diff --git a/.readthedocs.yaml b/.readthedocs.yaml
deleted file mode 100644
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--- a/.readthedocs.yaml
+++ /dev/null
@@ -1,35 +0,0 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
-version: 2
-
-# Set the OS, Python version and other tools you might need
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
-  commands: 
-    - mkdir --parents _readthedocs/html/
-    - cp --recursive docs/build/pre_built_html/* _readthedocs/html/
-
-# Build documentation in the "docs/" directory with Sphinx
-sphinx:
-  configuration: docs/source/conf.py
-
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
-#    - pdf
-#    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-python:
-   install:
-   - requirements: docs/docs_requirements.txt
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diff --git a/docs/build/pre_built_html/.buildinfo b/docs/build/html/.buildinfo
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index cc7ae95..1c5c78b 100644
--- a/docs/build/pre_built_html/utils.html
+++ b/docs/build/html/ENVI.html
@@ -2,12 +2,12 @@
 <html class="no-js" lang="en" data-content_root="./">
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
-    <meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
-<link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="prev" title="ENVI" href="ENVI.html" />
+    <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="tutorial/MOp_MERFISH_tutorial.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
-        <title>Utilities - scenvi 0.3.2 documentation</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=362ab14a" />
+        <title>ENVI - scenvi 0.3.2 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
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@@ -134,7 +134,7 @@
           <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg>
         </button>
       </div>
-      <label class="toc-overlay-icon toc-header-icon" for="__toc">
+      <label class="toc-overlay-icon toc-header-icon no-toc" for="__toc">
         <div class="visually-hidden">Toggle table of contents sidebar</div>
         <i class="icon"><svg><use href="#svg-toc"></use></svg></i>
       </label>
@@ -160,8 +160,8 @@
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="ENVI.html">ENVI</a></li>
-<li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Utilities</a></li>
+<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>
 </ul>
 
 </div>
@@ -190,41 +190,14 @@
               <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg>
             </button>
           </div>
-          <label class="toc-overlay-icon toc-content-icon" for="__toc">
+          <label class="toc-overlay-icon toc-content-icon no-toc" for="__toc">
             <div class="visually-hidden">Toggle table of contents sidebar</div>
             <i class="icon"><svg><use href="#svg-toc"></use></svg></i>
           </label>
         </div>
         <article role="main">
-          <section id="module-scenvi.utils">
-<span id="utilities"></span><h1>Utilities<a class="headerlink" href="#module-scenvi.utils" title="Link to this heading">¶</a></h1>
-<dl class="py function">
-<dt class="sig sig-object py" id="scenvi.utils.compute_covet">
-<span class="sig-prename descclassname"><span class="pre">scenvi.utils.</span></span><span class="sig-name descname"><span class="pre">compute_covet</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spatial_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">g</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">64</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">genes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spatial_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'spatial'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.utils.compute_covet" title="Link to this definition">¶</a></dt>
-<dd><p>Compute niche covariance matrices for spatial data, run with scenvi.compute_covet</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>(</strong><strong>anndata</strong><strong>)</strong> (<em>spatial_data</em>) – anndata with spatial data, with an obsm indicating spatial location of spot/segmented cell</p></li>
-<li><p><strong>(</strong><strong>int</strong><strong>)</strong> (<em>g</em>) – number of nearest neighbours to define niche (default 8)</p></li>
-<li><p><strong>(</strong><strong>int</strong><strong>)</strong> – number of HVG to compute COVET representation on (default 64)</p></li>
-<li><p><strong>str</strong><strong>)</strong> (<em>genes</em><em> (</em><em>list of</em>) – list of genes to keep for niche covariance (default []</p></li>
-<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>batch_key</em>) – obsm key name with physical location of spots/cells (default ‘spatial’)</p></li>
-<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – obs key name of batch/sample of spatial data (default ‘batch’ if in spatial_data.obs, else -1)</p></li>
-</ul>
-</dd>
-<dt class="field-even">Return COVET<span class="colon">:</span></dt>
-<dd class="field-even"><p>niche covariance matrices</p>
-</dd>
-<dt class="field-odd">Return COVET_SQRT<span class="colon">:</span></dt>
-<dd class="field-odd"><p>matrix square-root of niche covariance matrices for approximate OT</p>
-</dd>
-<dt class="field-even">Return CovGenes<span class="colon">:</span></dt>
-<dd class="field-even"><p>list of genes selected for COVET representation</p>
-</dd>
-</dl>
-</dd></dl>
-
+          <section id="envi">
+<h1>ENVI<a class="headerlink" href="#envi" title="Link to this heading">¶</a></h1>
 </section>
 
