Skip to content

Commit 55a82be

Browse files
committed
Deploying to gh-pages from @ 7cce3d5 🚀
1 parent 22f83c2 commit 55a82be

23 files changed

Lines changed: 192 additions & 106 deletions

.buildinfo

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: d6a81db725d1523ff60b473f57c98349
3+
config: 384002bc77b4ab6c4b67d534fe9440cf
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../genindex.html"><link rel="search" title="Search" href="../search.html">
66

77
<!-- Generated with Sphinx 8.2.3 and Furo 2025.12.19 -->
8-
<title>Overview: module code - SummarizedExperiment 0.6.4 documentation</title>
8+
<title>Overview: module code - SummarizedExperiment 0.6.5 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
1010
<link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=7bdb33bb" />
1111
<link rel="stylesheet" type="text/css" href="../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
161161
</label>
162162
</div>
163163
<div class="header-center">
164-
<a href="../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
164+
<a href="../index.html"><div class="brand">SummarizedExperiment 0.6.5 documentation</div></a>
165165
</div>
166166
<div class="header-right">
167167
<div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
182182

183183
<div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
184184

185-
<span class="sidebar-brand-text">SummarizedExperiment 0.6.4 documentation</span>
185+
<span class="sidebar-brand-text">SummarizedExperiment 0.6.5 documentation</span>
186186

187187
</a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
188188
<input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -270,7 +270,7 @@ <h1>All modules for which code is available</h1>
270270

271271
</aside>
272272
</div>
273-
</div><script src="../_static/documentation_options.js?v=73d9a94e"></script>
273+
</div><script src="../_static/documentation_options.js?v=d7a12d57"></script>
274274
<script src="../_static/doctools.js?v=9bcbadda"></script>
275275
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
276276
<script src="../_static/scripts/furo.js?v=46bd48cc"></script>

_modules/summarizedexperiment/RangedSummarizedExperiment.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../genindex.html"><link rel="search" title="Search" href="../../search.html">
66

77
<!-- Generated with Sphinx 8.2.3 and Furo 2025.12.19 -->
8-
<title>summarizedexperiment.RangedSummarizedExperiment - SummarizedExperiment 0.6.4 documentation</title>
8+
<title>summarizedexperiment.RangedSummarizedExperiment - SummarizedExperiment 0.6.5 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
1010
<link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=7bdb33bb" />
1111
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
161161
</label>
162162
</div>
163163
<div class="header-center">
164-
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
164+
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.5 documentation</div></a>
165165
</div>
166166
<div class="header-right">
167167
<div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
182182

183183
<div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
184184

185-
<span class="sidebar-brand-text">SummarizedExperiment 0.6.4 documentation</span>
185+
<span class="sidebar-brand-text">SummarizedExperiment 0.6.5 documentation</span>
186186

187187
</a><form class="sidebar-search-container" method="get" action="../../search.html" role="search">
188188
<input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -1526,7 +1526,7 @@ <h1>Source code for summarizedexperiment.RangedSummarizedExperiment</h1><div cla
15261526

15271527
</aside>
15281528
</div>
1529-
</div><script src="../../_static/documentation_options.js?v=73d9a94e"></script>
1529+
</div><script src="../../_static/documentation_options.js?v=d7a12d57"></script>
15301530
<script src="../../_static/doctools.js?v=9bcbadda"></script>
15311531
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
15321532
<script src="../../_static/scripts/furo.js?v=46bd48cc"></script>

_modules/summarizedexperiment/SummarizedExperiment.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../genindex.html"><link rel="search" title="Search" href="../../search.html">
66

77
<!-- Generated with Sphinx 8.2.3 and Furo 2025.12.19 -->
8-
<title>summarizedexperiment.SummarizedExperiment - SummarizedExperiment 0.6.4 documentation</title>
8+
<title>summarizedexperiment.SummarizedExperiment - SummarizedExperiment 0.6.5 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
1010
<link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=7bdb33bb" />
1111
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
161161
</label>
162162
</div>
163163
<div class="header-center">
164-
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
164+
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.5 documentation</div></a>
165165
</div>
166166
<div class="header-right">
167167
<div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
182182

183183
<div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
184184

185-
<span class="sidebar-brand-text">SummarizedExperiment 0.6.4 documentation</span>
185+
<span class="sidebar-brand-text">SummarizedExperiment 0.6.5 documentation</span>
186186

187187
</a><form class="sidebar-search-container" method="get" action="../../search.html" role="search">
188188
<input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -615,7 +615,7 @@ <h1>Source code for summarizedexperiment.SummarizedExperiment</h1><div class="hi
615615

