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diff --git a/.buildinfo b/.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: 447a37606b06e77bd4d352b6e07b819e
+config: 383563ece671bf12412f2e0552721ff9
 tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/_modules/index.html b/_modules/index.html
@@ -5,15 +5,15 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; paste3 1.2.0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
+  <title>Overview: module code &mdash; paste3 src documentation</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=b86133f3" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
       <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
 
 
       <script src="../_static/jquery.js?v=5d32c60e"></script>
       <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../_static/documentation_options.js?v=60341314"></script>
+      <script src="../_static/documentation_options.js?v=c8155056"></script>
       <script src="../_static/doctools.js?v=9bcbadda"></script>
       <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
       <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
@@ -43,6 +43,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../api.html">API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorials</a></li>
 </ul>
@@ -71,8 +72,7 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="paste3/glmpca.html">paste3.glmpca</a></li>
-<li><a href="paste3/helper.html">paste3.helper</a></li>
+<ul><li><a href="paste3/helper.html">paste3.helper</a></li>
 <li><a href="paste3/model_selection.html">paste3.model_selection</a></li>
 <li><a href="paste3/paste.html">paste3.paste</a></li>
 <li><a href="paste3/visualization.html">paste3.visualization</a></li>
@@ -85,7 +85,7 @@ <h1>All modules for which code is available</h1>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022, Raphael Lab.</p>
+    <p>&#169; Copyright 2024, Raphael Lab.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/_modules/paste3/glmpca.html b/_modules/paste3/glmpca.html
diff --git a/_modules/paste3/helper.html b/_modules/paste3/helper.html
diff --git a/_modules/paste3/model_selection.html b/_modules/paste3/model_selection.html
@@ -5,15 +5,15 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>paste3.model_selection &mdash; paste3 1.2.0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
+  <title>paste3.model_selection &mdash; paste3 src documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b86133f3" />
       <link rel="stylesheet" type="text/css" href="../../_static/css/theme.css?v=e59714d7" />
       <link rel="stylesheet" type="text/css" href="../../_static/sg_gallery.css?v=d2d258e8" />
 
 
       <script src="../../_static/jquery.js?v=5d32c60e"></script>
       <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../../_static/documentation_options.js?v=60341314"></script>
+      <script src="../../_static/documentation_options.js?v=c8155056"></script>
       <script src="../../_static/doctools.js?v=9bcbadda"></script>
       <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
       <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
@@ -43,6 +43,7 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
+<li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../api.html">API</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../tutorial.html">Tutorials</a></li>
 </ul>
@@ -77,25 +78,27 @@ <h1>Source code for paste3.model_selection</h1><div class="highlight"><pre>
 <span class="sd">two partially overlapped slices.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
-<span class="kn">import</span> <span class="nn">logging</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
 
-<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
-<span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-<span class="kn">import</span> <span class="nn">torch</span>
-<span class="kn">from</span> <span class="nn">matplotlib.path</span> <span class="kn">import</span> <span class="n">Path</span>
-<span class="kn">from</span> <span class="nn">scipy.spatial</span> <span class="kn">import</span> <span class="n">ConvexHull</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">matplotlib.pyplot</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">plt</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">networkx</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">nx</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">torch</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">matplotlib.path</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">scipy.spatial</span><span class="w"> </span><span class="kn">import</span> <span class="n">ConvexHull</span>
 
-<span class="kn">from</span> <span class="nn">paste3.helper</span> <span class="kn">import</span> <span class="p">(</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">paste3.helper</span><span class="w"> </span><span class="kn">import</span> <span class="p">(</span>
     <span class="n">get_common_genes</span><span class="p">,</span>
     <span class="n">glmpca_distance</span><span class="p">,</span>
     <span class="n">to_dense_array</span><span class="p">,</span>
 <span class="p">)</span>
-<span class="kn">from</span> <span class="nn">paste3.paste</span> <span class="kn">import</span> <span class="n">pairwise_align</span>
+<span class="kn">from</span><span class="w"> </span><span class="nn">paste3.paste</span><span class="w"> </span><span class="kn">import</span> <span class="n">pairwise_align</span>
 
 <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span>
 
 
-<span class="k">def</span> <span class="nf">generate_graph</span><span class="p">(</span><span class="nb">slice</span><span class="p">,</span> <span class="n">aligned_spots</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">degree</span><span class="o">=</span><span class="mi">4</span><span class="p">):</span>
+<div class="viewcode-block" id="generate_graph">
+<a class="viewcode-back" href="../../api/paste3.model_selection.generate_graph.html#paste3.model_selection.generate_graph">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">generate_graph</span><span class="p">(</span><span class="nb">slice</span><span class="p">,</span> <span class="n">aligned_spots</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">degree</span><span class="o">=</span><span class="mi">4</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Generates a graph using the networkx library where each node represents a spot</span>
 <span class="sd">    from the given `slice` object, and edges are formed between each node and its</span>
@@ -144,10 +147,13 @@ <h1>Source code for paste3.model_selection</h1><div class="highlight"><pre>
             <span class="k">if</span> <span class="nb">slice</span><span class="o">.</span><span class="n">obs</span><span class="o">.</span><span class="n">index</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">spot</span><span class="p">)]</span> <span class="ow">in</span> <span class="n">aligned_spots</span><span class="p">:</span>
                 <span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">spot</span><span class="p">))</span>
 