         </article>
@@ -232,15 +205,23 @@
       <footer>
         
         <div class="related-pages">
-          
-          <a class="prev-page" href="ENVI.html">
+          <a class="next-page" href="utils.html">
+              <div class="page-info">
+                <div class="context">
+                  <span>Next</span>
+                </div>
+                <div class="title">Utilities</div>
+              </div>
+              <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
+            </a>
+          <a class="prev-page" href="tutorial/MOp_MERFISH_tutorial.html">
               <svg class="furo-related-icon"><use href="#svg-arrow-right"></use></svg>
               <div class="page-info">
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-                <div class="title">ENVI</div>
+                <div class="title">ENVI Tutorial</div>
                 
               </div>
             </a>
@@ -262,28 +243,9 @@
         
       </footer>
     </div>
-    <aside class="toc-drawer">
+    <aside class="toc-drawer no-toc">
       
       
-      <div class="toc-sticky toc-scroll">
-        <div class="toc-title-container">
-          <span class="toc-title">
-            On this page
-          </span>
-        </div>
-        <div class="toc-tree-container">
-          <div class="toc-tree">
-            <ul>
-<li><a class="reference internal" href="#">Utilities</a><ul>
-<li><a class="reference internal" href="#scenvi.utils.compute_covet"><code class="docutils literal notranslate"><span class="pre">compute_covet()</span></code></a></li>
-</ul>
-</li>
-</ul>
-
-          </div>
-        </div>
-      </div>
-      
       
     </aside>
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diff --git a/docs/build/pre_built_html/_static/styles/furo-extensions.css.map b/docs/build/html/_static/styles/furo-extensions.css.map
similarity index 100%
rename from docs/build/pre_built_html/_static/styles/furo-extensions.css.map
rename to docs/build/html/_static/styles/furo-extensions.css.map
diff --git a/docs/build/pre_built_html/_static/styles/furo.css b/docs/build/html/_static/styles/furo.css
similarity index 100%
rename from docs/build/pre_built_html/_static/styles/furo.css
rename to docs/build/html/_static/styles/furo.css
diff --git a/docs/build/pre_built_html/_static/styles/furo.css.map b/docs/build/html/_static/styles/furo.css.map
similarity index 100%
rename from docs/build/pre_built_html/_static/styles/furo.css.map
rename to docs/build/html/_static/styles/furo.css.map
diff --git a/docs/build/pre_built_html/genindex.html b/docs/build/html/genindex.html
similarity index 75%
rename from docs/build/pre_built_html/genindex.html
rename to docs/build/html/genindex.html
index 9f0cff1..22334d2 100644
--- a/docs/build/pre_built_html/genindex.html
+++ b/docs/build/html/genindex.html
@@ -5,7 +5,7 @@
     <meta name="color-scheme" content="light dark"><link rel="index" title="Index" href="#" /><link rel="search" title="Search" href="search.html" />
 
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+<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
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@@ -196,105 +196,8 @@
           
