update docs

daler · Apr 20, 2024 · 82e3555 · 82e3555
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diff --git a/_modules/index.html b/_modules/index.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=eafc0fe6" />
+      <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
 
 
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=359c27e9"></script>
-        <script src="../_static/doctools.js?v=888ff710"></script>
-        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../_static/documentation_options.js?v=f2a433a1"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></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" /> 

diff --git a/_modules/trackhub/assembly.html b/_modules/trackhub/assembly.html
@@ -1,12 +1,12 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>trackhub.assembly &mdash; trackhub 1.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=eafc0fe6" />
+      <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
 
 
   <!--[if lt IE 9]>
@@ -15,9 +15,9 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=359c27e9"></script>
-        <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../../_static/documentation_options.js?v=f2a433a1"></script>
+        <script src="../../_static/doctools.js?v=9a2dae69"></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" /> 
@@ -154,8 +154,12 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="k">pass</span>
 
 
-<div class="viewcode-block" id="Assembly"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly">[docs]</a><span class="k">class</span> <span class="nc">Assembly</span><span class="p">(</span><span class="n">Genome</span><span class="p">):</span>
-<div class="viewcode-block" id="Assembly.__init__"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.__init__">[docs]</a>    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+<div class="viewcode-block" id="Assembly">
+<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly">[docs]</a>
+<span class="k">class</span> <span class="nc">Assembly</span><span class="p">(</span><span class="n">Genome</span><span class="p">):</span>
+<div class="viewcode-block" id="Assembly.__init__">
+<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.__init__">[docs]</a>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">,</span>
         <span class="n">genome</span><span class="p">,</span>
         <span class="n">twobit_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
@@ -200,6 +204,7 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">add_params</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span></div>
 
+
     <span class="k">def</span> <span class="nf">add_twobit</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">twobit</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">children</span> <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">TwoBitFile</span><span class="p">)]</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">add_child</span><span class="p">(</span><span class="n">twobit</span><span class="p">)</span>
@@ -224,7 +229,9 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;GenomesFile is level </span><span class="si">%s</span><span class="s2">, not -1&quot;</span> <span class="o">%</span> <span class="n">level</span><span class="p">)</span>
         <span class="k">return</span> <span class="n">obj</span>
 
-<div class="viewcode-block" id="Assembly.add_params"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.add_params">[docs]</a>    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
+<div class="viewcode-block" id="Assembly.add_params">
+<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.add_params">[docs]</a>
+    <span class="k">def</span> <span class="nf">add_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kw</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Add [possibly many] parameters to the Assembly.</span>
 
@@ -243,7 +250,10 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">kw</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
-<div class="viewcode-block" id="Assembly.remove_params"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.remove_params">[docs]</a>    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Assembly.remove_params">
+<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.remove_params">[docs]</a>
+    <span class="k">def</span> <span class="nf">remove_params</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Remove [possibly many] parameters from the Assembly.</span>
 
@@ -255,6 +265,7 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">a</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></div>
 
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">_html</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">html_string</span><span class="p">:</span>
@@ -289,8 +300,12 @@ <h1>Source code for trackhub.assembly</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_orig_kwargs</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="k">return</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&quot;</span>
 
-<div class="viewcode-block" id="Assembly.validate"><a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.validate">[docs]</a>    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="n">Genome</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div></div>
+<div class="viewcode-block" id="Assembly.validate">
+<a class="viewcode-back" href="../../autodocs/trackhub.Assembly.html#trackhub.Assembly.validate">[docs]</a>
+    <span class="k">def</span> <span class="nf">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="n">Genome</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
+</div>
+
         <span class="c1"># check for necessary params?</span>