fix build

dpeerlab · Apr 24, 2024 · fb73a08 · fb73a08
1 parent 1a0e2c9
commit fb73a08
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Showing 12 changed files with 40 additions and 65 deletions.
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/pre_built_html/.buildinfo b/docs/build/pre_built_html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 152f64c0f9d013d1a63b3ca9cd441292
+config: ef9216dd0783c9a330a1f77e3b1bbc54
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/pre_built_html/ENVI.html b/docs/build/pre_built_html/ENVI.html
@@ -3,10 +3,10 @@
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
-<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Utilities" href="utils.html" /><link rel="prev" title="ENVI Tutorial" href="notebooks/MOp_MERFISH_tutorial.html" />
+<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="Utilities" href="utils.html" /><link rel="prev" title="ENVI &amp; COVET" href="index.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
-        <title>ENVI - scenvi 3.0.2 documentation</title>
+        <title>ENVI - scenvi 0.3.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
@@ -123,7 +123,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">scenvi 3.0.2 documentation</div></a>
+      <a href="index.html"><div class="brand">scenvi 0.3.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -146,19 +146,15 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
-  <span class="sidebar-brand-text">scenvi 3.0.2 documentation</span>
+  <span class="sidebar-brand-text">scenvi 0.3.2 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">
   <input type="hidden" name="check_keywords" value="yes">
   <input type="hidden" name="area" value="default">
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
-  <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="notebooks/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
+  <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul class="current">
 <li class="toctree-l1 current current-page"><a class="current reference internal" href="#">ENVI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Utilities</a></li>
@@ -318,14 +314,14 @@
               </div>
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
             </a>
-          <a class="prev-page" href="notebooks/MOp_MERFISH_tutorial.html">
+          <a class="prev-page" href="index.html">
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
               <div class="page-info">
                 <div class="context">
                   <span>Previous</span>
                 </div>
 
-                <div class="title">ENVI Tutorial</div>
+                <div class="title">Home</div>
 
               </div>
             </a>
@@ -379,7 +375,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=3f474186"></script>
+</div><script src="_static/documentation_options.js?v=71d9d8e6"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/build/pre_built_html/_static/documentation_options.js b/docs/build/pre_built_html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '3.0.2',
+    VERSION: '0.3.2',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/pre_built_html/genindex.html b/docs/build/pre_built_html/genindex.html
@@ -4,7 +4,7 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />
 
-    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Index - scenvi 3.0.2 documentation</title>
+    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Index - scenvi 0.3.2 documentation</title>
 <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
@@ -121,7 +121,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">scenvi 3.0.2 documentation</div></a>
+      <a href="index.html"><div class="brand">scenvi 0.3.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -144,19 +144,15 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
-  <span class="sidebar-brand-text">scenvi 3.0.2 documentation</span>
+  <span class="sidebar-brand-text">scenvi 0.3.2 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">
   <input type="hidden" name="check_keywords" value="yes">
   <input type="hidden" name="area" value="default">
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
-  <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="notebooks/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
+  <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Utilities</a></li>
@@ -327,7 +323,7 @@ <h2>T</h2>
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=3f474186"></script>
+</div><script src="_static/documentation_options.js?v=71d9d8e6"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/build/pre_built_html/index.html b/docs/build/pre_built_html/index.html
@@ -3,10 +3,10 @@
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><meta name="viewport" content="width=device-width, initial-scale=1" />
-<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="ENVI Tutorial" href="notebooks/MOp_MERFISH_tutorial.html" />
+<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="ENVI" href="ENVI.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
-        <title>scenvi 3.0.2 documentation</title>
+        <title>scenvi 0.3.2 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
@@ -123,7 +123,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="#"><div class="brand">scenvi 3.0.2 documentation</div></a>
+      <a href="#"><div class="brand">scenvi 0.3.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -146,19 +146,15 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="#">
 