 <section class="genindex-section">
   <h1 id="index">Index</h1>
-  <div class="genindex-jumpbox"><a href="#C"><strong>C</strong></a> | <a href="#E"><strong>E</strong></a> | <a href="#I"><strong>I</strong></a> | <a href="#L"><strong>L</strong></a> | <a href="#M"><strong>M</strong></a> | <a href="#S"><strong>S</strong></a> | <a href="#T"><strong>T</strong></a></div>
+  <div class="genindex-jumpbox"></div>
 </section>
-<section id="C" class="genindex-section">
-  <h2>C</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="utils.html#scenvi.utils.compute_covet">compute_covet() (in module scenvi.utils)</a>
-</li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="E" class="genindex-section">
-  <h2>E</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI">ENVI (class in scenvi.ENVI)</a>
-</li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="I" class="genindex-section">
-  <h2>I</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI.impute_genes">impute_genes() (scenvi.ENVI.ENVI method)</a>
-</li>
-    </ul></td>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI.infer_niche_celltype">infer_niche_celltype() (scenvi.ENVI.ENVI method)</a>
-</li>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI.infer_niche_covet">infer_niche_covet() (scenvi.ENVI.ENVI method)</a>
-</li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="L" class="genindex-section">
-  <h2>L</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI.latent_rep">latent_rep() (scenvi.ENVI.ENVI method)</a>
-</li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="M" class="genindex-section">
-  <h2>M</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li>
-    module
-
-        <ul>
-          <li><a href="ENVI.html#module-scenvi.ENVI">scenvi.ENVI</a>
-</li>
-          <li><a href="utils.html#module-scenvi.utils">scenvi.utils</a>
-</li>
-        </ul></li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="S" class="genindex-section">
-  <h2>S</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li>
-    scenvi.ENVI
-
-        <ul>
-          <li><a href="ENVI.html#module-scenvi.ENVI">module</a>
-</li>
-        </ul></li>
-    </ul></td>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li>
-    scenvi.utils
-
-        <ul>
-          <li><a href="utils.html#module-scenvi.utils">module</a>
-</li>
-        </ul></li>
-    </ul></td>
-  </tr></table>
-</section>
-
-<section id="T" class="genindex-section">
-  <h2>T</h2>
-  <table style="width: 100%" class="indextable genindextable"><tr>
-    <td style="width: 33%; vertical-align: top;"><ul>
-        <li><a href="ENVI.html#scenvi.ENVI.ENVI.train">train() (scenvi.ENVI.ENVI method)</a>
-</li>
-    </ul></td>
-  </tr></table>
-</section>
-
 
         </article>
       </div>
diff --git a/docs/build/pre_built_html/index.html b/docs/build/html/index.html
similarity index 98%
rename from docs/build/pre_built_html/index.html
rename to docs/build/html/index.html
index a7ce1a6..850ea3d 100644
--- a/docs/build/pre_built_html/index.html
+++ b/docs/build/html/index.html
@@ -2,12 +2,12 @@
 <html class="no-js" lang="en" data-content_root="./">
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
-    <meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+    <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="tutorial/MOp_MERFISH_tutorial.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
         <title>scenvi 0.3.2 documentation</title>
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diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv
new file mode 100644
index 0000000..26d905c
--- /dev/null
+++ b/docs/build/html/objects.inv
@@ -0,0 +1,9 @@
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diff --git a/docs/build/pre_built_html/search.html b/docs/build/html/search.html
similarity index 99%
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rename to docs/build/html/search.html
index 4d8869e..0dde3a8 100644
--- a/docs/build/pre_built_html/search.html
+++ b/docs/build/html/search.html
@@ -4,7 +4,7 @@
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+    <!-- 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=a746c00c" />
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diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
new file mode 100644
index 0000000..de2aabf
--- /dev/null
+++ b/docs/build/html/searchindex.js
@@ -0,0 +1 @@
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diff --git a/docs/build/pre_built_html/tutorial/MOp_MERFISH_tutorial.html b/docs/build/html/tutorial/MOp_MERFISH_tutorial.html
similarity index 99%
rename from docs/build/pre_built_html/tutorial/MOp_MERFISH_tutorial.html
rename to docs/build/html/tutorial/MOp_MERFISH_tutorial.html
index 57264c5..ea7c9ce 100644
--- a/docs/build/pre_built_html/tutorial/MOp_MERFISH_tutorial.html
+++ b/docs/build/html/tutorial/MOp_MERFISH_tutorial.html
@@ -2,12 +2,12 @@
 <html class="no-js" lang="en" data-content_root="../">
   <head><meta charset="utf-8"/>
     <meta name="viewport" content="width=device-width,initial-scale=1"/>
-    <meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
+    <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" href="../ENVI.html" /><link rel="prev" title="ENVI &amp; COVET" href="../index.html" />
 
