diff --git a/0.1.28/_modules/index.html b/0.1.28/_modules/index.html
index fdf8e31..4bac276 100644
--- a/0.1.28/_modules/index.html
+++ b/0.1.28/_modules/index.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/index.html" />
   <!--[if lt IE 9]>
@@ -100,7 +102,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/cli.html b/0.1.28/_modules/mdacli/cli.html
index 8743e3b..0e49d80 100644
--- a/0.1.28/_modules/mdacli/cli.html
+++ b/0.1.28/_modules/mdacli/cli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.cli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/cli.html" />
   <!--[if lt IE 9]>
@@ -191,9 +193,6 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
     <span class="c1">#   sub parser in complete detail.</span>
     <span class="n">setup_clients</span><span class="p">(</span><span class="n">ap</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2"> Analysis Modules&quot;</span><span class="p">,</span> <span class="n">members</span><span class="o">=</span><span class="n">modules</span><span class="p">)</span>
 
-    <span class="c1"># Be case insensitive for the subcommand</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
-
     <span class="n">args</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
 
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
@@ -209,7 +208,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
             <span class="c1"># Get the correct ArgumentParser instance from all subparsers</span>
             <span class="c1"># `[0]` selects the first subparser where our analysises live in.</span>
-            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span>
             <span class="n">ap_sup</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">_subparsers</span><span class="o">.</span><span class="n">_group_actions</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">choices</span><span class="p">[</span><span class="n">_key</span><span class="p">]</span>
             <span class="n">arg_grouped_dict</span> <span class="o">=</span> <span class="n">split_argparse_into_groups</span><span class="p">(</span><span class="n">ap_sup</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
 
@@ -241,7 +240,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/colors.html b/0.1.28/_modules/mdacli/colors.html
index a470569..fffdc44 100644
--- a/0.1.28/_modules/mdacli/colors.html
+++ b/0.1.28/_modules/mdacli/colors.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.colors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/colors.html" />
   <!--[if lt IE 9]>
@@ -312,7 +314,7 @@ <h1>Source code for mdacli.colors</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/libcli.html b/0.1.28/_modules/mdacli/libcli.html
index d7181e5..590fead 100644
--- a/0.1.28/_modules/mdacli/libcli.html
+++ b/0.1.28/_modules/mdacli/libcli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.libcli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/libcli.html" />
   <!--[if lt IE 9]>
@@ -477,6 +479,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># creates the subparser</span>
     <span class="n">analysis_class_parser</span> <span class="o">=</span> <span class="n">sub_parser</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
         <span class="n">interface_name</span><span class="p">,</span>
+        <span class="n">aliases</span><span class="o">=</span><span class="p">[</span><span class="n">interface_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()],</span>
         <span class="n">help</span><span class="o">=</span><span class="n">parameters</span><span class="p">[</span><span class="s2">&quot;desc&quot;</span><span class="p">],</span>
         <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc&#39;</span><span class="p">]</span><span class="si">}</span><span class="se">\n\n</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc_long&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
         <span class="n">formatter_class</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">RawDescriptionHelpFormatter</span><span class="p">,</span>
@@ -888,7 +891,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># to be writen</span>
     <span class="k">for</span> <span class="n">member_name</span><span class="p">,</span> <span class="n">parameters</span> <span class="ow">in</span> <span class="n">analysis_interfaces</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
         <span class="n">create_cli</span><span class="p">(</span><span class="n">sub_parser</span><span class="o">=</span><span class="n">cli_subparser</span><span class="p">,</span>
-                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="p">,</span>
                    <span class="n">parameters</span><span class="o">=</span><span class="n">parameters</span><span class="p">)</span></div>
 
