rebuilt html docs for version 0.1.28 from branch main with sphinx at b…

…ad8581
MDAnalysis · Mar 21, 2024 · ca4d448 · ca4d448
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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>