Update docs for v1.5

pwollstadt · Dec 9, 2023 · 0a247b8 · 0a247b8
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diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/idtxl.doctree b/docs/doctrees/idtxl.doctree
diff --git a/docs/doctrees/idtxl_data_class.doctree b/docs/doctrees/idtxl_data_class.doctree
diff --git a/docs/doctrees/idtxl_estimators.doctree b/docs/doctrees/idtxl_estimators.doctree
diff --git a/docs/doctrees/idtxl_helper.doctree b/docs/doctrees/idtxl_helper.doctree
diff --git a/docs/doctrees/idtxl_network_comparison.doctree b/docs/doctrees/idtxl_network_comparison.doctree
diff --git a/docs/doctrees/idtxl_network_inference.doctree b/docs/doctrees/idtxl_network_inference.doctree
diff --git a/docs/doctrees/idtxl_postprocessing.doctree b/docs/doctrees/idtxl_postprocessing.doctree
diff --git a/docs/doctrees/idtxl_process_analysis.doctree b/docs/doctrees/idtxl_process_analysis.doctree
diff --git a/docs/doctrees/idtxl_results_class.doctree b/docs/doctrees/idtxl_results_class.doctree
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/modules.doctree b/docs/doctrees/modules.doctree
diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bbdc974144d9ca28a919aa38820edff7
+config: ac063bd26c9fc26cbf87edb5d4832784
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/_modules/idtxl/active_information_storage.html b/docs/html/_modules/idtxl/active_information_storage.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>idtxl.active_information_storage &#8212; IDTxl 1.4 documentation</title>
-    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <title>idtxl.active_information_storage &#8212; IDTxl 1.5 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pyramid.css" />
+    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
     <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -32,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.active_information_storage</a></li> 
       </ul>
@@ -678,7 +677,7 @@ <h1>Source code for idtxl.active_information_storage</h1><div class="highlight">
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -697,14 +696,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.active_information_storage</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>
diff --git a/docs/html/_modules/idtxl/bivariate_pid.html b/docs/html/_modules/idtxl/bivariate_pid.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>idtxl.bivariate_pid &#8212; IDTxl 1.4 documentation</title>
-    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <title>idtxl.bivariate_pid &#8212; IDTxl 1.5 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pyramid.css" />
+    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
     <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -32,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.bivariate_pid</a></li> 
       </ul>
@@ -53,7 +52,7 @@ <h1>Source code for idtxl.bivariate_pid</h1><div class="highlight"><pre>
 <span class="sd">&quot;&quot;&quot;</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">from</span> <span class="nn">.single_process_analysis</span> <span class="kn">import</span> <span class="n">SingleProcessAnalysis</span>
-<span class="kn">from</span> <span class="nn">.estimator</span> <span class="kn">import</span> <span class="n">find_estimator</span>
+<span class="kn">from</span> <span class="nn">.estimator</span> <span class="kn">import</span> <span class="n">get_estimator</span>
 <span class="kn">from</span> <span class="nn">.results</span> <span class="kn">import</span> <span class="n">ResultsPID</span>
 
 
@@ -252,11 +251,8 @@ <h1>Source code for idtxl.bivariate_pid</h1><div class="highlight"><pre>
     <span class="k">def</span> <span class="nf">_initialise</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">target</span><span class="p">,</span> <span class="n">sources</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Check input, set initial or default values for analysis settings.&quot;&quot;&quot;</span>
         <span class="c1"># Check requested PID estimator.</span>
-        <span class="k">try</span><span class="p">:</span>
-            <span class="n">EstimatorClass</span> <span class="o">=</span> <span class="n">find_estimator</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;pid_estimator&#39;</span><span class="p">])</span>
-        <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
-            <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s1">&#39;Estimator was not specified!&#39;</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_pid_estimator</span> <span class="o">=</span> <span class="n">EstimatorClass</span><span class="p">(</span><span class="n">settings</span><span class="p">)</span>
+        <span class="k">assert</span> <span class="s1">&#39;pid_estimator&#39;</span> <span class="ow">in</span> <span class="n">settings</span><span class="p">,</span> <span class="s1">&#39;Estimator was not specified!&#39;</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_pid_estimator</span> <span class="o">=</span> <span class="n">get_estimator</span><span class="p">(</span><span class="n">settings</span><span class="p">[</span><span class="s1">&#39;pid_estimator&#39;</span><span class="p">],</span> <span class="n">settings</span><span class="p">)</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">settings</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="s1">&#39;lags_pid&#39;</span><span class="p">,</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">])</span>
@@ -363,7 +359,7 @@ <h1>Source code for idtxl.bivariate_pid</h1><div class="highlight"><pre>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -382,14 +378,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.bivariate_pid</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>
diff --git a/docs/html/_modules/idtxl/estimators_Rudelt.html b/docs/html/_modules/idtxl/estimators_Rudelt.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>idtxl.estimators_Rudelt &#8212; IDTxl 1.4 documentation</title>
-    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <title>idtxl.estimators_Rudelt &#8212; IDTxl 1.5 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pyramid.css" />
+    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
     <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -32,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.estimators_Rudelt</a></li> 
       </ul>
@@ -1187,7 +1186,7 @@ <h1>Source code for idtxl.estimators_Rudelt</h1><div class="highlight"><pre>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -1206,14 +1205,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.estimators_Rudelt</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>
diff --git a/docs/html/_modules/idtxl/estimators_jidt.html b/docs/html/_modules/idtxl/estimators_jidt.html
@@ -5,14 +5,13 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>idtxl.estimators_jidt &#8212; IDTxl 1.4 documentation</title>
-    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
-    <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <title>idtxl.estimators_jidt &#8212; IDTxl 1.5 documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css" />
+    <link rel="stylesheet" type="text/css" href="../../_static/pyramid.css" />
+    <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js"></script>
     <script src="../../_static/jquery.js"></script>
     <script src="../../_static/underscore.js"></script>
     <script src="../../_static/doctools.js"></script>
-    <script src="../../_static/language_data.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
 <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Neuton&amp;subset=latin" type="text/css" media="screen" charset="utf-8" />
@@ -32,7 +31,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.estimators_jidt</a></li> 
       </ul>
@@ -396,7 +395,6 @@ <h1>Source code for idtxl.estimators_jidt</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="JidtGaussian.estimate_surrogates_analytic"><a class="viewcode-back" href="../../idtxl_estimators.html#idtxl.estimators_jidt.JidtGaussian.estimate_surrogates_analytic">[docs]</a>    <span class="k">def</span> <span class="nf">estimate_surrogates_analytic</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">n_perm</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span> <span class="o">**</span><span class="n">data</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Estimate the surrogate distribution analytically.</span>
-
 <span class="sd">        This method must be implemented because this class&#39;</span>
 <span class="sd">        is_analytic_null_estimator() method returns true</span>
 
@@ -1363,7 +1361,6 @@ <h1>Source code for idtxl.estimators_jidt</h1><div class="highlight"><pre>
 
 <span class="sd">    See parent class for references. Results are returned in nats.</span>
 
-
 <span class="sd">    Args:</span>
 <span class="sd">        settings : dict [optional]</span>
 <span class="sd">            sets estimation parameters:</span>
@@ -1858,7 +1855,7 @@ <h1>Source code for idtxl.estimators_jidt</h1><div class="highlight"><pre>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>
@@ -1877,14 +1874,14 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.4 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.5 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">idtxl.estimators_jidt</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2018, Patricia Wollstadt, Joseph T. Lizier, Raul Vicente, Conor Finn, Mario Martinez-Zarzuela, Pedro Mediano, Leonardo Novelli, Michael Wibral.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>