 
@@ -955,7 +958,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/logger.html b/0.1.28/_modules/mdacli/logger.html
index 7c1c49f..347b75c 100644
--- a/0.1.28/_modules/mdacli/logger.html
+++ b/0.1.28/_modules/mdacli/logger.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.logger &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/logger.html" />
   <!--[if lt IE 9]>
@@ -162,7 +164,7 @@ <h1>Source code for mdacli.logger</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/save.html b/0.1.28/_modules/mdacli/save.html
index 73ea254..3b1559f 100644
--- a/0.1.28/_modules/mdacli/save.html
+++ b/0.1.28/_modules/mdacli/save.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.save &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/save.html" />
   <!--[if lt IE 9]>
@@ -551,7 +553,7 @@ <h1>Source code for mdacli.save</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/_modules/mdacli/utils.html b/0.1.28/_modules/mdacli/utils.html
index 11c15e1..61706b7 100644
--- a/0.1.28/_modules/mdacli/utils.html
+++ b/0.1.28/_modules/mdacli/utils.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.utils &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/utils.html" />
   <!--[if lt IE 9]>
@@ -367,7 +369,7 @@ <h1>Source code for mdacli.utils</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api.html b/0.1.28/api.html
index 56826fa..ef6c650 100644
--- a/0.1.28/api.html
+++ b/0.1.28/api.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>API library documentation &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api.html" />
   <!--[if lt IE 9]>
@@ -125,7 +127,7 @@ <h1>API library documentation<a class="headerlink" href="#api-library-documentat
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/cli.html b/0.1.28/api/cli.html
index eaee9d9..06c7cb3 100644
--- a/0.1.28/api/cli.html
+++ b/0.1.28/api/cli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>High-Level API &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/cli.html" />
   <!--[if lt IE 9]>
@@ -104,7 +106,7 @@
 <p>The toplevel command line interface.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mdacli.cli.cli">
-<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140573603213664'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140499268142416'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
 <dd><p>Create the command-line interface.</p>
 <p>This function creates a command line interface with a given <cite>name</cite> based
 on a module list.</p>
@@ -158,7 +160,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/colors.html b/0.1.28/api/colors.html
index 0fe82bf..129096f 100644
--- a/0.1.28/api/colors.html
+++ b/0.1.28/api/colors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Coloring &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/colors.html" />
   <!--[if lt IE 9]>
@@ -128,15 +130,15 @@
 <dl class="field-list simple">
 <dt class="field-odd">Variables<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – bold attribute</p></li>
-<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – underline attribute</p></li>
-<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – gray color</p></li>
-<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – red color</p></li>
-<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – green color</p></li>
-<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – yellow color</p></li>
-<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – blue color</p></li>
-<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – pink color</p></li>
-<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – turquoise color</p></li>
+<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – bold attribute</p></li>
+<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – underline attribute</p></li>
+<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – gray color</p></li>
+<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – red color</p></li>
+<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – green color</p></li>
+<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – yellow color</p></li>
+<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – blue color</p></li>
+<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – pink color</p></li>
+<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – turquoise color</p></li>
 </ul>
 </dd>
 </dl>
@@ -328,7 +330,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/libcli.html b/0.1.28/api/libcli.html
index 7e73d1f..cfa5ed6 100644
--- a/0.1.28/api/libcli.html
+++ b/0.1.28/api/libcli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Support functions for CLI &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/libcli.html" />
   <!--[if lt IE 9]>
@@ -195,7 +197,7 @@
 of no ine is created</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
 </dd>
 </dl>
 </dd></dl>
@@ -261,25 +263,25 @@
 define the list of atoms. If the file includes bond information,
 partial charges, atom masses, … then these data will be available to
 MDAnalysis. Alternatively, an existing
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
 numpy coordinates, or None for an empty universe.</p></li>
 <li><p><strong>coordinates</strong> (<em>str, stream, list of str, list of stream</em>) – Coordinates can be provided as files of
 a single frame (eg a PDB, CRD, or GRO file); a list of single
 frames; or a trajectory file (in CHARMM/NAMD/LAMMPS DCD, Gromacs
 XTC/TRR, or generic XYZ format). The coordinates must be
 ordered in the same way as the list of atoms in the topology.
-See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.6.1)"><span>Table of supported coordinate formats</span></a> for what can be read
+See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.7.0)"><span>Table of supported coordinate formats</span></a> for what can be read
 as coordinates. Alternatively, streams can be given.</p></li>
 <li><p><strong>topology_format</strong> (<em>str, None</em>) – Provide the file format of the topology file; <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from
 the file extension. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
 reader to be used on the topology file.</p></li>
 <li><p><strong>trajectory_format</strong> (<em>str or list or object</em>) – provide the file format of the coordinate or trajectory file;
 <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from the file extension. Note that this
 keyword has no effect if a list of file names is supplied because
 the “chained” reader has to guess the file format for each
 individual list member [<code class="docutils literal notranslate"><span class="pre">None</span></code>]. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
 reader to be used on the trajectory file.</p></li>
 <li><p><strong>atom_style</strong> (<em>str</em>) – Customised LAMMPS <cite>atom_style</cite> information. Only works with
 <cite>topology_format = data</cite></p></li>
@@ -289,7 +291,7 @@
 </ul>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><cite>MDAnalysis.Universe</cite></p>
@@ -425,7 +427,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/logger.html b/0.1.28/api/logger.html
index da62aa8..09c7893 100644
--- a/0.1.28/api/logger.html
+++ b/0.1.28/api/logger.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Logging &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/logger.html" />
   <!--[if lt IE 9]>
@@ -133,7 +135,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/save.html b/0.1.28/api/save.html
index ec923a8..9cd1487 100644
--- a/0.1.28/api/save.html
+++ b/0.1.28/api/save.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Results Saving &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/save.html" />
   <!--[if lt IE 9]>
@@ -342,7 +344,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/api/utils.html b/0.1.28/api/utils.html
index 5c1cda8..665dd5e 100644
--- a/0.1.28/api/utils.html
+++ b/0.1.28/api/utils.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Utilities &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/utils.html" />
   <!--[if lt IE 9]>
@@ -123,7 +125,7 @@
 <dd class="field-even"><p><em>int</em> – frame number</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -182,7 +184,7 @@
 <dd class="field-odd"><p><em>tuple (float, str)</em> – Value as float, units as str.</p>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
     present in the start of the string.</p>
 </dd>
 </dl>
@@ -202,7 +204,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/authors.html b/0.1.28/authors.html
index 863562c..1e34430 100644
--- a/0.1.28/authors.html
+++ b/0.1.28/authors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Authors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/authors.html" />
   <!--[if lt IE 9]>
@@ -108,7 +110,7 @@ <h1>Authors<a class="headerlink" href="#authors" title="Link to this heading">
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/0.1.28/changelog.html b/0.1.28/changelog.html
index 3a139ed..d8607c8 100644
--- a/0.1.28/changelog.html
+++ b/0.1.28/changelog.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Changelog &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/changelog.html" />
   <!--[if lt IE 9]>
@@ -120,6 +122,9 @@
              
   <section id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading"></a></h1>
+<ul class="simple">
+<li><p>Change handling of lowercase module names</p></li>
+</ul>
 <section id="v0-1-28-2023-09-29">
 <h2>v0.1.28 (2023-09-29)<a class="headerlink" href="#v0-1-28-2023-09-29" title="Link to this heading"></a></h2>
 <ul class="simple">
@@ -326,7 +331,7 @@ <h2>v0.1.0 (2021-11-18)<a class="headerlink" href="#v0-1-0-2021-11-18" title="Li
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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index 4361cdb..8bc973f 100644
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+++ b/0.1.28/contributing.html
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@@ -249,7 +251,7 @@ <h2>Pull Request<a class="headerlink" href="#pull-request" title="Link to this h
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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diff --git a/0.1.28/genindex.html b/0.1.28/genindex.html
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     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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diff --git a/0.1.28/index.html b/0.1.28/index.html
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+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
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   <title>MDAnalysis command line interface &mdash; mdacli 0.1.28 documentation</title>
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-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
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+  
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@@ -107,8 +109,8 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
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     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
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diff --git a/0.1.28/installation.html b/0.1.28/installation.html
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@@ -141,7 +143,7 @@ <h2>conda<a class="headerlink" href="#conda" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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diff --git a/0.1.28/philosophy.html b/0.1.28/philosophy.html
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-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
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@@ -104,7 +106,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
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 scripts is very helpful for the day-to-day analysis.
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@@ -117,11 +119,11 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
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   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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-      <span class="lastupdated">Last updated on Sep 29, 2023.
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   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
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       </span></p>
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diff --git a/0.1.28/usage.html b/0.1.28/usage.html
index c536059..d4b658a 100644
--- a/0.1.28/usage.html
+++ b/0.1.28/usage.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Usage &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/usage.html" />
   <!--[if lt IE 9]>
@@ -149,7 +151,7 @@ <h1>Usage<a class="headerlink" href="#usage" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/index.html b/dev/_modules/index.html
index fdf8e31..4bac276 100644
--- a/dev/_modules/index.html
+++ b/dev/_modules/index.html
@@ -1,12 +1,14 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/index.html" />
   <!--[if lt IE 9]>
@@ -100,7 +102,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/cli.html b/dev/_modules/mdacli/cli.html
index 8743e3b..0e49d80 100644
--- a/dev/_modules/mdacli/cli.html
+++ b/dev/_modules/mdacli/cli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.cli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/cli.html" />
   <!--[if lt IE 9]>
@@ -191,9 +193,6 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
     <span class="c1">#   sub parser in complete detail.</span>
     <span class="n">setup_clients</span><span class="p">(</span><span class="n">ap</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2"> Analysis Modules&quot;</span><span class="p">,</span> <span class="n">members</span><span class="o">=</span><span class="n">modules</span><span class="p">)</span>
 