     <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
         <title>ENVI Tutorial - 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/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?v=135e06be" />
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diff --git a/docs/build/pre_built_html/tutorial/MOp_MERFISH_tutorial.ipynb b/docs/build/html/tutorial/MOp_MERFISH_tutorial.ipynb
similarity index 100%
rename from docs/build/pre_built_html/tutorial/MOp_MERFISH_tutorial.ipynb
rename to docs/build/html/tutorial/MOp_MERFISH_tutorial.ipynb
diff --git a/docs/build/pre_built_html/py-modindex.html b/docs/build/html/utils.html
similarity index 86%
rename from docs/build/pre_built_html/py-modindex.html
rename to docs/build/html/utils.html
index ad87422..b1e57d2 100644
--- a/docs/build/pre_built_html/py-modindex.html
+++ b/docs/build/html/utils.html
@@ -2,10 +2,12 @@
 <html class="no-js" lang="en" data-content_root="./">
   <head><meta charset="utf-8"/>
     <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" />
+    <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="prev" title="ENVI" href="ENVI.html" />
 
-    <!-- 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" />
+    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
+        <title>Utilities - scenvi 0.3.2 documentation</title>
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
     <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?v=135e06be" />
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@@ -157,9 +159,9 @@
 <li class="toctree-l1"><a class="reference internal" href="tutorial/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
-<ul>
+<ul class="current">
 <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>
+<li class="toctree-l1 current current-page"><a class="current reference internal" href="#">Utilities</a></li>
 </ul>
 
 </div>
@@ -179,7 +181,8 @@
           <span>Back to top</span>
         </a>
         <div class="content-icon-container">
-          <div class="theme-toggle-container theme-toggle-content">
+          
+<div class="theme-toggle-container theme-toggle-content">
             <button class="theme-toggle">
               <div class="visually-hidden">Toggle Light / Dark / Auto color theme</div>
               <svg class="theme-icon-when-auto"><use href="#svg-sun-half"></use></svg>
@@ -193,38 +196,9 @@
           </label>
         </div>
         <article role="main">
-          
-<section class="domainindex-section">
-  <h1>Python Module Index</h1>
-  <div class="domainindex-jumpbox"><a href="#cap-s"><strong>s</strong></a></div>
+          <section id="utilities">
+<h1>Utilities<a class="headerlink" href="#utilities" title="Link to this heading">¶</a></h1>
 </section>
-<table class="domainindex-table">
-  <tr class="pcap">
-    <td></td><td>&#160;</td><td></td>
-  </tr>
-  <tr class="cap" id="cap-s">
-    <td></td><td><strong>s</strong></td><td></td>
-  </tr>
-  <tr>
-    <td><img src="_static/minus.png" class="toggler"
-              id="toggle-1" style="display: none" alt="-" /></td>
-    <td>
-        <code class="xref">scenvi</code></td><td>
-    <em></em></td>
-  </tr>
-  <tr class="cg-1">
-    <td></td>
-    <td>&#160;&#160;&#160;
-        <a href="ENVI.html#module-scenvi.ENVI"><code class="xref">scenvi.ENVI</code></a></td><td>
-    <em></em></td>
-  </tr>
-  <tr class="cg-1">
-    <td></td>
-    <td>&#160;&#160;&#160;
-        <a href="utils.html#module-scenvi.utils"><code class="xref">scenvi.utils</code></a></td><td>
-    <em></em></td>
-  </tr>
-</table>
 
