update documentation

lehner-lab · Nov 22, 2023 · aeb9d33 · aeb9d33
1 parent 31947ed
commit aeb9d33
Show file tree

Hide file tree

Showing 33 changed files with 3,595 additions and 1,029 deletions.
diff --git a/docs/_build/doctrees/api.doctree b/docs/_build/doctrees/api.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -10,11 +10,11 @@
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-        <script src="../_static/jquery.js"></script>
-        <script src="../_static/underscore.js"></script>
-        <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script src="../_static/doctools.js"></script>
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=888ff710"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -25,11 +25,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="../index.html" class="icon icon-home"> MoCHI
+
+
+
+          <a href="../index.html" class="icon icon-home">
+            MoCHI
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -54,8 +58,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Overview: module code</li>
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Overview: module code</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>

diff --git a/docs/_build/html/_modules/pymochi/data.html b/docs/_build/html/_modules/pymochi/data.html
diff --git a/docs/_build/html/_modules/pymochi/misc.html b/docs/_build/html/_modules/pymochi/misc.html
@@ -10,11 +10,11 @@
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
-        <script src="../../_static/jquery.js"></script>
-        <script src="../../_static/underscore.js"></script>
-        <script src="../../_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script src="../../_static/doctools.js"></script>
+        <script src="../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -25,11 +25,15 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="../../index.html" class="icon icon-home"> MoCHI
+
+
+
+          <a href="../../index.html" class="icon icon-home">
+            MoCHI
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" />
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
@@ -54,9 +58,9 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../../index.html" class="icon icon-home"></a> &raquo;</li>
-          <li><a href="../index.html">Module code</a> &raquo;</li>
-      <li>pymochi.misc</li>
+      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">pymochi.misc</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -79,9 +83,11 @@ <h1>Source code for pymochi.misc</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">itertools</span>
 
-<div class="viewcode-block" id="getsize"><a class="viewcode-back" href="../../api.html#pymochi.misc.getsize">[docs]</a><span class="k">def</span> <span class="nf">getsize</span><span class="p">(</span>
+<div class="viewcode-block" id="getsize">
+<a class="viewcode-back" href="../../api.html#pymochi.misc.getsize">[docs]</a>
+<span class="k">def</span> <span class="nf">getsize</span><span class="p">(</span>
     <span class="n">obj_0</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Recursively iterate to sum size of object &amp; members.</span>
 
 <span class="sd">    :param obj_0: input object (required).</span>
@@ -109,11 +115,14 @@ <h1>Source code for pymochi.misc</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">size</span>
     <span class="k">return</span> <span class="n">inner</span><span class="p">(</span><span class="n">obj_0</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="scatterplot_matrix"><a class="viewcode-back" href="../../api.html#pymochi.misc.scatterplot_matrix">[docs]</a><span class="k">def</span> <span class="nf">scatterplot_matrix</span><span class="p">(</span>
+
+<div class="viewcode-block" id="scatterplot_matrix">
+<a class="viewcode-back" href="../../api.html#pymochi.misc.scatterplot_matrix">[docs]</a>
+<span class="k">def</span> <span class="nf">scatterplot_matrix</span><span class="p">(</span>
     <span class="n">data</span><span class="p">,</span> 
     <span class="n">names</span><span class="p">,</span> 
     <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Plots a scatterplot matrix of subplots.  Each row of &quot;data&quot; is plotted</span>
 <span class="sd">    against other rows, resulting in a nrows by nrows grid of subplots with the</span>
 <span class="sd">    diagonal subplots labeled with &quot;names&quot;.  Additional keyword arguments are</span>