-    <span class="c1"># Be case insensitive for the subcommand</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
-
     <span class="n">args</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
 
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
@@ -209,7 +208,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
             <span class="c1"># Get the correct ArgumentParser instance from all subparsers</span>
             <span class="c1"># `[0]` selects the first subparser where our analysises live in.</span>
-            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span>
             <span class="n">ap_sup</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">_subparsers</span><span class="o">.</span><span class="n">_group_actions</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">choices</span><span class="p">[</span><span class="n">_key</span><span class="p">]</span>
             <span class="n">arg_grouped_dict</span> <span class="o">=</span> <span class="n">split_argparse_into_groups</span><span class="p">(</span><span class="n">ap_sup</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
 
@@ -241,7 +240,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/colors.html b/dev/_modules/mdacli/colors.html
index a470569..fffdc44 100644
--- a/dev/_modules/mdacli/colors.html
+++ b/dev/_modules/mdacli/colors.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.colors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/colors.html" />
   <!--[if lt IE 9]>
@@ -312,7 +314,7 @@ <h1>Source code for mdacli.colors</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/libcli.html b/dev/_modules/mdacli/libcli.html
index d7181e5..590fead 100644
--- a/dev/_modules/mdacli/libcli.html
+++ b/dev/_modules/mdacli/libcli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.libcli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/libcli.html" />
   <!--[if lt IE 9]>
@@ -477,6 +479,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># creates the subparser</span>
     <span class="n">analysis_class_parser</span> <span class="o">=</span> <span class="n">sub_parser</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
         <span class="n">interface_name</span><span class="p">,</span>
+        <span class="n">aliases</span><span class="o">=</span><span class="p">[</span><span class="n">interface_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()],</span>
         <span class="n">help</span><span class="o">=</span><span class="n">parameters</span><span class="p">[</span><span class="s2">&quot;desc&quot;</span><span class="p">],</span>
         <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc&#39;</span><span class="p">]</span><span class="si">}</span><span class="se">\n\n</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc_long&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
         <span class="n">formatter_class</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">RawDescriptionHelpFormatter</span><span class="p">,</span>
@@ -888,7 +891,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># to be writen</span>
     <span class="k">for</span> <span class="n">member_name</span><span class="p">,</span> <span class="n">parameters</span> <span class="ow">in</span> <span class="n">analysis_interfaces</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
         <span class="n">create_cli</span><span class="p">(</span><span class="n">sub_parser</span><span class="o">=</span><span class="n">cli_subparser</span><span class="p">,</span>
-                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="p">,</span>
                    <span class="n">parameters</span><span class="o">=</span><span class="n">parameters</span><span class="p">)</span></div>
 
 
@@ -955,7 +958,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/logger.html b/dev/_modules/mdacli/logger.html
index 7c1c49f..347b75c 100644
--- a/dev/_modules/mdacli/logger.html
+++ b/dev/_modules/mdacli/logger.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.logger &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/logger.html" />
   <!--[if lt IE 9]>
@@ -162,7 +164,7 @@ <h1>Source code for mdacli.logger</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/save.html b/dev/_modules/mdacli/save.html
index 73ea254..3b1559f 100644
--- a/dev/_modules/mdacli/save.html
+++ b/dev/_modules/mdacli/save.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.save &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/save.html" />
   <!--[if lt IE 9]>
@@ -551,7 +553,7 @@ <h1>Source code for mdacli.save</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/_modules/mdacli/utils.html b/dev/_modules/mdacli/utils.html
index 11c15e1..61706b7 100644
--- a/dev/_modules/mdacli/utils.html
+++ b/dev/_modules/mdacli/utils.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.utils &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/utils.html" />
   <!--[if lt IE 9]>
@@ -367,7 +369,7 @@ <h1>Source code for mdacli.utils</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api.html b/dev/api.html
index 56826fa..ef6c650 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>API library documentation &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api.html" />
   <!--[if lt IE 9]>
@@ -125,7 +127,7 @@ <h1>API library documentation<a class="headerlink" href="#api-library-documentat
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/cli.html b/dev/api/cli.html
index eaee9d9..06c7cb3 100644
--- a/dev/api/cli.html
+++ b/dev/api/cli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>High-Level API &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/cli.html" />
   <!--[if lt IE 9]>
@@ -104,7 +106,7 @@
 <p>The toplevel command line interface.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mdacli.cli.cli">
-<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140573603213664'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140499268142416'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
 <dd><p>Create the command-line interface.</p>
 <p>This function creates a command line interface with a given <cite>name</cite> based
 on a module list.</p>
@@ -158,7 +160,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/colors.html b/dev/api/colors.html
index 0fe82bf..129096f 100644
--- a/dev/api/colors.html
+++ b/dev/api/colors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Coloring &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/colors.html" />
   <!--[if lt IE 9]>
@@ -128,15 +130,15 @@
 <dl class="field-list simple">
 <dt class="field-odd">Variables<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – bold attribute</p></li>
-<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – underline attribute</p></li>
-<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – gray color</p></li>
-<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – red color</p></li>
-<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – green color</p></li>
-<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – yellow color</p></li>
-<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – blue color</p></li>
-<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – pink color</p></li>
-<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – turquoise color</p></li>
+<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – bold attribute</p></li>
+<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – underline attribute</p></li>
+<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – gray color</p></li>
+<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – red color</p></li>
+<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – green color</p></li>
+<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – yellow color</p></li>
+<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – blue color</p></li>
+<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – pink color</p></li>
+<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – turquoise color</p></li>
 </ul>
 </dd>
 </dl>
@@ -328,7 +330,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/libcli.html b/dev/api/libcli.html
index 7e73d1f..cfa5ed6 100644
--- a/dev/api/libcli.html
+++ b/dev/api/libcli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Support functions for CLI &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/libcli.html" />
   <!--[if lt IE 9]>
@@ -195,7 +197,7 @@
 of no ine is created</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
 </dd>
 </dl>
 </dd></dl>
@@ -261,25 +263,25 @@
 define the list of atoms. If the file includes bond information,
 partial charges, atom masses, … then these data will be available to
 MDAnalysis. Alternatively, an existing
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
 numpy coordinates, or None for an empty universe.</p></li>
 <li><p><strong>coordinates</strong> (<em>str, stream, list of str, list of stream</em>) – Coordinates can be provided as files of
 a single frame (eg a PDB, CRD, or GRO file); a list of single
 frames; or a trajectory file (in CHARMM/NAMD/LAMMPS DCD, Gromacs
 XTC/TRR, or generic XYZ format). The coordinates must be
 ordered in the same way as the list of atoms in the topology.
-See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.6.1)"><span>Table of supported coordinate formats</span></a> for what can be read
+See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.7.0)"><span>Table of supported coordinate formats</span></a> for what can be read
 as coordinates. Alternatively, streams can be given.</p></li>
 <li><p><strong>topology_format</strong> (<em>str, None</em>) – Provide the file format of the topology file; <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from
 the file extension. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
 reader to be used on the topology file.</p></li>
 <li><p><strong>trajectory_format</strong> (<em>str or list or object</em>) – provide the file format of the coordinate or trajectory file;
 <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from the file extension. Note that this
 keyword has no effect if a list of file names is supplied because
 the “chained” reader has to guess the file format for each
 individual list member [<code class="docutils literal notranslate"><span class="pre">None</span></code>]. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
 reader to be used on the trajectory file.</p></li>
 <li><p><strong>atom_style</strong> (<em>str</em>) – Customised LAMMPS <cite>atom_style</cite> information. Only works with
 <cite>topology_format = data</cite></p></li>
@@ -289,7 +291,7 @@
 </ul>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><cite>MDAnalysis.Universe</cite></p>
@@ -425,7 +427,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/logger.html b/dev/api/logger.html
index da62aa8..09c7893 100644
--- a/dev/api/logger.html
+++ b/dev/api/logger.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Logging &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/logger.html" />
   <!--[if lt IE 9]>
@@ -133,7 +135,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/save.html b/dev/api/save.html
index ec923a8..9cd1487 100644
--- a/dev/api/save.html
+++ b/dev/api/save.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Results Saving &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/save.html" />
   <!--[if lt IE 9]>
@@ -342,7 +344,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/api/utils.html b/dev/api/utils.html
index 5c1cda8..665dd5e 100644
--- a/dev/api/utils.html
+++ b/dev/api/utils.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Utilities &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/utils.html" />
   <!--[if lt IE 9]>
@@ -123,7 +125,7 @@
 <dd class="field-even"><p><em>int</em> – frame number</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -182,7 +184,7 @@
 <dd class="field-odd"><p><em>tuple (float, str)</em> – Value as float, units as str.</p>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
     present in the start of the string.</p>
 </dd>
 </dl>
@@ -202,7 +204,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/authors.html b/dev/authors.html
index 863562c..1e34430 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Authors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/authors.html" />
   <!--[if lt IE 9]>
@@ -108,7 +110,7 @@ <h1>Authors<a class="headerlink" href="#authors" title="Link to this heading">
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/changelog.html b/dev/changelog.html
index 3a139ed..d8607c8 100644
--- a/dev/changelog.html
+++ b/dev/changelog.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Changelog &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/changelog.html" />
   <!--[if lt IE 9]>
@@ -120,6 +122,9 @@
              
