Rebuild documentation with updated citation.

Emad-COMBINE-lab · May 16, 2024 · 89e265f · 89e265f
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diff --git a/docs/_build/doctrees/citation.doctree b/docs/_build/doctrees/citation.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/factory.doctree b/docs/_build/doctrees/factory.doctree
diff --git a/docs/_build/doctrees/gans.doctree b/docs/_build/doctrees/gans.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/layers.doctree b/docs/_build/doctrees/layers.doctree
diff --git a/docs/_build/doctrees/main.doctree b/docs/_build/doctrees/main.doctree
diff --git a/docs/_build/doctrees/networks.doctree b/docs/_build/doctrees/networks.doctree
diff --git a/docs/_build/doctrees/preprocessing.doctree b/docs/_build/doctrees/preprocessing.doctree
diff --git a/docs/_build/doctrees/sc_dataset.doctree b/docs/_build/doctrees/sc_dataset.doctree
diff --git a/docs/_build/doctrees/tfrecord_loader.doctree b/docs/_build/doctrees/tfrecord_loader.doctree
diff --git a/docs/_build/html/_modules/custom_parser.html b/docs/_build/html/_modules/custom_parser.html
@@ -3,7 +3,7 @@
 <!DOCTYPE html>
 
 
-<html lang="en" data-theme="light">
+<html lang="en" data-content_root="" data-theme="light">
 
   <head>
     <meta charset="utf-8" />
@@ -18,30 +18,31 @@
   </script>
 
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-<link href="../_static/styles/pydata-sphinx-theme.css?digest=e353d410970836974a52" rel="stylesheet" />
+  <link href="../_static/styles/theme.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+<link href="../_static/styles/bootstrap.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
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-<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
+  <link href="../_static/vendor/fontawesome/6.5.1/css/all.min.css?digest=8d27b9dea8ad943066ae" rel="stylesheet" />
+  <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-solid-900.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-brands-400.woff2" />
+<link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.5.1/webfonts/fa-regular-400.woff2" />
 
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-    <link rel="stylesheet" href="../_static/styles/sphinx-book-theme.css?digest=14f4ca6b54d191a8c7657f6c759bf11a5fb86285" type="text/css" />
+    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
-<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae" />
+  <script src="../_static/vendor/fontawesome/6.5.1/js/all.min.js?digest=8d27b9dea8ad943066ae"></script>
 
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
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     <script src="../_static/clipboard.min.js"></script>
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-    <script src="../_static/scripts/sphinx-book-theme.js?digest=5a5c038af52cf7bc1a1ec88eea08e6366ee68824"></script>
+    <script src="../_static/scripts/sphinx-book-theme.js"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = '_modules/custom_parser';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -54,7 +55,15 @@
 
 
 
-  <a class="skip-link" href="#main-content">Skip to main content</a>
+  <a id="pst-skip-link" class="skip-link" href="#main-content">Skip to main content</a>
+
+  <div id="pst-scroll-pixel-helper"></div>
+
+  <button type="button" class="btn rounded-pill" id="pst-back-to-top">
+    <i class="fa-solid fa-arrow-up"></i>
+    Back to top
+  </button>
+
 
   <input type="checkbox"
           class="sidebar-toggle"
@@ -89,12 +98,17 @@
 </form></div>
   </div>
 
-    <nav class="bd-header navbar navbar-expand-lg bd-navbar">
-    </nav>
+    <header class="bd-header navbar navbar-expand-lg bd-navbar">
+    </header>
 
+
   <div class="bd-container">
     <div class="bd-container__inner bd-page-width">
 
+
+
+
+
       <div class="bd-sidebar-primary bd-sidebar">
 
 
@@ -108,13 +122,15 @@
 
     <div class="sidebar-primary-items__start sidebar-primary__section">
         <div class="sidebar-primary-item">
+
 
 
 <a class="navbar-brand logo" href="../index.html">
 
 
 
 
+
 
 
 
@@ -134,8 +150,8 @@
 
 
 
-          <a href="https://github.com/Emad-COMBINE-lab/GRouNdGAN" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github"></i></span>
-            <label class="sr-only">GitHub</label></a>
+          <a href="https://github.com/Emad-COMBINE-lab/GRouNdGAN" title="GitHub" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-github fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">GitHub</span></a>
         </li>
         <li class="nav-item">
 
@@ -146,8 +162,8 @@
 
 
 
-          <a href="https://hub.docker.com/repository/docker/yazdanz/groundgan/" title="Docker" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-docker"></i></span>
-            <label class="sr-only">Docker</label></a>
+          <a href="https://hub.docker.com/repository/docker/yazdanz/groundgan/" title="Docker" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-brands fa-docker fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Docker</span></a>
         </li>
         <li class="nav-item">
 
@@ -158,8 +174,8 @@
 
 
 
-          <a href="https://www.biorxiv.org/content/10.1101/2023.07.25.550225v2" title="Manuscript" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-book"></i></span>
-            <label class="sr-only">Manuscript</label></a>
+          <a href="https://www.biorxiv.org/content/10.1101/2023.07.25.550225v2" title="Manuscript" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><span><i class="fa-solid fa-book fa-lg" aria-hidden="true"></i></span>
+            <span class="sr-only">Manuscript</span></a>
         </li>
         <li class="nav-item">
 
