Update sphinx documentation

pwollstadt · Feb 28, 2022 · a95604f · a95604f
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diff --git a/docs/conf.py b/docs/conf.py
@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.2.1'
+version = u'1.3'
 # The full version, including alpha/beta/rc tags.
-release = u'1.2.1'
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

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_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: f717522005f8a2bcad31d42c004451be
+config: e9e58d63b14646ac556754d60eae5f9e
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/_modules/idtxl/embedding_optimization_ais_Rudelt.html b/docs/html/_modules/idtxl/embedding_optimization_ais_Rudelt.html
diff --git a/docs/html/_modules/idtxl/estimators_Rudelt.html b/docs/html/_modules/idtxl/estimators_Rudelt.html
diff --git a/docs/html/_modules/idtxl/results.html b/docs/html/_modules/idtxl/results.html
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
@@ -5,10 +5,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; IDTxl 1.2.1 documentation</title>
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/pyramid.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+    <title>Overview: module code &#8212; IDTxl 1.3 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>
@@ -31,7 +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 1.2.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">IDTxl 1.3 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
       </ul>
     </div>  
@@ -47,12 +47,13 @@ <h1>All modules for which code is available</h1>
 <li><a href="idtxl/bivariate_pid.html">idtxl.bivariate_pid</a></li>
 <li><a href="idtxl/bivariate_te.html">idtxl.bivariate_te</a></li>
 <li><a href="idtxl/data.html">idtxl.data</a></li>
+<li><a href="idtxl/embedding_optimization_ais_Rudelt.html">idtxl.embedding_optimization_ais_Rudelt</a></li>
+<li><a href="idtxl/estimators_Rudelt.html">idtxl.estimators_Rudelt</a></li>
 <li><a href="idtxl/estimators_jidt.html">idtxl.estimators_jidt</a></li>
 <li><a href="idtxl/estimators_multivariate_pid.html">idtxl.estimators_multivariate_pid</a></li>
 <li><a href="idtxl/estimators_opencl.html">idtxl.estimators_opencl</a></li>
 <li><a href="idtxl/estimators_pid.html">idtxl.estimators_pid</a></li>
 <li><a href="idtxl/idtxl_exceptions.html">idtxl.idtxl_exceptions</a></li>
-<li><a href="idtxl/idtxl_import.html">idtxl.idtxl_import</a></li>
 <li><a href="idtxl/idtxl_io.html">idtxl.idtxl_io</a></li>
 <li><a href="idtxl/idtxl_utils.html">idtxl.idtxl_utils</a></li>
 <li><a href="idtxl/multivariate_mi.html">idtxl.multivariate_mi</a></li>
@@ -77,7 +78,7 @@ <h1>All modules for which code is available</h1>
   <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>
@@ -96,13 +97,13 @@ <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 1.2.1 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">IDTxl 1.3 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Overview: module code</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> 3.5.1.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 4.4.0.
     </div>
   </body>
 </html>
diff --git a/docs/html/_sources/idtxl.rst.txt b/docs/html/_sources/idtxl.rst.txt
@@ -69,6 +69,22 @@ idtxl.active_information_storage module
     :undoc-members:
     :show-inheritance:
 
+idtxl.embedding_optimization_ais_Rudelt module
+----------------------------------------------
+
+.. automodule:: idtxl.embedding_optimization_ais_Rudelt
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+idtxl.estimators_Rudelt module
+------------------------------
+
+.. automodule:: idtxl.estimators_Rudelt
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 idtxl.estimators_jidt module
 ----------------------------
 
@@ -102,14 +118,6 @@ idtxl.estimators_pid module
     :show-inheritance:
 
 
-idtxl.idtxl_import module
--------------------------
-
-.. automodule:: idtxl.idtxl_import
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 idtxl.idtxl_exceptions module
 -----------------------------
 

diff --git a/docs/html/_sources/idtxl_process_analysis.rst.txt b/docs/html/_sources/idtxl_process_analysis.rst.txt
@@ -18,3 +18,16 @@ Bivariate Partial Information Decomposition (PID)
 .. autoclass:: idtxl.bivariate_pid.BivariatePID
     :members:
     :noindex:
+
+History-dependence estimator for neural spiking data
+----------------------------------------------------
+Embedding optimization
+^^^^^^^^^^^^^^^^^^^^^^
+.. autoclass:: idtxl.embedding_optimization_ais_Rudelt.OptimizationRudelt
+    :members:
+    :noindex:
+Estimators
+^^^^^^^^^^
+.. automodule:: idtxl.estimators_Rudelt
+    :members:
+    :noindex:
diff --git a/docs/html/_sources/idtxl_results_class.rst.txt b/docs/html/_sources/idtxl_results_class.rst.txt
@@ -24,3 +24,6 @@ Results node dynamics
 .. autoclass:: idtxl.results.ResultsMultivariatePID
     :members:
     :noindex:
+.. autoclass:: idtxl.results.ResultsSingleProcessRudelt
+    :members:
+    :noindex:
diff --git a/docs/html/_static/basic.css b/docs/html/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -130,7 +130,7 @@ ul.search li a {
     font-weight: bold;
 }
 
-ul.search li div.context {
+ul.search li p.context {
     color: #888;
     margin: 2px 0 0 30px;
     text-align: left;
@@ -277,25 +277,25 @@ p.rubric {
     font-weight: bold;
 }
 
-img.align-left, .figure.align-left, object.align-left {
+img.align-left, figure.align-left, .figure.align-left, object.align-left {
     clear: left;
     float: left;
     margin-right: 1em;
 }
 
-img.align-right, .figure.align-right, object.align-right {
+img.align-right, figure.align-right, .figure.align-right, object.align-right {
     clear: right;
     float: right;
     margin-left: 1em;
 }
 
-img.align-center, .figure.align-center, object.align-center {
+img.align-center, figure.align-center, .figure.align-center, object.align-center {
   display: block;
   margin-left: auto;
   margin-right: auto;
 }
 
-img.align-default, .figure.align-default {
+img.align-default, figure.align-default, .figure.align-default {
   display: block;
   margin-left: auto;
   margin-right: auto;
@@ -319,7 +319,8 @@ img.align-default, .figure.align-default {
 
 /* -- sidebars -------------------------------------------------------------- */
 
-div.sidebar {
+div.sidebar,
+aside.sidebar {
     margin: 0 0 0.5em 1em;
     border: 1px solid #ddb;
     padding: 7px;
@@ -377,12 +378,14 @@ div.body p.centered {
 /* -- content of sidebars/topics/admonitions -------------------------------- */
 
 div.sidebar > :last-child,
+aside.sidebar > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
+aside.sidebar::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -455,20 +458,22 @@ td > :last-child {
 
 /* -- figures --------------------------------------------------------------- */
 
-div.figure {
+div.figure, figure {
     margin: 0.5em;
     padding: 0.5em;
 }
 
-div.figure p.caption {
+div.figure p.caption, figcaption {
     padding: 0.3em;
 }
 
-div.figure p.caption span.caption-number {
+div.figure p.caption span.caption-number,
+figcaption span.caption-number {
     font-style: italic;
 }
 
-div.figure p.caption span.caption-text {
+div.figure p.caption span.caption-text,
+figcaption span.caption-text {
 }
 
 /* -- field list styles ----------------------------------------------------- */
@@ -503,6 +508,63 @@ table.hlist td {
     vertical-align: top;
 }
 
+/* -- object description styles --------------------------------------------- */
+
+.sig {
+	font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+}
+
+.sig-name, code.descname {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+.sig-name {
+	font-size: 1.1em;
+}
+
+code.descname {
+    font-size: 1.2em;
+}
+
+.sig-prename, code.descclassname {
+    background-color: transparent;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.sig-paren {
+    font-size: larger;
+}
+
+.sig-param.n {
+	font-style: italic;
+}
+
+/* C++ specific styling */
+
+.sig-inline.c-texpr,
+.sig-inline.cpp-texpr {
+	font-family: unset;
+}
+
+.sig.c   .k, .sig.c   .kt,
+.sig.cpp .k, .sig.cpp .kt {
+	color: #0033B3;
+}
+
+.sig.c   .m,
+.sig.cpp .m {
+	color: #1750EB;
+}
+
+.sig.c   .s, .sig.c   .sc,
+.sig.cpp .s, .sig.cpp .sc {
+	color: #067D17;
+}
+
 
 /* -- other body styles ----------------------------------------------------- */
 
@@ -629,14 +691,6 @@ dl.glossary dt {
     font-size: 1.1em;
 }
 
-.optional {
-    font-size: 1.3em;
-}
-
-.sig-paren {
-    font-size: larger;
-}
-
 .versionmodified {
     font-style: italic;
 }
@@ -677,8 +731,9 @@ dl.glossary dt {
 
 .classifier:before {
     font-style: normal;
-    margin: 0.5em;
+    margin: 0 0.5em;
     content: ":";
+    display: inline-block;
 }
 
 abbr, acronym {
@@ -702,6 +757,7 @@ span.pre {
     -ms-hyphens: none;
     -webkit-hyphens: none;
     hyphens: none;
+    white-space: nowrap;
 }
 
 div[class*="highlight-"] {
@@ -765,8 +821,12 @@ div.code-block-caption code {
 
 table.highlighttable td.linenos,
 span.linenos,
-div.doctest > div.highlight span.gp {  /* gp: Generic.Prompt */
-    user-select: none;
+div.highlight span.gp {  /* gp: Generic.Prompt */
+  user-select: none;
+  -webkit-user-select: text; /* Safari fallback only */
+  -webkit-user-select: none; /* Chrome/Safari */
+  -moz-user-select: none; /* Firefox */
+  -ms-user-select: none; /* IE10+ */
 }
 
 div.code-block-caption span.caption-number {
@@ -781,16 +841,6 @@ div.literal-block-wrapper {
     margin: 1em 0;
 }
 
-code.descname {
-    background-color: transparent;
-    font-weight: bold;
-    font-size: 1.2em;
-}
-
-code.descclassname {
-    background-color: transparent;
-}
-
 code.xref, a code {
     background-color: transparent;
     font-weight: bold;