   <section id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading"></a></h1>
+<ul class="simple">
+<li><p>Change handling of lowercase module names</p></li>
+</ul>
 <section id="v0-1-28-2023-09-29">
 <h2>v0.1.28 (2023-09-29)<a class="headerlink" href="#v0-1-28-2023-09-29" title="Link to this heading"></a></h2>
 <ul class="simple">
@@ -326,7 +331,7 @@ <h2>v0.1.0 (2021-11-18)<a class="headerlink" href="#v0-1-0-2021-11-18" title="Li
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/contributing.html b/dev/contributing.html
index 4361cdb..8bc973f 100644
--- a/dev/contributing.html
+++ b/dev/contributing.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Contributing &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/contributing.html" />
   <!--[if lt IE 9]>
@@ -249,7 +251,7 @@ <h2>Pull Request<a class="headerlink" href="#pull-request" title="Link to this h
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/genindex.html b/dev/genindex.html
index f761254..79cac88 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/genindex.html" />
   <!--[if lt IE 9]>
@@ -435,7 +437,7 @@ <h2 id="Y">Y</h2>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/index.html b/dev/index.html
index 2c0baa3..e17f1d2 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>MDAnalysis command line interface &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/index.html" />
   <!--[if lt IE 9]>
@@ -107,8 +109,8 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 <p>Currently the following analysis modules are available</p>
 <table class="docutils align-default">
 <colgroup>
-<col style="width: 33%" />
-<col style="width: 67%" />
+<col style="width: 33.3%" />
+<col style="width: 66.7%" />
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 <thead>
 <tr class="row-odd"><th class="head"><p>Module Name</p></th>
@@ -196,7 +198,7 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/installation.html b/dev/installation.html
index f9f8665..b1dbbdc 100644
--- a/dev/installation.html
+++ b/dev/installation.html
@@ -1,13 +1,15 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
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-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Installation &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
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     <link rel="canonical" href="https://mdacli.mdanalysis.org/installation.html" />
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@@ -141,7 +143,7 @@ <h2>conda<a class="headerlink" href="#conda" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/philosophy.html b/dev/philosophy.html
index bdfa055..2693969 100644
--- a/dev/philosophy.html
+++ b/dev/philosophy.html
@@ -1,13 +1,15 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Philosophy and approach &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
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@@ -104,7 +106,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 <li><p>…</p></li>
 </ul>
 <p>Some of these problems can be solved by using the
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class of MDA. However,
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class of MDA. However,
 this class is limited to python, and sometimes a direct CLI to these
 scripts is very helpful for the day-to-day analysis.
 A generic CLI wrapper for all classes based on the AnalysisBase could
@@ -117,11 +119,11 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 <cite>base.AnalysisBase</cite>.</p>
 <p>Starting from <cite>taurenmd</cite> and <cite>maicos</cite> we
 developed a general CLI for any
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class.
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class.
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+project that uses the <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a>
 as parent class. If new classes are added to the
 MDA codebase they are just they will show up without
 any adjustments to <cite>mdacli</cite> itself.</p>
@@ -129,7 +131,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 with an argument inspection using the <cite>inspect</cite> library. Based on
 a created dictionary containing
 each parameter of the class with its docstring and type, the actual command
-line interface is build using <a class="reference external" href="https://docs.python.org/3/library/argparse.html#module-argparse" title="(in Python v3.11)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">argparse</span></code></a>. The syntax of the
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 syntax.</p>
@@ -153,7 +155,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/py-modindex.html b/dev/py-modindex.html
index 51c39d7..7a5dc1e 100644
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-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
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+  
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@@ -144,7 +146,7 @@ <h1>Python Module Index</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/dev/readme.html b/dev/readme.html
index 0a42c99..8fc1a71 100644
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+++ b/dev/readme.html
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+<html class="writer-html5" lang="en" data-content_root="./">
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-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
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-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
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@@ -106,8 +108,8 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 <p>Currently the following analysis modules are available</p>
 <table class="docutils align-default">
 <colgroup>
-<col style="width: 33%" />
-<col style="width: 67%" />
+<col style="width: 33.3%" />
+<col style="width: 66.7%" />
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 <thead>
 <tr class="row-odd"><th class="head"><p>Module Name</p></th>
@@ -191,7 +193,7 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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index 4882e65..a4e8afe 100644
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-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
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@@ -107,7 +109,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
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\ No newline at end of file
