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VectorInstitute · Oct 24, 2023 · e15a4bc · e15a4bc
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diff --git a/.buildinfo b/.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: eac8c2cecab8f5f0d1617fa75830a8e4
+config: cac6a737651ef2763a249709de69e78f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/cycquery/base.html b/_modules/cycquery/base.html
@@ -1,3 +1,9 @@
+
+
+
+
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../../">
 <head>
@@ -7,6 +13,7 @@
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
     <link rel="stylesheet" type="text/css" href="../../_static/css/cyclops.css?v=fc0e58c9" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
+    <link rel="shortcut icon" href="../../_static/favicon.ico"/>
   <!--[if lt IE 9]>
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -24,28 +31,91 @@
     <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
-<body class="wy-body-for-nav"> 
+<body class="wy-body-for-nav">
+  <!--
+    Lie about what theme we really are when some RTD-injected JS fetches the
+    full versions panel from the RTD API.  RTD's JS replaces the stub versions
+    panel in the Sphinx-generated HTML with the full versions panel it fetches
+    from the RTD API.  If the API thinks we're not sphinx_rtd_theme, it will
+    serve us the wrong HTML and the panel will float as a "badge" when it
+    shouldn't.  As a customized version of sphinx_rtd_theme, we really do want
+    the same HTML it gets.  See also the diagnoses in
+    <https://github.com/nextstrain/docs.nextstrain.org/issues/76>.
+
+    This bit of JS finds the data RTD injects into the page and modifies it
+    before the code that RTD injects runs and looks at the data.  RTD's
+    <script>s (in <head>) run before this JS, but they wait until the DOM is
+    ready to actually do any work.  This gives us a chance to modify the data
+    during DOM load before the RTD code actually uses it.
+
+      -trs, 27 Jan 2022
+  -->
+  <script>
+    (() => {
+      try {
+        console.log("Lying about the theme to RTD's JS so the versions panel works properly. 🙈");
+
+        /* Update global variable, which is used in the request to get the RTD
+         * "footer" that includes the versions panel.
+         */
+        if (window.READTHEDOCS_DATA)
+          window.READTHEDOCS_DATA.theme = "sphinx_rtd_theme";
+
+        /* Update stored JSON in case anything else deserializes it later.
+         * Comments in the RTD-injected HTML source claim the global variable
+         * above is deprecated.
+         */
+        var script = document.querySelector("#READTHEDOCS_DATA");
+        if (script)
+          script.innerHTML = JSON.stringify({ ...JSON.parse(script.innerHTML), theme: "sphinx_rtd_theme" });
+      }
+      catch (err) {
+        console.log("Lying about the theme to RTD's JS failed… oh well. 🤷", err);
+      }
+    })();
+  </script>
+
   <div class="wy-grid-for-nav">
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search"  style="background: #efeeed" >
 
-
-
-          <a href="../../index.html" class="icon icon-home">
-            cyclops-query
-          </a>
+
+
+
+  <a href="https://vectorinstitute.github.io/cyclops/">
+    <img src="../../_static/cyclops_logo-dark.png" class="logo" alt="Logo"/>
+  </a>
+
+
+
+  <div class="subproject">
+    <a href="../../index.html" class="project-name" alt="Documentation Home">
+      cyclops-query
+    </a>
+
+
+
+
+
+  </div>
+
+
+
+
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
 </div>
+
+
         </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="../../intro.html"># cyclops-query</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../intro.html">cyclops-query</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#getting-started">🐣 Getting Started</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#developing">🧑🏿‍💻 Developing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#documentation">📚 Documentation</a></li>
@@ -68,9 +138,21 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
-      <li class="breadcrumb-item active">cycquery.base</li>
+
+
+
+
+    <li><a href="https://vectorinstitute.github.io/cyclops/">Home</a></li>
+    <li><a href="../../index.html">cyclops-query</a></li>
+
+
+
+
+    <li><a href="../index.html">Module code</a></li>
+
+
+
+
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -397,13 +479,44 @@ <h1>Source code for cycquery.base</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022, Vector AI Engineering.</p>
+    <p></p>
   </div>
 
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
-
+
+
+  <div class="footer-small-text">
+    All <a href="https://github.com/VectorInstitute/cyclops">source code for cyclops</a> is freely available under the terms of an <a href="https://opensource.org/licenses/Apache-2.0">Apache-2.0</a> license.
+  </div>
+
+  <div class="footer-small-text">
+      This work is made possible due to the data obtained from the <a href="https://www.geminimedicine.ca/">GEMINI study</a>.
+  </div>
+
+  <hr/>
+
+  <div class="logo">
+    <a class="logo" href="https://vectorinstitute.ai/">
+      <span class="logo"></span>
+      <img alt="Logo of the Vector Institute" style="width:90px; max-width:90px;" src="../../_static/logos/vector_logo.png" />
+    </a>
+    <a class="logo" href="https://www.geminimedicine.ca/">
+      <span class="logo"></span>
+      <img alt="Logo of GEMINI" style="width:90px; max-width:90px;" src="../../_static/logos/gemini_logo.png" />
+    </a>
+  </div>
+
+  <div class="copyright">
+    &copy; Copyright 2022, Vector AI Engineering
+  </div>
+
+  <div class="copyright">
+    </p>
+    Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using customised version of
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">base theme</a> provided by
+    <a href="https://readthedocs.org">Read the Docs</a>.
+  </div>
+
+
 