 
-  <span class="sidebar-brand-text">scenvi 3.0.2 documentation</span>
+  <span class="sidebar-brand-text">scenvi 0.3.2 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">
   <input type="hidden" name="check_keywords" value="yes">
   <input type="hidden" name="area" value="default">
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
-  <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="notebooks/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
+  <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Utilities</a></li>
@@ -241,6 +237,7 @@ <h1>ENVI &amp; COVET<a class="headerlink" href="#envi-covet" title="Link to this
 <div class="highlight-none notranslate"><div class="highlight"><pre><span></span>st_data.obsm[&#39;COVET&#39;], st_data.obsm[&#39;COVET_SQRT&#39;], st_data.uns[&#39;CovGenes&#39;] = scenvi.compute_covet(st_data)
 </pre></div>
 </div>
+<p>Please read our documentation at <a class="reference external" href="https://scenvi.readthedocs.io/">https://scenvi.readthedocs.io/</a> for more details!</p>
 </section>
 <section id="index">
 <h1>Index<a class="headerlink" href="#index" title="Link to this heading">¶</a></h1>
@@ -254,12 +251,12 @@ <h1>Index<a class="headerlink" href="#index" title="Link to this heading">¶</a>
       <footer>
 
         <div class="related-pages">
-          <a class="next-page" href="notebooks/MOp_MERFISH_tutorial.html">
+          <a class="next-page" href="ENVI.html">
               <div class="page-info">
                 <div class="context">
                   <span>Next</span>
                 </div>
-                <div class="title">ENVI Tutorial</div>
+                <div class="title">ENVI</div>
               </div>
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
             </a>
@@ -288,12 +285,10 @@ <h1>Index<a class="headerlink" href="#index" title="Link to this heading">¶</a>
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=3f474186"></script>
+</div><script src="_static/documentation_options.js?v=71d9d8e6"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></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>
-    <script>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
-    <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     </body>
 </html>
diff --git a/docs/build/pre_built_html/objects.inv b/docs/build/pre_built_html/objects.inv
diff --git a/docs/build/pre_built_html/py-modindex.html b/docs/build/pre_built_html/py-modindex.html
@@ -4,7 +4,7 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <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 7.3.7 and Furo 2024.01.29 --><title>Python Module Index - scenvi 3.0.2 documentation</title>
+    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Python Module Index - scenvi 0.3.2 documentation</title>
 <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
@@ -121,7 +121,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">scenvi 3.0.2 documentation</div></a>
+      <a href="index.html"><div class="brand">scenvi 0.3.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -144,19 +144,15 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
-  <span class="sidebar-brand-text">scenvi 3.0.2 documentation</span>
+  <span class="sidebar-brand-text">scenvi 0.3.2 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">
   <input type="hidden" name="check_keywords" value="yes">
   <input type="hidden" name="area" value="default">
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
-  <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="notebooks/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
+  <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Utilities</a></li>
@@ -257,7 +253,7 @@ <h1>Python Module Index</h1>
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=3f474186"></script>
+</div><script src="_static/documentation_options.js?v=71d9d8e6"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>

diff --git a/docs/build/pre_built_html/search.html b/docs/build/pre_built_html/search.html
@@ -4,7 +4,7 @@
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="#" />
 
-    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Search - scenvi 3.0.2 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
+    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 --><title>Search - scenvi 0.3.2 documentation</title><link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo-extensions.css?v=36a5483c" />
 
@@ -120,7 +120,7 @@
       </label>
     </div>
     <div class="header-center">
-      <a href="index.html"><div class="brand">scenvi 3.0.2 documentation</div></a>
+      <a href="index.html"><div class="brand">scenvi 0.3.2 documentation</div></a>
     </div>
     <div class="header-right">
       <div class="theme-toggle-container theme-toggle-header">
@@ -143,19 +143,15 @@
       <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
-  <span class="sidebar-brand-text">scenvi 3.0.2 documentation</span>
+  <span class="sidebar-brand-text">scenvi 0.3.2 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="#" role="search">
   <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
   <input type="hidden" name="check_keywords" value="yes">
   <input type="hidden" name="area" value="default">
 </form>
 <div id="searchbox"></div><div class="sidebar-scroll"><div class="sidebar-tree">
-  <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="notebooks/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
+  <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
 <li class="toctree-l1"><a class="reference internal" href="utils.html">Utilities</a></li>
@@ -235,7 +231,7 @@
 
     </aside>
   </div>
-</div><script src="_static/documentation_options.js?v=3f474186"></script>
+</div><script src="_static/documentation_options.js?v=71d9d8e6"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/scripts/furo.js?v=32e29ea5"></script>