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"module-mdacli.cli"], [2, "module-mdacli.colors"], [3, "module-mdacli.libcli"], [4, "module-mdacli.logger"], [5, "module-mdacli.save"], [6, "module-mdacli.utils"]], "emphasise (class in mdacli.colors)": [[2, "mdacli.colors.Emphasise"]], "blue (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.blue"]], "bold (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.bold"]], "debug() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.debug"]], "emphasise() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.emphasise"]], "error() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.error"]], "gray (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.gray"]], "green (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.green"]], "header() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.header"]], "info() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.info"]], "mdacli.colors": [[2, "module-mdacli.colors"]], "ok() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.ok"]], "pink (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.pink"]], "red (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.red"]], "turquoise (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.turquoise"]], "underline (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.underline"]], "warning() (mdacli.colors.emphasise static method)": [[2, "mdacli.colors.Emphasise.warning"]], "yellow (mdacli.colors.emphasise attribute)": [[2, "mdacli.colors.Emphasise.yellow"]], "kwargsdict (class in mdacli.libcli)": [[3, "mdacli.libcli.KwargsDict"]], "add_cli_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_cli_universe"]], "add_output_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_output_group"]], "add_run_group() (in module mdacli.libcli)": [[3, "mdacli.libcli.add_run_group"]], "convert_analysis_parameters() (in module mdacli.libcli)": [[3, "mdacli.libcli.convert_analysis_parameters"]], "create_cli() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_cli"]], "create_universe() (in module mdacli.libcli)": [[3, "mdacli.libcli.create_universe"]], "find_classes_in_modules() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_classes_in_modules"]], "find_cls_members() (in module mdacli.libcli)": [[3, "mdacli.libcli.find_cls_members"]], "init_base_argparse() (in module mdacli.libcli)": [[3, "mdacli.libcli.init_base_argparse"]], "mdacli.libcli": [[3, "module-mdacli.libcli"]], "run_analysis() (in module mdacli.libcli)": [[3, "mdacli.libcli.run_analysis"]], "setup_clients() (in module mdacli.libcli)": [[3, "mdacli.libcli.setup_clients"]], "split_argparse_into_groups() (in module mdacli.libcli)": [[3, "mdacli.libcli.split_argparse_into_groups"]], "mdacli.logger": [[4, "module-mdacli.logger"]], "setup_logging() (in module mdacli.logger)": [[4, "mdacli.logger.setup_logging"]], "get_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.get_1D_arrays"]], "get_cli_input() (in module mdacli.save)": [[5, "mdacli.save.get_cli_input"]], "is_1d_array() (in module mdacli.save)": [[5, "mdacli.save.is_1d_array"]], "is_2d_array() (in module mdacli.save)": [[5, "mdacli.save.is_2d_array"]], "is_3d_array() (in module mdacli.save)": [[5, "mdacli.save.is_3d_array"]], "is_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_dimension_array"]], "is_higher_dimension_array() (in module mdacli.save)": [[5, "mdacli.save.is_higher_dimension_array"]], "is_serializable() (in module mdacli.save)": [[5, "mdacli.save.is_serializable"]], "mdacli.save": [[5, "module-mdacli.save"]], "remove_files() (in module mdacli.save)": [[5, "mdacli.save.remove_files"]], "return_with_remove() (in module mdacli.save)": [[5, "mdacli.save.return_with_remove"]], "save() (in module mdacli.save)": [[5, "mdacli.save.save"]], "save_1d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_1D_arrays"]], "save_2d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_2D_arrays"]], "save_3d_array_to_2d_csv() (in module mdacli.save)": [[5, "mdacli.save.save_3D_array_to_2D_csv"]], "save_3d_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_3D_arrays"]], "save_results_object() (in module mdacli.save)": [[5, "mdacli.save.save_Results_object"]], "save_files_to_zip() (in module mdacli.save)": [[5, "mdacli.save.save_files_to_zip"]], "save_higher_dim_arrays() (in module mdacli.save)": [[5, "mdacli.save.save_higher_dim_arrays"]], "save_json_serializables() (in module mdacli.save)": [[5, "mdacli.save.save_json_serializables"]], "save_result_array() (in module mdacli.save)": [[5, "mdacli.save.save_result_array"]], "save_to_json() (in module mdacli.save)": [[5, "mdacli.save.save_to_json"]], "savetxt_w_command() (in module mdacli.save)": [[5, "mdacli.save.savetxt_w_command"]], "stack_1d_arrays_list() (in module mdacli.save)": [[5, "mdacli.save.stack_1d_arrays_list"]], "try_to_squeeze_me() (in module mdacli.save)": [[5, "mdacli.save.try_to_squeeze_me"]], "convert_str_time() (in module mdacli.utils)": [[6, "mdacli.utils.convert_str_time"]], "mdacli.utils": [[6, "module-mdacli.utils"]], "parse_callable_signature() (in module mdacli.utils)": [[6, "mdacli.utils.parse_callable_signature"]], "parse_docs() (in module mdacli.utils)": [[6, "mdacli.utils.parse_docs"]], "split_time_unit() (in module mdacli.utils)": [[6, "mdacli.utils.split_time_unit"]]}})
\ No newline at end of file
diff --git a/dev/usage.html b/dev/usage.html
index c536059..d4b658a 100644
--- a/dev/usage.html
+++ b/dev/usage.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Usage &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/usage.html" />
   <!--[if lt IE 9]>
@@ -149,7 +151,7 @@ <h1>Usage<a class="headerlink" href="#usage" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/index.html b/stable/_modules/index.html
index fdf8e31..4bac276 100644
--- a/stable/_modules/index.html
+++ b/stable/_modules/index.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Overview: module code &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/index.html" />
   <!--[if lt IE 9]>
@@ -100,7 +102,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/cli.html b/stable/_modules/mdacli/cli.html
index 8743e3b..0e49d80 100644
--- a/stable/_modules/mdacli/cli.html
+++ b/stable/_modules/mdacli/cli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.cli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/cli.html" />
   <!--[if lt IE 9]>
@@ -191,9 +193,6 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
     <span class="c1">#   sub parser in complete detail.</span>
     <span class="n">setup_clients</span><span class="p">(</span><span class="n">ap</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2"> Analysis Modules&quot;</span><span class="p">,</span> <span class="n">members</span><span class="o">=</span><span class="n">modules</span><span class="p">)</span>
 