@@ -173,11 +189,23 @@
           <a href="https://github.com/Emad-COMBINE-lab/GRouNdGAN/actions" title="Docs Build" class="nav-link" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><img src="https://github.com/Emad-COMBINE-lab/GRouNdGAN/actions/workflows/documentation.yaml/badge.svg?branch=master" class="icon-link-image" alt="Docs Build"/></a>
         </li>
 </ul></div>
-        <div class="sidebar-primary-item"><nav class="bd-links" id="bd-docs-nav" aria-label="Main">
+        <div class="sidebar-primary-item">
+
+ <script>
+ document.write(`
+   <button class="btn navbar-btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass"></i>
+    <span class="search-button__default-text">Search</span>
+    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+   </button>
+ `);
+ </script></div>
+        <div class="sidebar-primary-item"><nav class="bd-links bd-docs-nav" aria-label="Main">
     <div class="bd-toc-item navbar-nav active">
         <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorial.html">Tutorial</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../benchmarking.html">Benchmarking</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../citation.html">Citation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../license.html">License</a></li>
 </ul>
@@ -299,20 +327,22 @@
 </button>
 
 
+
 <script>
 document.write(`
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-    <span class="theme-switch" data-mode="light"><i class="fa-solid fa-sun"></i></span>
-    <span class="theme-switch" data-mode="dark"><i class="fa-solid fa-moon"></i></span>
-    <span class="theme-switch" data-mode="auto"><i class="fa-solid fa-circle-half-stroke"></i></span>
+  <button class="btn btn-sm navbar-btn theme-switch-button" title="light/dark" aria-label="light/dark" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <span class="theme-switch nav-link" data-mode="light"><i class="fa-solid fa-sun fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="dark"><i class="fa-solid fa-moon fa-lg"></i></span>
+    <span class="theme-switch nav-link" data-mode="auto"><i class="fa-solid fa-circle-half-stroke fa-lg"></i></span>
   </button>
 `);
 </script>
 
+
 <script>
 document.write(`
   <button class="btn btn-sm navbar-btn search-button search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
-    <i class="fa-solid fa-magnifying-glass"></i>
+    <i class="fa-solid fa-magnifying-glass fa-lg"></i>
   </button>
 `);
 </script>
@@ -339,7 +369,7 @@ <h1></h1>
 
 
 <div id="searchbox"></div>
-                <article class="bd-article" role="main">
+                <article class="bd-article">
 
   <h1>Source code for custom_parser</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">argparse</span>
@@ -424,22 +454,20 @@ <h1>Source code for custom_parser</h1><div class="highlight"><pre>
 
 
 
-                <footer class="bd-footer-article">
+
+
+                <footer class="prev-next-footer">
 
-<div class="footer-article-items footer-article__inner">
-
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 <div class="prev-next-area">
-</div></div>
-
 </div>
-
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+                <div class="bd-sidebar-secondary bd-toc"></div>
+
 
           </div>
           <footer class="bd-footer-content">
@@ -456,6 +484,7 @@ <h1>Source code for custom_parser</h1><div class="highlight"><pre>
 
   <div class="footer-item">
 
+
   <p class="copyright">
 
       © Copyright 2023, Emad&#39;s COMBINE Lab: Yazdan Zinati, Abdulrahman Takiddeen, and Amin Emad.
@@ -482,8 +511,8 @@ <h1>Source code for custom_parser</h1><div class="highlight"><pre>
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="../_static/scripts/bootstrap.js?digest=e353d410970836974a52"></script>
-<script src="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52"></script>
+  <script src="../_static/scripts/bootstrap.js?digest=8d27b9dea8ad943066ae"></script>
+<script src="../_static/scripts/pydata-sphinx-theme.js?digest=8d27b9dea8ad943066ae"></script>
 
   <footer class="bd-footer">
   </footer>

diff --git a/docs/_build/html/_modules/index.html b/docs/_build/html/_modules/index.html
@@ -374,23 +374,7 @@ <h1></h1>
   <h1>All modules for which code is available</h1>
 <ul><li><a href="_abc.html">_abc</a></li>
 <li><a href="custom_parser.html">custom_parser</a></li>
-<li><a href="factory.html">factory</a></li>
-<li><a href="gans/causal_gan.html">gans.causal_gan</a></li>
-<li><a href="gans/conditional_gan.html">gans.conditional_gan</a></li>
-<li><a href="gans/conditional_gan_cat.html">gans.conditional_gan_cat</a></li>
-<li><a href="gans/conditional_gan_proj.html">gans.conditional_gan_proj</a></li>
-<li><a href="gans/gan.html">gans.gan</a></li>
-<li><a href="layers/cbn.html">layers.cbn</a></li>
-<li><a href="layers/lsn.html">layers.lsn</a></li>
-<li><a href="layers/masked_linear.html">layers.masked_linear</a></li>
-<li><a href="networks/critic.html">networks.critic</a></li>
-<li><a href="networks/generator.html">networks.generator</a></li>
-<li><a href="networks/labeler.html">networks.labeler</a></li>
-<li><a href="networks/masked_causal_generator.html">networks.masked_causal_generator</a></li>
-<li><a href="preprocessing/grn_creation.html">preprocessing.grn_creation</a></li>
 <li><a href="preprocessing/preprocess.html">preprocessing.preprocess</a></li>
-<li><a href="sc_dataset.html">sc_dataset</a></li>
-<li><a href="tfrecord_loader.html">tfrecord_loader</a></li>
 </ul>
 
                 </article>