('fast');
+        return;
+      }
+    }
+
+    // If we get here, this comment rates lower than all the others,
+    // or it is the only comment in the list.
+    ul.append(li.html(div));
+    li.slideDown('fast');
+  }
+
+  function acceptComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.acceptCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        $('#cm' + id).fadeOut('fast');
+        $('#cd' + id).removeClass('moderate');
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem accepting the comment.');
+      }
+    });
+  }
+
+  function deleteComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.deleteCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        var div = $('#cd' + id);
+        if (data == 'delete') {
+          // Moderator mode: remove the comment and all children immediately
+          div.slideUp('fast', function() {
+            div.remove();
+          });
+          return;
+        }
+        // User mode: only mark the comment as deleted
+        div
+          .find('span.user-id:first')
+          .text('[deleted]').end()
+          .find('div.comment-text:first')
+          .text('[deleted]').end()
+          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+          .remove();
+        var comment = div.data('comment');
+        comment.username = '[deleted]';
+        comment.text = '[deleted]';
+        div.data('comment', comment);
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem deleting the comment.');
+      }
+    });
+  }
+
+  function showProposal(id) {
+    $('#sp' + id).hide();
+    $('#hp' + id).show();
+    $('#pr' + id).slideDown('fast');
+  }
+
+  function hideProposal(id) {
+    $('#hp' + id).hide();
+    $('#sp' + id).show();
+    $('#pr' + id).slideUp('fast');
+  }
+
+  function showProposeChange(id) {
+    $('#pc' + id).hide();
+    $('#hc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val(textarea.data('source'));
+    $.fn.autogrow.resize(textarea[0]);
+    textarea.slideDown('fast');
+  }
+
+  function hideProposeChange(id) {
+    $('#hc' + id).hide();
+    $('#pc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val('').removeAttr('disabled');
+    textarea.slideUp('fast');
+  }
+
+  function toggleCommentMarkupBox(id) {
+    $('#mb' + id).toggle();
+  }
+
+  /** Handle when the user clicks on a sort by link. */
+  function handleReSort(link) {
+    var classes = link.attr('class').split(/\s+/);
+    for (var i=0; i<classes.length; i++) {
+      if (classes[i] != 'sort-option') {
+	by = classes[i].substring(2);
+      }
+    }
+    setComparator();
+    // Save/update the sortBy cookie.
+    var expiration = new Date();
+    expiration.setDate(expiration.getDate() + 365);
+    document.cookie= 'sortBy=' + escape(by) +
+                     ';expires=' + expiration.toUTCString();
+    $('ul.comment-ul').each(function(index, ul) {
+      var comments = getChildren($(ul), true);
+      comments = sortComments(comments);
+      appendComments(comments, $(ul).empty());
+    });
+  }
+
+  /**
+   * Function to process a vote when a user clicks an arrow.
+   */
+  function handleVote(link) {
+    if (!opts.voting) {
+      showError("You'll need to login to vote.");
+      return;
+    }
+
+    var id = link.attr('id');
+    if (!id) {
+      // Didn't click on one of the voting arrows.
+      return;
+    }
+    // If it is an unvote, the new vote value is 0,
+    // Otherwise it's 1 for an upvote, or -1 for a downvote.
+    var value = 0;
+    if (id.charAt(1) != 'u') {
+      value = id.charAt(0) == 'u' ? 1 : -1;
+    }
+    // The data to be sent to the server.
+    var d = {
+      comment_id: id.substring(2),
+      value: value
+    };
+
+    // Swap the vote and unvote links.
+    link.hide();
+    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+      .show();
+
+    // The div the comment is displayed in.
+    var div = $('div#cd' + d.comment_id);
+    var data = div.data('comment');
+
+    // If this is not an unvote, and the other vote arrow has
+    // already been pressed, unpress it.
+    if ((d.value !== 0) && (data.vote === d.value * -1)) {
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+    }
+
+    // Update the comments rating in the local data.
+    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+    data.vote = d.value;
+    div.data('comment', data);
+
+    // Change the rating text.
+    div.find('.rating:first')
+      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+    // Send the vote information to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.processVoteURL,
+      data: d,
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem casting that vote.');
+      }
+    });
+  }
+
+  /**
+   * Open a reply form used to reply to an existing comment.
+   */
+  function openReply(id) {
+    // Swap out the reply link for the hide link
+    $('#rl' + id).hide();
+    $('#cr' + id).show();
+
+    // Add the reply li to the children ul.
+    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+    $('#cl' + id)
+      .prepend(div)
+      // Setup the submit handler for the reply form.
+      .find('#rf' + id)
+      .submit(function(event) {
+        event.preventDefault();
+        addComment($('#rf' + id));
+        closeReply(id);
+      })
+      .find('input[type=button]')
+      .click(function() {
+        closeReply(id);
+      });
+    div.slideDown('fast', function() {
+      $('#rf' + id).find('textarea').focus();
+    });
+  }
+
+  /**
+   * Close the reply form opened with openReply.