-    <span class="c1"># Be case insensitive for the subcommand</span>
-    <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
-
     <span class="n">args</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
 
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
@@ -209,7 +208,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
             <span class="c1"># Get the correct ArgumentParser instance from all subparsers</span>
             <span class="c1"># `[0]` selects the first subparser where our analysises live in.</span>
-            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+            <span class="n">_key</span> <span class="o">=</span> <span class="n">analysis_callable</span><span class="o">.</span><span class="vm">__name__</span>
             <span class="n">ap_sup</span> <span class="o">=</span> <span class="n">ap</span><span class="o">.</span><span class="n">_subparsers</span><span class="o">.</span><span class="n">_group_actions</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">choices</span><span class="p">[</span><span class="n">_key</span><span class="p">]</span>
             <span class="n">arg_grouped_dict</span> <span class="o">=</span> <span class="n">split_argparse_into_groups</span><span class="p">(</span><span class="n">ap_sup</span><span class="p">,</span> <span class="n">args</span><span class="p">)</span>
 
@@ -241,7 +240,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/colors.html b/stable/_modules/mdacli/colors.html
index a470569..fffdc44 100644
--- a/stable/_modules/mdacli/colors.html
+++ b/stable/_modules/mdacli/colors.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.colors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/colors.html" />
   <!--[if lt IE 9]>
@@ -312,7 +314,7 @@ <h1>Source code for mdacli.colors</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/libcli.html b/stable/_modules/mdacli/libcli.html
index d7181e5..590fead 100644
--- a/stable/_modules/mdacli/libcli.html
+++ b/stable/_modules/mdacli/libcli.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.libcli &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/libcli.html" />
   <!--[if lt IE 9]>
@@ -477,6 +479,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># creates the subparser</span>
     <span class="n">analysis_class_parser</span> <span class="o">=</span> <span class="n">sub_parser</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
         <span class="n">interface_name</span><span class="p">,</span>
+        <span class="n">aliases</span><span class="o">=</span><span class="p">[</span><span class="n">interface_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()],</span>
         <span class="n">help</span><span class="o">=</span><span class="n">parameters</span><span class="p">[</span><span class="s2">&quot;desc&quot;</span><span class="p">],</span>
         <span class="n">description</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc&#39;</span><span class="p">]</span><span class="si">}</span><span class="se">\n\n</span><span class="si">{</span><span class="n">parameters</span><span class="p">[</span><span class="s1">&#39;desc_long&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
         <span class="n">formatter_class</span><span class="o">=</span><span class="n">argparse</span><span class="o">.</span><span class="n">RawDescriptionHelpFormatter</span><span class="p">,</span>
@@ -888,7 +891,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
     <span class="c1"># to be writen</span>
     <span class="k">for</span> <span class="n">member_name</span><span class="p">,</span> <span class="n">parameters</span> <span class="ow">in</span> <span class="n">analysis_interfaces</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
         <span class="n">create_cli</span><span class="p">(</span><span class="n">sub_parser</span><span class="o">=</span><span class="n">cli_subparser</span><span class="p">,</span>
-                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="o">.</span><span class="n">lower</span><span class="p">(),</span>
+                   <span class="n">interface_name</span><span class="o">=</span><span class="n">member_name</span><span class="p">,</span>
                    <span class="n">parameters</span><span class="o">=</span><span class="n">parameters</span><span class="p">)</span></div>
 