-    <span class="k">return</span> <span class="n">G</span><span class="p">,</span> <span class="p">{</span><span class="n">n</span><span class="p">:</span> <span class="n">aligned_spots</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">}</span>
+    <span class="k">return</span> <span class="n">G</span><span class="p">,</span> <span class="p">{</span><span class="n">n</span><span class="p">:</span> <span class="n">aligned_spots</span><span class="p">[</span><span class="n">n</span><span class="p">]</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">}</span></div>
 
 
-<span class="k">def</span> <span class="nf">convex_hull_edge_inconsistency</span><span class="p">(</span><span class="nb">slice</span><span class="p">,</span> <span class="n">pi</span><span class="p">,</span> <span class="n">axis</span><span class="p">):</span>
+
+<div class="viewcode-block" id="convex_hull_edge_inconsistency">
+<a class="viewcode-back" href="../../api/paste3.model_selection.convex_hull_edge_inconsistency.html#paste3.model_selection.convex_hull_edge_inconsistency">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">convex_hull_edge_inconsistency</span><span class="p">(</span><span class="nb">slice</span><span class="p">,</span> <span class="n">pi</span><span class="p">,</span> <span class="n">axis</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Computes the edge inconsistency score for a convex hull formed by the aligned spots</span>
 <span class="sd">    in a slice, based on their probability masses (:math:`\pi`). This score reflects</span>
@@ -203,23 +209,23 @@ <h1>Source code for paste3.model_selection</h1><div class="highlight"><pre>
     <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">edges</span><span class="p">():</span>
         <span class="n">C</span><span class="p">[</span><span class="n">label</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">]]][</span><span class="n">label</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]]]</span> <span class="o">+=</span> <span class="mi">1</span>
 
-    <span class="k">return</span> <span class="nb">float</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">C</span><span class="p">)</span> <span class="o">-</span> <span class="n">torch</span><span class="o">.</span><span class="n">trace</span><span class="p">(</span><span class="n">C</span><span class="p">))</span> <span class="o">/</span> <span class="n">torch</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">C</span><span class="p">)</span>
+    <span class="k">return</span> <span class="nb">float</span><span class="p">(</span><span class="n">torch</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">C</span><span class="p">)</span> <span class="o">-</span> <span class="n">torch</span><span class="o">.</span><span class="n">trace</span><span class="p">(</span><span class="n">C</span><span class="p">))</span> <span class="o">/</span> <span class="n">torch</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">C</span><span class="p">)</span></div>
+
 
 
-<div class="viewcode-block" id="plot_edge_curve">
-<a class="viewcode-back" href="../../api/paste3.model_selection.plot_edge_curve.html#paste3.model_selection.plot_edge_curve">[docs]</a>
-<span class="k">def</span> <span class="nf">plot_edge_curve</span><span class="p">(</span><span class="n">overlap_fractions</span><span class="p">,</span> <span class="n">inconsistency_scores</span><span class="p">,</span> <span class="n">ax</span><span class="p">,</span> <span class="n">title</span><span class="p">):</span>
+<span class="k">def</span><span class="w"> </span><span class="nf">plot_edge_curve</span><span class="p">(</span><span class="n">overlap_fractions</span><span class="p">,</span> <span class="n">inconsistency_scores</span><span class="p">,</span> <span class="n">ax</span><span class="p">,</span> <span class="n">title</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Plots inconsistency_scores in relation to overlap fractions in a given axis&quot;&quot;&quot;</span>
     <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">overlap_fractions</span><span class="p">,</span> <span class="n">inconsistency_scores</span><span class="p">)</span>
     <span class="n">ax</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
     <span class="n">ax</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">([</span><span class="mf">0.99</span><span class="p">,</span> <span class="mf">0.9</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span> <span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.6</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="mf">0.3</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">])</span>
     <span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Overlap Fraction&quot;</span><span class="p">)</span>
     <span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;Edge Inconsistency Score&quot;</span><span class="p">)</span>
-    <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="n">title</span><span class="p">)</span></div>
+    <span class="n">ax</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span><span class="n">title</span><span class="p">)</span>
 
 
-
-<span class="k">def</span> <span class="nf">select_overlap_fraction</span><span class="p">(</span>
+<div class="viewcode-block" id="select_overlap_fraction">
+<a class="viewcode-back" href="../../api/paste3.model_selection.select_overlap_fraction.html#paste3.model_selection.select_overlap_fraction">[docs]</a>
+<span class="k">def</span><span class="w"> </span><span class="nf">select_overlap_fraction</span><span class="p">(</span>
     <span class="n">a_slice</span><span class="p">,</span> <span class="n">b_slice</span><span class="p">,</span> <span class="n">alpha</span><span class="o">=</span><span class="mf">0.1</span><span class="p">,</span> <span class="n">show_plot</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">numItermax</span><span class="o">=</span><span class="mi">1000</span>
 <span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
@@ -293,7 +299,8 @@ <h1>Source code for paste3.model_selection</h1><div class="highlight"><pre>
 
     <span class="n">estimated_overlap_fraction</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="nb">min</span><span class="p">(</span><span class="n">half_estimate_a</span><span class="p">,</span> <span class="n">half_estimate_b</span><span class="p">),</span> <span class="mi">1</span><span class="p">)</span>
     <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Estimation of overlap percentage is </span><span class="si">{</span><span class="n">estimated_overlap_fraction</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">estimated_overlap_fraction</span>
+    <span class="k">return</span> <span class="n">estimated_overlap_fraction</span></div>
+
 </pre></div>
 
            </div>
@@ -303,7 +310,7 @@ <h1>Source code for paste3.model_selection</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022, Raphael Lab.</p>
+    <p>&#169; Copyright 2024, Raphael Lab.</p>
   </div>
 
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