Deploying to gh-pages from @ db759fe 🚀

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: a80e041eefd02a56c8a7a0bcba2662d8
+config: 6b546c3ab49ef3f0969a78606285203b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/biocframe/frame.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>biocframe.frame - BiocFrame 0.7.0 documentation</title>
+        <title>biocframe.frame - BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</div></a>
+      <a href="../../index.html"><div class="brand">BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</span>
+  <span class="sidebar-brand-text">BiocFrame 0.7.1 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">
@@ -367,7 +367,7 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="BiocFrame">
 <a class="viewcode-back" href="../../api/biocframe.html#biocframe.frame.BiocFrame">[docs]</a>
-<span class="k">class</span><span class="w"> </span><span class="nc">BiocFrame</span><span class="p">:</span>
+<span class="k">class</span><span class="w"> </span><span class="nc">BiocFrame</span><span class="p">(</span><span class="n">ut</span><span class="o">.</span><span class="n">BiocObject</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;`BiocFrame` is an alternative to :class:`~pandas.DataFrame`, with support for nested and flexible column types.</span>
 <span class="sd">    Inspired by the ``DFrame`` class from Bioconductor&#39;s **S4Vectors** package. Any object may be used as a column,</span>
 <span class="sd">    provided it has:</span>
@@ -433,6 +433,12 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
 <span class="sd">            _validate:</span>
 <span class="sd">                Internal use only.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span>
+            <span class="n">metadata</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="n">_validate</span><span class="p">,</span>
+        <span class="p">)</span>
+
         <span class="k">if</span> <span class="n">data</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">data</span> <span class="o">=</span> <span class="p">{}</span>
 
@@ -441,7 +447,7 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
             <span class="c1"># making sure all column values are lists</span>
             <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
                 <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
-                    <span class="c1"># if its a scalar, make a list else corce to list</span>
+                    <span class="c1"># if its a scalar, make a list else coerce to list</span>
                     <span class="n">data</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">abc</span><span class="o">.</span><span class="n">Sequence</span><span class="p">)</span> <span class="k">else</span> <span class="p">[</span><span class="n">v</span><span class="p">]</span>
         <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">Sequence</span><span class="p">)</span> <span class="ow">and</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dict</span><span class="p">)):</span>
             <span class="k">if</span> <span class="n">column_names</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -471,20 +477,13 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">_column_names</span> <span class="o">=</span> <span class="n">column_names</span> <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">column_names</span><span class="p">,</span> <span class="n">ut</span><span class="o">.</span><span class="n">Names</span><span class="p">)</span> <span class="k">else</span> <span class="n">ut</span><span class="o">.</span><span class="n">Names</span><span class="p">(</span><span class="n">column_names</span><span class="p">)</span>
 
-        <span class="bp">self</span><span class="o">.</span><span class="n">_metadata</span> <span class="o">=</span> <span class="p">{}</span> <span class="k">if</span> <span class="n">metadata</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">metadata</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">_column_data</span> <span class="o">=</span> <span class="n">column_data</span>
 
         <span class="k">if</span> <span class="n">_validate</span><span class="p">:</span>
             <span class="n">_validate_rows</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_number_of_rows</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_row_names</span><span class="p">)</span>
             <span class="n">_validate_columns</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_column_names</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_column_data</span><span class="p">)</span></div>
 