 
@@ -955,7 +958,7 @@ <h1>Source code for mdacli.libcli</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/logger.html b/stable/_modules/mdacli/logger.html
index 7c1c49f..347b75c 100644
--- a/stable/_modules/mdacli/logger.html
+++ b/stable/_modules/mdacli/logger.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.logger &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/logger.html" />
   <!--[if lt IE 9]>
@@ -162,7 +164,7 @@ <h1>Source code for mdacli.logger</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/save.html b/stable/_modules/mdacli/save.html
index 73ea254..3b1559f 100644
--- a/stable/_modules/mdacli/save.html
+++ b/stable/_modules/mdacli/save.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.save &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/save.html" />
   <!--[if lt IE 9]>
@@ -551,7 +553,7 @@ <h1>Source code for mdacli.save</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/_modules/mdacli/utils.html b/stable/_modules/mdacli/utils.html
index 11c15e1..61706b7 100644
--- a/stable/_modules/mdacli/utils.html
+++ b/stable/_modules/mdacli/utils.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>mdacli.utils &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/_modules/mdacli/utils.html" />
   <!--[if lt IE 9]>
@@ -367,7 +369,7 @@ <h1>Source code for mdacli.utils</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api.html b/stable/api.html
index 56826fa..ef6c650 100644
--- a/stable/api.html
+++ b/stable/api.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>API library documentation &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api.html" />
   <!--[if lt IE 9]>
@@ -125,7 +127,7 @@ <h1>API library documentation<a class="headerlink" href="#api-library-documentat
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/cli.html b/stable/api/cli.html
index eaee9d9..06c7cb3 100644
--- a/stable/api/cli.html
+++ b/stable/api/cli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>High-Level API &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/cli.html" />
   <!--[if lt IE 9]>
@@ -104,7 +106,7 @@
 <p>The toplevel command line interface.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mdacli.cli.cli">
-<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140573603213664'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">mdacli.cli.</span></span><span class="sig-name descname"><span class="pre">cli</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_class=&lt;Mock</span> <span class="pre">name='mock.AnalysisBase'</span> <span class="pre">id='140499268142416'&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">version=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">description=''</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_modules=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ignore_warnings=False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/cli.html#cli"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.cli.cli" title="Link to this definition"></a></dt>
 <dd><p>Create the command-line interface.</p>
 <p>This function creates a command line interface with a given <cite>name</cite> based
 on a module list.</p>
@@ -158,7 +160,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/colors.html b/stable/api/colors.html
index 0fe82bf..129096f 100644
--- a/stable/api/colors.html
+++ b/stable/api/colors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Coloring &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/colors.html" />
   <!--[if lt IE 9]>
@@ -128,15 +130,15 @@
 <dl class="field-list simple">
 <dt class="field-odd">Variables<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – bold attribute</p></li>
-<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – underline attribute</p></li>
-<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – gray color</p></li>
-<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – red color</p></li>
-<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – green color</p></li>
-<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – yellow color</p></li>
-<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – blue color</p></li>
-<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – pink color</p></li>
-<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.11)"><em>str</em></a>) – turquoise color</p></li>
+<li><p><strong>bold</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – bold attribute</p></li>
+<li><p><strong>underline</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – underline attribute</p></li>
+<li><p><strong>gray</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – gray color</p></li>
+<li><p><strong>red</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – red color</p></li>
+<li><p><strong>green</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – green color</p></li>
+<li><p><strong>yellow</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – yellow color</p></li>
+<li><p><strong>blue</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – blue color</p></li>
+<li><p><strong>pink</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – pink color</p></li>
+<li><p><strong>turquoise</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – turquoise color</p></li>
 </ul>
 </dd>
 </dl>
@@ -328,7 +330,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/libcli.html b/stable/api/libcli.html
index 7e73d1f..cfa5ed6 100644
--- a/stable/api/libcli.html
+++ b/stable/api/libcli.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Support functions for CLI &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/libcli.html" />
   <!--[if lt IE 9]>
@@ -195,7 +197,7 @@
 of no ine is created</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – If an Atomgroup does not contain any atoms</p>
 </dd>
 </dl>
 </dd></dl>
@@ -261,25 +263,25 @@
 define the list of atoms. If the file includes bond information,
 partial charges, atom masses, … then these data will be available to
 MDAnalysis. Alternatively, an existing
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/core/topology.html#MDAnalysis.core.topology.Topology" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.core.topology.Topology</span></code></a> instance may be given,
 numpy coordinates, or None for an empty universe.</p></li>
 <li><p><strong>coordinates</strong> (<em>str, stream, list of str, list of stream</em>) – Coordinates can be provided as files of
 a single frame (eg a PDB, CRD, or GRO file); a list of single
 frames; or a trajectory file (in CHARMM/NAMD/LAMMPS DCD, Gromacs
 XTC/TRR, or generic XYZ format). The coordinates must be
 ordered in the same way as the list of atoms in the topology.
-See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.6.1)"><span>Table of supported coordinate formats</span></a> for what can be read
+See <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/init.html#id2" title="(in MDAnalysis v2.7.0)"><span>Table of supported coordinate formats</span></a> for what can be read
 as coordinates. Alternatively, streams can be given.</p></li>
 <li><p><strong>topology_format</strong> (<em>str, None</em>) – Provide the file format of the topology file; <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from
 the file extension. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/topology/base.html#MDAnalysis.topology.base.TopologyReaderBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.topology.base.TopologyReaderBase</span></code></a> to define a custom
 reader to be used on the topology file.</p></li>
 <li><p><strong>trajectory_format</strong> (<em>str or list or object</em>) – provide the file format of the coordinate or trajectory file;
 <code class="docutils literal notranslate"><span class="pre">None</span></code> guesses it from the file extension. Note that this
 keyword has no effect if a list of file names is supplied because
 the “chained” reader has to guess the file format for each
 individual list member [<code class="docutils literal notranslate"><span class="pre">None</span></code>]. Can also pass a subclass of
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html#MDAnalysis.coordinates.base.ProtoReader" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.coordinates.base.ProtoReader</span></code></a> to define a custom
 reader to be used on the trajectory file.</p></li>
 <li><p><strong>atom_style</strong> (<em>str</em>) – Customised LAMMPS <cite>atom_style</cite> information. Only works with
 <cite>topology_format = data</cite></p></li>
@@ -289,7 +291,7 @@
 </ul>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – If the dimesions of the <cite>dimensions</cite> argument are not 3 or 6.</p>
 </dd>
 <dt class="field-odd">Returns<span class="colon">:</span></dt>
 <dd class="field-odd"><p><cite>MDAnalysis.Universe</cite></p>
@@ -425,7 +427,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/logger.html b/stable/api/logger.html
index da62aa8..09c7893 100644
--- a/stable/api/logger.html
+++ b/stable/api/logger.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Logging &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/logger.html" />
   <!--[if lt IE 9]>
@@ -133,7 +135,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/save.html b/stable/api/save.html
index ec923a8..9cd1487 100644
--- a/stable/api/save.html
+++ b/stable/api/save.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Results Saving &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/save.html" />
   <!--[if lt IE 9]>
@@ -342,7 +344,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/api/utils.html b/stable/api/utils.html
index 5c1cda8..665dd5e 100644
--- a/stable/api/utils.html
+++ b/stable/api/utils.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Utilities &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="../_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="../_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/api/utils.html" />
   <!--[if lt IE 9]>
@@ -123,7 +125,7 @@
 <dd class="field-even"><p><em>int</em> – frame number</p>
 </dd>
 <dt class="field-odd">Raises<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.11)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#ValueError" title="(in Python v3.12)"><strong>ValueError</strong></a> – The input does not contain any units but is not an integer.</p>
 </dd>
 </dl>
 </dd></dl>
@@ -182,7 +184,7 @@
 <dd class="field-odd"><p><em>tuple (float, str)</em> – Value as float, units as str.</p>
 </dd>
 <dt class="field-even">Raises<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.11)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3/library/exceptions.html#IndexError" title="(in Python v3.12)"><strong>IndexError</strong></a> – Tuple could not be found. This happens when a number is not
     present in the start of the string.</p>
 </dd>
 </dl>
@@ -202,7 +204,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/authors.html b/stable/authors.html
index 863562c..1e34430 100644
--- a/stable/authors.html
+++ b/stable/authors.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Authors &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/authors.html" />
   <!--[if lt IE 9]>
@@ -108,7 +110,7 @@ <h1>Authors<a class="headerlink" href="#authors" title="Link to this heading">
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/changelog.html b/stable/changelog.html
index 3a139ed..d8607c8 100644
--- a/stable/changelog.html
+++ b/stable/changelog.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Changelog &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/changelog.html" />
   <!--[if lt IE 9]>
@@ -120,6 +122,9 @@
              