         </article>
       </div>
@@ -232,7 +206,17 @@ <h1>Python Module Index</h1>
         
         <div class="related-pages">
           
-          
+          <a class="prev-page" href="ENVI.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</div>
+                
+              </div>
+            </a>
         </div>
         <div class="bottom-of-page">
           <div class="left-details">
diff --git a/docs/build/pre_built_html/ENVI.html b/docs/build/pre_built_html/ENVI.html
deleted file mode 100644
index d4aaa34..0000000
--- a/docs/build/pre_built_html/ENVI.html
+++ /dev/null
@@ -1,388 +0,0 @@
-<!doctype html>
-<html class="no-js" lang="en" data-content_root="./">
-  <head><meta charset="utf-8"/>
-    <meta name="viewport" content="width=device-width,initial-scale=1"/>
-    <meta name="color-scheme" content="light dark"><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />
-<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="tutorial/MOp_MERFISH_tutorial.html" />
-
-    <!-- Generated with Sphinx 7.3.7 and Furo 2024.01.29 -->
-        <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" />
-    
-    
-
-
-<style>
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-      --color-code-background: #202020;
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-  
-    }
-    @media (prefers-color-scheme: dark) {
-      body:not([data-theme="light"]) {
-        --color-code-background: #202020;
-  --color-code-foreground: #d0d0d0;
-  
-      }
-    }
-  }
-</style></head>
-  <body>
-    
-    <script>
-      document.body.dataset.theme = localStorage.getItem("theme") || "auto";
-    </script>
-    
-
-<svg xmlns="http://www.w3.org/2000/svg" style="display: none;">
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-<ul>
-<li class="toctree-l1"><a class="reference internal" href="tutorial/MOp_MERFISH_tutorial.html">ENVI Tutorial</a></li>
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-        <article role="main">
-          <section id="module-scenvi.ENVI">
-<span id="envi"></span><h1>ENVI<a class="headerlink" href="#module-scenvi.ENVI" title="Link to this heading">¶</a></h1>
-<dl class="py class">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">scenvi.ENVI.</span></span><span class="sig-name descname"><span class="pre">ENVI</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">spatial_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sc_data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spatial_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'spatial'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'batch'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_layers</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_neurons</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1024</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">latent_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">512</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k_nearest</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_cov_genes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">64</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cov_genes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_HVG</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2048</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sc_genes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spatial_dist</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'pois'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sc_dist</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'nb'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">spatial_coeff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sc_coeff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cov_coeff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">kl_coeff</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.3</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_input</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stable_eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1e-06</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI" title="Link to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Initializes the ENVI model &amp; computes COVET for spatial data</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>spatial_data</strong> – (anndata) spatial transcriptomics data, with an obsm indicating spatial location of spot/segmented cell</p></li>
-<li><p><strong>sc_data</strong> – (anndata) complementary sinlge cell data</p></li>
-<li><p><strong>spatial_key</strong> – (str) obsm key name with physical location of spots/cells (default ‘spatial’)</p></li>
-<li><p><strong>batch_key</strong> – (str) obs key name of batch/sample of spatial data (default ‘batch’ if in spatial_data.obs, else -1)</p></li>
-<li><p><strong>num_layers</strong> – (int) number of neural network for decoders and encoders (default 3)</p></li>
-<li><p><strong>num_neurons</strong> – (int) number of neurons in each layer (default 1024)</p></li>
-<li><p><strong>latent_dim</strong> – (int) size of ENVI latent dimention (size 512)</p></li>
-<li><p><strong>k_nearest</strong> – (int) number of physical neighbours to describe niche (default 8)</p></li>