 
-    <span class="k">def</span><span class="w"> </span><span class="nf">_define_output</span><span class="p">(</span><span class="bp">self</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="n">BiocFrame</span><span class="p">:</span>
-        <span class="k">if</span> <span class="n">in_place</span> <span class="ow">is</span> <span class="kc">True</span><span class="p">:</span>
-            <span class="k">return</span> <span class="bp">self</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">__copy__</span><span class="p">()</span>
-
 <div class="viewcode-block" id="BiocFrame.__eq__">
 <a class="viewcode-back" href="../../api/biocframe.html#biocframe.frame.BiocFrame.__eq__">[docs]</a>
     <span class="k">def</span><span class="w"> </span><span class="fm">__eq__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">other</span><span class="p">:</span> <span class="n">Any</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">bool</span><span class="p">:</span>
@@ -982,57 +981,6 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
         <span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">set_column_data</span><span class="p">(</span><span class="n">column_data</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
-<div class="viewcode-block" id="BiocFrame.get_metadata">
-<a class="viewcode-back" href="../../api/biocframe.html#biocframe.frame.BiocFrame.get_metadata">[docs]</a>
-    <span class="k">def</span><span class="w"> </span><span class="nf">get_metadata</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Get the metadata.</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            Dictionary of metadata for this object.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_metadata</span></div>
-
-
-<div class="viewcode-block" id="BiocFrame.set_metadata">
-<a class="viewcode-back" href="../../api/biocframe.html#biocframe.frame.BiocFrame.set_metadata">[docs]</a>
-    <span class="k">def</span><span class="w"> </span><span class="nf">set_metadata</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">metadata</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="n">Any</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="n">BiocFrame</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Set new metadata.</span>
-
-<span class="sd">        Args:</span>
-<span class="sd">            metadata:</span>
-<span class="sd">                New metadata for this object.</span>
-
-<span class="sd">            in_place:</span>
-<span class="sd">                Whether to modify the ``BiocFrame`` object in place.</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            A modified ``BiocFrame`` object, either as a copy of the original</span>
-<span class="sd">            or as a reference to the (in-place-modified) original.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">metadata</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
-            <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;`metadata` must be a dictionary, provided </span><span class="si">{</span><span class="nb">type</span><span class="p">(</span><span class="n">metadata</span><span class="p">)</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">)</span>
-        <span class="n">output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_define_output</span><span class="p">(</span><span class="n">in_place</span><span class="p">)</span>
-        <span class="n">output</span><span class="o">.</span><span class="n">_metadata</span> <span class="o">=</span> <span class="n">metadata</span>
-        <span class="k">return</span> <span class="n">output</span></div>
-
-
-    <span class="nd">@property</span>
-    <span class="k">def</span><span class="w"> </span><span class="nf">metadata</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Alias for :py:attr:`~get_metadata`.&quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_metadata</span><span class="p">()</span>
-
-    <span class="nd">@metadata</span><span class="o">.</span><span class="n">setter</span>
-    <span class="k">def</span><span class="w"> </span><span class="nf">metadata</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">metadata</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="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Alias for :py:attr:`~set_metadata` with ``in_place = True``.</span>
-
-<span class="sd">        As this mutates the original object, a warning is raised.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">warn</span><span class="p">(</span>
-            <span class="s2">&quot;Setting property &#39;metadata&#39; is an in-place operation, use &#39;set_metadata&#39; instead&quot;</span><span class="p">,</span>
-            <span class="ne">UserWarning</span><span class="p">,</span>
-        <span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">set_metadata</span><span class="p">(</span><span class="n">metadata</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-
     <span class="c1">################################</span>
     <span class="c1">######&gt;&gt; Single getters &lt;&lt;######</span>
     <span class="c1">################################</span>
@@ -2625,7 +2573,7 @@ <h1>Source code for biocframe.frame</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../_static/documentation_options.js?v=fe7df9b0"></script>
+</div><script src="../../_static/documentation_options.js?v=5a057da9"></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/biocframe/io/from_pandas.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>biocframe.io.from_pandas - BiocFrame 0.7.0 documentation</title>
+        <title>biocframe.io.from_pandas - BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</div></a>
+      <a href="../../../index.html"><div class="brand">BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</span>
+  <span class="sidebar-brand-text">BiocFrame 0.7.1 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">
@@ -300,7 +300,7 @@ <h1>Source code for biocframe.io.from_pandas</h1><div class="highlight"><pre>
 
     </aside>
   </div>
-</div><script src="../../../_static/documentation_options.js?v=fe7df9b0"></script>
+</div><script src="../../../_static/documentation_options.js?v=5a057da9"></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/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 - BiocFrame 0.7.0 documentation</title>
+        <title>Overview: module code - BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</div></a>
+      <a href="../index.html"><div class="brand">BiocFrame 0.7.1 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">BiocFrame 0.7.0 documentation</span>
+  <span class="sidebar-brand-text">BiocFrame 0.7.1 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">
@@ -281,7 +281,7 @@ <h1>All modules for which code is available</h1>
 
     </aside>
   </div>
-</div><script src="../_static/documentation_options.js?v=fe7df9b0"></script>
+</div><script src="../_static/documentation_options.js?v=5a057da9"></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>

_static/documentation_options.js

@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.7.0',
+    VERSION: '0.7.1',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',