   <section id="changelog">
 <h1>Changelog<a class="headerlink" href="#changelog" title="Link to this heading"></a></h1>
+<ul class="simple">
+<li><p>Change handling of lowercase module names</p></li>
+</ul>
 <section id="v0-1-28-2023-09-29">
 <h2>v0.1.28 (2023-09-29)<a class="headerlink" href="#v0-1-28-2023-09-29" title="Link to this heading"></a></h2>
 <ul class="simple">
@@ -326,7 +331,7 @@ <h2>v0.1.0 (2021-11-18)<a class="headerlink" href="#v0-1-0-2021-11-18" title="Li
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/contributing.html b/stable/contributing.html
index 4361cdb..8bc973f 100644
--- a/stable/contributing.html
+++ b/stable/contributing.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Contributing &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/contributing.html" />
   <!--[if lt IE 9]>
@@ -249,7 +251,7 @@ <h2>Pull Request<a class="headerlink" href="#pull-request" title="Link to this h
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/genindex.html b/stable/genindex.html
index f761254..79cac88 100644
--- a/stable/genindex.html
+++ b/stable/genindex.html
@@ -1,12 +1,14 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/genindex.html" />
   <!--[if lt IE 9]>
@@ -435,7 +437,7 @@ <h2 id="Y">Y</h2>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/index.html b/stable/index.html
index 2c0baa3..e17f1d2 100644
--- a/stable/index.html
+++ b/stable/index.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>MDAnalysis command line interface &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/index.html" />
   <!--[if lt IE 9]>
@@ -107,8 +109,8 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 <p>Currently the following analysis modules are available</p>
 <table class="docutils align-default">
 <colgroup>
-<col style="width: 33%" />
-<col style="width: 67%" />
+<col style="width: 33.3%" />
+<col style="width: 66.7%" />
 </colgroup>
 <thead>
 <tr class="row-odd"><th class="head"><p>Module Name</p></th>
@@ -196,7 +198,7 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/installation.html b/stable/installation.html
index f9f8665..b1dbbdc 100644
--- a/stable/installation.html
+++ b/stable/installation.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Installation &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/installation.html" />
   <!--[if lt IE 9]>
@@ -141,7 +143,7 @@ <h2>conda<a class="headerlink" href="#conda" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/philosophy.html b/stable/philosophy.html
index bdfa055..2693969 100644
--- a/stable/philosophy.html
+++ b/stable/philosophy.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Philosophy and approach &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/philosophy.html" />
   <!--[if lt IE 9]>
@@ -104,7 +106,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 <li><p>…</p></li>
 </ul>
 <p>Some of these problems can be solved by using the
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class of MDA. However,
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class of MDA. However,
 this class is limited to python, and sometimes a direct CLI to these
 scripts is very helpful for the day-to-day analysis.
 A generic CLI wrapper for all classes based on the AnalysisBase could
@@ -117,11 +119,11 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 <cite>base.AnalysisBase</cite>.</p>
 <p>Starting from <cite>taurenmd</cite> and <cite>maicos</cite> we
 developed a general CLI for any
-<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class.
+<a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a> class.
 mdacli detects all analysis classes located inside the
 MDA project and builds a CLI wrapper around them. The wrapper
 is generic so it also applies to any downstream
-project that uses the <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.6.1)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a>
+project that uses the <a class="reference external" href="https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase" title="(in MDAnalysis v2.7.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">MDAnalysis.analysis.base.AnalysisBase</span></code></a>
 as parent class. If new classes are added to the
 MDA codebase they are just they will show up without
 any adjustments to <cite>mdacli</cite> itself.</p>
@@ -129,7 +131,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 with an argument inspection using the <cite>inspect</cite> library. Based on
 a created dictionary containing
 each parameter of the class with its docstring and type, the actual command
-line interface is build using <a class="reference external" href="https://docs.python.org/3/library/argparse.html#module-argparse" title="(in Python v3.11)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">argparse</span></code></a>. The syntax of the
+line interface is build using <a class="reference external" href="https://docs.python.org/3/library/argparse.html#module-argparse" title="(in Python v3.12)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">argparse</span></code></a>. The syntax of the
 topology and the trajectory flags (<cite>-f</cite>, <cite>-s</cite>, …) is inspired by the
 <a class="reference external" href="https://manual.gromacs.org/documentation/current/user-guide/cmdline.html">GROMACS CLI</a>
 syntax.</p>
@@ -153,7 +155,7 @@ <h1>Philosophy and approach<a class="headerlink" href="#philosophy-and-approach"
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/py-modindex.html b/stable/py-modindex.html
index 51c39d7..7a5dc1e 100644
--- a/stable/py-modindex.html
+++ b/stable/py-modindex.html
@@ -1,12 +1,14 @@
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+<html class="writer-html5" lang="en" data-content_root="./">
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Python Module Index &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/py-modindex.html" />
   <!--[if lt IE 9]>
@@ -144,7 +146,7 @@ <h1>Python Module Index</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/readme.html b/stable/readme.html
index 0a42c99..8fc1a71 100644
--- a/stable/readme.html
+++ b/stable/readme.html
@@ -1,13 +1,15 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>MDAnalysis command line interface &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/readme.html" />
   <!--[if lt IE 9]>
@@ -106,8 +108,8 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 <p>Currently the following analysis modules are available</p>
 <table class="docutils align-default">
 <colgroup>
-<col style="width: 33%" />
-<col style="width: 67%" />
+<col style="width: 33.3%" />
+<col style="width: 66.7%" />
 </colgroup>
 <thead>
 <tr class="row-odd"><th class="head"><p>Module Name</p></th>
@@ -191,7 +193,7 @@ <h2>Available modules<a class="headerlink" href="#available-modules" title="Link
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/search.html b/stable/search.html
index 4882e65..a4e8afe 100644
--- a/stable/search.html
+++ b/stable/search.html
@@ -1,12 +1,14 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Search &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
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+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
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+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/search.html" />
     
@@ -107,7 +109,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
diff --git a/stable/searchindex.js b/stable/searchindex.js
index 253a6df..31d327f 100644
--- a/stable/searchindex.js
+++ b/stable/searchindex.js
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\ No newline at end of file
diff --git a/stable/usage.html b/stable/usage.html
index c536059..d4b658a 100644
--- a/stable/usage.html
+++ b/stable/usage.html
@@ -1,13 +1,15 @@
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-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
-  <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Usage &mdash; mdacli 0.1.28 documentation</title>
-      <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="_static/css/msmb.css" type="text/css" />
-      <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d10597a4" />
+      <link rel="stylesheet" type="text/css" href="_static/css/msmb.css?v=51bd699f" />
+      <link rel="stylesheet" type="text/css" href="_static/custom.css?v=27e8b3b8" />
+
+  
     <link rel="shortcut icon" href="_static/mdanalysis-logo.ico"/>
     <link rel="canonical" href="https://mdacli.mdanalysis.org/usage.html" />
   <!--[if lt IE 9]>
@@ -149,7 +151,7 @@ <h1>Usage<a class="headerlink" href="#usage" title="Link to this heading"></a
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Sep 29, 2023.
+      <span class="lastupdated">Last updated on Mar 21, 2024.
       </span></p>
   </div>
 