616616
</aside>
617617
</div>
618-
</div><script src="../../_static/documentation_options.js?v=73d9a94e"></script>
618+
</div><script src="../../_static/documentation_options.js?v=d7a12d57"></script>
619619
<script src="../../_static/doctools.js?v=9bcbadda"></script>
620620
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
621621
<script src="../../_static/scripts/furo.js?v=46bd48cc"></script>

_modules/summarizedexperiment/base.html

Lines changed: 47 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../genindex.html"><link rel="search" title="Search" href="../../search.html">
66

77
<!-- Generated with Sphinx 8.2.3 and Furo 2025.12.19 -->
8-
<title>summarizedexperiment.base - SummarizedExperiment 0.6.4 documentation</title>
8+
<title>summarizedexperiment.base - SummarizedExperiment 0.6.5 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
1010
<link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=7bdb33bb" />
1111
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
161161
</label>
162162
</div>
163163
<div class="header-center">
164-
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
164+
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.5 documentation</div></a>
165165
</div>
166166
<div class="header-right">
167167
<div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
182182

183183
<div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
184184

185-
<span class="sidebar-brand-text">SummarizedExperiment 0.6.4 documentation</span>
185+
<span class="sidebar-brand-text">SummarizedExperiment 0.6.5 documentation</span>
186186

187187
</a><form class="sidebar-search-container" method="get" action="../../search.html" role="search">
188188
<input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -1511,9 +1511,9 @@ <h1>Source code for summarizedexperiment.base</h1><div class="highlight"><pre>
15111511
<span class="k">return</span> <span class="n">obj</span></div>
15121512

15131513

1514-
<span class="c1">######################################</span>
1515-
<span class="c1">######&gt;&gt; col_data accessors &lt;&lt;########</span>
1516-
<span class="c1">######################################</span>
1514+
<span class="c1">##########################################</span>
1515+
<span class="c1">######&gt;&gt; col/row data accessors &lt;&lt;########</span>
1516+
<span class="c1">##########################################</span>
15171517

15181518
<div class="viewcode-block" id="BaseSE.get_column_data_column">
15191519
<a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.base.BaseSE.get_column_data_column">[docs]</a>
@@ -1550,7 +1550,46 @@ <h1>Source code for summarizedexperiment.base</h1><div class="highlight"><pre>
15501550
<span class="sd"> or as a reference to the (in-place-modified) original.</span>
15511551
<span class="sd"> &quot;&quot;&quot;</span>
15521552
<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>
1553-
<span class="n">output</span><span class="o">.</span><span class="n">_cols</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">_cols</span><span class="o">.</span><span class="n">set_column</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
1553+
<span class="n">output</span><span class="o">.</span><span class="n">_cols</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">_cols</span><span class="o">.</span><span class="n">set_column</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="n">in_place</span><span class="p">)</span>
1554+
<span class="k">return</span> <span class="n">output</span></div>
1555+
1556+
1557+
<div class="viewcode-block" id="BaseSE.get_row_data_column">
1558+
<a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.base.BaseSE.get_row_data_column">[docs]</a>
1559+
<span class="k">def</span><span class="w"> </span><span class="nf">get_row_data_column</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Any</span><span class="p">:</span>
1560+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Access a column from the ``row_data``.</span>
1561+
1562+
<span class="sd"> Args:</span>
1563+
<span class="sd"> column:</span>
1564+
<span class="sd"> Name of the column to retrieve.</span>
1565+
1566+
<span class="sd"> Returns:</span>
1567+
<span class="sd"> The content of the column.</span>
1568+
<span class="sd"> &quot;&quot;&quot;</span>
1569+
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_rows</span><span class="o">.</span><span class="n">get_column</span><span class="p">(</span><span class="n">column</span><span class="p">)</span></div>
1570+
1571+
1572+
<div class="viewcode-block" id="BaseSE.set_row_data_column">
1573+
<a class="viewcode-back" href="../../api/summarizedexperiment.html#summarizedexperiment.base.BaseSE.set_row_data_column">[docs]</a>
1574+
<span class="k">def</span><span class="w"> </span><span class="nf">set_row_data_column</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">column</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">value</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">BaseSE</span><span class="p">:</span>
1575+
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Set or replace a column in ``row_data``.</span>
1576+
1577+
<span class="sd"> Args:</span>
1578+
<span class="sd"> column:</span>
1579+
<span class="sd"> Name of the column to set.</span>
1580+
1581+
<span class="sd"> value:</span>
1582+
<span class="sd"> Values for the column. Must match the number of features (rows).</span>
1583+
1584+
<span class="sd"> in_place:</span>
1585+
<span class="sd"> Whether to modify the ``BaseSE`` in place.</span>
1586+
1587+
<span class="sd"> Returns:</span>
1588+
<span class="sd"> A modified ``BaseSE`` object, either as a copy of the original</span>
1589+
<span class="sd"> or as a reference to the (in-place-modified) original.</span>
1590+
<span class="sd"> &quot;&quot;&quot;</span>
1591+
<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>
1592+
<span class="n">output</span><span class="o">.</span><span class="n">_rows</span> <span class="o">=</span> <span class="n">output</span><span class="o">.</span><span class="n">_rows</span><span class="o">.</span><span class="n">set_column</span><span class="p">(</span><span class="n">column</span><span class="p">,</span> <span class="n">value</span><span class="p">,</span> <span class="n">in_place</span><span class="o">=</span><span class="n">in_place</span><span class="p">)</span>
15541593
<span class="k">return</span> <span class="n">output</span></div>
15551594
</div>
15561595

