rebuilt html docs for version 0.1.29 from branch main with sphinx at 4…

…a1e53f

0.1.29/_modules/index.html

@@ -102,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/cli.html

@@ -90,7 +90,7 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 <span></span><span class="ch">#!/usr/bin/env python3</span>
 <span class="c1"># -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-</span>
 <span class="c1">#</span>
-<span class="c1"># Copyright (c) 2021 Authors and contributors</span>
+<span class="c1"># Copyright (c) 2024 Authors and contributors</span>
 <span class="c1">#</span>
 <span class="c1"># Released under the GNU Public Licence, v2 or any higher version</span>
 <span class="c1"># SPDX-License-Identifier: GPL-2.0-or-later</span>
@@ -195,13 +195,20 @@ <h1>Source code for mdacli.cli</h1><div class="highlight"><pre>
 
     <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="c1"># Set the logging level based on the verbose argument</span>
+    <span class="c1"># If verbose is not an argument, default to WARNING</span>
+    <span class="k">if</span> <span class="ow">not</span> <span class="nb">hasattr</span><span class="p">(</span><span class="n">args</span><span class="p">,</span> <span class="s2">&quot;verbose&quot;</span><span class="p">)</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">args</span><span class="o">.</span><span class="n">verbose</span><span class="p">:</span>
+        <span class="n">level</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">WARNING</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="n">level</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span>
+
     <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
-        <span class="n">args</span><span class="o">.</span><span class="n">verbose</span> <span class="o">=</span> <span class="kc">True</span>
+        <span class="n">level</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span>
     <span class="k">else</span><span class="p">:</span>
-        <span class="c1"># Ignore all warnings if not in debug mode</span>
+        <span class="c1"># Ignore all warnings if not in debug mode, because MDA is noisy</span>
         <span class="n">warnings</span><span class="o">.</span><span class="n">filterwarnings</span><span class="p">(</span><span class="s2">&quot;ignore&quot;</span><span class="p">)</span>
 
-    <span class="k">with</span> <span class="n">setup_logging</span><span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">logfile</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">):</span>
+    <span class="k">with</span> <span class="n">setup_logging</span><span class="p">(</span><span class="n">logger</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">logfile</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">level</span><span class="p">):</span>
         <span class="c1"># Execute the main client interface.</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">analysis_callable</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">analysis_callable</span>
@@ -240,7 +247,7 @@ <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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/colors.html

@@ -314,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/libcli.html

@@ -958,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/logger.html

@@ -106,7 +106,7 @@ <h1>Source code for mdacli.logger</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="setup_logging">
 <a class="viewcode-back" href="../../api/logger.html#mdacli.logger.setup_logging">[docs]</a>
 <span class="nd">@contextlib</span><span class="o">.</span><span class="n">contextmanager</span>
-<span class="k">def</span> <span class="nf">setup_logging</span><span class="p">(</span><span class="n">logobj</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<span class="k">def</span> <span class="nf">setup_logging</span><span class="p">(</span><span class="n">logobj</span><span class="p">,</span> <span class="n">logfile</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">WARNING</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Create a logging environment for a given logobj.</span>
 
