Deploying to gh-pages from @ 09a0c80 🚀

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6b1c8af229374d10a63d5e4da33bc228
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: bfbcc171519d303693eaa7b789862202
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/genomicranges/SeqInfo.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../genindex.html" /><link rel="search" title="Search" href="../../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>genomicranges.SeqInfo - GenomicRanges 0.4.34 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>genomicranges.SeqInfo - GenomicRanges 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.34 documentation</div></a>
+      <a href="../../index.html"><div class="brand">GenomicRanges 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.34 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -618,9 +618,7 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="SeqInfo.set_seqnames">
 <a class="viewcode-back" href="../../api/genomicranges.html#genomicranges.SeqInfo.SeqInfo.set_seqnames">[docs]</a>
-    <span class="k">def</span> <span class="nf">set_seqnames</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span> <span class="n">seqnames</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">in_place</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;SeqInfo&quot;</span><span class="p">:</span>
+    <span class="k">def</span> <span class="nf">set_seqnames</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">seqnames</span><span class="p">:</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">in_place</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="s2">&quot;SeqInfo&quot;</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Args:</span>
 <span class="sd">            seqnames:</span>
@@ -714,9 +712,7 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_seqlengths</span><span class="p">()</span>
 
     <span class="nd">@seqlengths</span><span class="o">.</span><span class="n">setter</span>
-    <span class="k">def</span> <span class="nf">seqlengths</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span> <span class="n">seqlengths</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">int</span><span class="p">]]]</span>
-    <span class="p">):</span>
+    <span class="k">def</span> <span class="nf">seqlengths</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">seqlengths</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">int</span><span class="p">]]]):</span>
         <span class="n">warn</span><span class="p">(</span>
             <span class="s2">&quot;Setting property &#39;seqlengths&#39; is an in-place operation, use &#39;set_seqlengths&#39; instead&quot;</span><span class="p">,</span>
             <span class="ne">UserWarning</span><span class="p">,</span>
@@ -782,9 +778,7 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_is_circular</span><span class="p">()</span>
 
     <span class="nd">@is_circular</span><span class="o">.</span><span class="n">setter</span>
-    <span class="k">def</span> <span class="nf">is_circular</span><span class="p">(</span>
-        <span class="bp">self</span><span class="p">,</span> <span class="n">is_circular</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">bool</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">bool</span><span class="p">],</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]]]</span>
-    <span class="p">):</span>
+    <span class="k">def</span> <span class="nf">is_circular</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">is_circular</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Union</span><span class="p">[</span><span class="nb">bool</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">[</span><span class="nb">bool</span><span class="p">],</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">bool</span><span class="p">]]]):</span>
         <span class="n">warn</span><span class="p">(</span>
             <span class="s2">&quot;Setting property &#39;is_circular&#39; is an in-place operation, use &#39;set_is_circular&#39; instead&quot;</span><span class="p">,</span>
             <span class="ne">UserWarning</span><span class="p">,</span>
@@ -1011,8 +1005,8 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=d6caa86d"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>

_modules/genomicranges/io/gtf.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>genomicranges.io.gtf - GenomicRanges 0.4.34 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>genomicranges.io.gtf - GenomicRanges 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.34 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">GenomicRanges 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.34 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -363,9 +363,7 @@ <h1>Source code for genomicranges.io.gtf</h1><div class="highlight"><pre>
             <span class="n">comment</span><span class="o">=</span><span class="n">comment</span><span class="p">,</span>
         <span class="p">)</span>
 
-    <span class="n">rows</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=-</span><span class="mi">2</span><span class="p">)(</span>
-        <span class="n">delayed</span><span class="p">(</span><span class="n">_parse_all_attribute</span><span class="p">)(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">iterrows</span><span class="p">()</span>
-    <span class="p">)</span>
+    <span class="n">rows</span> <span class="o">=</span> <span class="n">Parallel</span><span class="p">(</span><span class="n">n_jobs</span><span class="o">=-</span><span class="mi">2</span><span class="p">)(</span><span class="n">delayed</span><span class="p">(</span><span class="n">_parse_all_attribute</span><span class="p">)(</span><span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">iterrows</span><span class="p">())</span>
     <span class="n">gtf</span> <span class="o">=</span> <span class="n">DataFrame</span><span class="o">.</span><span class="n">from_records</span><span class="p">(</span><span class="n">rows</span><span class="p">)</span>
     <span class="n">gtf</span><span class="o">.</span><span class="n">drop</span><span class="p">([</span><span class="s2">&quot;group&quot;</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
 
@@ -434,8 +432,8 @@ <h1>Source code for genomicranges.io.gtf</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=d6caa86d"></script>
-    <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../../../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>

_modules/genomicranges/io/ucsc.html

@@ -4,8 +4,8 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../../genindex.html" /><link rel="search" title="Search" href="../../../search.html" />
 
-    <!-- Generated with Sphinx 7.4.7 and Furo 2024.08.06 -->
-        <title>genomicranges.io.ucsc - GenomicRanges 0.4.34 documentation</title>
+    <!-- Generated with Sphinx 8.1.3 and Furo 2024.08.06 -->
+        <title>genomicranges.io.ucsc - GenomicRanges 0.5.0 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../../_static/styles/furo.css?v=354aac6f" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -166,7 +166,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.34 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">GenomicRanges 0.5.0 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -190,7 +190,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.34 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../../../search.html" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -297,9 +297,7 @@ <h1>Source code for genomicranges.io.ucsc</h1><div class="highlight"><pre>
     <span class="n">base_path</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;http://hgdownload.cse.ucsc.edu/goldenPath/</span><span class="si">{</span><span class="n">genome</span><span class="si">}</span><span class="s2">/bigZips/genes/&quot;</span>
 
     <span class="k">if</span> <span class="nb">type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;refGene&quot;</span><span class="p">,</span> <span class="s2">&quot;ensGene&quot;</span><span class="p">,</span> <span class="s2">&quot;knownGene&quot;</span><span class="p">,</span> <span class="s2">&quot;ncbiRefSeq&quot;</span><span class="p">]:</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;type must be one of refGene, ensGene, knownGene or ncbiRefSeq, provided </span><span class="si">{</span><span class="nb">type</span><span class="si">}</span><span class="s2">&quot;</span>
-        <span class="p">)</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;type must be one of refGene, ensGene, knownGene or ncbiRefSeq, provided </span><span class="si">{</span><span class="nb">type</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
 
     <span class="n">full_path</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">base_path</span><span class="si">}</span><span class="s2">/</span><span class="si">{</span><span class="n">genome</span><span class="si">}</span><span class="s2">.</span><span class="si">{</span><span class="nb">type</span><span class="si">}</span><span class="s2">.gtf.gz&quot;</span>
 
@@ -365,8 +363,8 @@ <h1>Source code for genomicranges.io.ucsc</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=d6caa86d"></script>
-    <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+</div><script src="../../../_static/documentation_options.js?v=1dd76d02"></script>
+    <script src="../../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=5fa4622c"></script>
     </body>