+   */
+  function closeReply(id) {
+    // Remove the reply div from the DOM.
+    $('#rd' + id).slideUp('fast', function() {
+      $(this).remove();
+    });
+
+    // Swap out the hide link for the reply link
+    $('#cr' + id).hide();
+    $('#rl' + id).show();
+  }
+
+  /**
+   * Recursively sort a tree of comments using the comp comparator.
+   */
+  function sortComments(comments) {
+    comments.sort(comp);
+    $.each(comments, function() {
+      this.children = sortComments(this.children);
+    });
+    return comments;
+  }
+
+  /**
+   * Get the children comments from a ul. If recursive is true,
+   * recursively include childrens' children.
+   */
+  function getChildren(ul, recursive) {
+    var children = [];
+    ul.children().children("[id^='cd']")
+      .each(function() {
+        var comment = $(this).data('comment');
+        if (recursive)
+          comment.children = getChildren($(this).find('#cl' + comment.id), true);
+        children.push(comment);
+      });
+    return children;
+  }
+
+  /** Create a div to display a comment in. */
+  function createCommentDiv(comment) {
+    if (!comment.displayed && !opts.moderator) {
+      return $('<div class="moderate">Thank you!  Your comment will show up '
+               + 'once it is has been approved by a moderator.</div>');
+    }
+    // Prettify the comment rating.
+    comment.pretty_rating = comment.rating + ' point' +
+      (comment.rating == 1 ? '' : 's');
+    // Make a class (for displaying not yet moderated comments differently)
+    comment.css_class = comment.displayed ? '' : ' moderate';
+    // Create a div for this comment.
+    var context = $.extend({}, opts, comment);
+    var div = $(renderTemplate(commentTemplate, context));
+
+    // If the user has voted on this comment, highlight the correct arrow.
+    if (comment.vote) {
+      var direction = (comment.vote == 1) ? 'u' : 'd';
+      div.find('#' + direction + 'v' + comment.id).hide();
+      div.find('#' + direction + 'u' + comment.id).show();
+    }
+
+    if (opts.moderator || comment.text != '[deleted]') {
+      div.find('a.reply').show();
+      if (comment.proposal_diff)
+        div.find('#sp' + comment.id).show();
+      if (opts.moderator && !comment.displayed)
+        div.find('#cm' + comment.id).show();
+      if (opts.moderator || (opts.username == comment.username))
+        div.find('#dc' + comment.id).show();
+    }
+    return div;
+  }
+
+  /**
+   * A simple template renderer. Placeholders such as <%id%> are replaced
+   * by context['id'] with items being escaped. Placeholders such as <#id#>
+   * are not escaped.
+   */
+  function renderTemplate(template, context) {
+    var esc = $(document.createElement('div'));
+
+    function handle(ph, escape) {
+      var cur = context;
+      $.each(ph.split('.'), function() {
+        cur = cur[this];
+      });
+      return escape ? esc.text(cur || "").html() : cur;
+    }
+
+    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+      return handle(arguments[2], arguments[1] == '%' ? true : false);
+    });
+  }
+
+  /** Flash an error message briefly. */
+  function showError(message) {
+    $(document.createElement('div')).attr({'class': 'popup-error'})
+      .append($(document.createElement('div'))
+               .attr({'class': 'error-message'}).text(message))
+      .appendTo('body')
+      .fadeIn("slow")
+      .delay(2000)
+      .fadeOut("slow");
+  }
+
+  /** Add a link the user uses to open the comments popup. */
+  $.fn.comment = function() {
+    return this.each(function() {
+      var id = $(this).attr('id').substring(1);
+      var count = COMMENT_METADATA[id];
+      var title = count + ' comment' + (count == 1 ? '' : 's');
+      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+      var addcls = count == 0 ? ' nocomment' : '';
+      $(this)
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-open' + addcls,
+            id: 'ao' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: image,
+              alt: 'comment',
+              title: title
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              show($(this).attr('id').substring(2));
+            })
+        )
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-close hidden',
+            id: 'ah' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: opts.closeCommentImage,
+              alt: 'close',
+              title: 'close'
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              hide($(this).attr('id').substring(2));
+            })
+        );
+    });
+  };
+
+  var opts = {
+    processVoteURL: '/_process_vote',
+    addCommentURL: '/_add_comment',
+    getCommentsURL: '/_get_comments',
+    acceptCommentURL: '/_accept_comment',
+    deleteCommentURL: '/_delete_comment',
+    commentImage: '/static/_static/comment.png',
+    closeCommentImage: '/static/_static/comment-close.png',
+    loadingImage: '/static/_static/ajax-loader.gif',
+    commentBrightImage: '/static/_static/comment-bright.png',
+    upArrow: '/static/_static/up.png',
