Deploying to gh-pages from @ 1ab20d9 🚀

.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: 74b22998551cbaab68e319a96349d6cf
+config: 84a217acf94b0ccf0ddb6b6914f5f2db
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/genomicranges/GenomicRangesList.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 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges.GenomicRangesList - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges.GenomicRangesList - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -1335,7 +1335,7 @@ <h1>Source code for genomicranges.GenomicRangesList</h1><div class="highlight"><
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../../_static/documentation_options.js?v=6de75181"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_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 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges.SeqInfo - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges.SeqInfo - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -352,7 +352,7 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
 <a class="viewcode-back" href="../../api/genomicranges.html#genomicranges.SeqInfo.SeqInfoIterator.__next__">[docs]</a>
     <span class="k">def</span> <span class="fm">__next__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_current_index</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_sinfo</span><span class="p">):</span>
-            <span class="n">iter_row_index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sinfo</span><span class="o">.</span><span class="n">seqnames</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_current_index</span><span class="p">]</span>
+            <span class="n">iter_row_index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sinfo</span><span class="o">.</span><span class="n">_seqnames</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_current_index</span><span class="p">]</span>
 
             <span class="n">iter_slice</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_sinfo</span><span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">_current_index</span><span class="p">]</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_current_index</span> <span class="o">+=</span> <span class="mi">1</span>
@@ -1024,7 +1024,7 @@ <h1>Source code for genomicranges.SeqInfo</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../../_static/documentation_options.js?v=6de75181"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_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 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges.io.gtf - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges.io.gtf - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -447,7 +447,7 @@ <h1>Source code for genomicranges.io.gtf</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../../../_static/documentation_options.js?v=6de75181"></script>
     <script src="../../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=4e2eecee"></script>

_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 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges.io.ucsc - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges.io.ucsc - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -378,7 +378,7 @@ <h1>Source code for genomicranges.io.ucsc</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../../../_static/documentation_options.js?v=6de75181"></script>
     <script src="../../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/genomicranges/utils.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 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges.utils - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges.utils - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -540,7 +540,7 @@ <h1>Source code for genomicranges.utils</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../../_static/documentation_options.js?v=6de75181"></script>
     <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/scripts/furo.js?v=4e2eecee"></script>

_modules/index.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 7.4.3 and Furo 2024.05.06 -->
-        <title>Overview: module code - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>Overview: module code - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -179,7 +179,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -203,7 +203,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -313,7 +313,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../_static/documentation_options.js?v=6de75181"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=4e2eecee"></script>

_sources/changelog.md.txt

@@ -1,8 +1,11 @@
 # Changelog
 
-## Version 0.4.27
+## Version 0.4.27 - 0.4.28
 
 - Implement `subtract` method, add tests.
+- Use accessor methods to access properties especially `get_seqnames()`
+- Modify search and overlap methods for strand-awareness.
+- Update tests and documentation.
 
 ## Version 0.4.26
 

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.4.27',
+    VERSION: '0.4.28',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

api/genomicranges.html

@@ -5,8 +5,8 @@
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="genomicranges.io package" href="genomicranges.io.html" /><link rel="prev" title="genomicranges" href="modules.html" />
 
-    <!-- Generated with Sphinx 7.4.3 and Furo 2024.05.06 -->
-        <title>genomicranges package - GenomicRanges 0.4.27 documentation</title>
+    <!-- Generated with Sphinx 7.4.4 and Furo 2024.05.06 -->
+        <title>genomicranges package - GenomicRanges 0.4.28 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=387cc868" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
@@ -180,7 +180,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">GenomicRanges 0.4.27 documentation</div></a>
+      <a href="../index.html"><div class="brand">GenomicRanges 0.4.28 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -204,7 +204,7 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
-  <span class="sidebar-brand-text">GenomicRanges 0.4.27 documentation</span>
+  <span class="sidebar-brand-text">GenomicRanges 0.4.28 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">
@@ -877,7 +877,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <dd class="field-odd"><p><strong>as_type</strong> (<span class="sphinx_autodoc_typehints-type"><a class="reference external" href="https://docs.python.org/3.9/library/typing.html#typing.Literal" title="(in Python v3.9)"><code class="xref py py-data docutils literal notranslate"><span class="pre">Literal</span></code></a>[<code class="docutils literal notranslate"><span class="pre">'numpy'</span></code>, <code class="docutils literal notranslate"><span class="pre">'factor'</span></code>, <code class="docutils literal notranslate"><span class="pre">'list'</span></code>]</span>) – <dl class="simple">
 <dt>Access seqnames as factor codes, in which case, a numpy</dt><dd><p>vector is retuned.</p>
 </dd>
-<dt>If <code class="docutils literal notranslate"><span class="pre">factor</span></code>, a tuple width levels as a dictionary and</dt><dd><p>indices to <code class="docutils literal notranslate"><span class="pre">seqinfo.seqnames</span></code> is returned.</p>
+<dt>If <code class="docutils literal notranslate"><span class="pre">factor</span></code>, a tuple width levels as a dictionary and</dt><dd><p>indices to <code class="docutils literal notranslate"><span class="pre">seqinfo.get_seqnames()</span></code> is returned.</p>
 </dd>
 </dl>
 <p>If <code class="docutils literal notranslate"><span class="pre">list</span></code>, then codes are mapped to levels and returned.</p>
@@ -3199,7 +3199,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=85fdf243"></script>
+</div><script src="../_static/documentation_options.js?v=6de75181"></script>
     <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/scripts/furo.js?v=4e2eecee"></script>