update docs to link to new webpage

.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: 4b60f1f4abdfdf01b83f38bc77a57247
+config: 009c76ea65200dd5740c9445d6a3edc3
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/index.html

@@ -5,10 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Overview: module code &#8212; neutcurve 2.1.0 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=b76e3c8a" />
-    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=c878986b" />
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+    <link rel="stylesheet" type="text/css" href="../_static/basic.css?v=c058f7c8" />
+    <link rel="stylesheet" type="text/css" href="../_static/alabaster.css?v=877b1dcb" />
     <script src="../_static/documentation_options.js?v=20623aea"></script>
-    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></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>
     <link rel="index" title="Index" href="../genindex.html" />
@@ -40,7 +41,7 @@ <h1>All modules for which code is available</h1>
 
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <p class="logo">
   <a href="../index.html">
@@ -90,15 +91,15 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<div id="searchbox" style="display: none" role="search">
+<search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
       <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
-</div>
+</search>
 <script>document.getElementById('searchbox').style.display = "block"</script>
 
 
@@ -116,14 +117,14 @@ <h3 id="searchlabel">Quick search</h3>
       &#169;2019--2024, Bloom lab.
 
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
     </div>
 
 
     <a href="https://github.com/jbloomlab/neutcurve" class="github">
-        <img style="position: absolute; top: 0; right: 0; border: 0;" src="https://github.blog/wp-content/uploads/2008/12/forkme_right_darkblue_121621.png" alt="Fork me on GitHub"  class="github"/>
+        <img src="../_static/github-banner.svg" alt="Fork me on GitHub" class="github"/>
     </a>
 
 

_modules/neutcurve/hillcurve.html

@@ -5,10 +5,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>neutcurve.hillcurve &#8212; neutcurve 2.1.0 documentation</title>
-    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=b76e3c8a" />
-    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=c878986b" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
+    <link rel="stylesheet" type="text/css" href="../../_static/basic.css?v=c058f7c8" />
+    <link rel="stylesheet" type="text/css" href="../../_static/alabaster.css?v=877b1dcb" />
     <script src="../../_static/documentation_options.js?v=20623aea"></script>
-    <script src="../../_static/doctools.js?v=888ff710"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></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>
     <link rel="index" title="Index" href="../../genindex.html" />
@@ -646,7 +647,7 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
                 <span class="k">raise</span> <span class="n">HillCurveFittingError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;fit failed:</span><span class="se">\n</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="si">=}</span><span class="se">\n</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="si">=}</span><span class="s2">&quot;</span><span class="p">)</span>
 
         <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">param</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">([</span><span class="s2">&quot;midpoint&quot;</span><span class="p">,</span> <span class="s2">&quot;slope&quot;</span><span class="p">,</span> <span class="s2">&quot;bottom&quot;</span><span class="p">,</span> <span class="s2">&quot;top&quot;</span><span class="p">]):</span>
-            <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">param</span><span class="p">,</span> <span class="n">fit_tup</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+            <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">param</span><span class="p">,</span> <span class="nb">float</span><span class="p">(</span><span class="n">fit_tup</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
         <span class="c1"># debugging check</span>
         <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">fixval</span><span class="p">,</span> <span class="n">val</span> <span class="ow">in</span> <span class="p">[</span>
             <span class="p">(</span><span class="s2">&quot;slope&quot;</span><span class="p">,</span> <span class="n">fixslope</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">slope</span><span class="p">),</span>
@@ -664,20 +665,22 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">midpoint</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound_type</span> <span class="o">=</span> <span class="s2">&quot;interpolated&quot;</span>
         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">midpoint</span> <span class="o">&lt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound_type</span> <span class="o">=</span> <span class="s2">&quot;upper&quot;</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="k">assert</span> <span class="bp">self</span><span class="o">.</span><span class="n">midpoint</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">midpoint_bound_type</span> <span class="o">=</span> <span class="s2">&quot;lower&quot;</span>
 
         <span class="c1"># compute coefficient of determination</span>
         <span class="c1"># https://en.wikipedia.org/wiki/Coefficient_of_determination</span>
         <span class="k">assert</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="p">)</span>
-        <span class="n">sstot</span> <span class="o">=</span> <span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span> <span class="o">-</span> <span class="n">numpy</span><span class="o">.</span><span class="n">average</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="p">))</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
-        <span class="n">ssres</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">fracinfectivity</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">])</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span>
-        <span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+        <span class="n">sstot</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(((</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span> <span class="o">-</span> <span class="n">numpy</span><span class="o">.</span><span class="n">average</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="p">))</span> <span class="o">**</span> <span class="mi">2</span><span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">())</span>
+        <span class="n">ssres</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span>
+            <span class="p">(</span>
+                <span class="p">(</span><span class="n">numpy</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">fracinfectivity</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">cs</span><span class="p">])</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">fs</span><span class="p">)</span> <span class="o">**</span> <span class="mi">2</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span>
+        <span class="p">)</span>
         <span class="k">if</span> <span class="n">sstot</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">if</span> <span class="n">ssres</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">r2</span> <span class="o">=</span> <span class="mf">1.0</span>
@@ -1481,7 +1484,7 @@ <h1>Source code for neutcurve.hillcurve</h1><div class="highlight"><pre>
 
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <p class="logo">
   <a href="../../index.html">
@@ -1533,15 +1536,15 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<div id="searchbox" style="display: none" role="search">
+<search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
       <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
-</div>
+</search>
 <script>document.getElementById('searchbox').style.display = "block"</script>
 