-<li><p><strong>num_cov_genes</strong> – (int) number of HVGs to compute niche covariance with (default ֿ64), if -1 uses all genes</p></li>
-<li><p><strong>cov_genes</strong> – (list of str) manual genes to compute niche with (default [])</p></li>
-<li><p><strong>num_HVG</strong> – (int) number of HVGs to keep for single cell data (default 2048)</p></li>
-<li><p><strong>sc_genes</strong> – (list of str) manual genes to keep for sinlge cell data (default [])</p></li>
-<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>spatial_dist</em>) – distribution used to describe spatial data (default pois, could be ‘pois’, ‘nb’, ‘zinb’ or ‘norm’)</p></li>
-<li><p><strong>sc_dist</strong> – (str) distribution used to describe sinlge cell data (default nb, could be ‘pois’, ‘nb’, ‘zinb’ or ‘norm’)</p></li>
-<li><p><strong>spatial_coeff</strong> – (float) coefficient for spatial expression loss in total ELBO (default 1.0)</p></li>
-<li><p><strong>sc_coeff</strong> – (float) coefficient for sinlge cell expression loss in total ELBO (default 1.0)</p></li>
-<li><p><strong>cov_coeff</strong> – (float) coefficient for spatial niche loss in total ELBO (default 1.0)</p></li>
-<li><p><strong>kl_coeff</strong> – (float) coefficient for latent prior loss in total ELBO (default 1.0)</p></li>
-<li><p><strong>log_input</strong> – (float) if larger than zero, a log is applied to ENVI input with pseudocount of log_input (default 0.1)</p></li>
-<li><p><strong>stable_eps</strong> – (float) added value to log probabilty calculations to avoid NaNs during training (default 1e-6)</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>initialized ENVI model</p>
-</dd>
-</dl>
-<dl class="py method">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI.impute_genes">
-<span class="sig-name descname"><span class="pre">impute_genes</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI.impute_genes" title="Link to this definition">¶</a></dt>
-<dd><p>Impute full transcriptome for spatial data</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><p>nothing adds ‘imputation’ to self.spatial_data.obsm</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI.infer_niche_celltype">
-<span class="sig-name descname"><span class="pre">infer_niche_celltype</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cell_type_key</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'cell_type'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI.infer_niche_celltype" title="Link to this definition">¶</a></dt>
-<dd><p>Predict cell type abundence based one ENVI-inferred COVET representations</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>(</strong><strong>string</strong><strong>)</strong> (<em>cell_type_key</em>) – key in spatial_data.obs where cell types are stored for environment composition (default ‘cell_type’)</p>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>nothing, adds ‘niche_cell_type’ to self.sc_data.obsm &amp; self.spatial_data.obsm</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI.infer_niche_covet">
-<span class="sig-name descname"><span class="pre">infer_niche_covet</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI.infer_niche_covet" title="Link to this definition">¶</a></dt>
-<dd><p>Predict COVET representation for single-cell data</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><p>nothing adds ‘COVET_SQRT’ and ‘COVET’ to self.spatial_data.obsm</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI.latent_rep">
-<span class="sig-name descname"><span class="pre">latent_rep</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI.latent_rep" title="Link to this definition">¶</a></dt>
-<dd><p>Compute latent embeddings for spatial and single cell data, automatically performed after training</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns<span class="colon">:</span></dt>
-<dd class="field-odd"><p>nothing, adds ‘envi_latent’ self.spatial_data.obsm and self.spatial_data.obsm</p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="scenvi.ENVI.ENVI.train">
-<span class="sig-name descname"><span class="pre">train</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">training_steps=16000,</span> <span class="pre">batch_size=128,</span> <span class="pre">verbose=16,</span> <span class="pre">init_lr=0.0001,</span> <span class="pre">decay_steps=4000,</span> <span class="pre">key=Array((),</span> <span class="pre">dtype=key&lt;fry&gt;)</span> <span class="pre">overlaying:</span> <span class="pre">[0</span> <span class="pre">0]</span></em><span class="sig-paren">)</span><a class="headerlink" href="#scenvi.ENVI.ENVI.train" title="Link to this definition">¶</a></dt>
-<dd><p>Set up optimization parameters and train the ENVI moodel</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>training_steps</strong> – (int) number of gradient descent steps to train ENVI (default 16000)</p></li>
-<li><p><strong>batch_size</strong> – (int) size of spatial and single-cell profiles sampled for each training step  (default 128)</p></li>
-<li><p><strong>verbose</strong> – (int) amount of steps between each loss print statement (default 16)</p></li>
