rename library.

.gitignore

@@ -18,15 +18,19 @@ notebooks/results/*
 notebooks/check_gm/*
 notebooks/test_parallel/*
 requirements/*
-pygraph/model.py
-pygraph/kernels/*_sym.py
+gklearn/model.py
+gklearn/kernels/*_sym.py
 *.npy
 *.eps
 *.dat
 *.pyc
 
-preimage/*
-!preimage/*.py
+gklearn/preimage/*
+!gklearn/preimage/*.py
 
 __pycache__
 ##*#
+
+docs/build/*
+!docs/build/latex/*.pdf
+docs/log*

README.md

@@ -1,7 +1,7 @@
-# py-graph
-[![Build Status](https://travis-ci.org/jajupmochi/py-graph.svg?branch=ljia)](https://travis-ci.org/jajupmochi/py-graph)
-[![codecov](https://codecov.io/gh/jajupmochi/py-graph/branch/ljia/graph/badge.svg)](https://codecov.io/gh/jajupmochi/py-graph)
-[![Documentation Status](https://readthedocs.org/projects/py-graph/badge/?version=ljia)](https://py-graph.readthedocs.io/en/ljia/?badge=ljia)
+# graphkit-learn
+[![Build Status](https://travis-ci.org/jajupmochi/graphkit-learn.svg?branch=ljia)](https://travis-ci.org/jajupmochi/graphkit-learn)
+[![codecov](https://codecov.io/gh/jajupmochi/graphkit-learn/branch/ljia/graph/badge.svg)](https://codecov.io/gh/jajupmochi/graphkit-learn)
+[![Documentation Status](https://readthedocs.org/projects/graphkit-learn/badge/?version=ljia)](https://graphkit-learn.readthedocs.io/en/ljia/?badge=ljia)
 
 A python package for graph kernels.
 
@@ -20,11 +20,11 @@ A python package for graph kernels.
 
 ## How to use?
 
-Simply clone this repository and voilà! Then check [`notebooks`](https://github.com/jajupmochi/py-graph/tree/ljia/notebooks) directory for demos:
-* [`notebooks`](https://github.com/jajupmochi/py-graph/tree/ljia/notebooks) directory includes test codes of graph kernels based on linear patterns;
-* [`notebooks/tests`](https://github.com/jajupmochi/py-graph/tree/ljia/notebooks/tests) directory includes codes that test some libraries and functions;
-* [`notebooks/utils`](https://github.com/jajupmochi/py-graph/tree/ljia/notebooks/utils) directory includes some useful tools, such as a Gram matrix checker and a function to get properties of datasets;
-* [`notebooks/else`](https://github.com/jajupmochi/py-graph/tree/ljia/notebooks/else) directory includes other codes that we used for experiments.
+Simply clone this repository and voilà! Then check [`notebooks`](https://github.com/jajupmochi/graphkit-learn/tree/ljia/notebooks) directory for demos:
+* [`notebooks`](https://github.com/jajupmochi/graphkit-learn/tree/ljia/notebooks) directory includes test codes of graph kernels based on linear patterns;
+* [`notebooks/tests`](https://github.com/jajupmochi/graphkit-learn/tree/ljia/notebooks/tests) directory includes codes that test some libraries and functions;
+* [`notebooks/utils`](https://github.com/jajupmochi/graphkit-learn/tree/ljia/notebooks/utils) directory includes some useful tools, such as a Gram matrix checker and a function to get properties of datasets;
+* [`notebooks/else`](https://github.com/jajupmochi/graphkit-learn/tree/ljia/notebooks/else) directory includes other codes that we used for experiments.
 
 ## List of graph kernels
 
@@ -77,6 +77,8 @@ Check this paper for detailed description of graph kernels and experimental resu
 
 Linlin Jia, Benoit Gaüzère, and Paul Honeine. Graph Kernels Based on Linear Patterns: Theoretical and Experimental Comparisons. working paper or preprint, March 2019. URL https://hal-normandie-univ.archives-ouvertes.fr/hal-02053946.
 
+A comparison of performances of graph kernels on benchmark datasets can be found [here](https://graphkit-learn.readthedocs.io/en/ljia/index.html#experiments).
+
 ## References
 [1] Thomas Gärtner, Peter Flach, and Stefan Wrobel. On graph kernels: Hardness results and efficient alternatives. Learning Theory and Kernel Machines, pages 129–143, 2003.
 

docs/Makefile

@@ -4,8 +4,8 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:

docs/_build/html/.buildinfo

@@ -1,4 +0,0 @@
-# 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: b72b368ba10131aed8c3edbb863096bd
-tags: 645f666f9bcd5a90fca523b33c5a78b7

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@@ -1,196 +0,0 @@
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-            
-  <h1>All modules for which code is available</h1>
-<ul><li><a href="pygraph/utils/graphdataset.html">pygraph.utils.graphdataset</a></li>
-<li><a href="pygraph/utils/graphfiles.html">pygraph.utils.graphfiles</a></li>
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-            
-  <h1>Source code for pygraph.utils.graphdataset</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot; Obtain all kinds of attributes of a graph dataset.</span>
-<span class="sd">&quot;&quot;&quot;</span>
-
-
-<div class="viewcode-block" id="get_dataset_attributes"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphdataset.get_dataset_attributes">[docs]</a><span class="k">def</span> <span class="nf">get_dataset_attributes</span><span class="p">(</span><span class="n">Gn</span><span class="p">,</span>
-                           <span class="n">target</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                           <span class="n">attr_names</span><span class="o">=</span><span class="p">[],</span>
-                           <span class="n">node_label</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
-                           <span class="n">edge_label</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Returns the structure and property information of the graph dataset Gn.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    Gn : List of NetworkX graph</span>
-<span class="sd">        List of graphs whose information will be returned.</span>
-<span class="sd">    target : list</span>
-<span class="sd">        The list of classification targets corresponding to Gn. Only works for </span>
-<span class="sd">        classification problems.</span>
-<span class="sd">    attr_names : list</span>
-<span class="sd">        List of strings which indicate which informations will be returned. The</span>
-<span class="sd">        possible choices includes:</span>
-<span class="sd">        &#39;substructures&#39;: sub-structures Gn contains, including &#39;linear&#39;, &#39;non </span>
-<span class="sd">            linear&#39; and &#39;cyclic&#39;.</span>
-<span class="sd">        &#39;node_labeled&#39;: whether vertices have symbolic labels.</span>
-<span class="sd">        &#39;edge_labeled&#39;: whether egdes have symbolic labels.</span>
-<span class="sd">        &#39;is_directed&#39;: whether graphs in Gn are directed.</span>
-<span class="sd">        &#39;dataset_size&#39;: number of graphs in Gn.</span>
-<span class="sd">        &#39;ave_node_num&#39;: average number of vertices of graphs in Gn.</span>
-<span class="sd">        &#39;min_node_num&#39;: minimum number of vertices of graphs in Gn.</span>
-<span class="sd">        &#39;max_node_num&#39;: maximum number of vertices of graphs in Gn.</span>
-<span class="sd">        &#39;ave_edge_num&#39;: average number of edges of graphs in Gn.</span>
-<span class="sd">        &#39;min_edge_num&#39;: minimum number of edges of graphs in Gn.</span>
-<span class="sd">        &#39;max_edge_num&#39;: maximum number of edges of graphs in Gn.</span>
-<span class="sd">        &#39;ave_node_degree&#39;: average vertex degree of graphs in Gn.</span>
-<span class="sd">        &#39;min_node_degree&#39;: minimum vertex degree of graphs in Gn.</span>
-<span class="sd">        &#39;max_node_degree&#39;: maximum vertex degree of graphs in Gn.</span>
-<span class="sd">        &#39;ave_fill_factor&#39;: average fill factor (number_of_edges / </span>
-<span class="sd">            (number_of_nodes ** 2)) of graphs in Gn.</span>
-<span class="sd">        &#39;min_fill_factor&#39;: minimum fill factor of graphs in Gn.</span>
-<span class="sd">        &#39;max_fill_factor&#39;: maximum fill factor of graphs in Gn.</span>
-<span class="sd">        &#39;node_label_num&#39;: number of symbolic vertex labels.</span>
-<span class="sd">        &#39;edge_label_num&#39;: number of symbolic edge labels.</span>
-<span class="sd">        &#39;node_attr_dim&#39;: number of dimensions of non-symbolic vertex labels. </span>
-<span class="sd">            Extracted from the &#39;attributes&#39; attribute of graph nodes.</span>
-<span class="sd">        &#39;edge_attr_dim&#39;: number of dimensions of non-symbolic edge labels.</span>
-<span class="sd">            Extracted from the &#39;attributes&#39; attribute of graph edges.</span>
-<span class="sd">        &#39;class_number&#39;: number of classes. Only available for classification </span>
-<span class="sd">            problems.</span>
-<span class="sd">    node_label : string</span>
-<span class="sd">        Node attribute used as label. The default node label is atom. Mandatory</span>
-<span class="sd">        when &#39;node_labeled&#39; or &#39;node_label_num&#39; is required.</span>
-<span class="sd">    edge_label : string</span>
-<span class="sd">        Edge attribute used as label. The default edge label is bond_type. </span>
-<span class="sd">        Mandatory when &#39;edge_labeled&#39; or &#39;edge_label_num&#39; is required.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    attrs : dict</span>
-<span class="sd">        Value for each property.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-
-    <span class="n">attrs</span> <span class="o">=</span> <span class="p">{}</span>
-
-    <span class="k">def</span> <span class="nf">get_dataset_size</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_all_node_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="p">[</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">]</span>
-
-    <span class="k">def</span> <span class="nf">get_ave_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_min_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_max_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_all_edge_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="p">[</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">]</span>
-
-    <span class="k">def</span> <span class="nf">get_ave_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_min_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">get_max_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">is_node_labeled</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">node_label</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">True</span>
-
-    <span class="k">def</span> <span class="nf">get_node_label_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="n">nl</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-            <span class="n">nl</span> <span class="o">=</span> <span class="n">nl</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">get_node_attributes</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">node_label</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
-        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">nl</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">is_edge_labeled</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="kc">False</span> <span class="k">if</span> <span class="n">edge_label</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="kc">True</span>
-
-    <span class="k">def</span> <span class="nf">get_edge_label_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="n">el</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-            <span class="n">el</span> <span class="o">=</span> <span class="n">el</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">get_edge_attributes</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">edge_label</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
-        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">el</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">is_directed</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">nx</span><span class="o">.</span><span class="n">is_directed</span><span class="p">(</span><span class="n">Gn</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_ave_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">degree</span><span class="p">())</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_max_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">degree</span><span class="p">())</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_min_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">degree</span><span class="p">())</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-    
-    <span class="c1"># get fill factor, the number of non-zero entries in the adjacency matrix.</span>
-    <span class="k">def</span> <span class="nf">get_ave_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">([</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> 
-                                           <span class="o">*</span> <span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_max_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">([</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> 
-                                           <span class="o">*</span> <span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_min_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">([</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="o">/</span> <span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> 
-                                           <span class="o">*</span> <span class="n">nx</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(</span><span class="n">G</span><span class="p">))</span> <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">])</span>
-
-    <span class="k">def</span> <span class="nf">get_substructures</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="n">subs</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-            <span class="n">degrees</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">dict</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">degree</span><span class="p">())</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
-            <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">i</span> <span class="o">==</span> <span class="mi">2</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">degrees</span><span class="p">):</span>
-                <span class="n">subs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;linear&#39;</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">amax</span><span class="p">(</span><span class="n">degrees</span><span class="p">)</span> <span class="o">&gt;=</span> <span class="mi">3</span><span class="p">:</span>
-                <span class="n">subs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;non linear&#39;</span><span class="p">)</span>
-            <span class="k">if</span> <span class="s1">&#39;linear&#39;</span> <span class="ow">in</span> <span class="n">subs</span> <span class="ow">and</span> <span class="s1">&#39;non linear&#39;</span> <span class="ow">in</span> <span class="n">subs</span><span class="p">:</span>
-                <span class="k">break</span>
-
-        <span class="k">if</span> <span class="n">is_directed</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-            <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">find_cycle</span><span class="p">(</span><span class="n">G</span><span class="p">)))</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
-                    <span class="n">subs</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">&#39;cyclic&#39;</span><span class="p">)</span>
-                    <span class="k">break</span>
-        <span class="c1"># else:</span>
-        <span class="c1">#     # @todo: this method does not work for big graph with large amount of edges like D&amp;D, try a better way.</span>
-        <span class="c1">#     upper = np.amin([nx.number_of_edges(G) for G in Gn]) * 2 + 10</span>
-        <span class="c1">#     for G in Gn:</span>
-        <span class="c1">#         if (nx.number_of_edges(G) &lt; upper):</span>
-        <span class="c1">#             cyc = list(nx.simple_cycles(G.to_directed()))</span>
-        <span class="c1">#             if any(len(i) &gt; 2 for i in cyc):</span>
-        <span class="c1">#                 subs.add(&#39;cyclic&#39;)</span>
-        <span class="c1">#                 break</span>
-        <span class="c1">#     if &#39;cyclic&#39; not in subs:</span>
-        <span class="c1">#         for G in Gn:</span>
-        <span class="c1">#             cyc = list(nx.simple_cycles(G.to_directed()))</span>
-        <span class="c1">#             if any(len(i) &gt; 2 for i in cyc):</span>
-        <span class="c1">#                 subs.add(&#39;cyclic&#39;)</span>
-        <span class="c1">#                 break</span>
-
-        <span class="k">return</span> <span class="n">subs</span>
-
-    <span class="k">def</span> <span class="nf">get_class_num</span><span class="p">(</span><span class="n">target</span><span class="p">):</span>
-        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">target</span><span class="p">))</span>
-
-    <span class="k">def</span> <span class="nf">get_node_attr_dim</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-                <span class="k">if</span> <span class="s1">&#39;attributes&#39;</span> <span class="ow">in</span> <span class="n">n</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
-                    <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">n</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="s1">&#39;attributes&#39;</span><span class="p">])</span>
-        <span class="k">return</span> <span class="mi">0</span>
-
-    <span class="k">def</span> <span class="nf">get_edge_attr_dim</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-        <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">nx</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">(</span><span class="n">G</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-                    <span class="k">if</span> <span class="s1">&#39;attributes&#39;</span> <span class="ow">in</span> <span class="n">e</span><span class="p">[</span><span class="mi">2</span><span class="p">]:</span>
-                        <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">e</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="s1">&#39;attributes&#39;</span><span class="p">])</span>
-        <span class="k">return</span> <span class="mi">0</span>
-
-    <span class="k">if</span> <span class="n">attr_names</span> <span class="o">==</span> <span class="p">[]:</span>
-        <span class="n">attr_names</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="s1">&#39;substructures&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;node_labeled&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;edge_labeled&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;is_directed&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;dataset_size&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;ave_node_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;min_node_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;max_node_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;ave_edge_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;min_edge_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;max_edge_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;ave_node_degree&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;min_node_degree&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;max_node_degree&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;ave_fill_factor&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;min_fill_factor&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;max_fill_factor&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;node_label_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;edge_label_num&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;node_attr_dim&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;edge_attr_dim&#39;</span><span class="p">,</span>
-            <span class="s1">&#39;class_number&#39;</span><span class="p">,</span>
-        <span class="p">]</span>
-
-    <span class="c1"># dataset size</span>
-    <span class="k">if</span> <span class="s1">&#39;dataset_size&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;dataset_size&#39;</span><span class="p">:</span> <span class="n">get_dataset_size</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="c1"># graph node number</span>
-    <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">i</span> <span class="ow">in</span> <span class="n">attr_names</span>
-           <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;ave_node_num&#39;</span><span class="p">,</span> <span class="s1">&#39;min_node_num&#39;</span><span class="p">,</span> <span class="s1">&#39;max_node_num&#39;</span><span class="p">]):</span>
-
-        <span class="n">all_node_num</span> <span class="o">=</span> <span class="n">get_all_node_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="s1">&#39;ave_node_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;ave_node_num&#39;</span><span class="p">:</span> <span class="n">get_ave_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;min_node_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;min_node_num&#39;</span><span class="p">:</span> <span class="n">get_min_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;max_node_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;max_node_num&#39;</span><span class="p">:</span> <span class="n">get_max_node_num</span><span class="p">(</span><span class="n">all_node_num</span><span class="p">)})</span>
-
-    <span class="c1"># graph edge number</span>
-    <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">i</span> <span class="ow">in</span> <span class="n">attr_names</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span>
-           <span class="p">[</span><span class="s1">&#39;ave_edge_num&#39;</span><span class="p">,</span> <span class="s1">&#39;min_edge_num&#39;</span><span class="p">,</span> <span class="s1">&#39;max_edge_num&#39;</span><span class="p">]):</span>
-
-        <span class="n">all_edge_num</span> <span class="o">=</span> <span class="n">get_all_edge_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="s1">&#39;ave_edge_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;ave_edge_num&#39;</span><span class="p">:</span> <span class="n">get_ave_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;max_edge_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;max_edge_num&#39;</span><span class="p">:</span> <span class="n">get_max_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;min_edge_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;min_edge_num&#39;</span><span class="p">:</span> <span class="n">get_min_edge_num</span><span class="p">(</span><span class="n">all_edge_num</span><span class="p">)})</span>
-
-    <span class="c1"># label number</span>
-    <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">i</span> <span class="ow">in</span> <span class="n">attr_names</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;node_labeled&#39;</span><span class="p">,</span> <span class="s1">&#39;node_label_num&#39;</span><span class="p">]):</span>
-        <span class="n">is_nl</span> <span class="o">=</span> <span class="n">is_node_labeled</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-        <span class="n">node_label_num</span> <span class="o">=</span> <span class="n">get_node_label_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="s1">&#39;node_labeled&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="c1"># graphs are considered node unlabeled if all nodes have the same label.</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;node_labeled&#39;</span><span class="p">:</span> <span class="n">is_nl</span> <span class="k">if</span> <span class="n">node_label_num</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span> <span class="kc">False</span><span class="p">})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;node_label_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;node_label_num&#39;</span><span class="p">:</span> <span class="n">node_label_num</span><span class="p">})</span>
-
-    <span class="k">if</span> <span class="nb">any</span><span class="p">(</span><span class="n">i</span> <span class="ow">in</span> <span class="n">attr_names</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">&#39;edge_labeled&#39;</span><span class="p">,</span> <span class="s1">&#39;edge_label_num&#39;</span><span class="p">]):</span>
-        <span class="n">is_el</span> <span class="o">=</span> <span class="n">is_edge_labeled</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-        <span class="n">edge_label_num</span> <span class="o">=</span> <span class="n">get_edge_label_num</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="s1">&#39;edge_labeled&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="c1"># graphs are considered edge unlabeled if all edges have the same label.</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;edge_labeled&#39;</span><span class="p">:</span> <span class="n">is_el</span> <span class="k">if</span> <span class="n">edge_label_num</span> <span class="o">&gt;</span> <span class="mi">1</span> <span class="k">else</span> <span class="kc">False</span><span class="p">})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;edge_label_num&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;edge_label_num&#39;</span><span class="p">:</span> <span class="n">edge_label_num</span><span class="p">})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;is_directed&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;is_directed&#39;</span><span class="p">:</span> <span class="n">is_directed</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;ave_node_degree&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;ave_node_degree&#39;</span><span class="p">:</span> <span class="n">get_ave_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;max_node_degree&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;max_node_degree&#39;</span><span class="p">:</span> <span class="n">get_max_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;min_node_degree&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;min_node_degree&#39;</span><span class="p">:</span> <span class="n">get_min_node_degree</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-        
-    <span class="k">if</span> <span class="s1">&#39;ave_fill_factor&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;ave_fill_factor&#39;</span><span class="p">:</span> <span class="n">get_ave_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;max_fill_factor&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;max_fill_factor&#39;</span><span class="p">:</span> <span class="n">get_max_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;min_fill_factor&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;min_fill_factor&#39;</span><span class="p">:</span> <span class="n">get_min_fill_factor</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;substructures&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;substructures&#39;</span><span class="p">:</span> <span class="n">get_substructures</span><span class="p">(</span><span class="n">Gn</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;class_number&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="s1">&#39;class_number&#39;</span><span class="p">:</span> <span class="n">get_class_num</span><span class="p">(</span><span class="n">target</span><span class="p">)})</span>
-
-    <span class="k">if</span> <span class="s1">&#39;node_attr_dim&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;node_attr_dim&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_node_attr_dim</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="k">if</span> <span class="s1">&#39;edge_attr_dim&#39;</span> <span class="ow">in</span> <span class="n">attr_names</span><span class="p">:</span>
-        <span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;edge_attr_dim&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">get_edge_attr_dim</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span>
-
-    <span class="kn">from</span> <span class="nn">collections</span> <span class="k">import</span> <span class="n">OrderedDict</span>
-    <span class="k">return</span> <span class="n">OrderedDict</span><span class="p">(</span>
-        <span class="nb">sorted</span><span class="p">(</span><span class="n">attrs</span><span class="o">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">i</span><span class="p">:</span> <span class="n">attr_names</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">i</span><span class="p">[</span><span class="mi">0</span><span class="p">])))</span></div>
-</pre></div>
-
-           </div>
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-          </div>
-          <footer>
-  
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docs/_build/html/_modules/pygraph/utils/graphfiles.html

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-           <div itemprop="articleBody">
-            
-  <h1>Source code for pygraph.utils.graphfiles</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot; Utilities function to manage graph files</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="kn">from</span> <span class="nn">os.path</span> <span class="k">import</span> <span class="n">dirname</span><span class="p">,</span> <span class="n">splitext</span>
-
-<div class="viewcode-block" id="loadCT"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadCT">[docs]</a><span class="k">def</span> <span class="nf">loadCT</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;load data from a Chemical Table (.ct) file.</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    ------</span>
-<span class="sd">    a typical example of data in .ct is like this:</span>
-
-<span class="sd">     3 2  &lt;- number of nodes and edges</span>
-<span class="sd">        0.0000    0.0000    0.0000 C &lt;- each line describes a node (x,y,z + label)</span>
-<span class="sd">        0.0000    0.0000    0.0000 C</span>
-<span class="sd">        0.0000    0.0000    0.0000 O</span>
-<span class="sd">      1  3  1  1 &lt;- each line describes an edge : to, from, bond type, bond stereo</span>
-<span class="sd">      2  3  1  1</span>
-<span class="sd">      </span>
-<span class="sd">    Check https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=10&amp;ved=2ahUKEwivhaSdjsTlAhVhx4UKHczHA8gQFjAJegQIARAC&amp;url=https%3A%2F%2Fwww.daylight.com%2Fmeetings%2Fmug05%2FKappler%2Fctfile.pdf&amp;usg=AOvVaw1cDNrrmMClkFPqodlF2inS</span>
-<span class="sd">    for detailed format discription.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="kn">from</span> <span class="nn">os.path</span> <span class="k">import</span> <span class="n">basename</span>
-    <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
-        <span class="n">content</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span>
-            <span class="n">name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="mi">0</span><span class="p">]),</span>
-            <span class="n">filename</span> <span class="o">=</span> <span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">))</span>  <span class="c1"># set name of the graph</span>
-        <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;&#39;</span><span class="p">:</span>
-            <span class="n">nb_nodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>  <span class="c1"># number of the nodes</span>
-            <span class="n">nb_edges</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>  <span class="c1"># number of the edges</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">nb_nodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-            <span class="n">nb_edges</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-            <span class="c1"># patch for compatibility : label will be removed later</span>
-        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nb_nodes</span><span class="p">):</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">tmp</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span><span class="p">]</span>
-            <span class="n">g</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">atom</span><span class="o">=</span><span class="n">tmp</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span> 
-                       <span class="n">label</span><span class="o">=</span><span class="p">[</span><span class="n">item</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">3</span><span class="p">:]],</span> 
-                       <span class="n">attributes</span><span class="o">=</span><span class="p">[</span><span class="n">item</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">:</span><span class="mi">3</span><span class="p">]])</span>
-        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nb_edges</span><span class="p">):</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="n">g</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()</span> <span class="o">+</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot; &quot;</span><span class="p">)</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="p">[</span><span class="n">x</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">tmp</span> <span class="k">if</span> <span class="n">x</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span><span class="p">]</span>
-            <span class="n">g</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span>
-                       <span class="n">bond_type</span><span class="o">=</span><span class="n">tmp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span>
-                       <span class="n">label</span><span class="o">=</span><span class="p">[</span><span class="n">item</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">2</span><span class="p">:]])</span>
-    <span class="k">return</span> <span class="n">g</span></div>
-
-
-<div class="viewcode-block" id="loadGXL"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadGXL">[docs]</a><span class="k">def</span> <span class="nf">loadGXL</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="kn">from</span> <span class="nn">os.path</span> <span class="k">import</span> <span class="n">basename</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="kn">import</span> <span class="nn">xml.etree.ElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
-
-    <span class="n">tree</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="n">root</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
-    <span class="n">index</span> <span class="o">=</span> <span class="mi">0</span>
-    <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">name</span><span class="o">=</span><span class="n">root</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">])</span>
-    <span class="n">dic</span> <span class="o">=</span> <span class="p">{}</span>  <span class="c1"># used to retrieve incident nodes of edges</span>
-    <span class="k">for</span> <span class="n">node</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;node&#39;</span><span class="p">):</span>
-        <span class="n">dic</span><span class="p">[</span><span class="n">node</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">index</span>
-        <span class="n">labels</span> <span class="o">=</span> <span class="p">{}</span>
-        <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">node</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;attr&#39;</span><span class="p">):</span>
-            <span class="n">labels</span><span class="p">[</span><span class="n">attr</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">text</span>
-        <span class="k">if</span> <span class="s1">&#39;chem&#39;</span> <span class="ow">in</span> <span class="n">labels</span><span class="p">:</span>
-            <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;chem&#39;</span><span class="p">]</span>
-            <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;atom&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;chem&#39;</span><span class="p">]</span>
-        <span class="n">g</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-        <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>
-
-    <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;edge&#39;</span><span class="p">):</span>
-        <span class="n">labels</span> <span class="o">=</span> <span class="p">{}</span>
-        <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">edge</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;attr&#39;</span><span class="p">):</span>
-            <span class="n">labels</span><span class="p">[</span><span class="n">attr</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">]]</span> <span class="o">=</span> <span class="n">attr</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">text</span>
-        <span class="k">if</span> <span class="s1">&#39;valence&#39;</span> <span class="ow">in</span> <span class="n">labels</span><span class="p">:</span>
-            <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;label&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;valence&#39;</span><span class="p">]</span>
-            <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;bond_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">labels</span><span class="p">[</span><span class="s1">&#39;valence&#39;</span><span class="p">]</span>
-        <span class="n">g</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">dic</span><span class="p">[</span><span class="n">edge</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;from&#39;</span><span class="p">]],</span> <span class="n">dic</span><span class="p">[</span><span class="n">edge</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;to&#39;</span><span class="p">]],</span> <span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">g</span></div>
-
-
-<div class="viewcode-block" id="saveGXL"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.saveGXL">[docs]</a><span class="k">def</span> <span class="nf">saveGXL</span><span class="p">(</span><span class="n">graph</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="s1">&#39;benoit&#39;</span><span class="p">):</span>
-    <span class="k">if</span> <span class="n">method</span> <span class="o">==</span> <span class="s1">&#39;benoit&#39;</span><span class="p">:</span>
-        <span class="kn">import</span> <span class="nn">xml.etree.ElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
-        <span class="n">root_node</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">Element</span><span class="p">(</span><span class="s1">&#39;gxl&#39;</span><span class="p">)</span>
-        <span class="n">attr</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
-        <span class="n">attr</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">graph</span><span class="o">.</span><span class="n">graph</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">])</span>
-        <span class="n">attr</span><span class="p">[</span><span class="s1">&#39;edgeids&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;true&#39;</span>
-        <span class="n">attr</span><span class="p">[</span><span class="s1">&#39;edgemode&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="s1">&#39;undirected&#39;</span>
-        <span class="n">graph_node</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span><span class="n">root_node</span><span class="p">,</span> <span class="s1">&#39;graph&#39;</span><span class="p">,</span> <span class="n">attrib</span><span class="o">=</span><span class="n">attr</span><span class="p">)</span>
-    
-        <span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">graph</span><span class="p">:</span>
-            <span class="n">current_node</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span><span class="n">graph_node</span><span class="p">,</span> <span class="s1">&#39;node&#39;</span><span class="p">,</span> <span class="n">attrib</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;id&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)})</span>
-            <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">v</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-                <span class="n">cur_attr</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span>
-                    <span class="n">current_node</span><span class="p">,</span> <span class="s1">&#39;attr&#39;</span><span class="p">,</span> <span class="n">attrib</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">attr</span><span class="p">})</span>
-                <span class="n">cur_value</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span><span class="n">cur_attr</span><span class="p">,</span>
-                                          <span class="n">graph</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">v</span><span class="p">][</span><span class="n">attr</span><span class="p">]</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
-                <span class="n">cur_value</span><span class="o">.</span><span class="n">text</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">v</span><span class="p">][</span><span class="n">attr</span><span class="p">]</span>
-    
-        <span class="k">for</span> <span class="n">v1</span> <span class="ow">in</span> <span class="n">graph</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">v2</span> <span class="ow">in</span> <span class="n">graph</span><span class="p">[</span><span class="n">v1</span><span class="p">]:</span>
-                <span class="k">if</span> <span class="p">(</span><span class="n">v1</span> <span class="o">&lt;</span> <span class="n">v2</span><span class="p">):</span>  <span class="c1"># Non oriented graphs</span>
-                    <span class="n">cur_edge</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span>
-                        <span class="n">graph_node</span><span class="p">,</span>
-                        <span class="s1">&#39;edge&#39;</span><span class="p">,</span>
-                        <span class="n">attrib</span><span class="o">=</span><span class="p">{</span>
-                            <span class="s1">&#39;from&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">v1</span><span class="p">),</span>
-                            <span class="s1">&#39;to&#39;</span><span class="p">:</span> <span class="nb">str</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span>
-                        <span class="p">})</span>
-                    <span class="k">for</span> <span class="n">attr</span> <span class="ow">in</span> <span class="n">graph</span><span class="p">[</span><span class="n">v1</span><span class="p">][</span><span class="n">v2</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-                        <span class="n">cur_attr</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span>
-                            <span class="n">cur_edge</span><span class="p">,</span> <span class="s1">&#39;attr&#39;</span><span class="p">,</span> <span class="n">attrib</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="n">attr</span><span class="p">})</span>
-                        <span class="n">cur_value</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">SubElement</span><span class="p">(</span>
-                            <span class="n">cur_attr</span><span class="p">,</span> <span class="n">graph</span><span class="p">[</span><span class="n">v1</span><span class="p">][</span><span class="n">v2</span><span class="p">][</span><span class="n">attr</span><span class="p">]</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span><span class="p">)</span>
-                        <span class="n">cur_value</span><span class="o">.</span><span class="n">text</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">graph</span><span class="p">[</span><span class="n">v1</span><span class="p">][</span><span class="n">v2</span><span class="p">][</span><span class="n">attr</span><span class="p">])</span>
-    
-        <span class="n">tree</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">ElementTree</span><span class="p">(</span><span class="n">root_node</span><span class="p">)</span>
-        <span class="n">tree</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">method</span> <span class="o">==</span> <span class="s1">&#39;gedlib&#39;</span><span class="p">:</span>
-        <span class="c1"># reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22</span>
-<span class="c1">#        pass</span>
-        <span class="n">gxl_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;?xml version=</span><span class="se">\&quot;</span><span class="s2">1.0</span><span class="se">\&quot;</span><span class="s2"> encoding=</span><span class="se">\&quot;</span><span class="s2">UTF-8</span><span class="se">\&quot;</span><span class="s2">?&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;!DOCTYPE gxl SYSTEM </span><span class="se">\&quot;</span><span class="s2">http://www.gupro.de/GXL/gxl-1.0.dtd</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;gxl xmlns:xlink=</span><span class="se">\&quot;</span><span class="s2">http://www.w3.org/1999/xlink</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;graph id=</span><span class="se">\&quot;</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">graph</span><span class="o">.</span><span class="n">graph</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2"> edgeids=</span><span class="se">\&quot;</span><span class="s2">true</span><span class="se">\&quot;</span><span class="s2"> edgemode=</span><span class="se">\&quot;</span><span class="s2">undirected</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">v</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;node id=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;attr name=</span><span class="se">\&quot;</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="s2">&quot;chem&quot;</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">&gt;&lt;int&gt;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;chem&#39;</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;&lt;/int&gt;&lt;/attr&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/node&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;edge from=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2"> to=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;attr name=</span><span class="se">\&quot;</span><span class="s2">valence</span><span class="se">\&quot;</span><span class="s2">&gt;&lt;int&gt;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;valence&#39;</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;&lt;/int&gt;&lt;/attr&gt;&quot;</span><span class="p">)</span>
-<span class="c1">#            gxl_file.write(&quot;&lt;attr name=\&quot;valence\&quot;&gt;&lt;int&gt;&quot; + &quot;1&quot; + &quot;&lt;/int&gt;&lt;/attr&gt;&quot;)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/edge&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/graph&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/gxl&gt;&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-    <span class="k">elif</span> <span class="n">method</span> <span class="o">==</span> <span class="s1">&#39;gedlib-letter&#39;</span><span class="p">:</span>
-        <span class="c1"># reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22</span>
-        <span class="c1"># and https://github.com/dbblumenthal/gedlib/blob/master/data/datasets/Letter/HIGH/AP1_0000.gxl</span>
-        <span class="n">gxl_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;?xml version=</span><span class="se">\&quot;</span><span class="s2">1.0</span><span class="se">\&quot;</span><span class="s2"> encoding=</span><span class="se">\&quot;</span><span class="s2">UTF-8</span><span class="se">\&quot;</span><span class="s2">?&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;!DOCTYPE gxl SYSTEM </span><span class="se">\&quot;</span><span class="s2">http://www.gupro.de/GXL/gxl-1.0.dtd</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;gxl xmlns:xlink=</span><span class="se">\&quot;</span><span class="s2">http://www.w3.org/1999/xlink</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;graph id=</span><span class="se">\&quot;</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">graph</span><span class="o">.</span><span class="n">graph</span><span class="p">[</span><span class="s1">&#39;name&#39;</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2"> edgeids=</span><span class="se">\&quot;</span><span class="s2">false</span><span class="se">\&quot;</span><span class="s2"> edgemode=</span><span class="se">\&quot;</span><span class="s2">undirected</span><span class="se">\&quot;</span><span class="s2">&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">v</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;node id=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;attr name=</span><span class="se">\&quot;</span><span class="s2">x</span><span class="se">\&quot;</span><span class="s2">&gt;&lt;float&gt;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;attributes&#39;</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;&lt;/float&gt;&lt;/attr&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;attr name=</span><span class="se">\&quot;</span><span class="s2">y</span><span class="se">\&quot;</span><span class="s2">&gt;&lt;float&gt;&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;attributes&#39;</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;&lt;/float&gt;&lt;/attr&gt;&quot;</span><span class="p">)</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/node&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="k">for</span> <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">graph</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;edge from=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v1</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2"> to=</span><span class="se">\&quot;</span><span class="s2">_&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">v2</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">/&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/graph&gt;</span><span class="se">\n</span><span class="s2">&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;/gxl&gt;&quot;</span><span class="p">)</span>
-        <span class="n">gxl_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
-
-
-<div class="viewcode-block" id="loadSDF"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadSDF">[docs]</a><span class="k">def</span> <span class="nf">loadSDF</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;load data from structured data file (.sdf file).</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    ------</span>
-<span class="sd">    A SDF file contains a group of molecules, represented in the similar way as in MOL format.</span>
-<span class="sd">    Check http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx, 2018 for detailed structure.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="kn">from</span> <span class="nn">os.path</span> <span class="k">import</span> <span class="n">basename</span>
-    <span class="kn">from</span> <span class="nn">tqdm</span> <span class="k">import</span> <span class="n">tqdm</span>
-    <span class="kn">import</span> <span class="nn">sys</span>
-    <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
-        <span class="n">content</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="n">index</span> <span class="o">=</span> <span class="mi">0</span>
-        <span class="n">pbar</span> <span class="o">=</span> <span class="n">tqdm</span><span class="p">(</span><span class="n">total</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">desc</span><span class="o">=</span><span class="s1">&#39;load SDF&#39;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
-        <span class="k">while</span> <span class="n">index</span> <span class="o">&lt;</span> <span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">):</span>
-            <span class="n">index_old</span> <span class="o">=</span> <span class="n">index</span>
-
-            <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">content</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>  <span class="c1"># set name of the graph</span>
-
-            <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">index</span> <span class="o">+</span> <span class="mi">3</span><span class="p">]</span>
-            <span class="n">nb_nodes</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[:</span><span class="mi">3</span><span class="p">])</span>  <span class="c1"># number of the nodes</span>
-            <span class="n">nb_edges</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">3</span><span class="p">:</span><span class="mi">6</span><span class="p">])</span>  <span class="c1"># number of the edges</span>
-
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nb_nodes</span><span class="p">):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="n">index</span> <span class="o">+</span> <span class="mi">4</span><span class="p">]</span>
-                <span class="n">g</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">atom</span><span class="o">=</span><span class="n">tmp</span><span class="p">[</span><span class="mi">31</span><span class="p">:</span><span class="mi">34</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
-
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nb_edges</span><span class="p">):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span> <span class="o">+</span> <span class="n">index</span> <span class="o">+</span> <span class="n">g</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()</span> <span class="o">+</span> <span class="mi">4</span><span class="p">]</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="p">[</span><span class="n">tmp</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span> <span class="o">+</span> <span class="mi">3</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">tmp</span><span class="p">),</span> <span class="mi">3</span><span class="p">)]</span>
-                <span class="n">g</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span>
-                    <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">bond_type</span><span class="o">=</span><span class="n">tmp</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
-
-            <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
-
-            <span class="n">index</span> <span class="o">+=</span> <span class="mi">4</span> <span class="o">+</span> <span class="n">g</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()</span> <span class="o">+</span> <span class="n">g</span><span class="o">.</span><span class="n">number_of_edges</span><span class="p">()</span>
-            <span class="k">while</span> <span class="n">content</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="o">!=</span> <span class="s1">&#39;$$$$&#39;</span><span class="p">:</span>  <span class="c1"># seperator</span>
-                <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>
-            <span class="n">index</span> <span class="o">+=</span> <span class="mi">1</span>
-
-            <span class="n">pbar</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">index</span> <span class="o">-</span> <span class="n">index_old</span><span class="p">)</span>
-        <span class="n">pbar</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-        <span class="n">pbar</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
-
-    <span class="k">return</span> <span class="n">data</span></div>
-
-
-<div class="viewcode-block" id="loadMAT"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadMAT">[docs]</a><span class="k">def</span> <span class="nf">loadMAT</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Load graph data from a MATLAB (up to version 7.1) .mat file.</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    ------</span>
-<span class="sd">    A MAT file contains a struct array containing graphs, and a column vector lx containing a class label for each graph.</span>
-<span class="sd">    Check README in downloadable file in http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/, 2018 for detailed structure.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">scipy.io</span> <span class="k">import</span> <span class="n">loadmat</span>
-    <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="n">content</span> <span class="o">=</span> <span class="n">loadmat</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="n">order</span> <span class="o">=</span> <span class="n">extra_params</span><span class="p">[</span><span class="s1">&#39;am_sp_al_nl_el&#39;</span><span class="p">]</span>
-    <span class="c1"># print(content)</span>
-    <span class="c1"># print(&#39;----&#39;)</span>
-    <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">content</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-        <span class="k">if</span> <span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">&#39;l&#39;</span><span class="p">:</span>  <span class="c1"># class label</span>
-            <span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">value</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
-            <span class="c1"># print(y)</span>
-        <span class="k">elif</span> <span class="n">key</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;_&#39;</span><span class="p">:</span>
-            <span class="c1"># print(value[0][0][0])</span>
-            <span class="c1"># print()</span>
-            <span class="c1"># print(value[0][0][1])</span>
-            <span class="c1"># print()</span>
-            <span class="c1"># print(value[0][0][2])</span>
-            <span class="c1"># print()</span>
-            <span class="c1"># if len(value[0][0]) &gt; 3:</span>
-            <span class="c1">#     print(value[0][0][3])</span>
-            <span class="c1"># print(&#39;----&#39;)</span>
-            <span class="c1"># if adjacency matrix is not compressed / edge label exists</span>
-            <span class="k">if</span> <span class="n">order</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
-                    <span class="c1"># print(item)</span>
-                    <span class="c1"># print(&#39;------&#39;)</span>
-                    <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">i</span><span class="p">)</span>  <span class="c1"># set name of the graph</span>
-                    <span class="n">nl</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="n">order</span><span class="p">[</span><span class="mi">3</span><span class="p">]][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>  <span class="c1"># node label</span>
-                    <span class="c1"># print(item[order[3]])</span>
-                    <span class="c1"># print()</span>
-                    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">label</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nl</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
-                        <span class="n">g</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">atom</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">label</span><span class="p">))</span>
-                    <span class="n">el</span> <span class="o">=</span> <span class="n">item</span><span class="p">[</span><span class="n">order</span><span class="p">[</span><span class="mi">4</span><span class="p">]][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>  <span class="c1"># edge label</span>
-                    <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">el</span><span class="p">:</span>
-                        <span class="n">g</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span>
-                            <span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="mi">1</span><span class="p">,</span> <span class="n">bond_type</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
-                    <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="kn">from</span> <span class="nn">scipy.sparse</span> <span class="k">import</span> <span class="n">csc_matrix</span>
-                <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">item</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">value</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
-                    <span class="c1"># print(item)</span>
-                    <span class="c1"># print(&#39;------&#39;)</span>
-                    <span class="n">g</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">i</span><span class="p">)</span>  <span class="c1"># set name of the graph</span>
-                    <span class="n">nl</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="n">order</span><span class="p">[</span><span class="mi">3</span><span class="p">]][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">])</span>  <span class="c1"># node label</span>
-                    <span class="c1"># print(nl)</span>
-                    <span class="c1"># print()</span>
-                    <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">label</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">nl</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span>
-                        <span class="n">g</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">index</span><span class="p">,</span> <span class="n">atom</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">label</span><span class="p">))</span>
-                    <span class="n">sam</span> <span class="o">=</span> <span class="n">item</span><span class="p">[</span><span class="n">order</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>  <span class="c1"># sparse adjacency matrix</span>
-                    <span class="n">index_no0</span> <span class="o">=</span> <span class="n">sam</span><span class="o">.</span><span class="n">nonzero</span><span class="p">()</span>
-                    <span class="k">for</span> <span class="n">col</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">index_no0</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">index_no0</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span>
-                        <span class="c1"># print(col)</span>
-                        <span class="c1"># print(row)</span>
-                        <span class="n">g</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">col</span><span class="p">,</span> <span class="n">row</span><span class="p">)</span>
-                    <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
-                    <span class="c1"># print(g.edges(data=True))</span>
-    <span class="k">return</span> <span class="n">data</span><span class="p">,</span> <span class="n">y</span></div>
-
-
-<div class="viewcode-block" id="loadTXT"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadTXT">[docs]</a><span class="k">def</span> <span class="nf">loadTXT</span><span class="p">(</span><span class="n">dirname_dataset</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Load graph data from a .txt file.</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    ------</span>
-<span class="sd">    The graph data is loaded from separate files.</span>
-<span class="sd">    Check README in downloadable file http://tiny.cc/PK_MLJ_data, 2018 for detailed structure.</span>
-<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">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="kn">from</span> <span class="nn">os</span> <span class="k">import</span> <span class="n">listdir</span>
-    <span class="kn">from</span> <span class="nn">os.path</span> <span class="k">import</span> <span class="n">dirname</span>
-
-    <span class="c1"># load data file names</span>
-    <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">listdir</span><span class="p">(</span><span class="n">dirname_dataset</span><span class="p">):</span>
-        <span class="k">if</span> <span class="s1">&#39;_A&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fam</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_graph_indicator&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fgi</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_graph_labels&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fgl</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_node_labels&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fnl</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_edge_labels&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fel</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_edge_attributes&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fea</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_node_attributes&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fna</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="k">elif</span> <span class="s1">&#39;_graph_attributes&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fga</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-        <span class="c1"># this is supposed to be the node attrs, make sure to put this as the last &#39;elif&#39;</span>
-        <span class="k">elif</span> <span class="s1">&#39;_attributes&#39;</span> <span class="ow">in</span> <span class="n">name</span><span class="p">:</span>
-            <span class="n">fna</span> <span class="o">=</span> <span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">name</span>
-
-    <span class="n">content_gi</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fgi</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>  <span class="c1"># graph indicator</span>
-    <span class="n">content_am</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fam</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>  <span class="c1"># adjacency matrix</span>
-    <span class="n">content_gl</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fgl</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>  <span class="c1"># lass labels</span>
-
-    <span class="c1"># create graphs and add nodes</span>
-    <span class="n">data</span> <span class="o">=</span> <span class="p">[</span><span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">content_gl</span><span class="p">))]</span>
-    <span class="k">if</span> <span class="s1">&#39;fnl&#39;</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">():</span>
-        <span class="n">content_nl</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fnl</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>  <span class="c1"># node labels</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content_gi</span><span class="p">):</span>
-            <span class="c1"># transfer to int first in case of unexpected blanks</span>
-            <span class="n">data</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">atom</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">content_nl</span><span class="p">[</span><span class="n">i</span><span class="p">])))</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content_gi</span><span class="p">):</span>
-            <span class="n">data</span><span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">line</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-            
-    <span class="c1"># add edges</span>
-    <span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">content_am</span><span class="p">:</span>
-        <span class="n">tmp</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
-        <span class="n">n1</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span>
-        <span class="n">n2</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span>
-        <span class="c1"># ignore edge weight here.</span>
-        <span class="n">g</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">content_gi</span><span class="p">[</span><span class="n">n1</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span>
-        <span class="n">data</span><span class="p">[</span><span class="n">g</span><span class="p">]</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">n1</span><span class="p">,</span> <span class="n">n2</span><span class="p">)</span>
-
-    <span class="c1"># add edge labels</span>
-    <span class="k">if</span> <span class="s1">&#39;fel&#39;</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">():</span>
-        <span class="n">content_el</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fel</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content_el</span><span class="p">):</span>
-            <span class="n">label</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
-            <span class="n">n</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">content_am</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
-            <span class="n">g</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">content_gi</span><span class="p">[</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span> <span class="o">-</span> <span class="mi">1</span>
-            <span class="n">data</span><span class="p">[</span><span class="n">g</span><span class="p">]</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;bond_type&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">label</span>
-
-    <span class="c1"># add node attributes</span>
-    <span class="k">if</span> <span class="s1">&#39;fna&#39;</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">():</span>
-        <span class="n">content_na</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fna</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content_na</span><span class="p">):</span>
-            <span class="n">attrs</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
-            <span class="n">g</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">content_gi</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span>
-            <span class="n">data</span><span class="p">[</span><span class="n">g</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="s1">&#39;attributes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">attrs</span>
-
-    <span class="c1"># add edge attributes</span>
-    <span class="k">if</span> <span class="s1">&#39;fea&#39;</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">():</span>
-        <span class="n">content_ea</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">fea</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">line</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">content_ea</span><span class="p">):</span>
-            <span class="n">attrs</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
-            <span class="n">n</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">content_am</span><span class="p">[</span><span class="n">index</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)]</span>
-            <span class="n">g</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">content_gi</span><span class="p">[</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span> <span class="o">-</span> <span class="mi">1</span>
-            <span class="n">data</span><span class="p">[</span><span class="n">g</span><span class="p">]</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">n</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="s1">&#39;attributes&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">attrs</span>
-
-    <span class="c1"># load y</span>
-    <span class="n">y</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">content_gl</span><span class="p">]</span>
-
-    <span class="k">return</span> <span class="n">data</span><span class="p">,</span> <span class="n">y</span></div>
-
-
-<div class="viewcode-block" id="loadDataset"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadDataset">[docs]</a><span class="k">def</span> <span class="nf">loadDataset</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">filename_y</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">extra_params</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Read graph data from filename and load them as NetworkX graphs.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    filename : string</span>
-<span class="sd">        The name of the file from where the dataset is read.</span>
-<span class="sd">    filename_y : string</span>
-<span class="sd">        The name of file of the targets corresponding to graphs.</span>
-<span class="sd">    extra_params : dict</span>
-<span class="sd">        Extra parameters only designated to &#39;.mat&#39; format.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    data : List of NetworkX graph.</span>
-<span class="sd">    y : List</span>
-<span class="sd">        Targets corresponding to graphs.</span>
-<span class="sd">        </span>
-<span class="sd">    Notes</span>
-<span class="sd">    -----</span>
-<span class="sd">    This function supports following graph dataset formats:</span>
-<span class="sd">    &#39;ds&#39;: load data from .ds file. See comments of function loadFromDS for a example.</span>
-<span class="sd">    &#39;cxl&#39;: load data from Graph eXchange Language file (.cxl file). See </span>
-<span class="sd">        http://www.gupro.de/GXL/Introduction/background.html, 2019 for detail.</span>
-<span class="sd">    &#39;sdf&#39;: load data from structured data file (.sdf file). See </span>
-<span class="sd">        http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx, </span>
-<span class="sd">        2018 for details.</span>
-<span class="sd">    &#39;mat&#39;: Load graph data from a MATLAB (up to version 7.1) .mat file. See</span>
-<span class="sd">        README in downloadable file in http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/, </span>
-<span class="sd">        2018 for details.</span>
-<span class="sd">    &#39;txt&#39;: Load graph data from a special .txt file. See</span>
-<span class="sd">        https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets,</span>
-<span class="sd">        2019 for details. Note here filename is the name of either .txt file in</span>
-<span class="sd">        the dataset directory.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">extension</span> <span class="o">=</span> <span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
-    <span class="k">if</span> <span class="n">extension</span> <span class="o">==</span> <span class="s2">&quot;ds&quot;</span><span class="p">:</span>
-        <span class="n">data</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">loadFromDS</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">filename_y</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s2">&quot;cxl&quot;</span><span class="p">:</span>
-        <span class="kn">import</span> <span class="nn">xml.etree.ElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
-        
-        <span class="n">dirname_dataset</span> <span class="o">=</span> <span class="n">dirname</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-        <span class="n">tree</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-        <span class="n">root</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
-        <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">graph</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;graph&#39;</span><span class="p">):</span>
-            <span class="n">mol_filename</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;file&#39;</span><span class="p">]</span>
-            <span class="n">mol_class</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;class&#39;</span><span class="p">]</span>
-            <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loadGXL</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">mol_filename</span><span class="p">))</span>
-            <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mol_class</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;xml&#39;</span><span class="p">:</span>
-        <span class="n">data</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">loadFromXML</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s2">&quot;sdf&quot;</span><span class="p">:</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">tqdm</span> <span class="k">import</span> <span class="n">tqdm</span>
-        <span class="kn">import</span> <span class="nn">sys</span>
-
-        <span class="n">data</span> <span class="o">=</span> <span class="n">loadSDF</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-
-        <span class="n">y_raw</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename_y</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="n">y_raw</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
-        <span class="n">tmp0</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="n">tmp1</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">y_raw</span><span class="p">)):</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="n">y_raw</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
-            <span class="n">tmp0</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
-            <span class="n">tmp1</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
-
-        <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">tqdm</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">data</span><span class="p">)),</span> <span class="n">desc</span><span class="o">=</span><span class="s1">&#39;ajust data&#39;</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">):</span>
-            <span class="k">try</span><span class="p">:</span>
-                <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tmp1</span><span class="p">[</span><span class="n">tmp0</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">name</span><span class="p">)]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
-            <span class="k">except</span> <span class="ne">ValueError</span><span class="p">:</span>  <span class="c1"># if data[i].name not in tmp0</span>
-                <span class="n">data</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="n">data</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">filter</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span> <span class="o">!=</span> <span class="p">[],</span> <span class="n">data</span><span class="p">))</span>
-    <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s2">&quot;mat&quot;</span><span class="p">:</span>
-        <span class="n">data</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">loadMAT</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">)</span>
-    <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;txt&#39;</span><span class="p">:</span>
-        <span class="n">dirname_dataset</span> <span class="o">=</span> <span class="n">dirname</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-        <span class="n">data</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">loadTXT</span><span class="p">(</span><span class="n">dirname_dataset</span><span class="p">)</span>
-        <span class="c1"># print(len(y))</span>
-        <span class="c1"># print(y)</span>
-        <span class="c1"># print(data[0].nodes(data=True))</span>
-        <span class="c1"># print(&#39;----&#39;)</span>
-        <span class="c1"># print(data[0].edges(data=True))</span>
-        <span class="c1"># for g in data:</span>
-        <span class="c1">#     print(g.nodes(data=True))</span>
-        <span class="c1">#     print(&#39;----&#39;)</span>
-        <span class="c1">#     print(g.edges(data=True))</span>
-
-    <span class="k">return</span> <span class="n">data</span><span class="p">,</span> <span class="n">y</span></div>
-
-
-<div class="viewcode-block" id="loadFromXML"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadFromXML">[docs]</a><span class="k">def</span> <span class="nf">loadFromXML</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">extra_params</span><span class="p">):</span>
-    <span class="kn">import</span> <span class="nn">xml.etree.ElementTree</span> <span class="k">as</span> <span class="nn">ET</span>
-    
-    <span class="k">if</span> <span class="n">extra_params</span><span class="p">:</span>
-        <span class="n">dirname_dataset</span> <span class="o">=</span> <span class="n">extra_params</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">dirname_dataset</span> <span class="o">=</span> <span class="n">dirname</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="n">tree</span> <span class="o">=</span> <span class="n">ET</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="n">root</span> <span class="o">=</span> <span class="n">tree</span><span class="o">.</span><span class="n">getroot</span><span class="p">()</span>
-    <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">for</span> <span class="n">graph</span> <span class="ow">in</span> <span class="n">root</span><span class="o">.</span><span class="n">iter</span><span class="p">(</span><span class="s1">&#39;graph&#39;</span><span class="p">):</span>
-        <span class="n">mol_filename</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;file&#39;</span><span class="p">]</span>
-        <span class="n">mol_class</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">attrib</span><span class="p">[</span><span class="s1">&#39;class&#39;</span><span class="p">]</span>
-        <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loadGXL</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">mol_filename</span><span class="p">))</span>
-        <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mol_class</span><span class="p">)</span>
-        
-    <span class="k">return</span> <span class="n">data</span><span class="p">,</span> <span class="n">y</span></div>
-            
-
-<div class="viewcode-block" id="loadFromDS"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.loadFromDS">[docs]</a><span class="k">def</span> <span class="nf">loadFromDS</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">filename_y</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Load data from .ds file.</span>
-<span class="sd">    Possible graph formats include:</span>
-<span class="sd">        &#39;.ct&#39;: see function loadCT for detail.</span>
-<span class="sd">        &#39;.gxl&#39;: see dunction loadGXL for detail.</span>
-<span class="sd">    Note these graph formats are checked automatically by the extensions of </span>
-<span class="sd">    graph files.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">dirname_dataset</span> <span class="o">=</span> <span class="n">dirname</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="n">data</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="n">y</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="n">content</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-    <span class="n">extension</span> <span class="o">=</span> <span class="n">splitext</span><span class="p">(</span><span class="n">content</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">)[</span><span class="mi">0</span><span class="p">])[</span><span class="mi">1</span><span class="p">][</span><span class="mi">1</span><span class="p">:]</span>
-    <span class="k">if</span> <span class="n">filename_y</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">filename_y</span> <span class="o">==</span> <span class="s1">&#39;&#39;</span><span class="p">:</span>
-        <span class="k">if</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;ct&#39;</span><span class="p">:</span> 
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">)):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">)</span>
-                <span class="c1"># remove the &#39;#&#39;s in file names</span>
-                <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-                    <span class="n">loadCT</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)))</span>
-                <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
-        <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;gxl&#39;</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">)):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">)</span>
-                <span class="c1"># remove the &#39;#&#39;s in file names</span>
-                <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-                    <span class="n">loadGXL</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">tmp</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)))</span>
-                <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
-    <span class="k">else</span><span class="p">:</span>  <span class="c1"># y in a seperate file</span>
-        <span class="k">if</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;ct&#39;</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">)):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
-                <span class="c1"># remove the &#39;#&#39;s in file names</span>
-                <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-                    <span class="n">loadCT</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">tmp</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)))</span>
-        <span class="k">elif</span> <span class="n">extension</span> <span class="o">==</span> <span class="s1">&#39;gxl&#39;</span><span class="p">:</span>
-            <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">content</span><span class="p">)):</span>
-                <span class="n">tmp</span> <span class="o">=</span> <span class="n">content</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
-                <span class="c1"># remove the &#39;#&#39;s in file names</span>
-                <span class="n">data</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-                    <span class="n">loadGXL</span><span class="p">(</span><span class="n">dirname_dataset</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span> <span class="o">+</span> <span class="n">tmp</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;#&#39;</span><span class="p">,</span> <span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)))</span>                                                       
-                                                               
-        <span class="n">content_y</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename_y</span><span class="p">)</span><span class="o">.</span><span class="n">read</span><span class="p">()</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
-        <span class="c1"># assume entries in filename and filename_y have the same order.</span>
-        <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">content_y</span><span class="p">:</span>
-            <span class="n">tmp</span> <span class="o">=</span> <span class="n">item</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39; &#39;</span><span class="p">)</span>
-            <span class="c1"># assume the 3rd entry in a line is y (for Alkane dataset)</span>
-            <span class="n">y</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="nb">float</span><span class="p">(</span><span class="n">tmp</span><span class="p">[</span><span class="mi">2</span><span class="p">]))</span>
-            
-    <span class="k">return</span> <span class="n">data</span><span class="p">,</span> <span class="n">y</span></div>
-                
-
-<div class="viewcode-block" id="saveDataset"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.graphfiles.saveDataset">[docs]</a><span class="k">def</span> <span class="nf">saveDataset</span><span class="p">(</span><span class="n">Gn</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">gformat</span><span class="o">=</span><span class="s1">&#39;gxl&#39;</span><span class="p">,</span> <span class="n">group</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="s1">&#39;gfile&#39;</span><span class="p">,</span> <span class="n">xparams</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Save list of graphs.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">import</span> <span class="nn">os</span>
-    <span class="n">dirname_ds</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">dirname_ds</span> <span class="o">!=</span> <span class="s1">&#39;&#39;</span><span class="p">:</span>
-        <span class="n">dirname_ds</span> <span class="o">+=</span> <span class="s1">&#39;/&#39;</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">dirname_ds</span><span class="p">)</span> <span class="p">:</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">dirname_ds</span><span class="p">)</span>
-                
-    <span class="k">if</span> <span class="s1">&#39;graph_dir&#39;</span> <span class="ow">in</span> <span class="n">xparams</span><span class="p">:</span>
-        <span class="n">graph_dir</span> <span class="o">=</span> <span class="n">xparams</span><span class="p">[</span><span class="s1">&#39;graph_dir&#39;</span><span class="p">]</span> <span class="o">+</span> <span class="s1">&#39;/&#39;</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">graph_dir</span><span class="p">):</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">graph_dir</span><span class="p">)</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">graph_dir</span> <span class="o">=</span> <span class="n">dirname_ds</span> 
-            
-    <span class="k">if</span> <span class="n">group</span> <span class="o">==</span> <span class="s1">&#39;xml&#39;</span> <span class="ow">and</span> <span class="n">gformat</span> <span class="o">==</span> <span class="s1">&#39;gxl&#39;</span><span class="p">:</span>
-        <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">filename</span> <span class="o">+</span> <span class="s1">&#39;.xml&#39;</span><span class="p">,</span> <span class="s1">&#39;w&#39;</span><span class="p">)</span> <span class="k">as</span> <span class="n">fgroup</span><span class="p">:</span>
-            <span class="n">fgroup</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;&lt;?xml version=</span><span class="se">\&quot;</span><span class="s2">1.0</span><span class="se">\&quot;</span><span class="s2">?&gt;&quot;</span><span class="p">)</span>
-            <span class="n">fgroup</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&lt;!DOCTYPE GraphCollection SYSTEM </span><span class="se">\&quot;</span><span class="s2">http://www.inf.unibz.it/~blumenthal/dtd/GraphCollection.dtd</span><span class="se">\&quot;</span><span class="s2">&gt;&quot;</span><span class="p">)</span>
-            <span class="n">fgroup</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&lt;GraphCollection&gt;&quot;</span><span class="p">)</span>
-            <span class="k">for</span> <span class="n">idx</span><span class="p">,</span> <span class="n">g</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">Gn</span><span class="p">):</span>
-                <span class="n">fname_tmp</span> <span class="o">=</span> <span class="s2">&quot;graph&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span> <span class="o">+</span> <span class="s2">&quot;.gxl&quot;</span>
-                <span class="n">saveGXL</span><span class="p">(</span><span class="n">g</span><span class="p">,</span> <span class="n">graph_dir</span> <span class="o">+</span> <span class="n">fname_tmp</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="n">xparams</span><span class="p">[</span><span class="s1">&#39;method&#39;</span><span class="p">])</span>
-                <span class="n">fgroup</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n\t</span><span class="s2">&lt;graph file=</span><span class="se">\&quot;</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="n">fname_tmp</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2"> class=</span><span class="se">\&quot;</span><span class="s2">&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">y</span><span class="p">[</span><span class="n">idx</span><span class="p">])</span> <span class="o">+</span> <span class="s2">&quot;</span><span class="se">\&quot;</span><span class="s2">/&gt;&quot;</span><span class="p">)</span>
-            <span class="n">fgroup</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s2">&quot;</span><span class="se">\n</span><span class="s2">&lt;/GraphCollection&gt;&quot;</span><span class="p">)</span>
-            <span class="n">fgroup</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
-            
-            
-<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>    
-<span class="c1">#    ### Load dataset from .ds file.</span>
-<span class="c1">#    # .ct files.</span>
-<span class="c1">#    ds = {&#39;name&#39;: &#39;Alkane&#39;, &#39;dataset&#39;: &#39;../../datasets/Alkane/dataset.ds&#39;,</span>
-<span class="c1">#        &#39;dataset_y&#39;: &#39;../../datasets/Alkane/dataset_boiling_point_names.txt&#39;}</span>
-<span class="c1">#    Gn, y = loadDataset(ds[&#39;dataset&#39;], filename_y=ds[&#39;dataset_y&#39;])</span>
-<span class="c1">##    ds = {&#39;name&#39;: &#39;Acyclic&#39;, &#39;dataset&#39;: &#39;../../datasets/acyclic/dataset_bps.ds&#39;}  # node symb</span>
-<span class="c1">##    Gn, y = loadDataset(ds[&#39;dataset&#39;])</span>
-<span class="c1">##    ds = {&#39;name&#39;: &#39;MAO&#39;, &#39;dataset&#39;: &#39;../../datasets/MAO/dataset.ds&#39;} # node/edge symb</span>
-<span class="c1">##    Gn, y = loadDataset(ds[&#39;dataset&#39;])</span>
-<span class="c1">##    ds = {&#39;name&#39;: &#39;PAH&#39;, &#39;dataset&#39;: &#39;../../datasets/PAH/dataset.ds&#39;} # unlabeled</span>
-<span class="c1">##    Gn, y = loadDataset(ds[&#39;dataset&#39;])</span>
-<span class="c1">#    print(Gn[1].nodes(data=True))</span>
-<span class="c1">#    print(Gn[1].edges(data=True))</span>
-<span class="c1">#    print(y[1])</span>
-    
-<span class="c1">#    # .gxl file.</span>
-<span class="c1">#    ds = {&#39;name&#39;: &#39;monoterpenoides&#39;, </span>
-<span class="c1">#          &#39;dataset&#39;: &#39;../../datasets/monoterpenoides/dataset_10+.ds&#39;}  # node/edge symb</span>
-<span class="c1">#    Gn, y = loadDataset(ds[&#39;dataset&#39;])</span>
-<span class="c1">#    print(Gn[1].nodes(data=True))</span>
-<span class="c1">#    print(Gn[1].edges(data=True))</span>
-<span class="c1">#    print(y[1])</span>
-    
-    <span class="c1">### Convert graph from one format to another.</span>
-    <span class="c1"># .gxl file.</span>
-    <span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</span>
-    <span class="n">ds</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;name&#39;</span><span class="p">:</span> <span class="s1">&#39;monoterpenoides&#39;</span><span class="p">,</span> 
-          <span class="s1">&#39;dataset&#39;</span><span class="p">:</span> <span class="s1">&#39;../../datasets/monoterpenoides/dataset_10+.ds&#39;</span><span class="p">}</span>  <span class="c1"># node/edge symb</span>
-    <span class="n">Gn</span><span class="p">,</span> <span class="n">y</span> <span class="o">=</span> <span class="n">loadDataset</span><span class="p">(</span><span class="n">ds</span><span class="p">[</span><span class="s1">&#39;dataset&#39;</span><span class="p">])</span>
-    <span class="n">y</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">y</span><span class="p">]</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">Gn</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">Gn</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">y</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-    <span class="c1"># Convert a graph to the proper NetworkX format that can be recognized by library gedlib.</span>
-    <span class="n">Gn_new</span> <span class="o">=</span> <span class="p">[]</span>
-    <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-        <span class="n">G_new</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
-        <span class="k">for</span> <span class="n">nd</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">G_new</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">nd</span><span class="p">),</span> <span class="n">chem</span><span class="o">=</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;atom&#39;</span><span class="p">])</span>
-        <span class="k">for</span> <span class="n">nd1</span><span class="p">,</span> <span class="n">nd2</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-            <span class="n">G_new</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">nd1</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">nd2</span><span class="p">),</span> <span class="n">valence</span><span class="o">=</span><span class="n">attrs</span><span class="p">[</span><span class="s1">&#39;bond_type&#39;</span><span class="p">])</span>
-<span class="c1">#            G_new.add_edge(str(nd1), str(nd2))</span>
-        <span class="n">Gn_new</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">G_new</span><span class="p">)</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">Gn_new</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">Gn_new</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="nb">print</span><span class="p">(</span><span class="n">Gn_new</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-    <span class="n">filename</span> <span class="o">=</span> <span class="s1">&#39;/media/ljia/DATA/research-repo/codes/others/gedlib/tests_linlin/generated_datsets/monoterpenoides/gxl/monoterpenoides&#39;</span>
-    <span class="n">xparams</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;method&#39;</span><span class="p">:</span> <span class="s1">&#39;gedlib&#39;</span><span class="p">}</span>
-    <span class="n">saveDataset</span><span class="p">(</span><span class="n">Gn</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">gformat</span><span class="o">=</span><span class="s1">&#39;gxl&#39;</span><span class="p">,</span> <span class="n">group</span><span class="o">=</span><span class="s1">&#39;xml&#39;</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="n">filename</span><span class="p">,</span> <span class="n">xparams</span><span class="o">=</span><span class="n">xparams</span><span class="p">)</span>
-    
-<span class="c1">#    ds = {&#39;name&#39;: &#39;MUTAG&#39;, &#39;dataset&#39;: &#39;../../datasets/MUTAG/MUTAG.mat&#39;,</span>
-<span class="c1">#          &#39;extra_params&#39;: {&#39;am_sp_al_nl_el&#39;: [0, 0, 3, 1, 2]}}  # node/edge symb</span>
-<span class="c1">#    Gn, y = loadDataset(ds[&#39;dataset&#39;], extra_params=ds[&#39;extra_params&#39;])</span>
-<span class="c1">#    saveDataset(Gn, y, group=&#39;xml&#39;, filename=&#39;temp/temp&#39;)</span>
-</pre></div>
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-            
-  <h1>Source code for pygraph.utils.isNotebook</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot; Functions for python system.</span>
-<span class="sd">&quot;&quot;&quot;</span>
-
-<div class="viewcode-block" id="isNotebook"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.isNotebook.isNotebook">[docs]</a><span class="k">def</span> <span class="nf">isNotebook</span><span class="p">():</span>
-    <span class="sd">&quot;&quot;&quot;check if code is executed in the IPython notebook.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">try</span><span class="p">:</span>
-        <span class="n">shell</span> <span class="o">=</span> <span class="n">get_ipython</span><span class="p">()</span><span class="o">.</span><span class="vm">__class__</span><span class="o">.</span><span class="vm">__name__</span>
-        <span class="k">if</span> <span class="n">shell</span> <span class="o">==</span> <span class="s1">&#39;ZMQInteractiveShell&#39;</span><span class="p">:</span>
-            <span class="k">return</span> <span class="kc">True</span>   <span class="c1"># Jupyter notebook or qtconsole</span>
-        <span class="k">elif</span> <span class="n">shell</span> <span class="o">==</span> <span class="s1">&#39;TerminalInteractiveShell&#39;</span><span class="p">:</span>
-            <span class="k">return</span> <span class="kc">False</span>  <span class="c1"># Terminal running IPython</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="kc">False</span>  <span class="c1"># Other type (?)</span>
-    <span class="k">except</span> <span class="ne">NameError</span><span class="p">:</span>
-        <span class="k">return</span> <span class="kc">False</span>      <span class="c1"># Probably standard Python interpreter</span></div>
-</pre></div>
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docs/_build/html/_modules/pygraph/utils/kernels.html

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-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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-            
-  <h1>Source code for pygraph.utils.kernels</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Those who are not graph kernels. We can be kernels for nodes or edges!</span>
-<span class="sd">These kernels are defined between pairs of vectors.</span>
-<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>
-
-<div class="viewcode-block" id="deltakernel"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.deltakernel">[docs]</a><span class="k">def</span> <span class="nf">deltakernel</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Delta kernel. Return 1 if x == y, 0 otherwise.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    x, y : any</span>
-<span class="sd">        Two parts to compare.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    kernel : integer</span>
-<span class="sd">        Delta kernel.</span>
-
-<span class="sd">    References</span>
-<span class="sd">    ----------</span>
-<span class="sd">    [1] H. Kashima, K. Tsuda, and A. Inokuchi. Marginalized kernels between </span>
-<span class="sd">    labeled graphs. In Proceedings of the 20th International Conference on </span>
-<span class="sd">    Machine Learning, Washington, DC, United States, 2003.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">x</span> <span class="o">==</span> <span class="n">y</span>  <span class="c1">#(1 if condition else 0)</span></div>
-
-
-<div class="viewcode-block" id="gaussiankernel"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.gaussiankernel">[docs]</a><span class="k">def</span> <span class="nf">gaussiankernel</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">gamma</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Gaussian kernel.</span>
-<span class="sd">    Compute the rbf (gaussian) kernel between x and y:</span>
-
-<span class="sd">        K(x, y) = exp(-gamma ||x-y||^2).</span>
-
-<span class="sd">    Read more in the :ref:`User Guide &lt;rbf_kernel&gt;`.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    x, y : array</span>
-
-<span class="sd">    gamma : float, default None</span>
-<span class="sd">        If None, defaults to 1.0 / n_features</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">    -------</span>
-<span class="sd">    kernel : float</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="n">gamma</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-        <span class="n">gamma</span> <span class="o">=</span> <span class="mf">1.0</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
-
-    <span class="n">xt</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">itm</span><span class="p">)</span> <span class="k">for</span> <span class="n">itm</span> <span class="ow">in</span> <span class="n">x</span><span class="p">])</span>
-    <span class="n">yt</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="nb">float</span><span class="p">(</span><span class="n">itm</span><span class="p">)</span> <span class="k">for</span> <span class="n">itm</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span>
-    <span class="n">kernel</span> <span class="o">=</span> <span class="n">xt</span> <span class="o">-</span> <span class="n">yt</span>
-    <span class="n">kernel</span> <span class="o">=</span> <span class="n">kernel</span> <span class="o">**</span> <span class="mi">2</span>
-    <span class="n">kernel</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">kernel</span><span class="p">)</span>
-    <span class="n">kernel</span> <span class="o">*=</span> <span class="o">-</span><span class="n">gamma</span>
-    <span class="n">kernel</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">kernel</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">kernel</span></div>
-
-
-<div class="viewcode-block" id="polynomialkernel"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.polynomialkernel">[docs]</a><span class="k">def</span> <span class="nf">polynomialkernel</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">d</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Polynomial kernel.</span>
-<span class="sd">    Compute the polynomial kernel between x and y:</span>
-
-<span class="sd">        K(x, y) = &lt;x, y&gt; ^d + c.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    x, y : array</span>
-
-<span class="sd">    d : integer, default 1</span>
-<span class="sd">    </span>
-<span class="sd">    c : float, default 0</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">    -------</span>
-<span class="sd">    kernel : float</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span> <span class="o">**</span> <span class="n">d</span> <span class="o">+</span> <span class="n">c</span></div>
-
-
-<div class="viewcode-block" id="linearkernel"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.linearkernel">[docs]</a><span class="k">def</span> <span class="nf">linearkernel</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Polynomial kernel.</span>
-<span class="sd">    Compute the polynomial kernel between x and y:</span>
-
-<span class="sd">        K(x, y) = &lt;x, y&gt;.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    x, y : array</span>
-
-<span class="sd">    d : integer, default 1</span>
-<span class="sd">    </span>
-<span class="sd">    c : float, default 0</span>
-
-<span class="sd">    Returns</span>
-<span class="sd">    -------</span>
-<span class="sd">    kernel : float</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span></div>
-
-
-<div class="viewcode-block" id="kernelsum"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.kernelsum">[docs]</a><span class="k">def</span> <span class="nf">kernelsum</span><span class="p">(</span><span class="n">k1</span><span class="p">,</span> <span class="n">k2</span><span class="p">,</span> <span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">,</span> <span class="n">d21</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">d22</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">lamda1</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">lamda2</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Sum of a pair of kernels.</span>
-
-<span class="sd">    k = lamda1 * k1(d11, d12) + lamda2 * k2(d21, d22)</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    k1, k2 : function</span>
-<span class="sd">        A pair of kernel functions.</span>
-<span class="sd">    d11, d12:</span>
-<span class="sd">        Inputs of k1. If d21 or d22 is None, apply d11, d12 to both k1 and k2.</span>
-<span class="sd">    d21, d22:</span>
-<span class="sd">        Inputs of k2.</span>
-<span class="sd">    lamda1, lamda2: float</span>
-<span class="sd">        Coefficients of the product.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    kernel : integer</span>
-
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="n">d21</span> <span class="o">==</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">d22</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-        <span class="n">kernel</span> <span class="o">=</span> <span class="n">lamda1</span> <span class="o">*</span> <span class="n">k1</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span> <span class="o">+</span> <span class="n">lamda2</span> <span class="o">*</span> <span class="n">k2</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">kernel</span> <span class="o">=</span> <span class="n">lamda1</span> <span class="o">*</span> <span class="n">k1</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span> <span class="o">+</span> <span class="n">lamda2</span> <span class="o">*</span> <span class="n">k2</span><span class="p">(</span><span class="n">d21</span><span class="p">,</span> <span class="n">d22</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">kernel</span></div>
-
-
-<div class="viewcode-block" id="kernelproduct"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.kernels.kernelproduct">[docs]</a><span class="k">def</span> <span class="nf">kernelproduct</span><span class="p">(</span><span class="n">k1</span><span class="p">,</span> <span class="n">k2</span><span class="p">,</span> <span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">,</span> <span class="n">d21</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">d22</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">lamda</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Product of a pair of kernels.</span>
-
-<span class="sd">    k = lamda * k1(d11, d12) * k2(d21, d22)</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    k1, k2 : function</span>
-<span class="sd">        A pair of kernel functions.</span>
-<span class="sd">    d11, d12:</span>
-<span class="sd">        Inputs of k1. If d21 or d22 is None, apply d11, d12 to both k1 and k2.</span>
-<span class="sd">    d21, d22:</span>
-<span class="sd">        Inputs of k2.</span>
-<span class="sd">    lamda: float</span>
-<span class="sd">        Coefficient of the product.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    kernel : integer</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="n">d21</span> <span class="o">==</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">d22</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-        <span class="n">kernel</span> <span class="o">=</span> <span class="n">lamda</span> <span class="o">*</span> <span class="n">k1</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span> <span class="o">*</span> <span class="n">k2</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">kernel</span> <span class="o">=</span> <span class="n">lamda</span> <span class="o">*</span> <span class="n">k1</span><span class="p">(</span><span class="n">d11</span><span class="p">,</span> <span class="n">d12</span><span class="p">)</span> <span class="o">*</span> <span class="n">k2</span><span class="p">(</span><span class="n">d21</span><span class="p">,</span> <span class="n">d22</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">kernel</span></div>
-
-
-<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
-    <span class="n">o</span> <span class="o">=</span> <span class="n">polynomialkernel</span><span class="p">([</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="p">[</span><span class="mi">3</span><span class="p">,</span> <span class="mi">4</span><span class="p">],</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
-</pre></div>
-
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docs/_build/html/_modules/pygraph/utils/logger2file.html

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-           <div itemprop="articleBody">
-            
-  <h1>Source code for pygraph.utils.logger2file</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python3</span>
-<span class="c1"># -*- coding: utf-8 -*-</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">Created on Fri Nov  8 14:21:25 2019</span>
-
-<span class="sd">@author: ljia</span>
-<span class="sd">&quot;&quot;&quot;</span>
-
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">import</span> <span class="nn">time</span>
-
-<div class="viewcode-block" id="Logger"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.logger2file.Logger">[docs]</a><span class="k">class</span> <span class="nc">Logger</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">terminal</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">stdout</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">log</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="s2">&quot;log.&quot;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">time</span><span class="o">.</span><span class="n">time</span><span class="p">())</span> <span class="o">+</span> <span class="s2">&quot;.log&quot;</span><span class="p">,</span> <span class="s2">&quot;a&quot;</span><span class="p">)</span>
-
-<div class="viewcode-block" id="Logger.write"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.logger2file.Logger.write">[docs]</a>    <span class="k">def</span> <span class="nf">write</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">terminal</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">log</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>  </div>
-
-<div class="viewcode-block" id="Logger.flush"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.logger2file.Logger.flush">[docs]</a>    <span class="k">def</span> <span class="nf">flush</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="c1">#this flush method is needed for python 3 compatibility.</span>
-        <span class="c1">#this handles the flush command by doing nothing.</span>
-        <span class="c1">#you might want to specify some extra behavior here.</span>
-        <span class="k">pass</span>    </div></div>
-
-<span class="n">sys</span><span class="o">.</span><span class="n">stdout</span> <span class="o">=</span> <span class="n">Logger</span><span class="p">()</span>
-</pre></div>
-
-           </div>
-           
-          </div>
-          <footer>
-  
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-    <p>
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docs/_build/html/_modules/pygraph/utils/parallel.html

@@ -1,252 +0,0 @@
-
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-<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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-           <div itemprop="articleBody">
-            
-  <h1>Source code for pygraph.utils.parallel</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python3</span>
-<span class="c1"># -*- coding: utf-8 -*-</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">Created on Tue Dec 11 11:39:46 2018</span>
-<span class="sd">Parallel aid functions.</span>
-<span class="sd">@author: ljia</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="kn">import</span> <span class="nn">multiprocessing</span>
-<span class="kn">from</span> <span class="nn">multiprocessing</span> <span class="k">import</span> <span class="n">Pool</span>
-<span class="kn">from</span> <span class="nn">tqdm</span> <span class="k">import</span> <span class="n">tqdm</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-
-<div class="viewcode-block" id="parallel_me"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.parallel.parallel_me">[docs]</a><span class="k">def</span> <span class="nf">parallel_me</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">func_assign</span><span class="p">,</span> <span class="n">var_to_assign</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">len_itr</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">init_worker</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 
-                <span class="n">glbv</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">chunksize</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">itr_desc</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span>
-                <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-    <span class="sd">&#39;&#39;&#39;</span>
-<span class="sd">    &#39;&#39;&#39;</span>
-    <span class="k">if</span> <span class="n">method</span> <span class="o">==</span> <span class="s1">&#39;imap_unordered&#39;</span><span class="p">:</span>
-        <span class="k">if</span> <span class="n">glbv</span><span class="p">:</span> <span class="c1"># global varibles required.</span>
-<span class="c1">#            def init_worker(v_share):</span>
-<span class="c1">#                global G_var</span>
-<span class="c1">#                G_var = v_share</span>
-            <span class="k">if</span> <span class="n">n_jobs</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="n">n_jobs</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span>
-            <span class="k">with</span> <span class="n">Pool</span><span class="p">(</span><span class="n">processes</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">,</span> <span class="n">initializer</span><span class="o">=</span><span class="n">init_worker</span><span class="p">,</span> 
-                      <span class="n">initargs</span><span class="o">=</span><span class="n">glbv</span><span class="p">)</span> <span class="k">as</span> <span class="n">pool</span><span class="p">:</span>                
-                <span class="k">if</span> <span class="n">chunksize</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="n">len_itr</span> <span class="o">&lt;</span> <span class="mi">100</span> <span class="o">*</span> <span class="n">n_jobs</span><span class="p">:</span>
-                        <span class="n">chunksize</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">len_itr</span> <span class="o">/</span> <span class="n">n_jobs</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span>
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">chunksize</span> <span class="o">=</span> <span class="mi">100</span>
-                <span class="k">for</span> <span class="n">result</span> <span class="ow">in</span> <span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="n">pool</span><span class="o">.</span><span class="n">imap_unordered</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">chunksize</span><span class="p">),</span>
-                    <span class="n">desc</span><span class="o">=</span><span class="n">itr_desc</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span> <span class="k">if</span> <span class="n">verbose</span> <span class="k">else</span> 
-                    <span class="n">pool</span><span class="o">.</span><span class="n">imap_unordered</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">chunksize</span><span class="p">)):</span>
-                    <span class="n">func_assign</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">var_to_assign</span><span class="p">)</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">n_jobs</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="n">n_jobs</span> <span class="o">=</span> <span class="n">multiprocessing</span><span class="o">.</span><span class="n">cpu_count</span><span class="p">()</span>
-            <span class="k">with</span> <span class="n">Pool</span><span class="p">(</span><span class="n">processes</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">)</span> <span class="k">as</span> <span class="n">pool</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">chunksize</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
-                    <span class="k">if</span> <span class="n">len_itr</span> <span class="o">&lt;</span> <span class="mi">100</span> <span class="o">*</span> <span class="n">n_jobs</span><span class="p">:</span>
-                        <span class="n">chunksize</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">len_itr</span> <span class="o">/</span> <span class="n">n_jobs</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span>
-                    <span class="k">else</span><span class="p">:</span>
-                        <span class="n">chunksize</span> <span class="o">=</span> <span class="mi">100</span>
-                <span class="k">for</span> <span class="n">result</span> <span class="ow">in</span> <span class="p">(</span><span class="n">tqdm</span><span class="p">(</span><span class="n">pool</span><span class="o">.</span><span class="n">imap_unordered</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">chunksize</span><span class="p">),</span>
-                    <span class="n">desc</span><span class="o">=</span><span class="n">itr_desc</span><span class="p">,</span> <span class="n">file</span><span class="o">=</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span> <span class="k">if</span> <span class="n">verbose</span> <span class="k">else</span> 
-                    <span class="n">pool</span><span class="o">.</span><span class="n">imap_unordered</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">chunksize</span><span class="p">)):</span>
-                    <span class="n">func_assign</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">var_to_assign</span><span class="p">)</span></div>
-            
-                    
-
-<div class="viewcode-block" id="parallel_gm"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.parallel.parallel_gm">[docs]</a><span class="k">def</span> <span class="nf">parallel_gm</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">Kmatrix</span><span class="p">,</span> <span class="n">Gn</span><span class="p">,</span> <span class="n">init_worker</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">glbv</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 
-                <span class="n">method</span><span class="o">=</span><span class="s1">&#39;imap_unordered&#39;</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">chunksize</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> 
-                <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-    <span class="kn">from</span> <span class="nn">itertools</span> <span class="k">import</span> <span class="n">combinations_with_replacement</span>
-    <span class="k">def</span> <span class="nf">func_assign</span><span class="p">(</span><span class="n">result</span><span class="p">,</span> <span class="n">var_to_assign</span><span class="p">):</span>
-        <span class="n">var_to_assign</span><span class="p">[</span><span class="n">result</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">result</span><span class="p">[</span><span class="mi">1</span><span class="p">]]</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-        <span class="n">var_to_assign</span><span class="p">[</span><span class="n">result</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="n">result</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
-    <span class="n">itr</span> <span class="o">=</span> <span class="n">combinations_with_replacement</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">Gn</span><span class="p">)),</span> <span class="mi">2</span><span class="p">)</span>
-    <span class="n">len_itr</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span> <span class="o">*</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">Gn</span><span class="p">)</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">2</span><span class="p">)</span>
-    <span class="n">parallel_me</span><span class="p">(</span><span class="n">func</span><span class="p">,</span> <span class="n">func_assign</span><span class="p">,</span> <span class="n">Kmatrix</span><span class="p">,</span> <span class="n">itr</span><span class="p">,</span> <span class="n">len_itr</span><span class="o">=</span><span class="n">len_itr</span><span class="p">,</span>
-        <span class="n">init_worker</span><span class="o">=</span><span class="n">init_worker</span><span class="p">,</span> <span class="n">glbv</span><span class="o">=</span><span class="n">glbv</span><span class="p">,</span> <span class="n">method</span><span class="o">=</span><span class="n">method</span><span class="p">,</span> <span class="n">n_jobs</span><span class="o">=</span><span class="n">n_jobs</span><span class="p">,</span> 
-        <span class="n">chunksize</span><span class="o">=</span><span class="n">chunksize</span><span class="p">,</span> <span class="n">itr_desc</span><span class="o">=</span><span class="s1">&#39;calculating kernels&#39;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span></div>
-</pre></div>
-
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-           <div itemprop="articleBody">
-            
-  <h1>Source code for pygraph.utils.trie</h1><div class="highlight"><pre>
-<span></span><span class="ch">#!/usr/bin/env python3</span>
-<span class="c1"># -*- coding: utf-8 -*-</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">Created on Wed Jan 30 10:48:49 2019</span>
-
-<span class="sd">Trie (prefix tree)</span>
-<span class="sd">@author: ljia</span>
-<span class="sd">@references:</span>
-<span class="sd">        https://viblo.asia/p/nlp-build-a-trie-data-structure-from-scratch-with-python-3P0lPzroKox, 2019.1</span>
-<span class="sd">&quot;&quot;&quot;</span>
-
-<span class="kn">import</span> <span class="nn">pickle</span>
-<span class="kn">import</span> <span class="nn">json</span>
-
-<span class="sd">&quot;&quot;&quot; Trie class</span>
-<span class="sd">&quot;&quot;&quot;</span>
-<div class="viewcode-block" id="Trie"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie">[docs]</a><span class="k">class</span> <span class="nc">Trie</span><span class="p">:</span>
-    <span class="c1"># init Trie class</span>
-    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">root</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getNode</span><span class="p">()</span>
-
-<div class="viewcode-block" id="Trie.getNode"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.getNode">[docs]</a>    <span class="k">def</span> <span class="nf">getNode</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="p">{</span><span class="s2">&quot;isEndOfWord&quot;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s2">&quot;children&quot;</span><span class="p">:</span> <span class="p">{}}</span></div>
-
-<div class="viewcode-block" id="Trie.insertWord"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.insertWord">[docs]</a>    <span class="k">def</span> <span class="nf">insertWord</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">word</span><span class="p">):</span>
-        <span class="n">current</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span>
-        <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">word</span><span class="p">:</span>
-
-            <span class="k">if</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]:</span>
-                <span class="n">node</span> <span class="o">=</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">][</span><span class="n">ch</span><span class="p">]</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="n">node</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">getNode</span><span class="p">()</span>
-                <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">][</span><span class="n">ch</span><span class="p">]</span> <span class="o">=</span> <span class="n">node</span>
-
-            <span class="n">current</span> <span class="o">=</span> <span class="n">node</span>
-        <span class="n">current</span><span class="p">[</span><span class="s2">&quot;isEndOfWord&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">True</span>
-        <span class="k">if</span> <span class="s1">&#39;count&#39;</span> <span class="ow">in</span> <span class="n">current</span><span class="p">:</span>
-            <span class="n">current</span><span class="p">[</span><span class="s1">&#39;count&#39;</span><span class="p">]</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">current</span><span class="p">[</span><span class="s1">&#39;count&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span></div>
-
-<div class="viewcode-block" id="Trie.searchWord"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.searchWord">[docs]</a>    <span class="k">def</span> <span class="nf">searchWord</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">word</span><span class="p">):</span>
-        <span class="n">current</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span>
-        <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">word</span><span class="p">:</span>
-            <span class="k">if</span> <span class="n">ch</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]:</span>
-                <span class="k">return</span> <span class="mi">0</span>
-            <span class="n">node</span> <span class="o">=</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">][</span><span class="n">ch</span><span class="p">]</span>
-
-            <span class="n">current</span> <span class="o">=</span> <span class="n">node</span>
-        <span class="k">if</span> <span class="s1">&#39;count&#39;</span> <span class="ow">in</span> <span class="n">current</span><span class="p">:</span>
-            <span class="k">return</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;count&quot;</span><span class="p">]</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="k">return</span> <span class="mi">0</span></div>
-
-<div class="viewcode-block" id="Trie.searchWordPrefix"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.searchWordPrefix">[docs]</a>    <span class="k">def</span> <span class="nf">searchWordPrefix</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">word</span><span class="p">):</span>
-        <span class="n">current</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">root</span>
-        <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">word</span><span class="p">:</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">ch</span><span class="p">):</span>
-                <span class="k">return</span> <span class="kc">False</span>
-            <span class="n">node</span> <span class="o">=</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">][</span><span class="n">ch</span><span class="p">]</span>
-
-            <span class="n">current</span> <span class="o">=</span> <span class="n">node</span>
-        <span class="c1"># return True if children contain keys and values</span>
-        <span class="k">return</span> <span class="nb">bool</span><span class="p">(</span><span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">])</span></div>
-
-<div class="viewcode-block" id="Trie.deleteWord"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.deleteWord">[docs]</a>    <span class="k">def</span> <span class="nf">deleteWord</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">word</span><span class="p">):</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">_delete</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">word</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span></div>
-
-    <span class="k">def</span> <span class="nf">_delete</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">current</span><span class="p">,</span> <span class="n">word</span><span class="p">,</span> <span class="n">index</span><span class="p">):</span>
-        <span class="k">if</span><span class="p">(</span><span class="n">index</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">word</span><span class="p">)):</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;isEndOfWord&quot;</span><span class="p">]:</span>
-                <span class="k">return</span> <span class="kc">False</span>
-            <span class="n">current</span><span class="p">[</span><span class="s2">&quot;isEndOfWord&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="kc">False</span>
-            <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">==</span> <span class="mi">0</span>
-
-        <span class="n">ch</span> <span class="o">=</span> <span class="n">word</span><span class="p">[</span><span class="n">index</span><span class="p">]</span>
-        <span class="k">if</span> <span class="ow">not</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">ch</span><span class="p">):</span>
-            <span class="k">return</span> <span class="kc">False</span>
-        <span class="n">node</span> <span class="o">=</span> <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">][</span><span class="n">ch</span><span class="p">]</span>
-
-        <span class="n">should_delete_current_node</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_delete</span><span class="p">(</span><span class="n">node</span><span class="p">,</span> <span class="n">word</span><span class="p">,</span> <span class="n">index</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
-
-        <span class="k">if</span> <span class="n">should_delete_current_node</span><span class="p">:</span>
-            <span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="n">ch</span><span class="p">)</span>
-            <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">current</span><span class="p">[</span><span class="s2">&quot;children&quot;</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">==</span> <span class="mi">0</span>
-
-        <span class="k">return</span> <span class="kc">False</span>
-
-<div class="viewcode-block" id="Trie.save_to_pickle"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.save_to_pickle">[docs]</a>    <span class="k">def</span> <span class="nf">save_to_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name</span><span class="p">):</span>
-        <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span> <span class="o">+</span> <span class="s2">&quot;.pkl&quot;</span><span class="p">,</span> <span class="s2">&quot;wb&quot;</span><span class="p">)</span>
-        <span class="n">pickle</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">,</span> <span class="n">f</span><span class="p">)</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
-
-<div class="viewcode-block" id="Trie.load_from_pickle"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.load_from_pickle">[docs]</a>    <span class="k">def</span> <span class="nf">load_from_pickle</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name</span><span class="p">):</span>
-        <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span> <span class="o">+</span> <span class="s2">&quot;.pkl&quot;</span><span class="p">,</span> <span class="s2">&quot;rb&quot;</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">root</span> <span class="o">=</span> <span class="n">pickle</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
-        
-<div class="viewcode-block" id="Trie.to_json"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.to_json">[docs]</a>    <span class="k">def</span> <span class="nf">to_json</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span></div>
-
-<div class="viewcode-block" id="Trie.save_to_json"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.save_to_json">[docs]</a>    <span class="k">def</span> <span class="nf">save_to_json</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name</span><span class="p">):</span>
-        <span class="n">json_data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">dumps</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">root</span><span class="p">)</span>
-        <span class="n">f</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span> <span class="o">+</span> <span class="s2">&quot;.json&quot;</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">json_data</span><span class="p">)</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div>
-
-<div class="viewcode-block" id="Trie.load_from_json"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.trie.Trie.load_from_json">[docs]</a>    <span class="k">def</span> <span class="nf">load_from_json</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">file_name</span><span class="p">):</span>
-        <span class="n">json_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_name</span> <span class="o">+</span> <span class="s2">&quot;.json&quot;</span><span class="p">,</span> <span class="s2">&quot;r&quot;</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">root</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">json_file</span><span class="p">)</span>
-        <span class="n">json_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></div></div>
-</pre></div>
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-           <div itemprop="articleBody">
-            
-  <h1>Source code for pygraph.utils.utils</h1><div class="highlight"><pre>
-<span></span><span class="kn">import</span> <span class="nn">networkx</span> <span class="k">as</span> <span class="nn">nx</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">copy</span> <span class="k">import</span> <span class="n">deepcopy</span>
-<span class="c1">#from itertools import product</span>
-
-<span class="c1"># from tqdm import tqdm</span>
-
-
-<div class="viewcode-block" id="getSPLengths"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.getSPLengths">[docs]</a><span class="k">def</span> <span class="nf">getSPLengths</span><span class="p">(</span><span class="n">G1</span><span class="p">):</span>
-    <span class="n">sp</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">shortest_path</span><span class="p">(</span><span class="n">G1</span><span class="p">)</span>
-    <span class="n">distances</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="n">G1</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">(),</span> <span class="n">G1</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()))</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">sp</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">sp</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-            <span class="n">distances</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">sp</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">j</span><span class="p">])</span> <span class="o">-</span> <span class="mi">1</span>
-    <span class="k">return</span> <span class="n">distances</span></div>
-
-
-<div class="viewcode-block" id="getSPGraph"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.getSPGraph">[docs]</a><span class="k">def</span> <span class="nf">getSPGraph</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">edge_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Transform graph G to its corresponding shortest-paths graph.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    G : NetworkX graph</span>
-<span class="sd">        The graph to be tramsformed.</span>
-<span class="sd">    edge_weight : string</span>
-<span class="sd">        edge attribute corresponding to the edge weight.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    S : NetworkX graph</span>
-<span class="sd">        The shortest-paths graph corresponding to G.</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    ------</span>
-<span class="sd">    For an input graph G, its corresponding shortest-paths graph S contains the same set of nodes as G, while there exists an edge between all nodes in S which are connected by a walk in G. Every edge in S between two nodes is labeled by the shortest distance between these two nodes.</span>
-
-<span class="sd">    References</span>
-<span class="sd">    ----------</span>
-<span class="sd">    [1] Borgwardt KM, Kriegel HP. Shortest-path kernels on graphs. InData Mining, Fifth IEEE International Conference on 2005 Nov 27 (pp. 8-pp). IEEE.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">floydTransformation</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">edge_weight</span><span class="o">=</span><span class="n">edge_weight</span><span class="p">)</span></div>
-
-
-<div class="viewcode-block" id="floydTransformation"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.floydTransformation">[docs]</a><span class="k">def</span> <span class="nf">floydTransformation</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">edge_weight</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Transform graph G to its corresponding shortest-paths graph using Floyd-transformation.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    G : NetworkX graph</span>
-<span class="sd">        The graph to be tramsformed.</span>
-<span class="sd">    edge_weight : string</span>
-<span class="sd">        edge attribute corresponding to the edge weight. The default edge weight is bond_type.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    S : NetworkX graph</span>
-<span class="sd">        The shortest-paths graph corresponding to G.</span>
-
-<span class="sd">    References</span>
-<span class="sd">    ----------</span>
-<span class="sd">    [1] Borgwardt KM, Kriegel HP. Shortest-path kernels on graphs. InData Mining, Fifth IEEE International Conference on 2005 Nov 27 (pp. 8-pp). IEEE.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">spMatrix</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">floyd_warshall_numpy</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="n">edge_weight</span><span class="p">)</span>
-    <span class="n">S</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
-    <span class="n">S</span><span class="o">.</span><span class="n">add_nodes_from</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="n">ns</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">())</span>
-    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">G</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()):</span>
-        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">i</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">G</span><span class="o">.</span><span class="n">number_of_nodes</span><span class="p">()):</span>
-            <span class="k">if</span> <span class="n">spMatrix</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">!=</span> <span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">:</span>
-                <span class="n">S</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">ns</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">ns</span><span class="p">[</span><span class="n">j</span><span class="p">],</span> <span class="n">cost</span><span class="o">=</span><span class="n">spMatrix</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">])</span>
-    <span class="k">return</span> <span class="n">S</span></div>
-
-
-<div class="viewcode-block" id="untotterTransformation"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.untotterTransformation">[docs]</a><span class="k">def</span> <span class="nf">untotterTransformation</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">node_label</span><span class="p">,</span> <span class="n">edge_label</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Transform graph G according to Mahé et al.&#39;s work to filter out tottering patterns of marginalized kernel and tree pattern kernel.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    G : NetworkX graph</span>
-<span class="sd">        The graph to be tramsformed.</span>
-<span class="sd">    node_label : string</span>
-<span class="sd">        node attribute used as label. The default node label is &#39;atom&#39;.</span>
-<span class="sd">    edge_label : string</span>
-<span class="sd">        edge attribute used as label. The default edge label is &#39;bond_type&#39;.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    gt : NetworkX graph</span>
-<span class="sd">        The transformed graph corresponding to G.</span>
-
-<span class="sd">    References</span>
-<span class="sd">    ----------</span>
-<span class="sd">    [1] Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, and Jean-Philippe Vert. Extensions of marginalized graph kernels. In Proceedings of the twenty-first international conference on Machine learning, page 70. ACM, 2004.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># arrange all graphs in a list</span>
-    <span class="n">G</span> <span class="o">=</span> <span class="n">G</span><span class="o">.</span><span class="n">to_directed</span><span class="p">()</span>
-    <span class="n">gt</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>
-    <span class="n">gt</span><span class="o">.</span><span class="n">graph</span> <span class="o">=</span> <span class="n">G</span><span class="o">.</span><span class="n">graph</span>
-    <span class="n">gt</span><span class="o">.</span><span class="n">add_nodes_from</span><span class="p">(</span><span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">))</span>
-    <span class="k">for</span> <span class="n">edge</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">():</span>
-        <span class="n">gt</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">edge</span><span class="p">)</span>
-        <span class="n">gt</span><span class="o">.</span><span class="n">node</span><span class="p">[</span><span class="n">edge</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="n">node_label</span><span class="p">:</span> <span class="n">G</span><span class="o">.</span><span class="n">node</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="n">node_label</span><span class="p">]})</span>
-        <span class="n">gt</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">edge</span><span class="p">)</span>
-        <span class="n">gt</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">edge</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
-            <span class="n">edge_label</span><span class="p">:</span>
-            <span class="n">G</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="n">edge_label</span><span class="p">]</span>
-        <span class="p">})</span>
-        <span class="k">for</span> <span class="n">neighbor</span> <span class="ow">in</span> <span class="n">G</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]]:</span>
-            <span class="k">if</span> <span class="n">neighbor</span> <span class="o">!=</span> <span class="n">edge</span><span class="p">[</span><span class="mi">0</span><span class="p">]:</span>
-                <span class="n">gt</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">edge</span><span class="p">,</span> <span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">neighbor</span><span class="p">))</span>
-                <span class="n">gt</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">edge</span><span class="p">,</span> <span class="p">(</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">neighbor</span><span class="p">)]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
-                    <span class="n">edge_label</span><span class="p">:</span>
-                    <span class="n">G</span><span class="p">[</span><span class="n">edge</span><span class="p">[</span><span class="mi">1</span><span class="p">]][</span><span class="n">neighbor</span><span class="p">][</span><span class="n">edge_label</span><span class="p">]</span>
-                <span class="p">})</span>
-    <span class="c1"># nx.draw_networkx(gt)</span>
-    <span class="c1"># plt.show()</span>
-
-    <span class="c1"># relabel nodes using consecutive integers for convenience of kernel calculation.</span>
-    <span class="n">gt</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">convert_node_labels_to_integers</span><span class="p">(</span>
-        <span class="n">gt</span><span class="p">,</span> <span class="n">first_label</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">label_attribute</span><span class="o">=</span><span class="s1">&#39;label_orignal&#39;</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">gt</span></div>
-
-
-<div class="viewcode-block" id="direct_product"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.direct_product">[docs]</a><span class="k">def</span> <span class="nf">direct_product</span><span class="p">(</span><span class="n">G1</span><span class="p">,</span> <span class="n">G2</span><span class="p">,</span> <span class="n">node_label</span><span class="p">,</span> <span class="n">edge_label</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Return the direct/tensor product of directed graphs G1 and G2.</span>
-
-<span class="sd">    Parameters</span>
-<span class="sd">    ----------</span>
-<span class="sd">    G1, G2 : NetworkX graph</span>
-<span class="sd">        The original graphs.</span>
-<span class="sd">    node_label : string</span>
-<span class="sd">        node attribute used as label. The default node label is &#39;atom&#39;.</span>
-<span class="sd">    edge_label : string</span>
-<span class="sd">        edge attribute used as label. The default edge label is &#39;bond_type&#39;.</span>
-
-<span class="sd">    Return</span>
-<span class="sd">    ------</span>
-<span class="sd">    gt : NetworkX graph</span>
-<span class="sd">        The direct product graph of G1 and G2.</span>
-
-<span class="sd">    Notes</span>
-<span class="sd">    -----</span>
-<span class="sd">    This method differs from networkx.tensor_product in that this method only adds nodes and edges in G1 and G2 that have the same labels to the direct product graph.</span>
-
-<span class="sd">    References</span>
-<span class="sd">    ----------</span>
-<span class="sd">    [1] Thomas Gärtner, Peter Flach, and Stefan Wrobel. On graph kernels: Hardness results and efficient alternatives. Learning Theory and Kernel Machines, pages 129–143, 2003.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># arrange all graphs in a list</span>
-    <span class="kn">from</span> <span class="nn">itertools</span> <span class="k">import</span> <span class="n">product</span>
-    <span class="c1"># G = G.to_directed()</span>
-    <span class="n">gt</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">DiGraph</span><span class="p">()</span>
-    <span class="c1"># add nodes</span>
-    <span class="k">for</span> <span class="n">u</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="n">G1</span><span class="p">,</span> <span class="n">G2</span><span class="p">):</span>
-        <span class="k">if</span> <span class="n">G1</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">u</span><span class="p">][</span><span class="n">node_label</span><span class="p">]</span> <span class="o">==</span> <span class="n">G2</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">v</span><span class="p">][</span><span class="n">node_label</span><span class="p">]:</span>
-            <span class="n">gt</span><span class="o">.</span><span class="n">add_node</span><span class="p">((</span><span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">))</span>
-            <span class="n">gt</span><span class="o">.</span><span class="n">nodes</span><span class="p">[(</span><span class="n">u</span><span class="p">,</span> <span class="n">v</span><span class="p">)]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="n">node_label</span><span class="p">:</span> <span class="n">G1</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">u</span><span class="p">][</span><span class="n">node_label</span><span class="p">]})</span>
-    <span class="c1"># add edges, faster for sparse graphs (no so many edges), which is the most case for now.</span>
-    <span class="k">for</span> <span class="p">(</span><span class="n">u1</span><span class="p">,</span> <span class="n">v1</span><span class="p">),</span> <span class="p">(</span><span class="n">u2</span><span class="p">,</span> <span class="n">v2</span><span class="p">)</span> <span class="ow">in</span> <span class="n">product</span><span class="p">(</span><span class="n">G1</span><span class="o">.</span><span class="n">edges</span><span class="p">,</span> <span class="n">G2</span><span class="o">.</span><span class="n">edges</span><span class="p">):</span>
-        <span class="k">if</span> <span class="p">(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">)</span> <span class="ow">in</span> <span class="n">gt</span> <span class="ow">and</span> <span class="p">(</span>
-                <span class="n">v1</span><span class="p">,</span> <span class="n">v2</span>
-        <span class="p">)</span> <span class="ow">in</span> <span class="n">gt</span> <span class="ow">and</span> <span class="n">G1</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">u1</span><span class="p">,</span> <span class="n">v1</span><span class="p">][</span><span class="n">edge_label</span><span class="p">]</span> <span class="o">==</span> <span class="n">G2</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">u2</span><span class="p">,</span>
-                                                             <span class="n">v2</span><span class="p">][</span><span class="n">edge_label</span><span class="p">]:</span>
-            <span class="n">gt</span><span class="o">.</span><span class="n">add_edge</span><span class="p">((</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">),</span> <span class="p">(</span><span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">))</span>
-            <span class="n">gt</span><span class="o">.</span><span class="n">edges</span><span class="p">[(</span><span class="n">u1</span><span class="p">,</span> <span class="n">u2</span><span class="p">),</span> <span class="p">(</span><span class="n">v1</span><span class="p">,</span> <span class="n">v2</span><span class="p">)]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
-                <span class="n">edge_label</span><span class="p">:</span>
-                <span class="n">G1</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">u1</span><span class="p">,</span> <span class="n">v1</span><span class="p">][</span><span class="n">edge_label</span><span class="p">]</span>
-            <span class="p">})</span>
-
-    <span class="c1"># # add edges, faster for dense graphs (a lot of edges, complete graph would be super).</span>
-    <span class="c1"># for u, v in product(gt, gt):</span>
-    <span class="c1">#     if (u[0], v[0]) in G1.edges and (</span>
-    <span class="c1">#             u[1], v[1]</span>
-    <span class="c1">#     ) in G2.edges and G1.edges[u[0],</span>
-    <span class="c1">#                                v[0]][edge_label] == G2.edges[u[1],</span>
-    <span class="c1">#                                                              v[1]][edge_label]:</span>
-    <span class="c1">#         gt.add_edge((u[0], u[1]), (v[0], v[1]))</span>
-    <span class="c1">#         gt.edges[(u[0], u[1]), (v[0], v[1])].update({</span>
-    <span class="c1">#             edge_label:</span>
-    <span class="c1">#             G1.edges[u[0], v[0]][edge_label]</span>
-    <span class="c1">#         })</span>
-
-    <span class="c1"># relabel nodes using consecutive integers for convenience of kernel calculation.</span>
-    <span class="c1"># gt = nx.convert_node_labels_to_integers(</span>
-    <span class="c1">#     gt, first_label=0, label_attribute=&#39;label_orignal&#39;)</span>
-    <span class="k">return</span> <span class="n">gt</span></div>
-
-
-<div class="viewcode-block" id="graph_deepcopy"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.graph_deepcopy">[docs]</a><span class="k">def</span> <span class="nf">graph_deepcopy</span><span class="p">(</span><span class="n">G</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Deep copy a graph, including deep copy of all nodes, edges and </span>
-<span class="sd">    attributes of the graph, nodes and edges.</span>
-<span class="sd">    </span>
-<span class="sd">    Note</span>
-<span class="sd">    ----</span>
-<span class="sd">    It is the same as the NetworkX function graph.copy(), as far as I know.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># add graph attributes.</span>
-    <span class="n">labels</span> <span class="o">=</span> <span class="p">{}</span>
-    <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-        <span class="n">labels</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">G</span><span class="o">.</span><span class="n">is_directed</span><span class="p">():</span>
-        <span class="n">G_copy</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">DiGraph</span><span class="p">(</span><span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-    <span class="k">else</span><span class="p">:</span>
-        <span class="n">G_copy</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">(</span><span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-        
-    <span class="c1"># add nodes    </span>
-    <span class="k">for</span> <span class="n">nd</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-        <span class="n">labels</span> <span class="o">=</span> <span class="p">{}</span>
-        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">attrs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-            <span class="n">labels</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
-        <span class="n">G_copy</span><span class="o">.</span><span class="n">add_node</span><span class="p">(</span><span class="n">nd</span><span class="p">,</span> <span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-        
-    <span class="c1"># add edges.</span>
-    <span class="k">for</span> <span class="n">nd1</span><span class="p">,</span> <span class="n">nd2</span><span class="p">,</span> <span class="n">attrs</span> <span class="ow">in</span> <span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
-        <span class="n">labels</span> <span class="o">=</span> <span class="p">{}</span>
-        <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">attrs</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
-            <span class="n">labels</span><span class="p">[</span><span class="n">k</span><span class="p">]</span> <span class="o">=</span> <span class="n">deepcopy</span><span class="p">(</span><span class="n">v</span><span class="p">)</span>
-        <span class="n">G_copy</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="n">nd1</span><span class="p">,</span> <span class="n">nd2</span><span class="p">,</span> <span class="o">**</span><span class="n">labels</span><span class="p">)</span>
-    
-    <span class="k">return</span> <span class="n">G_copy</span></div>
-
-
-<div class="viewcode-block" id="graph_isIdentical"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.graph_isIdentical">[docs]</a><span class="k">def</span> <span class="nf">graph_isIdentical</span><span class="p">(</span><span class="n">G1</span><span class="p">,</span> <span class="n">G2</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Check if two graphs are identical, including: same nodes, edges, node</span>
-<span class="sd">    labels/attributes, edge labels/attributes.</span>
-<span class="sd">    </span>
-<span class="sd">    Notes</span>
-<span class="sd">    ----</span>
-<span class="sd">    1. The type of graphs has to be the same.</span>
-<span class="sd">    2. Global/Graph attributes are neglected as they may contain names for graphs.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># check nodes.</span>
-    <span class="n">nlist1</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G1</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
-    <span class="n">nlist2</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G2</span><span class="o">.</span><span class="n">nodes</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">nlist1</span> <span class="o">==</span> <span class="n">nlist2</span><span class="p">:</span>
-        <span class="k">return</span> <span class="kc">False</span>
-    <span class="c1"># check edges.</span>
-    <span class="n">elist1</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G1</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
-    <span class="n">elist2</span> <span class="o">=</span> <span class="p">[</span><span class="n">n</span> <span class="k">for</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">G2</span><span class="o">.</span><span class="n">edges</span><span class="p">(</span><span class="n">data</span><span class="o">=</span><span class="kc">True</span><span class="p">)]</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">elist1</span> <span class="o">==</span> <span class="n">elist2</span><span class="p">:</span>
-        <span class="k">return</span> <span class="kc">False</span>
-    <span class="c1"># check graph attributes.</span>
-    
-    <span class="k">return</span> <span class="kc">True</span></div>
-
-
-<div class="viewcode-block" id="get_node_labels"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.get_node_labels">[docs]</a><span class="k">def</span> <span class="nf">get_node_labels</span><span class="p">(</span><span class="n">Gn</span><span class="p">,</span> <span class="n">node_label</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Get node labels of dataset Gn.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">nl</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-    <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-        <span class="n">nl</span> <span class="o">=</span> <span class="n">nl</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">get_node_attributes</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">node_label</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
-    <span class="k">return</span> <span class="n">nl</span></div>
-
-
-<div class="viewcode-block" id="get_edge_labels"><a class="viewcode-back" href="../../../pygraph.utils.html#pygraph.utils.utils.get_edge_labels">[docs]</a><span class="k">def</span> <span class="nf">get_edge_labels</span><span class="p">(</span><span class="n">Gn</span><span class="p">,</span> <span class="n">edge_label</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;Get edge labels of dataset Gn.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">el</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-    <span class="k">for</span> <span class="n">G</span> <span class="ow">in</span> <span class="n">Gn</span><span class="p">:</span>
-        <span class="n">el</span> <span class="o">=</span> <span class="n">el</span> <span class="o">|</span> <span class="nb">set</span><span class="p">(</span><span class="n">nx</span><span class="o">.</span><span class="n">get_edge_attributes</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">edge_label</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">())</span>
-    <span class="k">return</span> <span class="n">el</span></div>
-</pre></div>
-
-           </div>
-           
-          </div>
-          <footer>
-  
-
-  <hr/>
-
-  <div role="contentinfo">
-    <p>
-        &copy; Copyright 2020, Linlin Jia
-
-    </p>
-  </div>
-  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 
-
-</footer>
-
-        </div>
-      </div>
-
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-
-  </div>
-  
-
-
-  <script type="text/javascript">
-      jQuery(function () {
-          SphinxRtdTheme.Navigation.enable(true);
-      });
-  </script>
-
-  
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-</body>
-</html>

docs/_build/html/_sources/index.rst.txt

@@ -1,20 +0,0 @@
-.. py-graph documentation master file, created by
-   sphinx-quickstart on Tue Jan 28 17:13:42 2020.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to py-graph's documentation!
-====================================
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

docs/_build/html/_sources/modules.rst.txt

@@ -1,7 +0,0 @@
-py-graph
-========
-
-.. toctree::
-   :maxdepth: 4
-
-   pygraph

docs/_build/html/_sources/pygraph.rst.txt

@@ -1,17 +0,0 @@
-pygraph package
-===============
-
-Subpackages
------------
-
-.. toctree::
-
-    pygraph.utils
-
-Module contents
----------------
-
-.. automodule:: pygraph
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/_build/html/_sources/pygraph.utils.rst.txt

@@ -1,94 +0,0 @@
-pygraph.utils package
-=====================
-
-Submodules
-----------
-
-pygraph.utils.graphdataset module
----------------------------------
-
-.. automodule:: pygraph.utils.graphdataset
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.graphfiles module
--------------------------------
-
-.. automodule:: pygraph.utils.graphfiles
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.ipython\_log module
----------------------------------
-
-.. automodule:: pygraph.utils.ipython_log
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.isNotebook module
--------------------------------
-
-.. automodule:: pygraph.utils.isNotebook
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.kernels module
-----------------------------
-
-.. automodule:: pygraph.utils.kernels
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.logger2file module
---------------------------------
-
-.. automodule:: pygraph.utils.logger2file
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.model\_selection\_precomputed module
---------------------------------------------------
-
-.. automodule:: pygraph.utils.model_selection_precomputed
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.parallel module
------------------------------
-
-.. automodule:: pygraph.utils.parallel
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.trie module
--------------------------
-
-.. automodule:: pygraph.utils.trie
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-pygraph.utils.utils module
---------------------------
-
-.. automodule:: pygraph.utils.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: pygraph.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:

docs/_build/html/_static/alabaster.css

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-        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
-        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
-          node.nextSibling));
-        node.nodeValue = val.substr(0, pos);
-        if (isInSVG) {
-          var bbox = span.getBBox();
-          var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
-       	  rect.x.baseVal.value = bbox.x;
-          rect.y.baseVal.value = bbox.y;
-          rect.width.baseVal.value = bbox.width;
-          rect.height.baseVal.value = bbox.height;
-          rect.setAttribute('class', className);
-          var parentOfText = node.parentNode.parentNode;
-          addItems.push({
-              "parent": node.parentNode,
-              "target": rect});
-        }
-      }
-    }
-    else if (!jQuery(node).is("button, select, textarea")) {
-      jQuery.each(node.childNodes, function() {
-        highlight(this, addItems);
-      });
-    }
-  }
-  var addItems = [];
-  var result = this.each(function() {
-    highlight(this, addItems);
-  });
-  for (var i = 0; i < addItems.length; ++i) {
-    jQuery(addItems[i].parent).before(addItems[i].target);
-  }
-  return result;
-};
-
-/*
- * backward compatibility for jQuery.browser
- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
-  jQuery.uaMatch = function(ua) {
-    ua = ua.toLowerCase();
-
-    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
-      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
-      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
-      /(msie) ([\w.]+)/.exec(ua) ||
-      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
-      [];
-
-    return {
-      browser: match[ 1 ] || "",
-      version: match[ 2 ] || "0"
-    };
-  };
-  jQuery.browser = {};
-  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
-}
-
-/**
- * Small JavaScript module for the documentation.
- */
-var Documentation = {
-
-  init : function() {
-    this.fixFirefoxAnchorBug();
-    this.highlightSearchWords();
-    this.initIndexTable();
-    if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) {
-      this.initOnKeyListeners();
-    }
-  },
-
-  /**
-   * i18n support
-   */
-  TRANSLATIONS : {},
-  PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
-  LOCALE : 'unknown',
-
-  // gettext and ngettext don't access this so that the functions
-  // can safely bound to a different name (_ = Documentation.gettext)
-  gettext : function(string) {
-    var translated = Documentation.TRANSLATIONS[string];
-    if (typeof translated === 'undefined')
-      return string;
-    return (typeof translated === 'string') ? translated : translated[0];
-  },
-
-  ngettext : function(singular, plural, n) {
-    var translated = Documentation.TRANSLATIONS[singular];
-    if (typeof translated === 'undefined')
-      return (n == 1) ? singular : plural;
-    return translated[Documentation.PLURALEXPR(n)];
-  },
-
-  addTranslations : function(catalog) {
-    for (var key in catalog.messages)
-      this.TRANSLATIONS[key] = catalog.messages[key];
-    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
-    this.LOCALE = catalog.locale;
-  },
-
-  /**
-   * add context elements like header anchor links
-   */
-  addContextElements : function() {
-    $('div[id] > :header:first').each(function() {
-      $('<a class="headerlink">\u00B6</a>').
-      attr('href', '#' + this.id).
-      attr('title', _('Permalink to this headline')).
-      appendTo(this);
-    });
-    $('dt[id]').each(function() {
-      $('<a class="headerlink">\u00B6</a>').
-      attr('href', '#' + this.id).
-      attr('title', _('Permalink to this definition')).
-      appendTo(this);
-    });
-  },
-
-  /**
-   * workaround a firefox stupidity
-   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
-   */
-  fixFirefoxAnchorBug : function() {
-    if (document.location.hash && $.browser.mozilla)
-      window.setTimeout(function() {
-        document.location.href += '';
-      }, 10);
-  },
-
-  /**
-   * highlight the search words provided in the url in the text
-   */
-  highlightSearchWords : function() {
-    var params = $.getQueryParameters();
-    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
-    if (terms.length) {
-      var body = $('div.body');
-      if (!body.length) {
-        body = $('body');
-      }
-      window.setTimeout(function() {
-        $.each(terms, function() {
-          body.highlightText(this.toLowerCase(), 'highlighted');
-        });
-      }, 10);
-      $('<p class="highlight-link"><a href="javascript:Documentation.' +
-        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
-          .appendTo($('#searchbox'));
-    }
-  },
-
-  /**
-   * init the domain index toggle buttons
-   */
-  initIndexTable : function() {
-    var togglers = $('img.toggler').click(function() {
-      var src = $(this).attr('src');
-      var idnum = $(this).attr('id').substr(7);
-      $('tr.cg-' + idnum).toggle();
-      if (src.substr(-9) === 'minus.png')
-        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
-      else
-        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
-    }).css('display', '');
-    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
-        togglers.click();
-    }
-  },
-
-  /**
-   * helper function to hide the search marks again
-   */
-  hideSearchWords : function() {
-    $('#searchbox .highlight-link').fadeOut(300);
-    $('span.highlighted').removeClass('highlighted');
-  },
-
-  /**
-   * make the url absolute
-   */
-  makeURL : function(relativeURL) {
-    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
-  },
-
-  /**
-   * get the current relative url
-   */
-  getCurrentURL : function() {
-    var path = document.location.pathname;
-    var parts = path.split(/\//);
-    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
-      if (this === '..')
-        parts.pop();
-    });
-    var url = parts.join('/');
-    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
-  },
-
-  initOnKeyListeners: function() {
-    $(document).keyup(function(event) {
-      var activeElementType = document.activeElement.tagName;
-      // don't navigate when in search box or textarea
-      if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
-        switch (event.keyCode) {
-          case 37: // left
-            var prevHref = $('link[rel="prev"]').prop('href');
-            if (prevHref) {
-              window.location.href = prevHref;
-              return false;
-            }
-          case 39: // right
-            var nextHref = $('link[rel="next"]').prop('href');
-            if (nextHref) {
-              window.location.href = nextHref;
-              return false;
-            }
-        }
-      }
-    });
-  }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
-  Documentation.init();
-});

docs/_build/html/_static/documentation_options.js

@@ -1,296 +0,0 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '',
-    LANGUAGE: 'None',
-    COLLAPSE_INDEX: false,
-    FILE_SUFFIX: '.html',
-    HAS_SOURCE: true,
-    SOURCELINK_SUFFIX: '.txt',
-    NAVIGATION_WITH_KEYS: false,
-    SEARCH_LANGUAGE_STOP_WORDS: ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]
-};
-
-
-
-/* Non-minified version JS is _stemmer.js if file is provided */ 
-/**
- * Porter Stemmer
- */
-var Stemmer = function() {
-
-  var step2list = {
-    ational: 'ate',
-    tional: 'tion',
-    enci: 'ence',
-    anci: 'ance',
-    izer: 'ize',
-    bli: 'ble',
-    alli: 'al',
-    entli: 'ent',
-    eli: 'e',
-    ousli: 'ous',
-    ization: 'ize',
-    ation: 'ate',
-    ator: 'ate',
-    alism: 'al',
-    iveness: 'ive',
-    fulness: 'ful',
-    ousness: 'ous',
-    aliti: 'al',
-    iviti: 'ive',
-    biliti: 'ble',
-    logi: 'log'
-  };
-
-  var step3list = {
-    icate: 'ic',
-    ative: '',
-    alize: 'al',
-    iciti: 'ic',
-    ical: 'ic',
-    ful: '',
-    ness: ''
-  };
-
-  var c = "[^aeiou]";          // consonant
-  var v = "[aeiouy]";          // vowel
-  var C = c + "[^aeiouy]*";    // consonant sequence
-  var V = v + "[aeiou]*";      // vowel sequence
-
-  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
-  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
-  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
-  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
-
-  this.stemWord = function (w) {
-    var stem;
-    var suffix;
-    var firstch;
-    var origword = w;
-
-    if (w.length < 3)
-      return w;
-
-    var re;
-    var re2;
-    var re3;
-    var re4;
-
-    firstch = w.substr(0,1);
-    if (firstch == "y")
-      w = firstch.toUpperCase() + w.substr(1);
-
-    // Step 1a
-    re = /^(.+?)(ss|i)es$/;
-    re2 = /^(.+?)([^s])s$/;
-
-    if (re.test(w))
-      w = w.replace(re,"$1$2");
-    else if (re2.test(w))
-      w = w.replace(re2,"$1$2");
-
-    // Step 1b
-    re = /^(.+?)eed$/;
-    re2 = /^(.+?)(ed|ing)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      re = new RegExp(mgr0);
-      if (re.test(fp[1])) {
-        re = /.$/;
-        w = w.replace(re,"");
-      }
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1];
-      re2 = new RegExp(s_v);
-      if (re2.test(stem)) {
-        w = stem;
-        re2 = /(at|bl|iz)$/;
-        re3 = new RegExp("([^aeiouylsz])\\1$");
-        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-        if (re2.test(w))
-          w = w + "e";
-        else if (re3.test(w)) {
-          re = /.$/;
-          w = w.replace(re,"");
-        }
-        else if (re4.test(w))
-          w = w + "e";
-      }
-    }
-
-    // Step 1c
-    re = /^(.+?)y$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(s_v);
-      if (re.test(stem))
-        w = stem + "i";
-    }
-
-    // Step 2
-    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step2list[suffix];
-    }
-
-    // Step 3
-    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      suffix = fp[2];
-      re = new RegExp(mgr0);
-      if (re.test(stem))
-        w = stem + step3list[suffix];
-    }
-
-    // Step 4
-    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
-    re2 = /^(.+?)(s|t)(ion)$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      if (re.test(stem))
-        w = stem;
-    }
-    else if (re2.test(w)) {
-      var fp = re2.exec(w);
-      stem = fp[1] + fp[2];
-      re2 = new RegExp(mgr1);
-      if (re2.test(stem))
-        w = stem;
-    }
-
-    // Step 5
-    re = /^(.+?)e$/;
-    if (re.test(w)) {
-      var fp = re.exec(w);
-      stem = fp[1];
-      re = new RegExp(mgr1);
-      re2 = new RegExp(meq1);
-      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
-      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
-        w = stem;
-    }
-    re = /ll$/;
-    re2 = new RegExp(mgr1);
-    if (re.test(w) && re2.test(w)) {
-      re = /.$/;
-      w = w.replace(re,"");
-    }
-
-    // and turn initial Y back to y
-    if (firstch == "y")
-      w = firstch.toLowerCase() + w.substr(1);
-    return w;
-  }
-}
-
-
-
-
-
-var splitChars = (function() {
-    var result = {};
-    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
-         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
-         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
-         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
-         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
-         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
-         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
-         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
-         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
-         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
-    var i, j, start, end;
-    for (i = 0; i < singles.length; i++) {
-        result[singles[i]] = true;
-    }
-    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
-         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
-         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
-         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
-         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
-         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
-         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
-         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
-         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
-         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
-         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
-         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
-         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
-         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
-         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
-         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
-         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
-         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
-         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
-         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
-         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
-         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
-         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
-         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
-         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
-         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
-         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
-         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
-         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
-         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
-         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
-         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
-         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
-         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
-         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
-         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
-         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
-         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
-         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
-         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
-         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
-         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
-         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
-         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
-         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
-         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
-         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
-         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
-         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
-    for (i = 0; i < ranges.length; i++) {
-        start = ranges[i][0];
-        end = ranges[i][1];
-        for (j = start; j <= end; j++) {
-            result[j] = true;
-        }
-    }
-    return result;
-})();
-
-function splitQuery(query) {
-    var result = [];
-    var start = -1;
-    for (var i = 0; i < query.length; i++) {
-        if (splitChars[query.charCodeAt(i)]) {
-            if (start !== -1) {
-                result.push(query.slice(start, i));
-                start = -1;
-            }
-        } else if (start === -1) {
-            start = i;
-        }
-    }
-    if (start !== -1) {
-        result.push(query.slice(start));
-    }
-    return result;
-}
-
-

docs/_build/html/_static/js/theme.js

@@ -1,3 +0,0 @@
-/* sphinx_rtd_theme version 0.4.3 | MIT license */
-/* Built 20190212 16:02 */
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docs/_build/html/_static/searchtools.js

@@ -1,482 +0,0 @@
-/*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
- * Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-if (!Scorer) {
-  /**
-   * Simple result scoring code.
-   */
-  var Scorer = {
-    // Implement the following function to further tweak the score for each result
-    // The function takes a result array [filename, title, anchor, descr, score]
-    // and returns the new score.
-    /*
-    score: function(result) {
-      return result[4];
-    },
-    */
-
-    // query matches the full name of an object
-    objNameMatch: 11,
-    // or matches in the last dotted part of the object name
-    objPartialMatch: 6,
-    // Additive scores depending on the priority of the object
-    objPrio: {0:  15,   // used to be importantResults
-              1:  5,   // used to be objectResults
-              2: -5},  // used to be unimportantResults
-    //  Used when the priority is not in the mapping.
-    objPrioDefault: 0,
-
-    // query found in title
-    title: 15,
-    // query found in terms
-    term: 5
-  };
-}
-
-if (!splitQuery) {
-  function splitQuery(query) {
-    return query.split(/\s+/);
-  }
-}
-
-/**
- * Search Module
- */
-var Search = {
-
-  _index : null,
-  _queued_query : null,
-  _pulse_status : -1,
-
-  init : function() {
-      var params = $.getQueryParameters();
-      if (params.q) {
-          var query = params.q[0];
-          $('input[name="q"]')[0].value = query;
-          this.performSearch(query);
-      }
-  },
-
-  loadIndex : function(url) {
-    $.ajax({type: "GET", url: url, data: null,
-            dataType: "script", cache: true,
-            complete: function(jqxhr, textstatus) {
-              if (textstatus != "success") {
-                document.getElementById("searchindexloader").src = url;
-              }
-            }});
-  },
-
-  setIndex : function(index) {
-    var q;
-    this._index = index;
-    if ((q = this._queued_query) !== null) {
-      this._queued_query = null;
-      Search.query(q);
-    }
-  },
-
-  hasIndex : function() {
-      return this._index !== null;
-  },
-
-  deferQuery : function(query) {
-      this._queued_query = query;
-  },
-
-  stopPulse : function() {
-      this._pulse_status = 0;
-  },
-
-  startPulse : function() {
-    if (this._pulse_status >= 0)
-        return;
-    function pulse() {
-      var i;
-      Search._pulse_status = (Search._pulse_status + 1) % 4;
-      var dotString = '';
-      for (i = 0; i < Search._pulse_status; i++)
-        dotString += '.';
-      Search.dots.text(dotString);
-      if (Search._pulse_status > -1)
-        window.setTimeout(pulse, 500);
-    }
-    pulse();
-  },
-
-  /**
-   * perform a search for something (or wait until index is loaded)
-   */
-  performSearch : function(query) {
-    // create the required interface elements
-    this.out = $('#search-results');
-    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
-    this.dots = $('<span></span>').appendTo(this.title);
-    this.status = $('<p style="display: none"></p>').appendTo(this.out);
-    this.output = $('<ul class="search"/>').appendTo(this.out);
-
-    $('#search-progress').text(_('Preparing search...'));
-    this.startPulse();
-
-    // index already loaded, the browser was quick!
-    if (this.hasIndex())
-      this.query(query);
-    else
-      this.deferQuery(query);
-  },
-
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  query : function(query) {
-    var i;
-    var stopwords = DOCUMENTATION_OPTIONS.SEARCH_LANGUAGE_STOP_WORDS;
-
-    // stem the searchterms and add them to the correct list
-    var stemmer = new Stemmer();
-    var searchterms = [];
-    var excluded = [];
-    var hlterms = [];
-    var tmp = splitQuery(query);
-    var objectterms = [];
-    for (i = 0; i < tmp.length; i++) {
-      if (tmp[i] !== "") {
-          objectterms.push(tmp[i].toLowerCase());
-      }
-
-      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] === "") {
-        // skip this "word"
-        continue;
-      }
-      // stem the word
-      var word = stemmer.stemWord(tmp[i].toLowerCase());
-      // prevent stemmer from cutting word smaller than two chars
-      if(word.length < 3 && tmp[i].length >= 3) {
-        word = tmp[i];
-      }
-      var toAppend;
-      // select the correct list
-      if (word[0] == '-') {
-        toAppend = excluded;
-        word = word.substr(1);
-      }
-      else {
-        toAppend = searchterms;
-        hlterms.push(tmp[i].toLowerCase());
-      }
-      // only add if not already in the list
-      if (!$u.contains(toAppend, word))
-        toAppend.push(word);
-    }
-    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
-
-    // console.debug('SEARCH: searching for:');
-    // console.info('required: ', searchterms);
-    // console.info('excluded: ', excluded);
-
-    // prepare search
-    var terms = this._index.terms;
-    var titleterms = this._index.titleterms;
-
-    // array of [filename, title, anchor, descr, score]
-    var results = [];
-    $('#search-progress').empty();
-
-    // lookup as object
-    for (i = 0; i < objectterms.length; i++) {
-      var others = [].concat(objectterms.slice(0, i),
-                             objectterms.slice(i+1, objectterms.length));
-      results = results.concat(this.performObjectSearch(objectterms[i], others));
-    }
-
-    // lookup as search terms in fulltext
-    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
-
-    // let the scorer override scores with a custom scoring function
-    if (Scorer.score) {
-      for (i = 0; i < results.length; i++)
-        results[i][4] = Scorer.score(results[i]);
-    }
-
-    // now sort the results by score (in opposite order of appearance, since the
-    // display function below uses pop() to retrieve items) and then
-    // alphabetically
-    results.sort(function(a, b) {
-      var left = a[4];
-      var right = b[4];
-      if (left > right) {
-        return 1;
-      } else if (left < right) {
-        return -1;
-      } else {
-        // same score: sort alphabetically
-        left = a[1].toLowerCase();
-        right = b[1].toLowerCase();
-        return (left > right) ? -1 : ((left < right) ? 1 : 0);
-      }
-    });
-
-    // for debugging
-    //Search.lastresults = results.slice();  // a copy
-    //console.info('search results:', Search.lastresults);
-
-    // print the results
-    var resultCount = results.length;
-    function displayNextItem() {
-      // results left, load the summary and display it
-      if (results.length) {
-        var item = results.pop();
-        var listItem = $('<li style="display:none"></li>');
-        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
-          // dirhtml builder
-          var dirname = item[0] + '/';
-          if (dirname.match(/\/index\/$/)) {
-            dirname = dirname.substring(0, dirname.length-6);
-          } else if (dirname == 'index/') {
-            dirname = '';
-          }
-          listItem.append($('<a/>').attr('href',
-            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
-            highlightstring + item[2]).html(item[1]));
-        } else {
-          // normal html builders
-          listItem.append($('<a/>').attr('href',
-            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
-            highlightstring + item[2]).html(item[1]));
-        }
-        if (item[3]) {
-          listItem.append($('<span> (' + item[3] + ')</span>'));
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
-          if (suffix === undefined) {
-            suffix = '.txt';
-          }
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
-                  dataType: "text",
-                  complete: function(jqxhr, textstatus) {
-                    var data = jqxhr.responseText;
-                    if (data !== '' && data !== undefined) {
-                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
-                    }
-                    Search.output.append(listItem);
-                    listItem.slideDown(5, function() {
-                      displayNextItem();
-                    });
-                  }});
-        } else {
-          // no source available, just display title
-          Search.output.append(listItem);
-          listItem.slideDown(5, function() {
-            displayNextItem();
-          });
-        }
-      }
-      // search finished, update title and status message
-      else {
-        Search.stopPulse();
-        Search.title.text(_('Search Results'));
-        if (!resultCount)
-          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
-        else
-            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
-        Search.status.fadeIn(500);
-      }
-    }
-    displayNextItem();
-  },
-
-  /**
-   * search for object names
-   */
-  performObjectSearch : function(object, otherterms) {
-    var filenames = this._index.filenames;
-    var docnames = this._index.docnames;
-    var objects = this._index.objects;
-    var objnames = this._index.objnames;
-    var titles = this._index.titles;
-
-    var i;
-    var results = [];
-
-    for (var prefix in objects) {
-      for (var name in objects[prefix]) {
-        var fullname = (prefix ? prefix + '.' : '') + name;
-        if (fullname.toLowerCase().indexOf(object) > -1) {
-          var score = 0;
-          var parts = fullname.split('.');
-          // check for different match types: exact matches of full name or
-          // "last name" (i.e. last dotted part)
-          if (fullname == object || parts[parts.length - 1] == object) {
-            score += Scorer.objNameMatch;
-          // matches in last name
-          } else if (parts[parts.length - 1].indexOf(object) > -1) {
-            score += Scorer.objPartialMatch;
-          }
-          var match = objects[prefix][name];
-          var objname = objnames[match[1]][2];
-          var title = titles[match[0]];
-          // If more than one term searched for, we require other words to be
-          // found in the name/title/description
-          if (otherterms.length > 0) {
-            var haystack = (prefix + ' ' + name + ' ' +
-                            objname + ' ' + title).toLowerCase();
-            var allfound = true;
-            for (i = 0; i < otherterms.length; i++) {
-              if (haystack.indexOf(otherterms[i]) == -1) {
-                allfound = false;
-                break;
-              }
-            }
-            if (!allfound) {
-              continue;
-            }
-          }
-          var descr = objname + _(', in ') + title;
-
-          var anchor = match[3];
-          if (anchor === '')
-            anchor = fullname;
-          else if (anchor == '-')
-            anchor = objnames[match[1]][1] + '-' + fullname;
-          // add custom score for some objects according to scorer
-          if (Scorer.objPrio.hasOwnProperty(match[2])) {
-            score += Scorer.objPrio[match[2]];
-          } else {
-            score += Scorer.objPrioDefault;
-          }
-          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
-        }
-      }
-    }
-
-    return results;
-  },
-
-  /**
-   * search for full-text terms in the index
-   */
-  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
-    var docnames = this._index.docnames;
-    var filenames = this._index.filenames;
-    var titles = this._index.titles;
-
-    var i, j, file;
-    var fileMap = {};
-    var scoreMap = {};
-    var results = [];
-
-    // perform the search on the required terms
-    for (i = 0; i < searchterms.length; i++) {
-      var word = searchterms[i];
-      var files = [];
-      var _o = [
-        {files: terms[word], score: Scorer.term},
-        {files: titleterms[word], score: Scorer.title}
-      ];
-
-      // no match but word was a required one
-      if ($u.every(_o, function(o){return o.files === undefined;})) {
-        break;
-      }
-      // found search word in contents
-      $u.each(_o, function(o) {
-        var _files = o.files;
-        if (_files === undefined)
-          return
-
-        if (_files.length === undefined)
-          _files = [_files];
-        files = files.concat(_files);
-
-        // set score for the word in each file to Scorer.term
-        for (j = 0; j < _files.length; j++) {
-          file = _files[j];
-          if (!(file in scoreMap))
-            scoreMap[file] = {}
-          scoreMap[file][word] = o.score;
-        }
-      });
-
-      // create the mapping
-      for (j = 0; j < files.length; j++) {
-        file = files[j];
-        if (file in fileMap)
-          fileMap[file].push(word);
-        else
-          fileMap[file] = [word];
-      }
-    }
-
-    // now check if the files don't contain excluded terms
-    for (file in fileMap) {
-      var valid = true;
-
-      // check if all requirements are matched
-      if (fileMap[file].length != searchterms.length)
-          continue;
-
-      // ensure that none of the excluded terms is in the search result
-      for (i = 0; i < excluded.length; i++) {
-        if (terms[excluded[i]] == file ||
-            titleterms[excluded[i]] == file ||
-            $u.contains(terms[excluded[i]] || [], file) ||
-            $u.contains(titleterms[excluded[i]] || [], file)) {
-          valid = false;
-          break;
-        }
-      }
-
-      // if we have still a valid result we can add it to the result list
-      if (valid) {
-        // select one (max) score for the file.
-        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
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docs/_build/html/_static/underscore.js

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docs/_build/html/_static/websupport.js

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-       $('#cf' + id)
-         .find('textarea[name="proposal"]')
-         .data('source', data.source);
-
-       if (data.comments.length === 0) {
-         ul.html('<li>No comments yet.</li>');
-         ul.data('empty', true);
-       } else {
-         // If there are comments, sort them and put them in the list.
-         var comments = sortComments(data.comments);
-         speed = data.comments.length * 100;
-         appendComments(comments, ul);
-         ul.data('empty', false);
-       }
-       $('#cn' + id).slideUp(speed + 200);
-       ul.slideDown(speed);
-     },
-     error: function(request, textStatus, error) {
-       showError('Oops, there was a problem retrieving the comments.');
-     },
-     dataType: 'json'
-    });
-  }
-
-  /**
-   * Add a comment via ajax and insert the comment into the comment tree.
-   */
-  function addComment(form) {
-    var node_id = form.find('input[name="node"]').val();
-    var parent_id = form.find('input[name="parent"]').val();
-    var text = form.find('textarea[name="comment"]').val();
-    var proposal = form.find('textarea[name="proposal"]').val();
-
-    if (text == '') {
-      showError('Please enter a comment.');
-      return;
-    }
-
-    // Disable the form that is being submitted.
-    form.find('textarea,input').attr('disabled', 'disabled');
-
-    // Send the comment to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.addCommentURL,
-      dataType: 'json',
-      data: {
-        node: node_id,
-        parent: parent_id,
-        text: text,
-        proposal: proposal
-      },
-      success: function(data, textStatus, error) {
-        // Reset the form.
-        if (node_id) {
-          hideProposeChange(node_id);
-        }
-        form.find('textarea')
-          .val('')
-          .add(form.find('input'))
-          .removeAttr('disabled');
-	var ul = $('#cl' + (node_id || parent_id));
-        if (ul.data('empty')) {
-          $(ul).empty();
-          ul.data('empty', false);
-        }
-        insertComment(data.comment);
-        var ao = $('#ao' + node_id);
-        ao.find('img').attr({'src': opts.commentBrightImage});
-        if (node_id) {
-          // if this was a "root" comment, remove the commenting box
-          // (the user can get it back by reopening the comment popup)
-          $('#ca' + node_id).slideUp();
-        }
-      },
-      error: function(request, textStatus, error) {
-        form.find('textarea,input').removeAttr('disabled');
-        showError('Oops, there was a problem adding the comment.');
-      }
-    });
-  }
-
-  /**
-   * Recursively append comments to the main comment list and children
-   * lists, creating the comment tree.
-   */
-  function appendComments(comments, ul) {
-    $.each(comments, function() {
-      var div = createCommentDiv(this);
-      ul.append($(document.createElement('li')).html(div));
-      appendComments(this.children, div.find('ul.comment-children'));
-      // To avoid stagnating data, don't store the comments children in data.
-      this.children = null;
-      div.data('comment', this);
-    });
-  }
-
-  /**
-   * After adding a new comment, it must be inserted in the correct
-   * location in the comment tree.
-   */
-  function insertComment(comment) {
-    var div = createCommentDiv(comment);
-
-    // To avoid stagnating data, don't store the comments children in data.
-    comment.children = null;
-    div.data('comment', comment);
-
-    var ul = $('#cl' + (comment.node || comment.parent));
-    var siblings = getChildren(ul);
-
-    var li = $(document.createElement('li'));
-    li.hide();
-
-    // Determine where in the parents children list to insert this comment.
-    for(var i=0; i < siblings.length; i++) {
-      if (comp(comment, siblings[i]) <= 0) {
-        $('#cd' + siblings[i].id)
-          .parent()
-          .before(li.html(div));
-        li.slideDown('fast');
-        return;
-      }
-    }
-
-    // If we get here, this comment rates lower than all the others,
-    // or it is the only comment in the list.
-    ul.append(li.html(div));
-    li.slideDown('fast');
-  }
-
-  function acceptComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.acceptCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        $('#cm' + id).fadeOut('fast');
-        $('#cd' + id).removeClass('moderate');
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem accepting the comment.');
-      }
-    });
-  }
-
-  function deleteComment(id) {
-    $.ajax({
-      type: 'POST',
-      url: opts.deleteCommentURL,
-      data: {id: id},
-      success: function(data, textStatus, request) {
-        var div = $('#cd' + id);
-        if (data == 'delete') {
-          // Moderator mode: remove the comment and all children immediately
-          div.slideUp('fast', function() {
-            div.remove();
-          });
-          return;
-        }
-        // User mode: only mark the comment as deleted
-        div
-          .find('span.user-id:first')
-          .text('[deleted]').end()
-          .find('div.comment-text:first')
-          .text('[deleted]').end()
-          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
-                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
-          .remove();
-        var comment = div.data('comment');
-        comment.username = '[deleted]';
-        comment.text = '[deleted]';
-        div.data('comment', comment);
-      },
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem deleting the comment.');
-      }
-    });
-  }
-
-  function showProposal(id) {
-    $('#sp' + id).hide();
-    $('#hp' + id).show();
-    $('#pr' + id).slideDown('fast');
-  }
-
-  function hideProposal(id) {
-    $('#hp' + id).hide();
-    $('#sp' + id).show();
-    $('#pr' + id).slideUp('fast');
-  }
-
-  function showProposeChange(id) {
-    $('#pc' + id).hide();
-    $('#hc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val(textarea.data('source'));
-    $.fn.autogrow.resize(textarea[0]);
-    textarea.slideDown('fast');
-  }
-
-  function hideProposeChange(id) {
-    $('#hc' + id).hide();
-    $('#pc' + id).show();
-    var textarea = $('#pt' + id);
-    textarea.val('').removeAttr('disabled');
-    textarea.slideUp('fast');
-  }
-
-  function toggleCommentMarkupBox(id) {
-    $('#mb' + id).toggle();
-  }
-
-  /** Handle when the user clicks on a sort by link. */
-  function handleReSort(link) {
-    var classes = link.attr('class').split(/\s+/);
-    for (var i=0; i<classes.length; i++) {
-      if (classes[i] != 'sort-option') {
-	by = classes[i].substring(2);
-      }
-    }
-    setComparator();
-    // Save/update the sortBy cookie.
-    var expiration = new Date();
-    expiration.setDate(expiration.getDate() + 365);
-    document.cookie= 'sortBy=' + escape(by) +
-                     ';expires=' + expiration.toUTCString();
-    $('ul.comment-ul').each(function(index, ul) {
-      var comments = getChildren($(ul), true);
-      comments = sortComments(comments);
-      appendComments(comments, $(ul).empty());
-    });
-  }
-
-  /**
-   * Function to process a vote when a user clicks an arrow.
-   */
-  function handleVote(link) {
-    if (!opts.voting) {
-      showError("You'll need to login to vote.");
-      return;
-    }
-
-    var id = link.attr('id');
-    if (!id) {
-      // Didn't click on one of the voting arrows.
-      return;
-    }
-    // If it is an unvote, the new vote value is 0,
-    // Otherwise it's 1 for an upvote, or -1 for a downvote.
-    var value = 0;
-    if (id.charAt(1) != 'u') {
-      value = id.charAt(0) == 'u' ? 1 : -1;
-    }
-    // The data to be sent to the server.
-    var d = {
-      comment_id: id.substring(2),
-      value: value
-    };
-
-    // Swap the vote and unvote links.
-    link.hide();
-    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
-      .show();
-
-    // The div the comment is displayed in.
-    var div = $('div#cd' + d.comment_id);
-    var data = div.data('comment');
-
-    // If this is not an unvote, and the other vote arrow has
-    // already been pressed, unpress it.
-    if ((d.value !== 0) && (data.vote === d.value * -1)) {
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
-      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
-    }
-
-    // Update the comments rating in the local data.
-    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
-    data.vote = d.value;
-    div.data('comment', data);
-
-    // Change the rating text.
-    div.find('.rating:first')
-      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
-
-    // Send the vote information to the server.
-    $.ajax({
-      type: "POST",
-      url: opts.processVoteURL,
-      data: d,
-      error: function(request, textStatus, error) {
-        showError('Oops, there was a problem casting that vote.');
-      }
-    });
-  }
-
-  /**
-   * Open a reply form used to reply to an existing comment.
-   */
-  function openReply(id) {
-    // Swap out the reply link for the hide link
-    $('#rl' + id).hide();
-    $('#cr' + id).show();
-
-    // Add the reply li to the children ul.
-    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
-    $('#cl' + id)
-      .prepend(div)
-      // Setup the submit handler for the reply form.
-      .find('#rf' + id)
-      .submit(function(event) {
-        event.preventDefault();
-        addComment($('#rf' + id));
-        closeReply(id);
-      })
-      .find('input[type=button]')
-      .click(function() {
-        closeReply(id);
-      });
-    div.slideDown('fast', function() {
-      $('#rf' + id).find('textarea').focus();
-    });
-  }
-
-  /**
-   * Close the reply form opened with openReply.
-   */
-  function closeReply(id) {
-    // Remove the reply div from the DOM.
-    $('#rd' + id).slideUp('fast', function() {
-      $(this).remove();
-    });
-
-    // Swap out the hide link for the reply link
-    $('#cr' + id).hide();
-    $('#rl' + id).show();
-  }
-
-  /**
-   * Recursively sort a tree of comments using the comp comparator.
-   */
-  function sortComments(comments) {
-    comments.sort(comp);
-    $.each(comments, function() {
-      this.children = sortComments(this.children);
-    });
-    return comments;
-  }
-
-  /**
-   * Get the children comments from a ul. If recursive is true,
-   * recursively include childrens' children.
-   */
-  function getChildren(ul, recursive) {
-    var children = [];
-    ul.children().children("[id^='cd']")
-      .each(function() {
-        var comment = $(this).data('comment');
-        if (recursive)
-          comment.children = getChildren($(this).find('#cl' + comment.id), true);
-        children.push(comment);
-      });
-    return children;
-  }
-
-  /** Create a div to display a comment in. */
-  function createCommentDiv(comment) {
-    if (!comment.displayed && !opts.moderator) {
-      return $('<div class="moderate">Thank you!  Your comment will show up '
-               + 'once it is has been approved by a moderator.</div>');
-    }
-    // Prettify the comment rating.
-    comment.pretty_rating = comment.rating + ' point' +
-      (comment.rating == 1 ? '' : 's');
-    // Make a class (for displaying not yet moderated comments differently)
-    comment.css_class = comment.displayed ? '' : ' moderate';
-    // Create a div for this comment.
-    var context = $.extend({}, opts, comment);
-    var div = $(renderTemplate(commentTemplate, context));
-
-    // If the user has voted on this comment, highlight the correct arrow.
-    if (comment.vote) {
-      var direction = (comment.vote == 1) ? 'u' : 'd';
-      div.find('#' + direction + 'v' + comment.id).hide();
-      div.find('#' + direction + 'u' + comment.id).show();
-    }
-
-    if (opts.moderator || comment.text != '[deleted]') {
-      div.find('a.reply').show();
-      if (comment.proposal_diff)
-        div.find('#sp' + comment.id).show();
-      if (opts.moderator && !comment.displayed)
-        div.find('#cm' + comment.id).show();
-      if (opts.moderator || (opts.username == comment.username))
-        div.find('#dc' + comment.id).show();
-    }
-    return div;
-  }
-
-  /**
-   * A simple template renderer. Placeholders such as <%id%> are replaced
-   * by context['id'] with items being escaped. Placeholders such as <#id#>
-   * are not escaped.
-   */
-  function renderTemplate(template, context) {
-    var esc = $(document.createElement('div'));
-
-    function handle(ph, escape) {
-      var cur = context;
-      $.each(ph.split('.'), function() {
-        cur = cur[this];
-      });
-      return escape ? esc.text(cur || "").html() : cur;
-    }
-
-    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
-      return handle(arguments[2], arguments[1] == '%' ? true : false);
-    });
-  }
-
-  /** Flash an error message briefly. */
-  function showError(message) {
-    $(document.createElement('div')).attr({'class': 'popup-error'})
-      .append($(document.createElement('div'))
-               .attr({'class': 'error-message'}).text(message))
-      .appendTo('body')
-      .fadeIn("slow")
-      .delay(2000)
-      .fadeOut("slow");
-  }
-
-  /** Add a link the user uses to open the comments popup. */
-  $.fn.comment = function() {
-    return this.each(function() {
-      var id = $(this).attr('id').substring(1);
-      var count = COMMENT_METADATA[id];
-      var title = count + ' comment' + (count == 1 ? '' : 's');
-      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
-      var addcls = count == 0 ? ' nocomment' : '';
-      $(this)
-        .append(
-          $(document.createElement('a')).attr({
-            href: '#',
-            'class': 'sphinx-comment-open' + addcls,
-            id: 'ao' + id
-          })
-            .append($(document.createElement('img')).attr({
-              src: image,
-              alt: 'comment',
-              title: title
-            }))
-            .click(function(event) {
-              event.preventDefault();
-              show($(this).attr('id').substring(2));
-            })
-        )
-        .append(
-          $(document.createElement('a')).attr({
-            href: '#',
-            'class': 'sphinx-comment-close hidden',
-            id: 'ah' + id
-          })
-            .append($(document.createElement('img')).attr({
-              src: opts.closeCommentImage,
-              alt: 'close',
-              title: 'close'
-            }))
-            .click(function(event) {
-              event.preventDefault();
-              hide($(this).attr('id').substring(2));
-            })
-        );
-    });
-  };
-
-  var opts = {
-    processVoteURL: '/_process_vote',
-    addCommentURL: '/_add_comment',
-    getCommentsURL: '/_get_comments',
-    acceptCommentURL: '/_accept_comment',
-    deleteCommentURL: '/_delete_comment',
-    commentImage: '/static/_static/comment.png',
-    closeCommentImage: '/static/_static/comment-close.png',
-    loadingImage: '/static/_static/ajax-loader.gif',
-    commentBrightImage: '/static/_static/comment-bright.png',
-    upArrow: '/static/_static/up.png',
-    downArrow: '/static/_static/down.png',
-    upArrowPressed: '/static/_static/up-pressed.png',
-    downArrowPressed: '/static/_static/down-pressed.png',
-    voting: false,
-    moderator: false
-  };
-
-  if (typeof COMMENT_OPTIONS != "undefined") {
-    opts = jQuery.extend(opts, COMMENT_OPTIONS);
-  }
-
-  var popupTemplate = '\
-    <div class="sphinx-comments" id="sc<%id%>">\
-      <p class="sort-options">\
-        Sort by:\
-        <a href="#" class="sort-option byrating">best rated</a>\
-        <a href="#" class="sort-option byascage">newest</a>\
-        <a href="#" class="sort-option byage">oldest</a>\
-      </p>\
-      <div class="comment-header">Comments</div>\
-      <div class="comment-loading" id="cn<%id%>">\
-        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
-      <ul id="cl<%id%>" class="comment-ul"></ul>\
-      <div id="ca<%id%>">\
-      <p class="add-a-comment">Add a comment\
-        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
-      <div class="comment-markup-box" id="mb<%id%>">\
-        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
-        <code>``code``</code>, \
-        code blocks: <code>::</code> and an indented block after blank line</div>\
-      <form method="post" id="cf<%id%>" class="comment-form" action="">\
-        <textarea name="comment" cols="80"></textarea>\
-        <p class="propose-button">\
-          <a href="#" id="pc<%id%>" class="show-propose-change">\
-            Propose a change &#9657;\
-          </a>\
-          <a href="#" id="hc<%id%>" class="hide-propose-change">\
-            Propose a change &#9663;\
-          </a>\
-        </p>\
-        <textarea name="proposal" id="pt<%id%>" cols="80"\
-                  spellcheck="false"></textarea>\
-        <input type="submit" value="Add comment" />\
-        <input type="hidden" name="node" value="<%id%>" />\
-        <input type="hidden" name="parent" value="" />\
-      </form>\
-      </div>\
-    </div>';
-
-  var commentTemplate = '\
-    <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
-      <div class="vote">\
-        <div class="arrow">\
-          <a href="#" id="uv<%id%>" class="vote" title="vote up">\
-            <img src="<%upArrow%>" />\
-          </a>\
-          <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
-            <img src="<%upArrowPressed%>" />\
-          </a>\
-        </div>\
-        <div class="arrow">\
-          <a href="#" id="dv<%id%>" class="vote" title="vote down">\
-            <img src="<%downArrow%>" id="da<%id%>" />\
-          </a>\
-          <a href="#" id="du<%id%>" class="un vote" title="vote down">\
-            <img src="<%downArrowPressed%>" />\
-          </a>\
-        </div>\
-      </div>\
-      <div class="comment-content">\
-        <p class="tagline comment">\
-          <span class="user-id"><%username%></span>\
-          <span class="rating"><%pretty_rating%></span>\
-          <span class="delta"><%time.delta%></span>\
-        </p>\
-        <div class="comment-text comment"><#text#></div>\
-        <p class="comment-opts comment">\
-          <a href="#" class="reply hidden" id="rl<%id%>">reply &#9657;</a>\
-          <a href="#" class="close-reply" id="cr<%id%>">reply &#9663;</a>\
-          <a href="#" id="sp<%id%>" class="show-proposal">proposal &#9657;</a>\
-          <a href="#" id="hp<%id%>" class="hide-proposal">proposal &#9663;</a>\
-          <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
-          <span id="cm<%id%>" class="moderation hidden">\
-            <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
-          </span>\
-        </p>\
-        <pre class="proposal" id="pr<%id%>">\
-<#proposal_diff#>\
-        </pre>\
-          <ul class="comment-children" id="cl<%id%>"></ul>\
-        </div>\
-        <div class="clearleft"></div>\
-      </div>\
-    </div>';
-
-  var replyTemplate = '\
-    <li>\
-      <div class="reply-div" id="rd<%id%>">\
-        <form id="rf<%id%>">\
-          <textarea name="comment" cols="80"></textarea>\
-          <input type="submit" value="Add reply" />\
-          <input type="button" value="Cancel" />\
-          <input type="hidden" name="parent" value="<%id%>" />\
-          <input type="hidden" name="node" value="" />\
-        </form>\
-      </div>\
-    </li>';
-
-  $(document).ready(function() {
-    init();
-  });
-})(jQuery);
-
-$(document).ready(function() {
-  // add comment anchors for all paragraphs that are commentable
-  $('.sphinx-has-comment').comment();
-
-  // highlight search words in search results
-  $("div.context").each(function() {
-    var params = $.getQueryParameters();
-    var terms = (params.q) ? params.q[0].split(/\s+/) : [];
-    var result = $(this);
-    $.each(terms, function() {
-      result.highlightText(this.toLowerCase(), 'highlighted');
-    });
-  });
-
-  // directly open comment window if requested
-  var anchor = document.location.hash;
-  if (anchor.substring(0, 9) == '#comment-') {
-    $('#ao' + anchor.substring(9)).click();
-    document.location.hash = '#s' + anchor.substring(9);
-  }
-});

docs/_build/html/genindex.html

@@ -1,431 +0,0 @@
-
-
-
-<!DOCTYPE html>
-<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
-<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
-<head>
-  <meta charset="utf-8">
-  
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  
-  <title>Index &mdash; py-graph  documentation</title>
-  
-
-  
-  
-  
-  
-
-  
-  <script type="text/javascript" src="_static/js/modernizr.min.js"></script>
-  
-    
-      <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>
-        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    
-    <script type="text/javascript" src="_static/js/theme.js"></script>
-
-    
-
-  
-  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-    <link rel="index" title="Index" href="#" />
-    <link rel="search" title="Search" href="search.html" /> 
-</head>
-
-<body class="wy-body-for-nav">
-
-   
-  <div class="wy-grid-for-nav">
-    
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-scroll">
-        <div class="wy-side-nav-search" >
-          
-
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-<h2 id="C">C</h2>
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-      <li><a href="pygraph.utils.html#pygraph.utils.kernels.gaussiankernel">gaussiankernel() (in module pygraph.utils.kernels)</a>
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-<h2 id="I">I</h2>
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-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.insertWord">insertWord() (pygraph.utils.trie.Trie method)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.kernels.kernelproduct">kernelproduct() (in module pygraph.utils.kernels)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.kernels.kernelsum">kernelsum() (in module pygraph.utils.kernels)</a>
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-<h2 id="L">L</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
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-      <li><a href="pygraph.utils.html#pygraph.utils.kernels.linearkernel">linearkernel() (in module pygraph.utils.kernels)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.load_from_json">load_from_json() (pygraph.utils.trie.Trie method)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.graphfiles.loadSDF">loadSDF() (in module pygraph.utils.graphfiles)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.graphfiles.loadTXT">loadTXT() (in module pygraph.utils.graphfiles)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.logger2file.Logger">Logger (class in pygraph.utils.logger2file)</a>
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-<h2 id="M">M</h2>
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-      <li><a href="pygraph.utils.html#pygraph.utils.model_selection_precomputed.model_selection_for_precomputed_kernel">model_selection_for_precomputed_kernel() (in module pygraph.utils.model_selection_precomputed)</a>
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-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
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-      <li><a href="pygraph.utils.html#pygraph.utils.parallel.parallel_gm">parallel_gm() (in module pygraph.utils.parallel)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.parallel.parallel_me">parallel_me() (in module pygraph.utils.parallel)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.model_selection_precomputed.parallel_trial_do">parallel_trial_do() (in module pygraph.utils.model_selection_precomputed)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.kernels.polynomialkernel">polynomialkernel() (in module pygraph.utils.kernels)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.model_selection_precomputed.printResultsInTable">printResultsInTable() (in module pygraph.utils.model_selection_precomputed)</a>
-</li>
-      <li><a href="pygraph.html#module-pygraph">pygraph (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils">pygraph.utils (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.graphdataset">pygraph.utils.graphdataset (module)</a>
-</li>
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-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.graphfiles">pygraph.utils.graphfiles (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.isNotebook">pygraph.utils.isNotebook (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.kernels">pygraph.utils.kernels (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.logger2file">pygraph.utils.logger2file (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.model_selection_precomputed">pygraph.utils.model_selection_precomputed (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.parallel">pygraph.utils.parallel (module)</a>
-</li>
-      <li><a href="pygraph.utils.html#module-pygraph.utils.trie">pygraph.utils.trie (module)</a>
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-      <li><a href="pygraph.utils.html#module-pygraph.utils.utils">pygraph.utils.utils (module)</a>
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-<h2 id="R">R</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.model_selection_precomputed.read_gram_matrices_from_file">read_gram_matrices_from_file() (in module pygraph.utils.model_selection_precomputed)</a>
-</li>
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-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.save_to_json">save_to_json() (pygraph.utils.trie.Trie method)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.save_to_pickle">save_to_pickle() (pygraph.utils.trie.Trie method)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.graphfiles.saveDataset">saveDataset() (in module pygraph.utils.graphfiles)</a>
-</li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.graphfiles.saveGXL">saveGXL() (in module pygraph.utils.graphfiles)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.searchWord">searchWord() (pygraph.utils.trie.Trie method)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.searchWordPrefix">searchWordPrefix() (pygraph.utils.trie.Trie method)</a>
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-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie.to_json">to_json() (pygraph.utils.trie.Trie method)</a>
-</li>
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-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.model_selection_precomputed.trial_do">trial_do() (in module pygraph.utils.model_selection_precomputed)</a>
-</li>
-      <li><a href="pygraph.utils.html#pygraph.utils.trie.Trie">Trie (class in pygraph.utils.trie)</a>
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-<h2 id="U">U</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.utils.untotterTransformation">untotterTransformation() (in module pygraph.utils.utils)</a>
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-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="pygraph.utils.html#pygraph.utils.logger2file.Logger.write">write() (pygraph.utils.logger2file.Logger method)</a>
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-            
-  <div class="section" id="pygraph-utils-package">
-<h1>pygraph.utils package<a class="headerlink" href="#pygraph-utils-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
-<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-pygraph.utils.graphdataset">
-<span id="pygraph-utils-graphdataset-module"></span><h2>pygraph.utils.graphdataset module<a class="headerlink" href="#module-pygraph.utils.graphdataset" title="Permalink to this headline">¶</a></h2>
-<p>Obtain all kinds of attributes of a graph dataset.</p>
-<dl class="function">
-<dt id="pygraph.utils.graphdataset.get_dataset_attributes">
-<code class="descclassname">pygraph.utils.graphdataset.</code><code class="descname">get_dataset_attributes</code><span class="sig-paren">(</span><em>Gn</em>, <em>target=None</em>, <em>attr_names=[]</em>, <em>node_label=None</em>, <em>edge_label=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphdataset.html#get_dataset_attributes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphdataset.get_dataset_attributes" title="Permalink to this definition">¶</a></dt>
-<dd><p>Returns the structure and property information of the graph dataset Gn.</p>
-<dl class="docutils">
-<dt>Gn <span class="classifier-delimiter">:</span> <span class="classifier">List of NetworkX graph</span></dt>
-<dd>List of graphs whose information will be returned.</dd>
-<dt>target <span class="classifier-delimiter">:</span> <span class="classifier">list</span></dt>
-<dd>The list of classification targets corresponding to Gn. Only works for 
-classification problems.</dd>
-<dt>attr_names <span class="classifier-delimiter">:</span> <span class="classifier">list</span></dt>
-<dd><p class="first">List of strings which indicate which informations will be returned. The
-possible choices includes:
-‘substructures’: sub-structures Gn contains, including ‘linear’, ‘non</p>
-<blockquote>
-<div>linear’ and ‘cyclic’.</div></blockquote>
-<p>‘node_labeled’: whether vertices have symbolic labels.
-‘edge_labeled’: whether egdes have symbolic labels.
-‘is_directed’: whether graphs in Gn are directed.
-‘dataset_size’: number of graphs in Gn.
-‘ave_node_num’: average number of vertices of graphs in Gn.
-‘min_node_num’: minimum number of vertices of graphs in Gn.
-‘max_node_num’: maximum number of vertices of graphs in Gn.
-‘ave_edge_num’: average number of edges of graphs in Gn.
-‘min_edge_num’: minimum number of edges of graphs in Gn.
-‘max_edge_num’: maximum number of edges of graphs in Gn.
-‘ave_node_degree’: average vertex degree of graphs in Gn.
-‘min_node_degree’: minimum vertex degree of graphs in Gn.
-‘max_node_degree’: maximum vertex degree of graphs in Gn.
-‘ave_fill_factor’: average fill factor (number_of_edges /</p>
-<blockquote>
-<div>(number_of_nodes ** 2)) of graphs in Gn.</div></blockquote>
-<p>‘min_fill_factor’: minimum fill factor of graphs in Gn.
-‘max_fill_factor’: maximum fill factor of graphs in Gn.
-‘node_label_num’: number of symbolic vertex labels.
-‘edge_label_num’: number of symbolic edge labels.
-‘node_attr_dim’: number of dimensions of non-symbolic vertex labels.</p>
-<blockquote>
-<div>Extracted from the ‘attributes’ attribute of graph nodes.</div></blockquote>
-<dl class="last docutils">
-<dt>‘edge_attr_dim’: number of dimensions of non-symbolic edge labels.</dt>
-<dd>Extracted from the ‘attributes’ attribute of graph edges.</dd>
-<dt>‘class_number’: number of classes. Only available for classification </dt>
-<dd>problems.</dd>
-</dl>
-</dd>
-<dt>node_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Node attribute used as label. The default node label is atom. Mandatory
-when ‘node_labeled’ or ‘node_label_num’ is required.</dd>
-<dt>edge_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Edge attribute used as label. The default edge label is bond_type. 
-Mandatory when ‘edge_labeled’ or ‘edge_label_num’ is required.</dd>
-</dl>
-<dl class="docutils">
-<dt>attrs <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
-<dd>Value for each property.</dd>
-</dl>
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.graphfiles">
-<span id="pygraph-utils-graphfiles-module"></span><h2>pygraph.utils.graphfiles module<a class="headerlink" href="#module-pygraph.utils.graphfiles" title="Permalink to this headline">¶</a></h2>
-<p>Utilities function to manage graph files</p>
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadCT">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadCT</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadCT"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadCT" title="Permalink to this definition">¶</a></dt>
-<dd><p>load data from a Chemical Table (.ct) file.</p>
-<p>a typical example of data in .ct is like this:</p>
-<blockquote>
-<div><dl class="docutils">
-<dt>3 2  &lt;- number of nodes and edges</dt>
-<dd><blockquote class="first">
-<div>0.0000    0.0000    0.0000 C &lt;- each line describes a node (x,y,z + label)
-0.0000    0.0000    0.0000 C
-0.0000    0.0000    0.0000 O</div></blockquote>
-<p class="last">1  3  1  1 &lt;- each line describes an edge : to, from, bond type, bond stereo
-2  3  1  1</p>
-</dd>
-</dl>
-</div></blockquote>
-<p>Check <a class="reference external" href="https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=10&amp;ved=2ahUKEwivhaSdjsTlAhVhx4UKHczHA8gQFjAJegQIARAC&amp;url=https%3A%2F%2Fwww.daylight.com%2Fmeetings%2Fmug05%2FKappler%2Fctfile.pdf&amp;usg=AOvVaw1cDNrrmMClkFPqodlF2inS">https://www.google.com/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=10&amp;ved=2ahUKEwivhaSdjsTlAhVhx4UKHczHA8gQFjAJegQIARAC&amp;url=https%3A%2F%2Fwww.daylight.com%2Fmeetings%2Fmug05%2FKappler%2Fctfile.pdf&amp;usg=AOvVaw1cDNrrmMClkFPqodlF2inS</a>
-for detailed format discription.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadDataset">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadDataset</code><span class="sig-paren">(</span><em>filename</em>, <em>filename_y=None</em>, <em>extra_params=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadDataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadDataset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Read graph data from filename and load them as NetworkX graphs.</p>
-<dl class="docutils">
-<dt>filename <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>The name of the file from where the dataset is read.</dd>
-<dt>filename_y <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>The name of file of the targets corresponding to graphs.</dd>
-<dt>extra_params <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
-<dd>Extra parameters only designated to ‘.mat’ format.</dd>
-</dl>
-<p>data : List of NetworkX graph.
-y : List</p>
-<blockquote>
-<div>Targets corresponding to graphs.</div></blockquote>
-<p>This function supports following graph dataset formats:
-‘ds’: load data from .ds file. See comments of function loadFromDS for a example.
-‘cxl’: load data from Graph eXchange Language file (.cxl file). See</p>
-<blockquote>
-<div><a class="reference external" href="http://www.gupro.de/GXL/Introduction/background.html">http://www.gupro.de/GXL/Introduction/background.html</a>, 2019 for detail.</div></blockquote>
-<dl class="docutils">
-<dt>‘sdf’: load data from structured data file (.sdf file). See </dt>
-<dd><a class="reference external" href="http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx">http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx</a>, 
-2018 for details.</dd>
-<dt>‘mat’: Load graph data from a MATLAB (up to version 7.1) .mat file. See</dt>
-<dd>README in downloadable file in <a class="reference external" href="http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/">http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/</a>, 
-2018 for details.</dd>
-<dt>‘txt’: Load graph data from a special .txt file. See</dt>
-<dd><a class="reference external" href="https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets">https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets</a>,
-2019 for details. Note here filename is the name of either .txt file in
-the dataset directory.</dd>
-</dl>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadFromDS">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadFromDS</code><span class="sig-paren">(</span><em>filename</em>, <em>filename_y</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadFromDS"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadFromDS" title="Permalink to this definition">¶</a></dt>
-<dd><p>Load data from .ds file.
-Possible graph formats include:</p>
-<blockquote>
-<div>‘.ct’: see function loadCT for detail.
-‘.gxl’: see dunction loadGXL for detail.</div></blockquote>
-<p>Note these graph formats are checked automatically by the extensions of 
-graph files.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadFromXML">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadFromXML</code><span class="sig-paren">(</span><em>filename</em>, <em>extra_params</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadFromXML"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadFromXML" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadGXL">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadGXL</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadGXL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadGXL" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadMAT">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadMAT</code><span class="sig-paren">(</span><em>filename</em>, <em>extra_params</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadMAT"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadMAT" title="Permalink to this definition">¶</a></dt>
-<dd><p>Load graph data from a MATLAB (up to version 7.1) .mat file.</p>
-<p>A MAT file contains a struct array containing graphs, and a column vector lx containing a class label for each graph.
-Check README in downloadable file in <a class="reference external" href="http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/">http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/</a>, 2018 for detailed structure.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadSDF">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadSDF</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadSDF"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadSDF" title="Permalink to this definition">¶</a></dt>
-<dd><p>load data from structured data file (.sdf file).</p>
-<p>A SDF file contains a group of molecules, represented in the similar way as in MOL format.
-Check <a class="reference external" href="http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx">http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx</a>, 2018 for detailed structure.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.loadTXT">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">loadTXT</code><span class="sig-paren">(</span><em>dirname_dataset</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#loadTXT"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.loadTXT" title="Permalink to this definition">¶</a></dt>
-<dd><p>Load graph data from a .txt file.</p>
-<p>The graph data is loaded from separate files.
-Check README in downloadable file <a class="reference external" href="http://tiny.cc/PK_MLJ_data">http://tiny.cc/PK_MLJ_data</a>, 2018 for detailed structure.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.saveDataset">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">saveDataset</code><span class="sig-paren">(</span><em>Gn</em>, <em>y</em>, <em>gformat='gxl'</em>, <em>group=None</em>, <em>filename='gfile'</em>, <em>xparams=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#saveDataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.saveDataset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Save list of graphs.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.graphfiles.saveGXL">
-<code class="descclassname">pygraph.utils.graphfiles.</code><code class="descname">saveGXL</code><span class="sig-paren">(</span><em>graph</em>, <em>filename</em>, <em>method='benoit'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/graphfiles.html#saveGXL"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.graphfiles.saveGXL" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</div>
-<div class="section" id="pygraph-utils-ipython-log-module">
-<h2>pygraph.utils.ipython_log module<a class="headerlink" href="#pygraph-utils-ipython-log-module" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-pygraph.utils.isNotebook">
-<span id="pygraph-utils-isnotebook-module"></span><h2>pygraph.utils.isNotebook module<a class="headerlink" href="#module-pygraph.utils.isNotebook" title="Permalink to this headline">¶</a></h2>
-<p>Functions for python system.</p>
-<dl class="function">
-<dt id="pygraph.utils.isNotebook.isNotebook">
-<code class="descclassname">pygraph.utils.isNotebook.</code><code class="descname">isNotebook</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/isNotebook.html#isNotebook"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.isNotebook.isNotebook" title="Permalink to this definition">¶</a></dt>
-<dd><p>check if code is executed in the IPython notebook.</p>
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.kernels">
-<span id="pygraph-utils-kernels-module"></span><h2>pygraph.utils.kernels module<a class="headerlink" href="#module-pygraph.utils.kernels" title="Permalink to this headline">¶</a></h2>
-<p>Those who are not graph kernels. We can be kernels for nodes or edges!
-These kernels are defined between pairs of vectors.</p>
-<dl class="function">
-<dt id="pygraph.utils.kernels.deltakernel">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">deltakernel</code><span class="sig-paren">(</span><em>x</em>, <em>y</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#deltakernel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.deltakernel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Delta kernel. Return 1 if x == y, 0 otherwise.</p>
-<dl class="docutils">
-<dt>x, y <span class="classifier-delimiter">:</span> <span class="classifier">any</span></dt>
-<dd>Two parts to compare.</dd>
-</dl>
-<dl class="docutils">
-<dt>kernel <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
-<dd>Delta kernel.</dd>
-</dl>
-<p>[1] H. Kashima, K. Tsuda, and A. Inokuchi. Marginalized kernels between 
-labeled graphs. In Proceedings of the 20th International Conference on 
-Machine Learning, Washington, DC, United States, 2003.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.kernels.gaussiankernel">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">gaussiankernel</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>gamma=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#gaussiankernel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.gaussiankernel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Gaussian kernel.
-Compute the rbf (gaussian) kernel between x and y:</p>
-<blockquote>
-<div>K(x, y) = exp(-gamma ||x-y||^2).</div></blockquote>
-<p>Read more in the <span class="xref std std-ref">User Guide</span>.</p>
-<p>x, y : array</p>
-<dl class="docutils">
-<dt>gamma <span class="classifier-delimiter">:</span> <span class="classifier">float, default None</span></dt>
-<dd>If None, defaults to 1.0 / n_features</dd>
-</dl>
-<p>kernel : float</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.kernels.kernelproduct">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">kernelproduct</code><span class="sig-paren">(</span><em>k1</em>, <em>k2</em>, <em>d11</em>, <em>d12</em>, <em>d21=None</em>, <em>d22=None</em>, <em>lamda=1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#kernelproduct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.kernelproduct" title="Permalink to this definition">¶</a></dt>
-<dd><p>Product of a pair of kernels.</p>
-<p>k = lamda * k1(d11, d12) * k2(d21, d22)</p>
-<dl class="docutils">
-<dt>k1, k2 <span class="classifier-delimiter">:</span> <span class="classifier">function</span></dt>
-<dd>A pair of kernel functions.</dd>
-<dt>d11, d12:</dt>
-<dd>Inputs of k1. If d21 or d22 is None, apply d11, d12 to both k1 and k2.</dd>
-<dt>d21, d22:</dt>
-<dd>Inputs of k2.</dd>
-<dt>lamda: float</dt>
-<dd>Coefficient of the product.</dd>
-</dl>
-<p>kernel : integer</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.kernels.kernelsum">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">kernelsum</code><span class="sig-paren">(</span><em>k1</em>, <em>k2</em>, <em>d11</em>, <em>d12</em>, <em>d21=None</em>, <em>d22=None</em>, <em>lamda1=1</em>, <em>lamda2=1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#kernelsum"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.kernelsum" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sum of a pair of kernels.</p>
-<p>k = lamda1 * k1(d11, d12) + lamda2 * k2(d21, d22)</p>
-<dl class="docutils">
-<dt>k1, k2 <span class="classifier-delimiter">:</span> <span class="classifier">function</span></dt>
-<dd>A pair of kernel functions.</dd>
-<dt>d11, d12:</dt>
-<dd>Inputs of k1. If d21 or d22 is None, apply d11, d12 to both k1 and k2.</dd>
-<dt>d21, d22:</dt>
-<dd>Inputs of k2.</dd>
-<dt>lamda1, lamda2: float</dt>
-<dd>Coefficients of the product.</dd>
-</dl>
-<p>kernel : integer</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.kernels.linearkernel">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">linearkernel</code><span class="sig-paren">(</span><em>x</em>, <em>y</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#linearkernel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.linearkernel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Polynomial kernel.
-Compute the polynomial kernel between x and y:</p>
-<blockquote>
-<div>K(x, y) = &lt;x, y&gt;.</div></blockquote>
-<p>x, y : array</p>
-<p>d : integer, default 1</p>
-<p>c : float, default 0</p>
-<p>kernel : float</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.kernels.polynomialkernel">
-<code class="descclassname">pygraph.utils.kernels.</code><code class="descname">polynomialkernel</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>d=1</em>, <em>c=0</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/kernels.html#polynomialkernel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.kernels.polynomialkernel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Polynomial kernel.
-Compute the polynomial kernel between x and y:</p>
-<blockquote>
-<div>K(x, y) = &lt;x, y&gt; ^d + c.</div></blockquote>
-<p>x, y : array</p>
-<p>d : integer, default 1</p>
-<p>c : float, default 0</p>
-<p>kernel : float</p>
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.logger2file">
-<span id="pygraph-utils-logger2file-module"></span><h2>pygraph.utils.logger2file module<a class="headerlink" href="#module-pygraph.utils.logger2file" title="Permalink to this headline">¶</a></h2>
-<p>Created on Fri Nov  8 14:21:25 2019</p>
-<p>&#64;author: ljia</p>
-<dl class="class">
-<dt id="pygraph.utils.logger2file.Logger">
-<em class="property">class </em><code class="descclassname">pygraph.utils.logger2file.</code><code class="descname">Logger</code><a class="reference internal" href="_modules/pygraph/utils/logger2file.html#Logger"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.logger2file.Logger" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<dl class="method">
-<dt id="pygraph.utils.logger2file.Logger.flush">
-<code class="descname">flush</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/logger2file.html#Logger.flush"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.logger2file.Logger.flush" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.logger2file.Logger.write">
-<code class="descname">write</code><span class="sig-paren">(</span><em>message</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/logger2file.html#Logger.write"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.logger2file.Logger.write" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.model_selection_precomputed">
-<span id="pygraph-utils-model-selection-precomputed-module"></span><h2>pygraph.utils.model_selection_precomputed module<a class="headerlink" href="#module-pygraph.utils.model_selection_precomputed" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.compute_gram_matrices">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">compute_gram_matrices</code><span class="sig-paren">(</span><em>dataset</em>, <em>y</em>, <em>estimator</em>, <em>param_list_precomputed</em>, <em>results_dir</em>, <em>ds_name</em>, <em>n_jobs=1</em>, <em>str_fw=''</em>, <em>verbose=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#compute_gram_matrices"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.compute_gram_matrices" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.model_selection_for_precomputed_kernel">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">model_selection_for_precomputed_kernel</code><span class="sig-paren">(</span><em>datafile</em>, <em>estimator</em>, <em>param_grid_precomputed</em>, <em>param_grid</em>, <em>model_type</em>, <em>NUM_TRIALS=30</em>, <em>datafile_y=None</em>, <em>extra_params=None</em>, <em>ds_name='ds-unknown'</em>, <em>n_jobs=1</em>, <em>read_gm_from_file=False</em>, <em>verbose=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#model_selection_for_precomputed_kernel"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.model_selection_for_precomputed_kernel" title="Permalink to this definition">¶</a></dt>
-<dd><p>Perform model selection, fitting and testing for precomputed kernels 
-using nested CV. Print out neccessary data during the process then finally 
-the results.</p>
-<dl class="docutils">
-<dt>datafile <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Path of dataset file.</dd>
-<dt>estimator <span class="classifier-delimiter">:</span> <span class="classifier">function</span></dt>
-<dd>kernel function used to estimate. This function needs to return a gram matrix.</dd>
-<dt>param_grid_precomputed <span class="classifier-delimiter">:</span> <span class="classifier">dictionary</span></dt>
-<dd>Dictionary with names (string) of parameters used to calculate gram 
-matrices as keys and lists of parameter settings to try as values. This 
-enables searching over any sequence of parameter settings. Params with 
-length 1 will be omitted.</dd>
-<dt>param_grid <span class="classifier-delimiter">:</span> <span class="classifier">dictionary</span></dt>
-<dd>Dictionary with names (string) of parameters used as penelties as keys 
-and lists of parameter settings to try as values. This enables 
-searching over any sequence of parameter settings. Params with length 1
-will be omitted.</dd>
-<dt>model_type <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Type of the problem, can be ‘regression’ or ‘classification’.</dd>
-<dt>NUM_TRIALS <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
-<dd>Number of random trials of outer cv loop. The default is 30.</dd>
-<dt>datafile_y <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Path of file storing y data. This parameter is optional depending on 
-the given dataset file.</dd>
-<dt>extra_params <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
-<dd>Extra parameters for loading dataset. See function pygraph.utils.
-graphfiles.loadDataset for detail.</dd>
-<dt>ds_name <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>Name of the dataset.</dd>
-<dt>n_jobs <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
-<dd>Number of jobs for parallelization.</dd>
-<dt>read_gm_from_file <span class="classifier-delimiter">:</span> <span class="classifier">boolean</span></dt>
-<dd>Whether gram matrices are loaded from a file.</dd>
-</dl>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>&gt;&gt;&gt; import numpy as np
-&gt;&gt;&gt; import sys
-&gt;&gt;&gt; sys.path.insert(0, &quot;../&quot;)
-&gt;&gt;&gt; from pygraph.utils.model_selection_precomputed import model_selection_for_precomputed_kernel
-&gt;&gt;&gt; from pygraph.kernels.untilHPathKernel import untilhpathkernel
-&gt;&gt;&gt;
-&gt;&gt;&gt; datafile = &#39;../datasets/MUTAG/MUTAG_A.txt&#39;
-&gt;&gt;&gt; estimator = untilhpathkernel
-&gt;&gt;&gt; param_grid_precomputed = {’depth’:  np.linspace(1, 10, 10), ’k_func’:
-        [’MinMax’, ’tanimoto’], ’compute_method’:  [’trie’]}
-&gt;&gt;&gt; # ’C’ for classification problems and ’alpha’ for regression problems.
-&gt;&gt;&gt; param_grid = [{’C’: np.logspace(-10, 10, num=41, base=10)}, {’alpha’:
-        np.logspace(-10, 10, num=41, base=10)}]
-&gt;&gt;&gt;
-&gt;&gt;&gt; model_selection_for_precomputed_kernel(datafile, estimator, 
-        param_grid_precomputed, param_grid[0], &#39;classification&#39;, ds_name=’MUTAG’)
-</pre></div>
-</div>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.parallel_trial_do">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">parallel_trial_do</code><span class="sig-paren">(</span><em>param_list_pre_revised</em>, <em>param_list</em>, <em>y</em>, <em>model_type</em>, <em>trial</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#parallel_trial_do"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.parallel_trial_do" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.printResultsInTable">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">printResultsInTable</code><span class="sig-paren">(</span><em>param_list</em>, <em>param_list_pre_revised</em>, <em>average_val_scores</em>, <em>std_val_scores</em>, <em>average_perf_scores</em>, <em>std_perf_scores</em>, <em>average_train_scores</em>, <em>std_train_scores</em>, <em>gram_matrix_time</em>, <em>model_type</em>, <em>verbose</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#printResultsInTable"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.printResultsInTable" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.read_gram_matrices_from_file">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">read_gram_matrices_from_file</code><span class="sig-paren">(</span><em>results_dir</em>, <em>ds_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#read_gram_matrices_from_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.read_gram_matrices_from_file" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.model_selection_precomputed.trial_do">
-<code class="descclassname">pygraph.utils.model_selection_precomputed.</code><code class="descname">trial_do</code><span class="sig-paren">(</span><em>param_list_pre_revised</em>, <em>param_list</em>, <em>gram_matrices</em>, <em>y</em>, <em>model_type</em>, <em>trial</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/model_selection_precomputed.html#trial_do"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.model_selection_precomputed.trial_do" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.parallel">
-<span id="pygraph-utils-parallel-module"></span><h2>pygraph.utils.parallel module<a class="headerlink" href="#module-pygraph.utils.parallel" title="Permalink to this headline">¶</a></h2>
-<p>Created on Tue Dec 11 11:39:46 2018
-Parallel aid functions.
-&#64;author: ljia</p>
-<dl class="function">
-<dt id="pygraph.utils.parallel.parallel_gm">
-<code class="descclassname">pygraph.utils.parallel.</code><code class="descname">parallel_gm</code><span class="sig-paren">(</span><em>func</em>, <em>Kmatrix</em>, <em>Gn</em>, <em>init_worker=None</em>, <em>glbv=None</em>, <em>method='imap_unordered'</em>, <em>n_jobs=None</em>, <em>chunksize=None</em>, <em>verbose=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/parallel.html#parallel_gm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.parallel.parallel_gm" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.parallel.parallel_me">
-<code class="descclassname">pygraph.utils.parallel.</code><code class="descname">parallel_me</code><span class="sig-paren">(</span><em>func</em>, <em>func_assign</em>, <em>var_to_assign</em>, <em>itr</em>, <em>len_itr=None</em>, <em>init_worker=None</em>, <em>glbv=None</em>, <em>method=None</em>, <em>n_jobs=None</em>, <em>chunksize=None</em>, <em>itr_desc=''</em>, <em>verbose=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/parallel.html#parallel_me"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.parallel.parallel_me" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.trie">
-<span id="pygraph-utils-trie-module"></span><h2>pygraph.utils.trie module<a class="headerlink" href="#module-pygraph.utils.trie" title="Permalink to this headline">¶</a></h2>
-<p>Created on Wed Jan 30 10:48:49 2019</p>
-<p>Trie (prefix tree)
-&#64;author: ljia
-&#64;references:</p>
-<blockquote>
-<div><a class="reference external" href="https://viblo.asia/p/nlp-build-a-trie-data-structure-from-scratch-with-python-3P0lPzroKox">https://viblo.asia/p/nlp-build-a-trie-data-structure-from-scratch-with-python-3P0lPzroKox</a>, 2019.1</div></blockquote>
-<dl class="class">
-<dt id="pygraph.utils.trie.Trie">
-<em class="property">class </em><code class="descclassname">pygraph.utils.trie.</code><code class="descname">Trie</code><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.deleteWord">
-<code class="descname">deleteWord</code><span class="sig-paren">(</span><em>word</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.deleteWord"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.deleteWord" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.getNode">
-<code class="descname">getNode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.getNode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.getNode" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.insertWord">
-<code class="descname">insertWord</code><span class="sig-paren">(</span><em>word</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.insertWord"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.insertWord" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.load_from_json">
-<code class="descname">load_from_json</code><span class="sig-paren">(</span><em>file_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.load_from_json"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.load_from_json" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.load_from_pickle">
-<code class="descname">load_from_pickle</code><span class="sig-paren">(</span><em>file_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.load_from_pickle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.load_from_pickle" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.save_to_json">
-<code class="descname">save_to_json</code><span class="sig-paren">(</span><em>file_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.save_to_json"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.save_to_json" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.save_to_pickle">
-<code class="descname">save_to_pickle</code><span class="sig-paren">(</span><em>file_name</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.save_to_pickle"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.save_to_pickle" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.searchWord">
-<code class="descname">searchWord</code><span class="sig-paren">(</span><em>word</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.searchWord"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.searchWord" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.searchWordPrefix">
-<code class="descname">searchWordPrefix</code><span class="sig-paren">(</span><em>word</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.searchWordPrefix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.searchWordPrefix" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt id="pygraph.utils.trie.Trie.to_json">
-<code class="descname">to_json</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/trie.html#Trie.to_json"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.trie.Trie.to_json" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils.utils">
-<span id="pygraph-utils-utils-module"></span><h2>pygraph.utils.utils module<a class="headerlink" href="#module-pygraph.utils.utils" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="pygraph.utils.utils.direct_product">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">direct_product</code><span class="sig-paren">(</span><em>G1</em>, <em>G2</em>, <em>node_label</em>, <em>edge_label</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#direct_product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.direct_product" title="Permalink to this definition">¶</a></dt>
-<dd><p>Return the direct/tensor product of directed graphs G1 and G2.</p>
-<dl class="docutils">
-<dt>G1, G2 <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The original graphs.</dd>
-<dt>node_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>node attribute used as label. The default node label is ‘atom’.</dd>
-<dt>edge_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>edge attribute used as label. The default edge label is ‘bond_type’.</dd>
-</dl>
-<dl class="docutils">
-<dt>gt <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The direct product graph of G1 and G2.</dd>
-</dl>
-<p>This method differs from networkx.tensor_product in that this method only adds nodes and edges in G1 and G2 that have the same labels to the direct product graph.</p>
-<p>[1] Thomas Gärtner, Peter Flach, and Stefan Wrobel. On graph kernels: Hardness results and efficient alternatives. Learning Theory and Kernel Machines, pages 129–143, 2003.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.floydTransformation">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">floydTransformation</code><span class="sig-paren">(</span><em>G</em>, <em>edge_weight=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#floydTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.floydTransformation" title="Permalink to this definition">¶</a></dt>
-<dd><p>Transform graph G to its corresponding shortest-paths graph using Floyd-transformation.</p>
-<dl class="docutils">
-<dt>G <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The graph to be tramsformed.</dd>
-<dt>edge_weight <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>edge attribute corresponding to the edge weight. The default edge weight is bond_type.</dd>
-</dl>
-<dl class="docutils">
-<dt>S <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The shortest-paths graph corresponding to G.</dd>
-</dl>
-<p>[1] Borgwardt KM, Kriegel HP. Shortest-path kernels on graphs. InData Mining, Fifth IEEE International Conference on 2005 Nov 27 (pp. 8-pp). IEEE.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.getSPGraph">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">getSPGraph</code><span class="sig-paren">(</span><em>G</em>, <em>edge_weight=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#getSPGraph"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.getSPGraph" title="Permalink to this definition">¶</a></dt>
-<dd><p>Transform graph G to its corresponding shortest-paths graph.</p>
-<dl class="docutils">
-<dt>G <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The graph to be tramsformed.</dd>
-<dt>edge_weight <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>edge attribute corresponding to the edge weight.</dd>
-</dl>
-<dl class="docutils">
-<dt>S <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The shortest-paths graph corresponding to G.</dd>
-</dl>
-<p>For an input graph G, its corresponding shortest-paths graph S contains the same set of nodes as G, while there exists an edge between all nodes in S which are connected by a walk in G. Every edge in S between two nodes is labeled by the shortest distance between these two nodes.</p>
-<p>[1] Borgwardt KM, Kriegel HP. Shortest-path kernels on graphs. InData Mining, Fifth IEEE International Conference on 2005 Nov 27 (pp. 8-pp). IEEE.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.getSPLengths">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">getSPLengths</code><span class="sig-paren">(</span><em>G1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#getSPLengths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.getSPLengths" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.get_edge_labels">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">get_edge_labels</code><span class="sig-paren">(</span><em>Gn</em>, <em>edge_label</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#get_edge_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.get_edge_labels" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get edge labels of dataset Gn.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.get_node_labels">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">get_node_labels</code><span class="sig-paren">(</span><em>Gn</em>, <em>node_label</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#get_node_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.get_node_labels" title="Permalink to this definition">¶</a></dt>
-<dd><p>Get node labels of dataset Gn.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.graph_deepcopy">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">graph_deepcopy</code><span class="sig-paren">(</span><em>G</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#graph_deepcopy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.graph_deepcopy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Deep copy a graph, including deep copy of all nodes, edges and 
-attributes of the graph, nodes and edges.</p>
-<p>It is the same as the NetworkX function graph.copy(), as far as I know.</p>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.graph_isIdentical">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">graph_isIdentical</code><span class="sig-paren">(</span><em>G1</em>, <em>G2</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#graph_isIdentical"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.graph_isIdentical" title="Permalink to this definition">¶</a></dt>
-<dd><p>Check if two graphs are identical, including: same nodes, edges, node
-labels/attributes, edge labels/attributes.</p>
-<ol class="arabic simple">
-<li>The type of graphs has to be the same.</li>
-<li>Global/Graph attributes are neglected as they may contain names for graphs.</li>
-</ol>
-</dd></dl>
-
-<dl class="function">
-<dt id="pygraph.utils.utils.untotterTransformation">
-<code class="descclassname">pygraph.utils.utils.</code><code class="descname">untotterTransformation</code><span class="sig-paren">(</span><em>G</em>, <em>node_label</em>, <em>edge_label</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pygraph/utils/utils.html#untotterTransformation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pygraph.utils.utils.untotterTransformation" title="Permalink to this definition">¶</a></dt>
-<dd><p>Transform graph G according to Mahé et al.’s work to filter out tottering patterns of marginalized kernel and tree pattern kernel.</p>
-<dl class="docutils">
-<dt>G <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The graph to be tramsformed.</dd>
-<dt>node_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>node attribute used as label. The default node label is ‘atom’.</dd>
-<dt>edge_label <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
-<dd>edge attribute used as label. The default edge label is ‘bond_type’.</dd>
-</dl>
-<dl class="docutils">
-<dt>gt <span class="classifier-delimiter">:</span> <span class="classifier">NetworkX graph</span></dt>
-<dd>The transformed graph corresponding to G.</dd>
-</dl>
-<p>[1] Pierre Mahé, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, and Jean-Philippe Vert. Extensions of marginalized graph kernels. In Proceedings of the twenty-first international conference on Machine learning, page 70. ACM, 2004.</p>
-</dd></dl>
-
-</div>
-<div class="section" id="module-pygraph.utils">
-<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-pygraph.utils" title="Permalink to this headline">¶</a></h2>
-<p>Pygraph - utils module</p>
-<dl class="docutils">
-<dt>Implement some methods to manage graphs</dt>
-<dd>graphfiles.py : load .gxl and .ct files
-utils.py : compute some properties on networkX graphs</dd>
-</dl>
-</div>
-</div>
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-(merge-rule "\IeC {\cyrl }" "л" :string)
-(merge-rule "\IeC {\cyrlje }" "љ" :string)
-(merge-rule "\IeC {\cyrm }" "м" :string)
-(merge-rule "\IeC {\cyrn }" "н" :string)
-(merge-rule "\IeC {\cyrnje }" "њ" :string)
-(merge-rule "\IeC {\cyro }" "о" :string)
-(merge-rule "\IeC {\cyrp }" "п" :string)
-(merge-rule "\IeC {\cyrr }" "р" :string)
-(merge-rule "\IeC {\cyrs }" "с" :string)
-(merge-rule "\IeC {\cyrsftsn }" "ь" :string)
-(merge-rule "\IeC {\cyrsh }" "ш" :string)
-(merge-rule "\IeC {\cyrshch }" "щ" :string)
-(merge-rule "\IeC {\cyrt }" "т" :string)
-(merge-rule "\IeC {\cyrtshe }" "ћ" :string)
-(merge-rule "\IeC {\cyru }" "у" :string)
-(merge-rule "\IeC {\cyrushrt }" "ў" :string)
-(merge-rule "\IeC {\cyrv }" "в" :string)
-(merge-rule "\IeC {\cyrya }" "я" :string)
-(merge-rule "\IeC {\cyryi }" "ї" :string)
-(merge-rule "\IeC {\cyryo }" "ё" :string)
-(merge-rule "\IeC {\cyryu }" "ю" :string)
-(merge-rule "\IeC {\cyrz }" "з" :string)
-(merge-rule "\IeC {\cyrzh }" "ж" :string)

docs/_build/latex/LICRlatin2utf8.xdy

@@ -1,236 +0,0 @@
-;; style file for xindy
-;; filename: LICRlatin2utf8.xdy
-;; description: style file for xindy which maps back LaTeX Internal
-;;   Character Representation of letters (as arising in .idx index
-;;   file) to UTF-8 encoding for correct sorting by xindy.
-;; usage: for use with the pdflatex engine,
-;;        *not* for use with xelatex or lualatex.
-;;
-;; This is based upon xindy's distributed file tex/inputenc/utf8.xdy.
-;; The modifications include:
-;;
-;; - Updates for compatibility with current LaTeX macro encoding.
-;;
-;; - Systematic usage of the \IeC {...} mark-up, because mark-up in
-;;   tex/inputenc/utf8.xdy was using it on seemingly random basis, and
-;;   Sphinx coercing of xindy usability for both Latin and Cyrillic scripts
-;;   with pdflatex requires its systematic presence here.
-;;
-;; - Support for some extra letters: Ÿ, Ŋ, ŋ, Œ, œ, IJ, ij, ȷ and ẞ.
-;;
-;;   Indeed Sphinx needs to support for pdflatex engine all Unicode letters
-;;   available in TeX T1 font encoding.  The above letters are found in
-;;   that encoding but not in the Latin1, 2, 3 charsets which are those
-;;   covered by original tex/inputenc/utf8.xdy.
-;;
-;; - There is a problem that ȷ is not supported out-of-the box by LaTeX
-;;   with inputenc, one must add explicitely
-;;       \DeclareUnicodeCharacter{0237}{\j}
-;;   to preamble of LaTeX document.  However this character is not supported
-;;   by the TeX "times" font used by default by Sphinx for pdflatex engine.
-;;
-;; - ẞ needs \DeclareUnicodeCharacter{1E9E}{\SS} (but ß needs no extra set-up).
-;;
-;; - U+02DB (˛) and U+02D9 (˙) are also not supported by inputenc
-;;   out of the box and require
-;;       \DeclareUnicodeCharacter{02DB}{\k{}}
-;;       \DeclareUnicodeCharacter{02D9}{\.{}}
-;;   to be added to preamble.
-;;
-;; - U+0127 ħ and U+0126 Ħ are absent from TeX T1+TS1 font encodings.
-;;
-;; - Characters Ŋ and ŋ are not supported by TeX font "times" used by
-;;   default by Sphinx for pdflatex engine but they are supported by
-;;   some TeX fonts, in particular by the default LaTeX font for T1
-;;   encoding.
-;;
-;; - " and ~ must be escaped as ~" and resp. ~~ in xindy merge rules.
-;;
-;; Contributed by the Sphinx team, July 2018.
-;;
-;; See sphinx.xdy for superior figures, as they are escaped by LaTeX writer.
-(merge-rule "\IeC {\textonesuperior }" "¹" :string)
-(merge-rule "\IeC {\texttwosuperior }" "²" :string)
-(merge-rule "\IeC {\textthreesuperior }" "³" :string)
-(merge-rule "\IeC {\'a}" "á" :string)
-(merge-rule "\IeC {\'A}" "Á" :string)
-(merge-rule "\IeC {\`a}" "à" :string)
-(merge-rule "\IeC {\`A}" "À" :string)
-(merge-rule "\IeC {\^a}" "â" :string)
-(merge-rule "\IeC {\^A}" "Â" :string)
-(merge-rule "\IeC {\~"a}" "ä" :string)
-(merge-rule "\IeC {\~"A}" "Ä" :string)
-(merge-rule "\IeC {\~~a}" "ã" :string)
-(merge-rule "\IeC {\~~A}" "Ã" :string)
-(merge-rule "\IeC {\c c}" "ç" :string)
-(merge-rule "\IeC {\c C}" "Ç" :string)
-(merge-rule "\IeC {\'c}" "ć" :string)
-(merge-rule "\IeC {\'C}" "Ć" :string)
-(merge-rule "\IeC {\^c}" "ĉ" :string)
-(merge-rule "\IeC {\^C}" "Ĉ" :string)
-(merge-rule "\IeC {\.c}" "ċ" :string)
-(merge-rule "\IeC {\.C}" "Ċ" :string)
-(merge-rule "\IeC {\c s}" "ş" :string)
-(merge-rule "\IeC {\c S}" "Ş" :string)
-(merge-rule "\IeC {\c t}" "ţ" :string)
-(merge-rule "\IeC {\c T}" "Ţ" :string)
-(merge-rule "\IeC {\-}" "­" :string); soft hyphen
-(merge-rule "\IeC {\textdiv }" "÷" :string)
-(merge-rule "\IeC {\'e}" "é" :string)
-(merge-rule "\IeC {\'E}" "É" :string)
-(merge-rule "\IeC {\`e}" "è" :string)
-(merge-rule "\IeC {\`E}" "È" :string)
-(merge-rule "\IeC {\^e}" "ê" :string)
-(merge-rule "\IeC {\^E}" "Ê" :string)
-(merge-rule "\IeC {\~"e}" "ë" :string)
-(merge-rule "\IeC {\~"E}" "Ë" :string)
-(merge-rule "\IeC {\^g}" "ĝ" :string)
-(merge-rule "\IeC {\^G}" "Ĝ" :string)
-(merge-rule "\IeC {\.g}" "ġ" :string)
-(merge-rule "\IeC {\.G}" "Ġ" :string)
-(merge-rule "\IeC {\^h}" "ĥ" :string)
-(merge-rule "\IeC {\^H}" "Ĥ" :string)
-(merge-rule "\IeC {\H o}" "ő" :string)
-(merge-rule "\IeC {\H O}" "Ő" :string)
-(merge-rule "\IeC {\textacutedbl }" "˝" :string)
-(merge-rule "\IeC {\H u}" "ű" :string)
-(merge-rule "\IeC {\H U}" "Ű" :string)
-(merge-rule "\IeC {\ae }" "æ" :string)
-(merge-rule "\IeC {\AE }" "Æ" :string)
-(merge-rule "\IeC {\textcopyright }" "©" :string)
-(merge-rule "\IeC {\c \ }" "¸" :string)
-(merge-rule "\IeC {\dh }" "ð" :string)
-(merge-rule "\IeC {\DH }" "Ð" :string)
-(merge-rule "\IeC {\dj }" "đ" :string)
-(merge-rule "\IeC {\DJ }" "Đ" :string)
-(merge-rule "\IeC {\guillemotleft }" "«" :string)
-(merge-rule "\IeC {\guillemotright }" "»" :string)
-(merge-rule "\IeC {\'\i }" "í" :string)
-(merge-rule "\IeC {\`\i }" "ì" :string)
-(merge-rule "\IeC {\^\i }" "î" :string)
-(merge-rule "\IeC {\~"\i }" "ï" :string)
-(merge-rule "\IeC {\i }" "ı" :string)
-(merge-rule "\IeC {\^\j }" "ĵ" :string)
-(merge-rule "\IeC {\k {}}" "˛" :string)
-(merge-rule "\IeC {\l }" "ł" :string)
-(merge-rule "\IeC {\L }" "Ł" :string)
-(merge-rule "\IeC {\nobreakspace }" " " :string)
-(merge-rule "\IeC {\o }" "ø" :string)
-(merge-rule "\IeC {\O }" "Ø" :string)
-(merge-rule "\IeC {\textsterling }" "£" :string)
-(merge-rule "\IeC {\textparagraph }" "¶" :string)
-(merge-rule "\IeC {\ss }" "ß" :string)
-(merge-rule "\IeC {\textsection }" "§" :string)
-(merge-rule "\IeC {\textbrokenbar }" "¦" :string)
-(merge-rule "\IeC {\textcent }" "¢" :string)
-(merge-rule "\IeC {\textcurrency }" "¤" :string)
-(merge-rule "\IeC {\textdegree }" "°" :string)
-(merge-rule "\IeC {\textexclamdown }" "¡" :string)
-(merge-rule "\IeC {\texthbar }" "ħ" :string)
-(merge-rule "\IeC {\textHbar }" "Ħ" :string)
-(merge-rule "\IeC {\textonehalf }" "½" :string)
-(merge-rule "\IeC {\textonequarter }" "¼" :string)
-(merge-rule "\IeC {\textordfeminine }" "ª" :string)
-(merge-rule "\IeC {\textordmasculine }" "º" :string)
-(merge-rule "\IeC {\textperiodcentered }" "·" :string)
-(merge-rule "\IeC {\textquestiondown }" "¿" :string)
-(merge-rule "\IeC {\textregistered }" "®" :string)
-(merge-rule "\IeC {\textthreequarters }" "¾" :string)
-(merge-rule "\IeC {\textyen }" "¥" :string)
-(merge-rule "\IeC {\th }" "þ" :string)
-(merge-rule "\IeC {\TH }" "Þ" :string)
-(merge-rule "\IeC {\'I}" "Í" :string)
-(merge-rule "\IeC {\`I}" "Ì" :string)
-(merge-rule "\IeC {\^I}" "Î" :string)
-(merge-rule "\IeC {\~"I}" "Ï" :string)
-(merge-rule "\IeC {\.I}" "İ" :string)
-(merge-rule "\IeC {\^J}" "Ĵ" :string)
-(merge-rule "\IeC {\k a}" "ą" :string)
-(merge-rule "\IeC {\k A}" "Ą" :string)
-(merge-rule "\IeC {\k e}" "ę" :string)
-(merge-rule "\IeC {\k E}" "Ę" :string)
-(merge-rule "\IeC {\'l}" "ĺ" :string)
-(merge-rule "\IeC {\'L}" "Ĺ" :string)
-(merge-rule "\IeC {\textlnot }" "¬" :string)
-(merge-rule "\IeC {\textmu }" "µ" :string)
-(merge-rule "\IeC {\'n}" "ń" :string)
-(merge-rule "\IeC {\'N}" "Ń" :string)
-(merge-rule "\IeC {\~~n}" "ñ" :string)
-(merge-rule "\IeC {\~~N}" "Ñ" :string)
-(merge-rule "\IeC {\'o}" "ó" :string)
-(merge-rule "\IeC {\'O}" "Ó" :string)
-(merge-rule "\IeC {\`o}" "ò" :string)
-(merge-rule "\IeC {\`O}" "Ò" :string)
-(merge-rule "\IeC {\^o}" "ô" :string)
-(merge-rule "\IeC {\^O}" "Ô" :string)
-(merge-rule "\IeC {\~"o}" "ö" :string)
-(merge-rule "\IeC {\~"O}" "Ö" :string)
-(merge-rule "\IeC {\~~o}" "õ" :string)
-(merge-rule "\IeC {\~~O}" "Õ" :string)
-(merge-rule "\IeC {\textpm }" "±" :string)
-(merge-rule "\IeC {\r a}" "å" :string)
-(merge-rule "\IeC {\r A}" "Å" :string)
-(merge-rule "\IeC {\'r}" "ŕ" :string)
-(merge-rule "\IeC {\'R}" "Ŕ" :string)
-(merge-rule "\IeC {\r u}" "ů" :string)
-(merge-rule "\IeC {\r U}" "Ů" :string)
-(merge-rule "\IeC {\'s}" "ś" :string)
-(merge-rule "\IeC {\'S}" "Ś" :string)
-(merge-rule "\IeC {\^s}" "ŝ" :string)
-(merge-rule "\IeC {\^S}" "Ŝ" :string)
-(merge-rule "\IeC {\textasciidieresis }" "¨" :string)
-(merge-rule "\IeC {\textasciimacron }" "¯" :string)
-(merge-rule "\IeC {\.{}}" "˙" :string)
-(merge-rule "\IeC {\textasciiacute }" "´" :string)
-(merge-rule "\IeC {\texttimes }" "×" :string)
-(merge-rule "\IeC {\u a}" "ă" :string)
-(merge-rule "\IeC {\u A}" "Ă" :string)
-(merge-rule "\IeC {\u g}" "ğ" :string)
-(merge-rule "\IeC {\u G}" "Ğ" :string)
-(merge-rule "\IeC {\textasciibreve }" "˘" :string)
-(merge-rule "\IeC {\'u}" "ú" :string)
-(merge-rule "\IeC {\'U}" "Ú" :string)
-(merge-rule "\IeC {\`u}" "ù" :string)
-(merge-rule "\IeC {\`U}" "Ù" :string)
-(merge-rule "\IeC {\^u}" "û" :string)
-(merge-rule "\IeC {\^U}" "Û" :string)
-(merge-rule "\IeC {\~"u}" "ü" :string)
-(merge-rule "\IeC {\~"U}" "Ü" :string)
-(merge-rule "\IeC {\u u}" "ŭ" :string)
-(merge-rule "\IeC {\u U}" "Ŭ" :string)
-(merge-rule "\IeC {\v c}" "č" :string)
-(merge-rule "\IeC {\v C}" "Č" :string)
-(merge-rule "\IeC {\v d}" "ď" :string)
-(merge-rule "\IeC {\v D}" "Ď" :string)
-(merge-rule "\IeC {\v e}" "ě" :string)
-(merge-rule "\IeC {\v E}" "Ě" :string)
-(merge-rule "\IeC {\v l}" "ľ" :string)
-(merge-rule "\IeC {\v L}" "Ľ" :string)
-(merge-rule "\IeC {\v n}" "ň" :string)
-(merge-rule "\IeC {\v N}" "Ň" :string)
-(merge-rule "\IeC {\v r}" "ř" :string)
-(merge-rule "\IeC {\v R}" "Ř" :string)
-(merge-rule "\IeC {\v s}" "š" :string)
-(merge-rule "\IeC {\v S}" "Š" :string)
-(merge-rule "\IeC {\textasciicaron }" "ˇ" :string)
-(merge-rule "\IeC {\v t}" "ť" :string)
-(merge-rule "\IeC {\v T}" "Ť" :string)
-(merge-rule "\IeC {\v z}" "ž" :string)
-(merge-rule "\IeC {\v Z}" "Ž" :string)
-(merge-rule "\IeC {\'y}" "ý" :string)
-(merge-rule "\IeC {\'Y}" "Ý" :string)
-(merge-rule "\IeC {\~"y}" "ÿ" :string)
-(merge-rule "\IeC {\'z}" "ź" :string)
-(merge-rule "\IeC {\'Z}" "Ź" :string)
-(merge-rule "\IeC {\.z}" "ż" :string)
-(merge-rule "\IeC {\.Z}" "Ż" :string)
-;; letters not in Latin1, 2, 3 but available in TeX T1 font encoding
-(merge-rule "\IeC {\~"Y}" "Ÿ" :string)
-(merge-rule "\IeC {\NG }" "Ŋ" :string)
-(merge-rule "\IeC {\ng }" "ŋ" :string)
-(merge-rule "\IeC {\OE }" "Œ" :string)
-(merge-rule "\IeC {\oe }" "œ" :string)
-(merge-rule "\IeC {\IJ }" "IJ" :string)
-(merge-rule "\IeC {\ij }" "ij" :string)
-(merge-rule "\IeC {\j }" "ȷ" :string)
-(merge-rule "\IeC {\SS }" "ẞ" :string)