 </footer>
         </div>

diff --git a/_modules/cycquery/eicu.html b/_modules/cycquery/eicu.html
@@ -1,3 +1,9 @@
+
+
+
+
+
+
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../../">
 <head>
@@ -7,6 +13,7 @@
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=80d5e7a1" />
     <link rel="stylesheet" type="text/css" href="../../_static/css/cyclops.css?v=fc0e58c9" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
+    <link rel="shortcut icon" href="../../_static/favicon.ico"/>
   <!--[if lt IE 9]>
     <script src="../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -24,28 +31,91 @@
     <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
-<body class="wy-body-for-nav"> 
+<body class="wy-body-for-nav">
+  <!--
+    Lie about what theme we really are when some RTD-injected JS fetches the
+    full versions panel from the RTD API.  RTD's JS replaces the stub versions
+    panel in the Sphinx-generated HTML with the full versions panel it fetches
+    from the RTD API.  If the API thinks we're not sphinx_rtd_theme, it will
+    serve us the wrong HTML and the panel will float as a "badge" when it
+    shouldn't.  As a customized version of sphinx_rtd_theme, we really do want
+    the same HTML it gets.  See also the diagnoses in
+    <https://github.com/nextstrain/docs.nextstrain.org/issues/76>.
+
+    This bit of JS finds the data RTD injects into the page and modifies it
+    before the code that RTD injects runs and looks at the data.  RTD's
+    <script>s (in <head>) run before this JS, but they wait until the DOM is
+    ready to actually do any work.  This gives us a chance to modify the data
+    during DOM load before the RTD code actually uses it.
+
+      -trs, 27 Jan 2022
+  -->
+  <script>
+    (() => {
+      try {
+        console.log("Lying about the theme to RTD's JS so the versions panel works properly. 🙈");
+
+        /* Update global variable, which is used in the request to get the RTD
+         * "footer" that includes the versions panel.
+         */
+        if (window.READTHEDOCS_DATA)
+          window.READTHEDOCS_DATA.theme = "sphinx_rtd_theme";
+
+        /* Update stored JSON in case anything else deserializes it later.
+         * Comments in the RTD-injected HTML source claim the global variable
+         * above is deprecated.
+         */
+        var script = document.querySelector("#READTHEDOCS_DATA");
+        if (script)
+          script.innerHTML = JSON.stringify({ ...JSON.parse(script.innerHTML), theme: "sphinx_rtd_theme" });
+      }
+      catch (err) {
+        console.log("Lying about the theme to RTD's JS failed… oh well. 🤷", err);
+      }
+    })();
+  </script>
+
   <div class="wy-grid-for-nav">
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search"  style="background: #efeeed" >
 
-
-
-          <a href="../../index.html" class="icon icon-home">
-            cyclops-query
-          </a>
+
+
+
+  <a href="https://vectorinstitute.github.io/cyclops/">
+    <img src="../../_static/cyclops_logo-dark.png" class="logo" alt="Logo"/>
+  </a>
+
+
+
+  <div class="subproject">
+    <a href="../../index.html" class="project-name" alt="Documentation Home">
+      cyclops-query
+    </a>
+
+
+
+
+
+  </div>
+
+
+
+
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>
 </div>
+
+
         </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="../../intro.html"># cyclops-query</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../intro.html">cyclops-query</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#getting-started">🐣 Getting Started</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#developing">🧑🏿‍💻 Developing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../intro.html#documentation">📚 Documentation</a></li>
@@ -68,9 +138,21 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../index.html">Module code</a></li>
-      <li class="breadcrumb-item active">cycquery.eicu</li>
+
+
+
+
+    <li><a href="https://vectorinstitute.github.io/cyclops/">Home</a></li>
+    <li><a href="../../index.html">cyclops-query</a></li>
+
+
+
+
+    <li><a href="../index.html">Module code</a></li>
+
+
+
+
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -111,13 +193,44 @@ <h1>Source code for cycquery.eicu</h1><div class="highlight"><pre>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2022, Vector AI Engineering.</p>
+    <p></p>
   </div>
 
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
-    provided by <a href="https://readthedocs.org">Read the Docs</a>.
-
+
+
+  <div class="footer-small-text">
+    All <a href="https://github.com/VectorInstitute/cyclops">source code for cyclops</a> is freely available under the terms of an <a href="https://opensource.org/licenses/Apache-2.0">Apache-2.0</a> license.
+  </div>
+
+  <div class="footer-small-text">
+      This work is made possible due to the data obtained from the <a href="https://www.geminimedicine.ca/">GEMINI study</a>.
+  </div>
+
+  <hr/>
+
+  <div class="logo">
+    <a class="logo" href="https://vectorinstitute.ai/">
+      <span class="logo"></span>
+      <img alt="Logo of the Vector Institute" style="width:90px; max-width:90px;" src="../../_static/logos/vector_logo.png" />
+    </a>
+    <a class="logo" href="https://www.geminimedicine.ca/">
+      <span class="logo"></span>
+      <img alt="Logo of GEMINI" style="width:90px; max-width:90px;" src="../../_static/logos/gemini_logo.png" />
+    </a>
+  </div>
+
+  <div class="copyright">
+    &copy; Copyright 2022, Vector AI Engineering
+  </div>
+
+  <div class="copyright">
+    </p>
+    Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using customised version of
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">base theme</a> provided by
+    <a href="https://readthedocs.org">Read the Docs</a>.
+  </div>
+
+
 
 </footer>
         </div>