 
@@ -1559,14 +1562,14 @@ <h3 id="searchlabel">Quick search</h3>
       &#169;2019--2024, Bloom lab.
 
       |
-      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 7.2.6</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.0.2</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
     </div>
 
 
     <a href="https://github.com/jbloomlab/neutcurve" class="github">
-        <img style="position: absolute; top: 0; right: 0; border: 0;" src="https://github.blog/wp-content/uploads/2008/12/forkme_right_darkblue_121621.png" alt="Fork me on GitHub"  class="github"/>
+        <img src="../../_static/github-banner.svg" alt="Fork me on GitHub" class="github"/>
     </a>
 
 

_sources/acknowledgments.rst.txt

@@ -1,6 +1,6 @@
 Acknowledgements
 -----------------
-`neutcurve` is written by the `Bloom lab  <https://research.fhcrc.org/bloom/en.html>`_.
+`neutcurve` is written by the `Bloom lab  <https://jbloomlab.org>`_.
 
 See https://github.com/jbloomlab/neutcurve/graphs/contributors for the full list of contributors.
 

_sources/index.rst.txt

@@ -1,7 +1,7 @@
 ``neutcurve`` documentation
 ======================================
 
-`neutcurve` is a Python package written by the `Bloom lab <https://research.fhcrc.org/bloom/en.html>`_ for fitting and plotting neutralization curves.
+`neutcurve` is a Python package written by the `Bloom lab <https://jbloomlab.org>`_ for fitting and plotting neutralization curves.
 
 See below for information and examples of how to use this package.
 

_static/alabaster.css

@@ -1,5 +1,3 @@
-@import url("basic.css");
-
 /* -- page layout ----------------------------------------------------------- */
 
 body {
@@ -160,8 +158,8 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
-div.sphinxsidebar #searchbox input[type="text"] {
-    width: 160px;
+div.sphinxsidebar #searchbox {
+    margin: 1em 0;
 }
 
 div.sphinxsidebar .search > div {
@@ -263,10 +261,6 @@ div.admonition p.last {
     margin-bottom: 0;
 }
 
-div.highlight {
-    background-color: #fff;
-}
-
 dt:target, .highlight {
     background: #FAF3E8;
 }
@@ -454,7 +448,7 @@ ul, ol {
 }
 
 pre {
-    background: #EEE;
+    background: unset;
     padding: 7px 30px;
     margin: 15px 0px;
     line-height: 1.3em;
@@ -485,15 +479,15 @@ a.reference {
     border-bottom: 1px dotted #004B6B;
 }
 
+a.reference:hover {
+    border-bottom: 1px solid #6D4100;
+}
+
 /* Don't put an underline on images */
 a.image-reference, a.image-reference:hover {
     border-bottom: none;
 }
 
-a.reference:hover {
-    border-bottom: 1px solid #6D4100;
-}
-
 a.footnote-reference {
     text-decoration: none;
     font-size: 0.7em;
@@ -509,68 +503,7 @@ a:hover tt, a:hover code {
     background: #EEE;
 }
 
-
-@media screen and (max-width: 870px) {
-
-    div.sphinxsidebar {
-    	display: none;
-    }
-
-    div.document {
-       width: 100%;
-
-    }
-
-    div.documentwrapper {
-    	margin-left: 0;
-    	margin-top: 0;
-    	margin-right: 0;
-    	margin-bottom: 0;
-    }
-
-    div.bodywrapper {
-    	margin-top: 0;
-    	margin-right: 0;
-    	margin-bottom: 0;
-    	margin-left: 0;
-    }
-
-    ul {
-    	margin-left: 0;
-    }
-
-	li > ul {
-        /* Matches the 30px from the "ul, ol" selector above */
-		margin-left: 30px;
-	}
-
-    .document {
-    	width: auto;
-    }
-
-    .footer {
-    	width: auto;
-    }
-
-    .bodywrapper {
-    	margin: 0;
-    }
-
-    .footer {
-    	width: auto;
-    }
-
-    .github {
-        display: none;
-    }
-
-
-
-}
-
-
-
-@media screen and (max-width: 875px) {
+@media screen and (max-width: 940px) {
 
     body {
         margin: 0;
@@ -580,12 +513,16 @@ a:hover tt, a:hover code {
     div.documentwrapper {
         float: none;
         background: #fff;
+        margin-left: 0;
+        margin-top: 0;
+        margin-right: 0;
+        margin-bottom: 0;
     }
 
     div.sphinxsidebar {
         display: block;
         float: none;
-        width: 102.5%;
+        width: unset;
         margin: 50px -30px -20px -30px;
         padding: 10px 20px;
         background: #333;
@@ -620,8 +557,14 @@ a:hover tt, a:hover code {
 
     div.body {
         min-height: 0;
+        min-width: auto; /* fixes width on small screens, breaks .hll */
         padding: 0;
     }
+
+    .hll {
+        /* "fixes" the breakage */
+        width: max-content;
+    }
 
     .rtd_doc_footer {
         display: none;
@@ -635,13 +578,18 @@ a:hover tt, a:hover code {
         width: auto;
     }
 
-    .footer {
-        width: auto;
-    }
-
     .github {
         display: none;
     }
+
+    ul {
+        margin-left: 0;
+    }
+
+    li > ul {
+       /* Matches the 30px from the "ul, ol" selector above */
+        margin-left: 30px;
+    }
 }
 
 
@@ -705,4 +653,11 @@ nav#breadcrumbs li+li:before {
     div.related {
         display: none;
     }
+}
+
+img.github  {
+    position: absolute;
+    top: 0;
+    border: 0;
+    right: 0;
 }

_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */