Update gh-pages to v1.2.1

Fixes #51.
pwollstadt · Feb 25, 2021 · d225f38 · d225f38
1 parent bb23244
commit d225f38
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Showing 71 changed files with 24,454 additions and 9,029 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'1.0'
+version = u'1.2.1'
 # The full version, including alpha/beta/rc tags.
-release = u'1.0'
+release = u'1.2.1'
 
 # 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: 6c4e3c84cb60f8ef29d1bd405463eb1f
+config: f717522005f8a2bcad31d42c004451be
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/_modules/idtxl/active_information_storage.html b/docs/html/_modules/idtxl/active_information_storage.html
diff --git a/docs/html/_modules/idtxl/bivariate_mi.html b/docs/html/_modules/idtxl/bivariate_mi.html
@@ -1,18 +1,17 @@
 
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
-  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!DOCTYPE html>
 
-<html xmlns="http://www.w3.org/1999/xhtml">
+<html>
   <head>
-    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>idtxl.bivariate_mi &#8212; IDTxl 1.0 documentation</title>
-    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
-    <script type="text/javascript" src="../../_static/jquery.js"></script>
-    <script type="text/javascript" src="../../_static/underscore.js"></script>
-    <script type="text/javascript" src="../../_static/doctools.js"></script>
+    <link rel="stylesheet" href="../../_static/pyramid.css" type="text/css" />
+    <script id="documentation_options" data-url_root="../../" src="../../_static/documentation_options.js"></script>
+    <script src="../../_static/jquery.js"></script>
+    <script src="../../_static/underscore.js"></script>
+    <script src="../../_static/doctools.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" />
@@ -33,7 +32,8 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.0 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-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">idtxl.bivariate_mi</a></li> 
       </ul>
     </div>  
 
@@ -185,6 +185,11 @@ <h1>Source code for idtxl.bivariate_mi</h1><div class="highlight"><pre>
         <span class="k">assert</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">sources</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">targets</span><span class="p">)),</span> <span class="p">(</span>
             <span class="s1">&#39;List of targets and list of sources have to have the same length&#39;</span><span class="p">)</span>
 
+        <span class="c1"># Check and set defaults for checkpointing. If requested, initialise</span>
+        <span class="c1"># checkpointing.</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">settings</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_set_checkpointing_defaults</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">sources</span><span class="p">,</span> <span class="n">targets</span><span class="p">)</span>
+
         <span class="c1"># Perform MI estimation for each target individually</span>
         <span class="n">results</span> <span class="o">=</span> <span class="n">ResultsNetworkInference</span><span class="p">(</span><span class="n">n_nodes</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">n_processes</span><span class="p">,</span>
                                           <span class="n">n_realisations</span><span class="o">=</span><span class="n">data</span><span class="o">.</span><span class="n">n_realisations</span><span class="p">(),</span>
@@ -289,6 +294,12 @@ <h1>Source code for idtxl.bivariate_mi</h1><div class="highlight"><pre>
 <span class="sd">                  further settings (default=False)</span>
 <span class="sd">                - verbose : bool [optional] - toggle console output</span>
 <span class="sd">                  (default=True)</span>
+<span class="sd">                - write_ckp : bool [optional] - enable checkpointing, writes</span>
+<span class="sd">                  analysis state to disk every time a variable is selected;</span>
+<span class="sd">                  resume crashed analysis using</span>
+<span class="sd">                  network_analysis.resume_checkpoint() (default=False)</span>
+<span class="sd">                - filename_ckp : str [optional] - checkpoint file name (without</span>
+<span class="sd">                  extension) (default=&#39;./idtxl_checkpoint&#39;)</span>
 
 <span class="sd">            data : Data instance</span>
 <span class="sd">                raw data for analysis</span>
@@ -352,23 +363,22 @@ <h1>Source code for idtxl.bivariate_mi</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">results</span></div></div>
 </pre></div>
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
 <div id="searchbox" style="display: none" role="search">
-  <h3>Quick search</h3>
+  <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../search.html" method="get">
-      <input type="text" name="q" />
+      <input type="text" name="q" aria-labelledby="searchlabel" />
       <input type="submit" value="Go" />
-      <input type="hidden" name="check_keywords" value="yes" />
-      <input type="hidden" name="area" value="default" />
     </form>
     </div>
 </div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
+<script>$('#searchbox').show(0);</script>
         </div>
       </div>
       <div class="clearer"></div>
@@ -383,12 +393,13 @@ <h3>Navigation</h3>
           <a href="../../py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
         <li class="nav-item nav-item-0"><a href="../../index.html">IDTxl 1.0 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-1"><a href="../index.html" >Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">idtxl.bivariate_mi</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="http://sphinx-doc.org/">Sphinx</a> 1.8.2.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.5.1.
     </div>
   </body>
 </html>