@@ -116,19 +116,20 @@ <h1>Source code for mdacli.logger</h1><div class="highlight"><pre>
 <span class="sd">        A logging instance</span>
 <span class="sd">    logfile : str</span>
 <span class="sd">        Name of the log file</span>
-<span class="sd">    debug : bool</span>
-<span class="sd">        If ``True`` detailed debug logs inludcing filename and function name</span>
-<span class="sd">        are displayed. If ``False`` only the message logged from</span>
-<span class="sd">        errors, warnings and infos will be displayed.</span>
+<span class="sd">    level : int</span>
+<span class="sd">        Set the root logger level to the specified level. If for example set</span>
+<span class="sd">        to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and</span>
+<span class="sd">        function name are displayed. For :py:obj:`logging.INFO only the message</span>
+<span class="sd">        logged from errors, warnings and infos will be displayed.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">try</span><span class="p">:</span>
-        <span class="nb">format</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">{message}</span><span class="s1">&#39;</span>
-        <span class="k">if</span> <span class="n">debug</span><span class="p">:</span>
-            <span class="nb">format</span> <span class="o">=</span> <span class="s2">&quot;[</span><span class="si">{levelname}</span><span class="s2">] </span><span class="si">{filename}</span><span class="s2">:</span><span class="si">{name}</span><span class="s2">:</span><span class="si">{funcName}</span><span class="s2">:</span><span class="si">{lineno}</span><span class="s2">: &quot;</span> \
-                     <span class="o">+</span> <span class="nb">format</span>
-            <span class="n">level</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span>
+        <span class="k">if</span> <span class="n">level</span> <span class="o">==</span> <span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">:</span>
+            <span class="nb">format</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="s2">&quot;[</span><span class="si">{levelname}</span><span class="s2">] </span><span class="si">{filename}</span><span class="s2">:</span><span class="si">{name}</span><span class="s2">:</span><span class="si">{funcName}</span><span class="s2">:</span><span class="si">{lineno}</span><span class="s2">: &quot;</span>
+                <span class="s2">&quot;</span><span class="si">{message}</span><span class="s2">&quot;</span>
+            <span class="p">)</span>
         <span class="k">else</span><span class="p">:</span>
-            <span class="n">level</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span>
+            <span class="nb">format</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="si">{message}</span><span class="s2">&quot;</span>
 
         <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="nb">format</span><span class="o">=</span><span class="nb">format</span><span class="p">,</span>
                             <span class="n">handlers</span><span class="o">=</span><span class="p">[</span><span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)],</span>
@@ -164,7 +165,7 @@ <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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/save.html

@@ -553,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/_modules/mdacli/utils.html

@@ -369,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api.html

@@ -127,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/cli.html

@@ -106,7 +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='140119435511120'&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='140259180724288'&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>
@@ -160,7 +160,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/colors.html

@@ -330,7 +330,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/libcli.html

@@ -427,7 +427,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/logger.html

@@ -106,16 +106,17 @@
 <p>Logging.</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="mdacli.logger.setup_logging">
-<span class="sig-prename descclassname"><span class="pre">mdacli.logger.</span></span><span class="sig-name descname"><span class="pre">setup_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logobj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">debug</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/logger.html#setup_logging"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.logger.setup_logging" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">mdacli.logger.</span></span><span class="sig-name descname"><span class="pre">setup_logging</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logobj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">logfile</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">30</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/mdacli/logger.html#setup_logging"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#mdacli.logger.setup_logging" title="Link to this definition"></a></dt>
 <dd><p>Create a logging environment for a given logobj.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>logobj</strong> (<code class="docutils literal notranslate"><span class="pre">logging.Logger</span></code>) – A logging instance</p></li>
 <li><p><strong>logfile</strong> (<em>str</em>) – Name of the log file</p></li>
-<li><p><strong>debug</strong> (<em>bool</em>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code> detailed debug logs inludcing filename and function name
-are displayed. If <code class="docutils literal notranslate"><span class="pre">False</span></code> only the message logged from
-errors, warnings and infos will be displayed.</p></li>
+<li><p><strong>level</strong> (<em>int</em>) – Set the root logger level to the specified level. If for example set
+to <a class="reference external" href="https://docs.python.org/3/library/logging.html#logging.DEBUG" title="(in Python v3.12)"><code class="xref py py-obj docutils literal notranslate"><span class="pre">logging.DEBUG</span></code></a> detailed debug logs inludcing filename and
+function name are displayed. For :py:obj:<a href="#id1"><span class="problematic" id="id2">`</span></a>logging.INFO only the message
+logged from errors, warnings and infos will be displayed.</p></li>
 </ul>
 </dd>
 </dl>
@@ -135,7 +136,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/save.html

@@ -344,7 +344,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/api/utils.html

@@ -204,7 +204,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      <span class="lastupdated">Last updated on Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>
 

0.1.29/authors.html

@@ -110,7 +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 Mar 21, 2024.
+      <span class="lastupdated">Last updated on Apr 03, 2024.
       </span></p>
   </div>