+    downArrow: '/static/_static/down.png',
+    upArrowPressed: '/static/_static/up-pressed.png',
+    downArrowPressed: '/static/_static/down-pressed.png',
+    voting: false,
+    moderator: false
+  };
+
+  if (typeof COMMENT_OPTIONS != "undefined") {
+    opts = jQuery.extend(opts, COMMENT_OPTIONS);
+  }
+
+  var popupTemplate = '\
+    <div class="sphinx-comments" id="sc<%id%>">\
+      <p class="sort-options">\
+        Sort by:\
+        <a href="#" class="sort-option byrating">best rated</a>\
+        <a href="#" class="sort-option byascage">newest</a>\
+        <a href="#" class="sort-option byage">oldest</a>\
+      </p>\
+      <div class="comment-header">Comments</div>\
+      <div class="comment-loading" id="cn<%id%>">\
+        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+      <ul id="cl<%id%>" class="comment-ul"></ul>\
+      <div id="ca<%id%>">\
+      <p class="add-a-comment">Add a comment\
+        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+      <div class="comment-markup-box" id="mb<%id%>">\
+        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+        <code>``code``</code>, \
+        code blocks: <code>::</code> and an indented block after blank line</div>\
+      <form method="post" id="cf<%id%>" class="comment-form" action="">\
+        <textarea name="comment" cols="80"></textarea>\
+        <p class="propose-button">\
+          <a href="#" id="pc<%id%>" class="show-propose-change">\
+            Propose a change &#9657;\
+          </a>\
+          <a href="#" id="hc<%id%>" class="hide-propose-change">\
+            Propose a change &#9663;\
+          </a>\
+        </p>\
+        <textarea name="proposal" id="pt<%id%>" cols="80"\
+                  spellcheck="false"></textarea>\
+        <input type="submit" value="Add comment" />\
+        <input type="hidden" name="node" value="<%id%>" />\
+        <input type="hidden" name="parent" value="" />\
+      </form>\
+      </div>\
+    </div>';
+
+  var commentTemplate = '\
+    <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+      <div class="vote">\
+        <div class="arrow">\
+          <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+            <img src="<%upArrow%>" />\
+          </a>\
+          <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+            <img src="<%upArrowPressed%>" />\
+          </a>\
+        </div>\
+        <div class="arrow">\
+          <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+            <img src="<%downArrow%>" id="da<%id%>" />\
+          </a>\
+          <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+            <img src="<%downArrowPressed%>" />\
+          </a>\
+        </div>\
+      </div>\
+      <div class="comment-content">\
+        <p class="tagline comment">\
+          <span class="user-id"><%username%></span>\
+          <span class="rating"><%pretty_rating%></span>\
+          <span class="delta"><%time.delta%></span>\
+        </p>\
+        <div class="comment-text comment"><#text#></div>\
+        <p class="comment-opts comment">\
+          <a href="#" class="reply hidden" id="rl<%id%>">reply &#9657;</a>\
+          <a href="#" class="close-reply" id="cr<%id%>">reply &#9663;</a>\
+          <a href="#" id="sp<%id%>" class="show-proposal">proposal &#9657;</a>\
+          <a href="#" id="hp<%id%>" class="hide-proposal">proposal &#9663;</a>\
+          <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+          <span id="cm<%id%>" class="moderation hidden">\
+            <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+          </span>\
+        </p>\
+        <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+        </pre>\
+          <ul class="comment-children" id="cl<%id%>"></ul>\
+        </div>\
+        <div class="clearleft"></div>\
+      </div>\
+    </div>';
+
+  var replyTemplate = '\
+    <li>\
+      <div class="reply-div" id="rd<%id%>">\
+        <form id="rf<%id%>">\
+          <textarea name="comment" cols="80"></textarea>\
+          <input type="submit" value="Add reply" />\
+          <input type="button" value="Cancel" />\
+          <input type="hidden" name="parent" value="<%id%>" />\
+          <input type="hidden" name="node" value="" />\
+        </form>\
+      </div>\
+    </li>';
+
+  $(document).ready(function() {
+    init();
+  });
+})(jQuery);
+
+$(document).ready(function() {
+  // add comment anchors for all paragraphs that are commentable
+  $('.sphinx-has-comment').comment();
+
+  // highlight search words in search results
+  $("div.context").each(function() {
+    var params = $.getQueryParameters();
+    var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+    var result = $(this);
+    $.each(terms, function() {
+      result.highlightText(this.toLowerCase(), 'highlighted');
+    });
+  });
+
+  // directly open comment window if requested
+  var anchor = document.location.hash;
+  if (anchor.substring(0, 9) == '#comment-') {
+    $('#ao' + anchor.substring(9)).click();
+    document.location.hash = '#s' + anchor.substring(9);
+  }
+});