-<li><p><strong>init_lr</strong> – (float) initial learning rate for ADAM optimizer with exponential decay (default 1e-4)</p></li>
-<li><p><strong>decay_steps</strong> – (int) number of steps before each learning rate decay (default 4000)</p></li>
-<li><p><strong>key</strong> – (jax.random.key) random seed (default jax.random.key(0))</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>nothing</p>
-</dd>
-</dl>
-</dd></dl>
-
-</dd></dl>
-
-</section>
-
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-            <ul>
-<li><a class="reference internal" href="#">ENVI</a><ul>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI"><code class="docutils literal notranslate"><span class="pre">ENVI</span></code></a><ul>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI.impute_genes"><code class="docutils literal notranslate"><span class="pre">ENVI.impute_genes()</span></code></a></li>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI.infer_niche_celltype"><code class="docutils literal notranslate"><span class="pre">ENVI.infer_niche_celltype()</span></code></a></li>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI.infer_niche_covet"><code class="docutils literal notranslate"><span class="pre">ENVI.infer_niche_covet()</span></code></a></li>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI.latent_rep"><code class="docutils literal notranslate"><span class="pre">ENVI.latent_rep()</span></code></a></li>
-<li><a class="reference internal" href="#scenvi.ENVI.ENVI.train"><code class="docutils literal notranslate"><span class="pre">ENVI.train()</span></code></a></li>
-</ul>
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diff --git a/docs/build/pre_built_html/objects.inv b/docs/build/pre_built_html/objects.inv
deleted file mode 100644
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diff --git a/docs/build/pre_built_html/searchindex.js b/docs/build/pre_built_html/searchindex.js
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--- a/docs/build/pre_built_html/searchindex.js
+++ /dev/null
@@ -1 +0,0 @@
-Search.setIndex({"alltitles": {"Calculating FDL and DC on COVET": [[2, "Calculating-FDL-and-DC-on-COVET"]], "Data": [[2, "Data"]], "ENVI": [[0, "module-scenvi.ENVI"]], "ENVI & COVET": [[1, "envi-covet"]], "ENVI COVET analysis": [[2, "ENVI-COVET-analysis"]], "ENVI Tutorial": [[2, "ENVI-Tutorial"]], "ENVI imputation on Spatial Data": [[2, "ENVI-imputation-on-Spatial-Data"]], "Importing": [[2, "Importing"]], "Index": [[1, "index"]], "Install ENVI": [[2, "Install-ENVI"]], "Niche Cell Type Composition": [[2, "Niche-Cell-Type-Composition"]], "Plot DC and Depth": [[2, "Plot-DC-and-Depth"]], "Plot UMAPs of ENVI latent": [[2, "Plot-UMAPs-of-ENVI-latent"]], "Plot as Stacked Bar Plots": [[2, "Plot-as-Stacked-Bar-Plots"]], "Plotting the Motor Cortex MERFISH": [[2, "Plotting-the-Motor-Cortex-MERFISH"]], "Plotting the Motor Cortex scRNAseq": [[2, "Plotting-the-Motor-Cortex-scRNAseq"]], "Reverse DC if needed": [[2, "Reverse-DC-if-needed"]], "Running ENVI": [[2, "Running-ENVI"]], "Subtype Depth": [[2, "Subtype-Depth"]], "Utilities": [[3, "module-scenvi.utils"]], "Utility Functions:": [[2, "Utility-Functions:"]], "What is COVET?": [[2, "What-is-COVET?"]], "What is ENVI?": [[2, "What-is-ENVI?"]]}, "docnames": ["ENVI", "index", "tutorial/MOp_MERFISH_tutorial", "utils"], "envversion": {"nbsphinx": 4, "sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["ENVI.rst", "index.rst", "tutorial/MOp_MERFISH_tutorial.ipynb", "utils.rst"], "indexentries": {"compute_covet() (in module scenvi.utils)": [[3, "scenvi.utils.compute_covet", false]], "envi (class in scenvi.envi)": [[0, "scenvi.ENVI.ENVI", false]], "impute_genes() (scenvi.envi.envi method)": [[0, "scenvi.ENVI.ENVI.impute_genes", false]], "infer_niche_celltype() (scenvi.envi.envi method)": 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\ No newline at end of file
diff --git a/readthedocs.yaml b/readthedocs.yaml
new file mode 100644
index 0000000..01d7142
--- /dev/null
+++ b/readthedocs.yaml
@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+
+sphinx:
+   configuration: docs/source/conf.py
+
+python:
+   install:
+   - requirements: docs/docs_requirements.txt
+   - method: pip
+     path: .
\ No newline at end of file
diff --git a/scenvi/ENVI.py b/scenvi/ENVI.py
index 5ee25a8..3a43467 100644
--- a/scenvi/ENVI.py
+++ b/scenvi/ENVI.py
@@ -44,7 +44,7 @@ class ENVI():
     :param cov_genes: (list of str) manual genes to compute niche with (default [])
     :param num_HVG: (int) number of HVGs to keep for single cell data (default 2048)
     :param sc_genes: (list of str) manual genes to keep for sinlge cell data (default [])
-    :param spatial_dist (str): distribution used to describe spatial data (default pois, could be 'pois', 'nb', 'zinb' or 'norm') 
+    :param spatial_dist: (str) distribution used to describe spatial data (default pois, could be 'pois', 'nb', 'zinb' or 'norm') 
     :param sc_dist: (str) distribution used to describe sinlge cell data (default nb, could be 'pois', 'nb', 'zinb' or 'norm')
     :param spatial_coeff: (float) coefficient for spatial expression loss in total ELBO (default 1.0)
     :param sc_coeff: (float) coefficient for sinlge cell expression loss in total ELBO (default 1.0)
