Deploying to gh-pages from @ de42252 🚀

Author: cklamann

Diff for: _modules/starling/utility.html

@@ -89,6 +89,8 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">scanpy.external</span> <span class="k">as</span> <span class="nn">sce</span>
 <span class="kn">import</span> <span class="nn">torch</span>
 
+<span class="c1"># patch outdated flowsom dependencies</span>
+<span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">as_matrix</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="o">.</span><span class="n">to_numpy</span>
 <span class="n">collections</span><span class="o">.</span><span class="n">MutableMapping</span> <span class="o">=</span> <span class="n">abc</span><span class="o">.</span><span class="n">MutableMapping</span>
 <span class="kn">from</span> <span class="nn">flowsom</span> <span class="kn">import</span> <span class="n">flowsom</span>
 <span class="kn">from</span> <span class="nn">scanpy</span> <span class="kn">import</span> <span class="n">AnnData</span>
@@ -192,7 +194,7 @@ <h1>Source code for starling.utility</h1><div class="highlight"><pre>
     <span class="k">elif</span> <span class="n">initial_clustering_method</span> <span class="o">==</span> <span class="s2">&quot;FS&quot;</span><span class="p">:</span>
         <span class="c1">## needs to output to csv first</span>
         <span class="c1"># ofn = OPATH + &quot;fs_&quot; + ONAME + &quot;.csv&quot;</span>
-        <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">X</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;fs.csv&quot;</span><span class="p">)</span>
+        <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">adata</span><span class="o">.</span><span class="n">X</span><span class="p">)</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="s2">&quot;fs.csv&quot;</span><span class="p">)</span>
         <span class="n">fsom</span> <span class="o">=</span> <span class="n">flowsom</span><span class="p">(</span><span class="s2">&quot;fs.csv&quot;</span><span class="p">,</span> <span class="n">if_fcs</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">if_drop</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">drop_col</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;Unnamed: 0&quot;</span><span class="p">])</span>
 
         <span class="n">fsom</span><span class="o">.</span><span class="n">som_mapping</span><span class="p">(</span>

Diff for: _static/searchtools.js

@@ -178,7 +178,7 @@ const Search = {
 
   htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    for (const removalQuery of [".headerlinks", "script", "style"]) {
+    for (const removalQuery of [".headerlink", "script", "style"]) {
       htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
     }
     if (anchor) {
@@ -328,13 +328,14 @@ const Search = {
     for (const [title, foundTitles] of Object.entries(allTitles)) {
       if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
           normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }

Diff for: index.html

@@ -87,7 +87,9 @@
 <h1>SegmentaTion AwaRe cLusterING (STARLING)<a class="headerlink" href="#segmentation-aware-clustering-starling" title="Link to this heading"></a></h1>
 <p><img alt="build" src="https://github.com/camlab-bioml/starling/actions/workflows/main.yml/badge.svg" />
 <img alt="" src="https://img.shields.io/badge/Python-3.9-blue" />
-<img alt="" src="https://img.shields.io/badge/Python-3.10-blue" /></p>
+<img alt="" src="https://img.shields.io/badge/Python-3.10-blue" />
+<img alt="" src="https://img.shields.io/badge/Python-3.11-blue" />
+<img alt="" src="https://img.shields.io/badge/Python-3.12-blue" /></p>
 <p>STARLING is a probabilistic model for clustering cells measured with spatial expression assays (e.g. IMC, MIBI, etc…) while accounting for segmentation errors.</p>
 <p>It outputs:</p>
 <ol class="arabic simple">