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fjclark · Sep 24, 2024 · e47af0f · e47af0f
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diff --git a/latest/development/index.html b/latest/development/index.html
@@ -776,6 +776,17 @@
 
 
 
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+
+
+  <span class="md-ellipsis">
+    Development
+  </span>
+
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+
       <a href="./" class="md-nav__link md-nav__link--active">
 
 
@@ -786,6 +797,58 @@
 
       </a>
 
+
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+
+
+
+
+
+
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+
+        <li class="md-nav__item">
+  <a href="#writing-code" class="md-nav__link">
+    <span class="md-ellipsis">
+      Writing Code
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#publishing" class="md-nav__link">
+    <span class="md-ellipsis">
+      Publishing
+    </span>
+  </a>
+
+    <nav class="md-nav" aria-label="Publishing">
+      <ul class="md-nav__list">
+
+          <li class="md-nav__item">
+  <a href="#pypi" class="md-nav__link">
+    <span class="md-ellipsis">
+      PyPI
+    </span>
+  </a>
+
+</li>
+
+      </ul>
+    </nav>
+
+</li>
+
+    </ul>
+
+</nav>
+
     </li>
 
 
@@ -830,6 +893,47 @@
 
 
 
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+
+        <li class="md-nav__item">
+  <a href="#writing-code" class="md-nav__link">
+    <span class="md-ellipsis">
+      Writing Code
+    </span>
+  </a>
+
+</li>
+
+        <li class="md-nav__item">
+  <a href="#publishing" class="md-nav__link">
+    <span class="md-ellipsis">
+      Publishing
+    </span>
+  </a>
+
+    <nav class="md-nav" aria-label="Publishing">
+      <ul class="md-nav__list">
+
+          <li class="md-nav__item">
+  <a href="#pypi" class="md-nav__link">
+    <span class="md-ellipsis">
+      PyPI
+    </span>
+  </a>
+
+</li>
+
+      </ul>
+    </nav>
+
+</li>
+
+    </ul>
+
 </nav>
                   </div>
                 </div>
@@ -847,6 +951,7 @@
 
 
 <h1 id="development">Development<a class="headerlink" href="#development" title="Permanent link">#</a></h1>
+<h2 id="writing-code">Writing Code<a class="headerlink" href="#writing-code" title="Permanent link">#</a></h2>
 <p>To create a development environment, you must have <a href="https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html"><code>mamba</code> installed</a>.</p>
 <p>A development conda environment can be created and activated with:</p>
 <div class="language-shell highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>make<span class="w"> </span>env
@@ -861,6 +966,13 @@ <h1 id="development">Development<a class="headerlink" href="#development" title=
 <p>To serve the documentation locally:</p>
 <div class="language-shell highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>mkdocs<span class="w"> </span>serve
 </span></code></pre></div>
+<h2 id="publishing">Publishing<a class="headerlink" href="#publishing" title="Permanent link">#</a></h2>
+<h3 id="pypi">PyPI<a class="headerlink" href="#pypi" title="Permanent link">#</a></h3>
+<div class="language-shell highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>pip<span class="w"> </span>install<span class="w"> </span>build<span class="w"> </span>twine
+</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>python<span class="w"> </span>-m<span class="w"> </span>build
+</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a>twine<span class="w"> </span>check<span class="w"> </span>dist/*
+</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a>twine<span class="w"> </span>upload<span class="w"> </span>dist/*
+</span></code></pre></div>
 
 
 

diff --git a/latest/index.html b/latest/index.html
@@ -935,7 +935,7 @@ <h2 align="center">Robust Equilibration Detection</h2>
 </p>
 
 <hr />
-<p>A Python package for detecting equilibration in timeseries data where an initial transient is followed by a stationary distribution. Two main approaches are implemented, which differ in the way they account for autocorrelation:</p>
+<p>A Python package for detecting equilibration in time series where an initial transient is followed by a stationary distribution. Two main approaches are implemented, which differ in the way they account for autocorrelation:</p>
 <ul>
 <li><code>detect_equilibration_init_seq</code>: This uses the initial sequence methods of Geyer (<a href="https://www.jstor.org/stable/2246094">Geyer, 1992</a>) to determine the truncation point of the sum of autocovariances. Chodera's method (<a href="https://pubs.acs.org/doi/full/10.1021/acs.jctc.5b00784">Chodera, 2016</a>) of simply truncating the autocovariance series at the first negative value is also implemented.</li>
 <li><code>detect_equilibration_window</code>: This uses window methods (see <a href="https://www.jstor.org/stable/2246094">Geyer</a> again) when calculating the

diff --git a/latest/search/search_index.json b/latest/search/search_index.json