Deploying to gh-pages from @ 54a89ad 🚀

Author: jkanche

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: a154bff7e2351a7d3ba2a9eef4c86de0
+config: d6a81db725d1523ff60b473f57c98349
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -5,7 +5,7 @@
     <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 8.2.3 and Furo 2025.12.19 -->
-        <title>Overview: module code - SummarizedExperiment 0.6.3 documentation</title>
+        <title>Overview: module code - SummarizedExperiment 0.6.4 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=7bdb33bb" />
     <link rel="stylesheet" type="text/css" href="../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../index.html"><div class="brand">SummarizedExperiment 0.6.3 documentation</div></a>
+      <a href="../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
 
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
-  <span class="sidebar-brand-text">SummarizedExperiment 0.6.3 documentation</span>
+  <span class="sidebar-brand-text">SummarizedExperiment 0.6.4 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">
@@ -270,7 +270,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=b8503983"></script>
+</div><script src="../_static/documentation_options.js?v=73d9a94e"></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=46bd48cc"></script>

_modules/summarizedexperiment/RangedSummarizedExperiment.html

@@ -5,7 +5,7 @@
     <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 8.2.3 and Furo 2025.12.19 -->
-        <title>summarizedexperiment.RangedSummarizedExperiment - SummarizedExperiment 0.6.3 documentation</title>
+        <title>summarizedexperiment.RangedSummarizedExperiment - SummarizedExperiment 0.6.4 documentation</title>
       <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
     <link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=7bdb33bb" />
     <link rel="stylesheet" type="text/css" href="../../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.3 documentation</div></a>
+      <a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
 
       <div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
 
-  <span class="sidebar-brand-text">SummarizedExperiment 0.6.3 documentation</span>
+  <span class="sidebar-brand-text">SummarizedExperiment 0.6.4 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">
@@ -1258,20 +1258,63 @@ <h1>Source code for summarizedexperiment.RangedSummarizedExperiment</h1><div cla
     <span class="c1">######&gt;&gt; to se &lt;&lt;#####</span>
     <span class="c1">######################</span>
 
+<div class="viewcode-block" id="RangedSummarizedExperiment.from_summarizedexperiment">
+<a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment.from_summarizedexperiment">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">from_summarizedexperiment</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">se</span><span class="p">:</span> <span class="n">SummarizedExperiment</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">RangedSummarizedExperiment</span><span class="p">:</span>
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
+            <span class="n">assays</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_assays</span><span class="p">(),</span>
+            <span class="n">row_data</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_row_data</span><span class="p">(),</span>
+            <span class="n">column_data</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_column_data</span><span class="p">(),</span>
+            <span class="n">row_names</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_row_names</span><span class="p">(),</span>
+            <span class="n">column_names</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_column_names</span><span class="p">(),</span>
+            <span class="n">metadata</span><span class="o">=</span><span class="n">se</span><span class="o">.</span><span class="n">get_metadata</span><span class="p">(),</span>
+        <span class="p">)</span></div>
+
+
+<div class="viewcode-block" id="RangedSummarizedExperiment.from_se">
+<a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment.from_se">[docs]</a>
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span><span class="w"> </span><span class="nf">from_se</span><span class="p">(</span><span class="bp">cls</span><span class="p">,</span> <span class="n">se</span><span class="p">:</span> <span class="n">SummarizedExperiment</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">RangedSummarizedExperiment</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Alias for :py:meth:`~to_summarizedexperiment`.&quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">RangedSummarizedExperiment</span><span class="o">.</span><span class="n">from_summarizedexperiment</span><span class="p">(</span><span class="n">se</span><span class="p">)</span></div>
+
+
 <div class="viewcode-block" id="RangedSummarizedExperiment.to_summarizedexperiment">
 <a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.RangedSummarizedExperiment.RangedSummarizedExperiment.to_summarizedexperiment">[docs]</a>
     <span class="k">def</span><span class="w"> </span><span class="nf">to_summarizedexperiment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Coerce to :py:class:`summarizedexperiment.SummarizedExperiment.SummarizedExperiment`&quot;&quot;&quot;</span>
 
-        <span class="n">warn</span><span class="p">(</span><span class="s2">&quot;SE does not containg a slot for ranges, dropping ranges.&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span>
+        <span class="n">warn</span><span class="p">(</span><span class="s2">&quot;SE does not containg a slot for ranges, merging ranges with row_data.&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span>
+
+        <span class="n">new_row_data</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rows</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_row_ranges</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">try</span><span class="p">:</span>
+                <span class="kn">import</span><span class="w"> </span><span class="nn">copy</span>
+
+                <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_row_ranges</span><span class="p">,</span> <span class="n">CompressedGenomicRangesList</span><span class="p">):</span>
+                    <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_row_ranges</span><span class="o">.</span><span class="n">get_unlist_data</span><span class="p">()</span><span class="o">.</span><span class="n">to_pandas</span><span class="p">()</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_row_ranges</span><span class="o">.</span><span class="n">to_pandas</span><span class="p">()</span>
+
+                <span class="n">range_bf</span> <span class="o">=</span> <span class="n">biocframe</span><span class="o">.</span><span class="n">BiocFrame</span><span class="o">.</span><span class="n">from_pandas</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">new_row_data</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">new_row_data</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                    <span class="n">new_row_data</span> <span class="o">=</span> <span class="n">range_bf</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">new_row_data</span> <span class="o">=</span> <span class="n">copy</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">new_row_data</span><span class="p">)</span>
+                    <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">range_bf</span><span class="o">.</span><span class="n">column_names</span><span class="p">:</span>
+                        <span class="n">new_row_data</span><span class="p">[</span><span class="n">col</span><span class="p">]</span> <span class="o">=</span> <span class="n">range_bf</span><span class="p">[</span><span class="n">col</span><span class="p">]</span>
+            <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+                <span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Failed to transfer row_ranges to row_data: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span> <span class="ne">UserWarning</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="n">SummarizedExperiment</span><span class="p">(</span>
             <span class="n">assays</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_assays</span><span class="p">,</span>
-            <span class="n">row_data</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_rows</span><span class="p">,</span>
+            <span class="n">row_data</span><span class="o">=</span><span class="n">new_row_data</span><span class="p">,</span>
             <span class="n">column_data</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_cols</span><span class="p">,</span>
             <span class="n">row_names</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_row_names</span><span class="p">,</span>
             <span class="n">column_names</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_column_names</span><span class="p">,</span>
             <span class="n">metadata</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_metadata</span><span class="p">,</span>
+            <span class="n">_validate</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
         <span class="p">)</span></div>
 
 
@@ -1483,7 +1526,7 @@ <h1>Source code for summarizedexperiment.RangedSummarizedExperiment</h1><div cla
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=b8503983"></script>
+</div><script src="../../_static/documentation_options.js?v=73d9a94e"></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=46bd48cc"></script>