@@ -1586,7 +1625,7 @@ <h1>Source code for summarizedexperiment.base</h1><div class="highlight"><pre>
15861625

15871626
</aside>
15881627
</div>
1589-
</div><script src="../../_static/documentation_options.js?v=73d9a94e"></script>
1628+
</div><script src="../../_static/documentation_options.js?v=d7a12d57"></script>
15901629
<script src="../../_static/doctools.js?v=9bcbadda"></script>
15911630
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
15921631
<script src="../../_static/scripts/furo.js?v=46bd48cc"></script>

_modules/summarizedexperiment/type_checks.html

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="../../genindex.html"><link rel="search" title="Search" href="../../search.html">
66

77
<!-- Generated with Sphinx 8.2.3 and Furo 2025.12.19 -->
8-
<title>summarizedexperiment.type_checks - SummarizedExperiment 0.6.4 documentation</title>
8+
<title>summarizedexperiment.type_checks - SummarizedExperiment 0.6.5 documentation</title>
99
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=03e43079" />
1010
<link rel="stylesheet" type="text/css" href="../../_static/styles/furo.css?v=7bdb33bb" />
1111
<link rel="stylesheet" type="text/css" href="../../_static/mystnb.8ecb98da25f57f5357bf6f572d296f466b2cfe2517ffebfabe82451661e28f02.css" />
@@ -161,7 +161,7 @@
161161
</label>
162162
</div>
163163
<div class="header-center">
164-
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.4 documentation</div></a>
164+
<a href="../../index.html"><div class="brand">SummarizedExperiment 0.6.5 documentation</div></a>
165165
</div>
166166
<div class="header-right">
167167
<div class="theme-toggle-container theme-toggle-header">
@@ -182,7 +182,7 @@
182182

183183
<div class="sidebar-sticky"><a class="sidebar-brand" href="../../index.html">
184184

185-
<span class="sidebar-brand-text">SummarizedExperiment 0.6.4 documentation</span>
185+
<span class="sidebar-brand-text">SummarizedExperiment 0.6.5 documentation</span>
186186

187187
</a><form class="sidebar-search-container" method="get" action="../../search.html" role="search">
188188
<input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -326,7 +326,7 @@ <h1>Source code for summarizedexperiment.type_checks</h1><div class="highlight">
326326

327327
</aside>
328328
</div>
329-
</div><script src="../../_static/documentation_options.js?v=73d9a94e"></script>
329+
</div><script src="../../_static/documentation_options.js?v=d7a12d57"></script>
330330
<script src="../../_static/doctools.js?v=9bcbadda"></script>
331331
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
332332
<script src="../../_static/scripts/furo.js?v=46bd48cc"></script>

_sources/changelog.md.txt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
# Changelog
22

3-
## Version 0.6.0 - 0.6.4
3+
## Version 0.6.0 - 0.6.5
44

55
- Classes now extend `BiocObject` from biocutils, which provides a metadata field.
66
- `valdiate` is renamed to `_validate` for consistency with other classes and packages.

_static/documentation_options.js

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
const DOCUMENTATION_OPTIONS = {
2-
VERSION: '0.6.4',
2+
VERSION: '0.6.5',
33
LANGUAGE: 'en',
44
COLLAPSE_INDEX: false,
55
BUILDER: 'html',

0 commit comments

Comments
 (0)