docs/_build/latex/LatinRules.xdy

@@ -1,607 +0,0 @@
-;; style file for xindy
-;; filename: LatinRules.xdy
-;;
-;; It is based upon xindy's files lang/general/utf8.xdy and
-;; lang/general/utf8-lang.xdy which implement
-;; "a general sorting order for Western European languages"
-;;
-;; The aim for Sphinx is to be able to index in a Cyrillic document
-;; also terms using the Latin alphabets, inclusive of letters
-;; with diacritics.  To this effect the xindy rules from lang/general
-;; got manually re-coded to avoid collisions with the encoding
-;; done by xindy for sorting words in Cyrillic languages, which was
-;; observed not to use bytes with octal encoding 0o266 or higher.
-;;
-;; So here we use only 0o266 or higher bytes.
-;; (Ŋ, ŋ, IJ, and ij are absent from
-;; lang/general/utf8.xdy and not included here)
-;; Contributed by the Sphinx team, 2018.
-
-(define-letter-group "A" :prefixes ("¶"))
-(define-letter-group "B" :after "A" :prefixes ("·"))
-(define-letter-group "C" :after "B" :prefixes ("¸"))
-(define-letter-group "D" :after "C" :prefixes ("¹"))
-(define-letter-group "E" :after "D" :prefixes ("º"))
-(define-letter-group "F" :after "E" :prefixes ("»"))
-(define-letter-group "G" :after "F" :prefixes ("¼"))
-(define-letter-group "H" :after "G" :prefixes ("½"))
-(define-letter-group "I" :after "H" :prefixes ("¾"))
-(define-letter-group "J" :after "I" :prefixes ("¿"))
-(define-letter-group "K" :after "J" :prefixes ("À"))
-(define-letter-group "L" :after "K" :prefixes ("Á"))
-(define-letter-group "M" :after "L" :prefixes ("Â"))
-(define-letter-group "N" :after "M" :prefixes ("Ã"))
-(define-letter-group "O" :after "N" :prefixes ("Ä"))
-(define-letter-group "P" :after "O" :prefixes ("È"))
-(define-letter-group "Q" :after "P" :prefixes ("Ê"))
-(define-letter-group "R" :after "Q" :prefixes ("Ë"))
-(define-letter-group "S" :after "R" :prefixes ("Ð"))
-(define-letter-group "T" :after "S" :prefixes ("Ú"))
-(define-letter-group "U" :after "T" :prefixes ("à"))
-(define-letter-group "V" :after "U" :prefixes ("å"))
-(define-letter-group "W" :after "V" :prefixes ("æ"))
-(define-letter-group "X" :after "W" :prefixes ("ë"))
-(define-letter-group "Y" :after "X" :prefixes ("í"))
-(define-letter-group "Z" :after "Y" :prefixes ("ð"))
-
-(define-rule-set "sphinx-xy-alphabetize"
-
-  :rules  (("À" "¶" :string)
-           ("Ä‚" "¶" :string)
-           ("â" "¶" :string)
-           ("Ä" "¶" :string)
-           ("à" "¶" :string)
-           ("Ã…" "¶" :string)
-           ("Ã" "¶" :string)
-           ("Ã�" "¶" :string)
-           ("á" "¶" :string)
-           ("ã" "¶" :string)
-           ("Â" "¶" :string)
-           ("ă" "¶" :string)
-           ("Ã¥" "¶" :string)
-           ("Ä…" "¶" :string)
-           ("ä" "¶" :string)
-           ("Ä„" "¶" :string)
-           ("æ" "¶º" :string)
-           ("Æ" "¶º" :string)
-           ("ć" "¸" :string)
-           ("ĉ" "¸" :string)
-           ("ç" "¸" :string)
-           ("ÄŒ" "¸" :string)
-           ("Ä�" "¸" :string)
-           ("Ĉ" "¸" :string)
-           ("Ç" "¸" :string)
-           ("Ć" "¸" :string)
-           ("Ä�" "¹" :string)
-           ("Ä�" "¹" :string)
-           ("ÄŽ" "¹" :string)
-           ("Ä‘" "¹" :string)
-           ("ê" "º" :string)
-           ("Ę" "º" :string)
-           ("Äš" "º" :string)
-           ("ë" "º" :string)
-           ("Ä›" "º" :string)
-           ("é" "º" :string)
-           ("È" "º" :string)
-           ("Ë" "º" :string)
-           ("É" "º" :string)
-           ("è" "º" :string)
-           ("Ê" "º" :string)
-           ("Ä™" "º" :string)
-           ("Ä�" "¼" :string)
-           ("ÄŸ" "¼" :string)
-           ("Äž" "¼" :string)
-           ("Äœ" "¼" :string)
-           ("Ä¥" "½" :string)
-           ("Ĥ" "½" :string)
-           ("Ã�" "¾" :string)
-           ("Ã�" "¾" :string)
-           ("ï" "¾" :string)
-           ("ÃŽ" "¾" :string)
-           ("î" "¾" :string)
-           ("ı" "¾" :string)
-           ("Ä°" "¾" :string)
-           ("í" "¾" :string)
-           ("ÃŒ" "¾" :string)
-           ("ì" "¾" :string)
-           ("Ä´" "¿" :string)
-           ("ĵ" "¿" :string)
-           ("Å‚" "Á" :string)
-           ("Å�" "Á" :string)
-           ("ľ" "Á" :string)
-           ("Ľ" "Á" :string)
-           ("Å„" "Ã" :string)
-           ("Ń" "Ã" :string)
-           ("ñ" "Ã" :string)
-           ("ň" "Ã" :string)
-           ("Ñ" "Ã" :string)
-           ("Ň" "Ã" :string)
-           ("Õ" "Ä" :string)
-           ("Å�" "Ä" :string)
-           ("ó" "Ä" :string)
-           ("ö" "Ä" :string)
-           ("ô" "Ä" :string)
-           ("Å‘" "Ä" :string)
-           ("Ø" "Ä" :string)
-           ("Ö" "Ä" :string)
-           ("õ" "Ä" :string)
-           ("Ô" "Ä" :string)
-           ("ø" "Ä" :string)
-           ("Ó" "Ä" :string)
-           ("Ã’" "Ä" :string)
-           ("ò" "Ä" :string)
-           ("œ" "ĺ" :string)
-           ("Œ" "ĺ" :string)
-           ("Ř" "Ë" :string)
-           ("Å™" "Ë" :string)
-           ("Å”" "Ë" :string)
-           ("Å•" "Ë" :string)
-           ("Å�" "Ð" :string)
-           ("Åš" "Ð" :string)
-           ("È™" "Ð" :string)
-           ("ÅŸ" "Ð" :string)
-           ("Åœ" "Ð" :string)
-           ("Å›" "Ð" :string)
-           ("Ș" "Ð" :string)
-           ("Å¡" "Ð" :string)
-           ("Åž" "Ð" :string)
-           ("Å " "Ð" :string)
-           ("ß" "ÐÐ" :string)
-           ("Èš" "Ú" :string)
-           ("Ť" "Ú" :string)
-           ("È›" "Ú" :string)
-           ("Å¥" "Ú" :string)
-           ("û" "à" :string)
-           ("Å­" "à" :string)
-           ("ů" "à" :string)
-           ("ű" "à" :string)
-           ("ù" "à" :string)
-           ("Ŭ" "à" :string)
-           ("Ù" "à" :string)
-           ("Å°" "à" :string)
-           ("Ãœ" "à" :string)
-           ("Å®" "à" :string)
-           ("ú" "à" :string)
-           ("Ú" "à" :string)
-           ("Û" "à" :string)
-           ("ü" "à" :string)
-           ("ÿ" "í" :string)
-           ("Ã�" "í" :string)
-           ("Ÿ" "í" :string)
-           ("ý" "í" :string)
-           ("Å»" "ð" :string)
-           ("Ž" "ð" :string)
-           ("Ź" "ð" :string)
-           ("ž" "ð" :string)
-           ("ż" "ð" :string)
-           ("ź" "ð" :string)
-           ("a" "¶" :string)
-           ("A" "¶" :string)
-           ("b" "·" :string)
-           ("B" "·" :string)
-           ("c" "¸" :string)
-           ("C" "¸" :string)
-           ("d" "¹" :string)
-           ("D" "¹" :string)
-           ("e" "º" :string)
-           ("E" "º" :string)
-           ("F" "»" :string)
-           ("f" "»" :string)
-           ("G" "¼" :string)
-           ("g" "¼" :string)
-           ("H" "½" :string)
-           ("h" "½" :string)
-           ("i" "¾" :string)
-           ("I" "¾" :string)
-           ("J" "¿" :string)
-           ("j" "¿" :string)
-           ("K" "À" :string)
-           ("k" "À" :string)
-           ("L" "Á" :string)
-           ("l" "Á" :string)
-           ("M" "Â" :string)
-           ("m" "Â" :string)
-           ("n" "Ã" :string)
-           ("N" "Ã" :string)
-           ("O" "Ä" :string)
-           ("o" "Ä" :string)
-           ("p" "È" :string)
-           ("P" "È" :string)
-           ("Q" "Ê" :string)
-           ("q" "Ê" :string)
-           ("r" "Ë" :string)
-           ("R" "Ë" :string)
-           ("S" "Ð" :string)
-           ("s" "Ð" :string)
-           ("t" "Ú" :string)
-           ("T" "Ú" :string)
-           ("u" "à" :string)
-           ("U" "à" :string)
-           ("v" "å" :string)
-           ("V" "å" :string)
-           ("W" "æ" :string)
-           ("w" "æ" :string)
-           ("x" "ë" :string)
-           ("X" "ë" :string)
-           ("Y" "í" :string)
-           ("y" "í" :string)
-           ("z" "ð" :string)
-           ("Z" "ð" :string)
-           ))
-
-(define-rule-set "sphinx-xy-resolve-diacritics"
-
-  :rules  (("Ĥ" "£" :string)
-           ("ó" "£" :string)
-           ("ľ" "£" :string)
-           ("Ř" "£" :string)
-           ("Ä�" "£" :string)
-           ("Ä�" "£" :string)
-           ("Äš" "£" :string)
-           ("Ä¥" "£" :string)
-           ("ÄŒ" "£" :string)
-           ("Ä´" "£" :string)
-           ("Ä›" "£" :string)
-           ("ž" "£" :string)
-           ("ÄŽ" "£" :string)
-           ("Å™" "£" :string)
-           ("Ž" "£" :string)
-           ("ı" "£" :string)
-           ("Ť" "£" :string)
-           ("á" "£" :string)
-           ("Ä�" "£" :string)
-           ("Ã�" "£" :string)
-           ("ň" "£" :string)
-           ("Å " "£" :string)
-           ("Ň" "£" :string)
-           ("ĵ" "£" :string)
-           ("Å¥" "£" :string)
-           ("Ó" "£" :string)
-           ("ý" "£" :string)
-           ("Äœ" "£" :string)
-           ("Ú" "£" :string)
-           ("Ľ" "£" :string)
-           ("Å¡" "£" :string)
-           ("Ã�" "£" :string)
-           ("ú" "£" :string)
-           ("Åš" "¤" :string)
-           ("ć" "¤" :string)
-           ("Å�" "¤" :string)
-           ("Å‚" "¤" :string)
-           ("Å„" "¤" :string)
-           ("À" "¤" :string)
-           ("Ź" "¤" :string)
-           ("à" "¤" :string)
-           ("Ń" "¤" :string)
-           ("Ä�" "¤" :string)
-           ("ÿ" "¤" :string)
-           ("Å›" "¤" :string)
-           ("Äž" "¤" :string)
-           ("ÄŸ" "¤" :string)
-           ("Ù" "¤" :string)
-           ("Ä°" "¤" :string)
-           ("Ä‘" "¤" :string)
-           ("ù" "¤" :string)
-           ("Èš" "¤" :string)
-           ("é" "¤" :string)
-           ("Å•" "¤" :string)
-           ("Ć" "¤" :string)
-           ("È›" "¤" :string)
-           ("ò" "¤" :string)
-           ("ź" "¤" :string)
-           ("Ã’" "¤" :string)
-           ("Ÿ" "¤" :string)
-           ("Å”" "¤" :string)
-           ("É" "¤" :string)
-           ("ĉ" "¥" :string)
-           ("ô" "¥" :string)
-           ("Ã�" "¥" :string)
-           ("Å�" "¥" :string)
-           ("Å»" "¥" :string)
-           ("Ä‚" "¥" :string)
-           ("Åœ" "¥" :string)
-           ("ñ" "¥" :string)
-           ("Å­" "¥" :string)
-           ("í" "¥" :string)
-           ("È" "¥" :string)
-           ("Ô" "¥" :string)
-           ("Ŭ" "¥" :string)
-           ("ż" "¥" :string)
-           ("Ñ" "¥" :string)
-           ("è" "¥" :string)
-           ("Ĉ" "¥" :string)
-           ("ă" "¥" :string)
-           ("â" "¦" :string)
-           ("û" "¦" :string)
-           ("ê" "¦" :string)
-           ("Õ" "¦" :string)
-           ("õ" "¦" :string)
-           ("È™" "¦" :string)
-           ("ç" "¦" :string)
-           ("Â" "¦" :string)
-           ("Ê" "¦" :string)
-           ("Û" "¦" :string)
-           ("Ç" "¦" :string)
-           ("ì" "¦" :string)
-           ("ÃŒ" "¦" :string)
-           ("Ș" "¦" :string)
-           ("ö" "§" :string)
-           ("Ö" "§" :string)
-           ("ÅŸ" "§" :string)
-           ("ů" "§" :string)
-           ("ë" "§" :string)
-           ("ã" "§" :string)
-           ("î" "§" :string)
-           ("ÃŽ" "§" :string)
-           ("Ã" "§" :string)
-           ("Åž" "§" :string)
-           ("Å®" "§" :string)
-           ("Ë" "§" :string)
-           ("ï" "¨" :string)
-           ("Å�" "¨" :string)
-           ("Ã�" "¨" :string)
-           ("Ę" "¨" :string)
-           ("Å‘" "¨" :string)
-           ("Ãœ" "¨" :string)
-           ("Ã…" "¨" :string)
-           ("ü" "¨" :string)
-           ("Ä™" "¨" :string)
-           ("Ã¥" "¨" :string)
-           ("Ä" "©" :string)
-           ("ű" "©" :string)
-           ("Ø" "©" :string)
-           ("ø" "©" :string)
-           ("Å°" "©" :string)
-           ("ä" "©" :string)
-           ("Ä„" "ª" :string)
-           ("Ä…" "ª" :string)
-           ("Å“" "ÿ" :string)
-           ("ß" "ÿ" :string)
-           ("Æ" "ÿ" :string)
-           ("Å’" "ÿ" :string)
-           ("æ" "ÿ" :string)
-           ("e" "¢" :string)
-           ("t" "¢" :string)
-           ("L" "¢" :string)
-           ("Y" "¢" :string)
-           ("J" "¢" :string)
-           ("a" "¢" :string)
-           ("p" "¢" :string)
-           ("u" "¢" :string)
-           ("j" "¢" :string)
-           ("b" "¢" :string)
-           ("G" "¢" :string)
-           ("U" "¢" :string)
-           ("F" "¢" :string)
-           ("H" "¢" :string)
-           ("i" "¢" :string)
-           ("z" "¢" :string)
-           ("c" "¢" :string)
-           ("l" "¢" :string)
-           ("A" "¢" :string)
-           ("Q" "¢" :string)
-           ("w" "¢" :string)
-           ("D" "¢" :string)
-           ("R" "¢" :string)
-           ("d" "¢" :string)
-           ("s" "¢" :string)
-           ("r" "¢" :string)
-           ("k" "¢" :string)
-           ("v" "¢" :string)
-           ("m" "¢" :string)
-           ("P" "¢" :string)
-           ("y" "¢" :string)
-           ("K" "¢" :string)
-           ("q" "¢" :string)
-           ("S" "¢" :string)
-           ("I" "¢" :string)
-           ("C" "¢" :string)
-           ("M" "¢" :string)
-           ("Z" "¢" :string)
-           ("T" "¢" :string)
-           ("W" "¢" :string)
-           ("B" "¢" :string)
-           ("h" "¢" :string)
-           ("x" "¢" :string)
-           ("X" "¢" :string)
-           ("f" "¢" :string)
-           ("E" "¢" :string)
-           ("V" "¢" :string)
-           ("N" "¢" :string)
-           ("O" "¢" :string)
-           ("o" "¢" :string)
-           ("g" "¢" :string)
-           ("n" "¢" :string)
-           ))
-
-(define-rule-set "sphinx-xy-resolve-case"
-
-  :rules  (("Ú" "8" :string)
-           ("Ÿ" "8" :string)
-           ("Ç" "8" :string)
-           ("Ĉ" "8" :string)
-           ("Å”" "8" :string)
-           ("Ľ" "8" :string)
-           ("Å®" "8" :string)
-           ("�" "8" :string)
-           ("É" "8" :string)
-           ("Ë" "8" :string)
-           ("Ș" "8" :string)
-           ("Ì" "8" :string)
-           ("Ê" "8" :string)
-           ("Ň" "8" :string)
-           ("Ä„" "8" :string)
-           ("Å " "8" :string)
-           ("Û" "8" :string)
-           ("Åž" "8" :string)
-           ("Ć" "8" :string)
-           ("Ã’" "8" :string)
-           ("Ĝ" "8" :string)
-           ("Ñ" "8" :string)
-           ("Ó" "8" :string)
-           ("ÃŽ" "8" :string)
-           ("�" "8" :string)
-           ("Ã" "8" :string)
-           ("Èš" "8" :string)
-           ("Ã…" "8" :string)
-           ("Äž" "8" :string)
-           ("Ü" "8" :string)
-           ("È" "8" :string)
-           ("Ô" "8" :string)
-           ("Ä°" "8" :string)
-           ("Å°" "8" :string)
-           ("Ù" "8" :string)
-           ("Ŭ" "8" :string)
-           ("Â" "8" :string)
-           ("Ť" "8" :string)
-           ("Ń" "8" :string)
-           ("ÄŽ" "8" :string)
-           ("Ź" "8" :string)
-           ("Ž" "8" :string)
-           ("�" "8" :string)
-           ("Ŝ" "8" :string)
-           ("Č" "8" :string)
-           ("Ä´" "8" :string)
-           ("Ö" "8" :string)
-           ("Ø" "8" :string)
-           ("Å»" "8" :string)
-           ("�" "8" :string)
-           ("Ä‚" "8" :string)
-           ("Äš" "8" :string)
-           ("�" "8" :string)
-           ("Õ" "8" :string)
-           ("Ę" "8" :string)
-           ("�" "8" :string)
-           ("À" "8" :string)
-           ("Ĥ" "8" :string)
-           ("Ä" "8" :string)
-           ("Åš" "8" :string)
-           ("Ř" "8" :string)
-           ("�" "8" :string)
-           ("Å’" "89" :string)
-           ("Æ" "89" :string)
-           ("ì" "9" :string)
-           ("è" "9" :string)
-           ("Ä…" "9" :string)
-           ("Å¡" "9" :string)
-           ("ú" "9" :string)
-           ("Ã¥" "9" :string)
-           ("ă" "9" :string)
-           ("Ä™" "9" :string)
-           ("ü" "9" :string)
-           ("ź" "9" :string)
-           ("ò" "9" :string)
-           ("Å¥" "9" :string)
-           ("È›" "9" :string)
-           ("ĵ" "9" :string)
-           ("Å•" "9" :string)
-           ("ż" "9" :string)
-           ("ä" "9" :string)
-           ("ý" "9" :string)
-           ("ù" "9" :string)
-           ("á" "9" :string)
-           ("é" "9" :string)
-           ("�" "9" :string)
-           ("ň" "9" :string)
-           ("Å›" "9" :string)
-           ("ø" "9" :string)
-           ("í" "9" :string)
-           ("Ä‘" "9" :string)
-           ("ı" "9" :string)
-           ("ÄŸ" "9" :string)
-           ("î" "9" :string)
-           ("ã" "9" :string)
-           ("à" "9" :string)
-           ("Å™" "9" :string)
-           ("Å‘" "9" :string)
-           ("ů" "9" :string)
-           ("È™" "9" :string)
-           ("ÿ" "9" :string)
-           ("ë" "9" :string)
-           ("Å­" "9" :string)
-           ("ç" "9" :string)
-           ("ű" "9" :string)
-           ("ñ" "9" :string)
-           ("õ" "9" :string)
-           ("Ä›" "9" :string)
-           ("ÅŸ" "9" :string)
-           ("ž" "9" :string)
-           ("�" "9" :string)
-           ("�" "9" :string)
-           ("Å„" "9" :string)
-           ("û" "9" :string)
-           ("Å‚" "9" :string)
-           ("�" "9" :string)
-           ("Ä¥" "9" :string)
-           ("ê" "9" :string)
-           ("ô" "9" :string)
-           ("ĉ" "9" :string)
-           ("â" "9" :string)
-           ("ć" "9" :string)
-           ("ï" "9" :string)
-           ("ö" "9" :string)
-           ("ľ" "9" :string)
-           ("ó" "9" :string)
-           ("æ" "99" :string)
-           ("ß" "99" :string)
-           ("Å“" "99" :string)
-           ("N" "8" :string)
-           ("V" "8" :string)
-           ("O" "8" :string)
-           ("X" "8" :string)
-           ("E" "8" :string)
-           ("P" "8" :string)
-           ("K" "8" :string)
-           ("T" "8" :string)
-           ("Z" "8" :string)
-           ("M" "8" :string)
-           ("C" "8" :string)
-           ("I" "8" :string)
-           ("S" "8" :string)
-           ("B" "8" :string)
-           ("W" "8" :string)
-           ("D" "8" :string)
-           ("R" "8" :string)
-           ("H" "8" :string)
-           ("F" "8" :string)
-           ("Q" "8" :string)
-           ("A" "8" :string)
-           ("G" "8" :string)
-           ("U" "8" :string)
-           ("J" "8" :string)
-           ("Y" "8" :string)
-           ("L" "8" :string)
-           ("o" "9" :string)
-           ("n" "9" :string)
-           ("g" "9" :string)
-           ("x" "9" :string)
-           ("f" "9" :string)
-           ("y" "9" :string)
-           ("q" "9" :string)
-           ("h" "9" :string)
-           ("w" "9" :string)
-           ("s" "9" :string)
-           ("d" "9" :string)
-           ("v" "9" :string)
-           ("k" "9" :string)
-           ("r" "9" :string)
-           ("m" "9" :string)
-           ("z" "9" :string)
-           ("c" "9" :string)
-           ("i" "9" :string)
-           ("l" "9" :string)
-           ("b" "9" :string)
-           ("j" "9" :string)
-           ("a" "9" :string)
-           ("p" "9" :string)
-           ("u" "9" :string)
-           ("t" "9" :string)
-           ("e" "9" :string)
-           ))
-
-(use-rule-set :run 0
-	      :rule-set ("sphinx-xy-alphabetize"))
-(use-rule-set :run 1
-	      :rule-set ("sphinx-xy-resolve-diacritics"))
-(use-rule-set :run 2
-	      :rule-set ("sphinx-xy-resolve-case"))

docs/_build/latex/Makefile

@@ -1,68 +0,0 @@
-# Makefile for Sphinx LaTeX output
-
-ALLDOCS = $(basename $(wildcard *.tex))
-ALLPDF = $(addsuffix .pdf,$(ALLDOCS))
-ALLDVI = $(addsuffix .dvi,$(ALLDOCS))
-ALLXDV =
-ALLPS  = $(addsuffix .ps,$(ALLDOCS))
-ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg)
-
-# Prefix for archive names
-ARCHIVEPREFIX =
-# Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file)
-export LATEXOPTS =
-# Additional latexmk options
-LATEXMKOPTS =
-# format: pdf or dvi (used only by archive targets)
-FMT = pdf
-
-LATEX = latexmk -dvi
-PDFLATEX = latexmk -pdf -dvi- -ps-
-
-
-%.png %.gif %.jpg %.jpeg: FORCE_MAKE
-	extractbb '$@'
-
-%.dvi: %.tex FORCE_MAKE
-	$(LATEX) $(LATEXMKOPTS) '$<'
-
-%.ps: %.dvi
-	dvips '$<'
-
-%.pdf: %.tex FORCE_MAKE
-	$(PDFLATEX) $(LATEXMKOPTS) '$<'
-
-all: $(ALLPDF)
-
-all-dvi: $(ALLDVI)
-
-all-ps: $(ALLPS)
-
-all-pdf: $(ALLPDF)
-
-zip: all-$(FMT)
-	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
-	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
-	zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT)
-	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
-
-tar: all-$(FMT)
-	mkdir $(ARCHIVEPREFIX)docs-$(FMT)
-	cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT)
-	tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT)
-	rm -r $(ARCHIVEPREFIX)docs-$(FMT)
-
-gz: tar
-	gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz
-
-bz2: tar
-	bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
-
-xz: tar
-	xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar
-
-clean:
-	rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk
-
-.PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz
-.PHONY: FORCE_MAKE

docs/_build/latex/footnotehyper-sphinx.sty

@@ -1,269 +0,0 @@
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{footnotehyper-sphinx}%
- [2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)]
-%%
-%% Package: footnotehyper-sphinx
-%% Version: based on footnotehyper.sty 2017/03/07 v1.0
-%% as available at https://www.ctan.org/pkg/footnotehyper
-%% License: the one applying to Sphinx
-%%
-%% Refer to the PDF documentation  at https://www.ctan.org/pkg/footnotehyper for
-%% the code comments.
-%%
-%% Differences:
-%% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up),
-%% 2. use of \spx@opt@BeforeFootnote from sphinx.sty,
-%% 3. use of \sphinxunactivateextrasandspace from sphinx.sty,
-%% 4. macro definition \sphinxfootnotemark,
-%% 5. macro definition \sphinxlongtablepatch
-%% 6. replaced an \undefined by \@undefined
-\DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}%
-\ProcessOptions\relax
-\newbox\FNH@notes
-\newdimen\FNH@width
-\let\FNH@colwidth\columnwidth
-\newif\ifFNH@savingnotes
-\AtBeginDocument {%
-    \let\FNH@latex@footnote    \footnote
-    \let\FNH@latex@footnotetext\footnotetext
-    \let\FNH@H@@footnotetext   \@footnotetext
-    \newenvironment{savenotes}
-        {\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}%
-    \let\spewnotes      \FNH@spewnotes
-    \let\footnote       \FNH@footnote
-    \let\footnotetext   \FNH@footnotetext
-    \let\endfootnote    \FNH@endfntext
-    \let\endfootnotetext\FNH@endfntext
-    \@ifpackageloaded{hyperref}
-     {\ifHy@hyperfootnotes
-         \let\FNH@H@@footnotetext\H@@footnotetext
-      \else
-         \let\FNH@hyper@fntext\FNH@nohyp@fntext
-      \fi}%
-     {\let\FNH@hyper@fntext\FNH@nohyp@fntext}%
-}%
-\def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}%
-\def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}%
-\def\FNH@fntext #1{%
-  \ifx\ifmeasuring@\@undefined
-    \expandafter\@secondoftwo\else\expandafter\@firstofone\fi
-% these two lines modified for Sphinx (tabulary compatibility):
-    {\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}%
-    {\ifx\equation$\expandafter\@gobbletwo\fi #1}%$
-}%
-\long\def\FNH@hyper@fntext@i#1{%
-  \global\setbox\FNH@notes\vbox
-  {\unvbox\FNH@notes
-   \FNH@startnote
-   \@makefntext
-    {\rule\z@\footnotesep\ignorespaces
-     \ifHy@nesting\expandafter\ltx@firstoftwo
-             \else\expandafter\ltx@secondoftwo
-     \fi
-     {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}%
-     {\Hy@raisedlink
-       {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}%
-       {\relax}}%
-      \let\@currentHref\Hy@footnote@currentHref
-      \let\@currentlabelname\@empty
-      #1}%
-     \@finalstrut\strutbox
-    }%
-   \FNH@endnote
-  }%
-}%
-\long\def\FNH@nohyp@fntext@i#1{%
-  \global\setbox\FNH@notes\vbox
-  {\unvbox\FNH@notes
-   \FNH@startnote
-   \@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}%
-   \FNH@endnote
-  }%
-}%
-\def\FNH@startnote{%
-  \hsize\FNH@colwidth
-  \interlinepenalty\interfootnotelinepenalty
-  \reset@font\footnotesize
-  \floatingpenalty\@MM
-  \@parboxrestore
-  \protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}%
-  \color@begingroup
-}%
-\def\FNH@endnote{\color@endgroup}%
-\def\FNH@savenotes{%
-  \begingroup
-  \ifFNH@savingnotes\else
-    \FNH@savingnotestrue
-    \let\@footnotetext    \FNH@hyper@fntext
-    \let\@mpfootnotetext  \FNH@hyper@fntext
-    \let\H@@mpfootnotetext\FNH@nohyp@fntext
-    \FNH@width\columnwidth
-    \let\FNH@colwidth\FNH@width
-    \global\setbox\FNH@notes\box\voidb@x
-    \let\FNH@thempfn\thempfn
-    \let\FNH@mpfn\@mpfn
-    \ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi
-    \expandafter\def\expandafter\@minipagerestore\expandafter{%
-      \@minipagerestore
-      \let\thempfn\FNH@thempfn
-      \let\@mpfn\FNH@mpfn
-    }%
-  \fi
-}%
-\def\FNH@spewnotes {%
-  \endgroup
-  \ifFNH@savingnotes\else
-   \ifvoid\FNH@notes\else
-    \begingroup
-     \let\@makefntext\@empty
-     \let\@finalstrut\@gobble
-     \let\rule\@gobbletwo
-     \FNH@H@@footnotetext{\unvbox\FNH@notes}%
-    \endgroup
-   \fi
-  \fi
-}%
-\def\FNH@footnote@envname    {footnote}%
-\def\FNH@footnotetext@envname{footnotetext}%
-\def\FNH@footnote{%
-% this line added for Sphinx:
-    \spx@opt@BeforeFootnote
-    \ifx\@currenvir\FNH@footnote@envname
-        \expandafter\FNH@footnoteenv
-    \else
-        \expandafter\FNH@latex@footnote
-    \fi
-}%
-\def\FNH@footnoteenv{%
-% this line added for Sphinx (footnotes in parsed literal blocks):
-    \catcode13=5 \sphinxunactivateextrasandspace
-    \@ifnextchar[%
-      \FNH@footnoteenv@i %]
-      {\stepcounter\@mpfn
-       \protected@xdef\@thefnmark{\thempfn}%
-       \@footnotemark
-       \def\FNH@endfntext@fntext{\@footnotetext}%
-       \FNH@startfntext}%
-}%
-\def\FNH@footnoteenv@i[#1]{%
-    \begingroup
-     \csname c@\@mpfn\endcsname #1\relax
-     \unrestored@protected@xdef\@thefnmark{\thempfn}%
-    \endgroup
-    \@footnotemark
-    \def\FNH@endfntext@fntext{\@footnotetext}%
-    \FNH@startfntext
-}%
-\def\FNH@footnotetext{%
-    \ifx\@currenvir\FNH@footnotetext@envname
-        \expandafter\FNH@footnotetextenv
-    \else
-        \expandafter\FNH@latex@footnotetext
-    \fi
-}%
-\def\FNH@footnotetextenv{%
-    \@ifnextchar[%
-      \FNH@footnotetextenv@i %]
-      {\protected@xdef\@thefnmark{\thempfn}%
-       \def\FNH@endfntext@fntext{\@footnotetext}%
-       \FNH@startfntext}%
-}%
-\def\FNH@footnotetextenv@i[#1]{%
-    \begingroup
-     \csname c@\@mpfn\endcsname #1\relax
-     \unrestored@protected@xdef\@thefnmark{\thempfn}%
-    \endgroup
-    \ifFNH@savingnotes
-      \def\FNH@endfntext@fntext{\FNH@nohyp@fntext}%
-    \else
-      \def\FNH@endfntext@fntext{\FNH@H@@footnotetext}%
-    \fi
-    \FNH@startfntext
-}%
-\def\FNH@startfntext{%
-  \setbox\z@\vbox\bgroup
-    \FNH@startnote
-    \FNH@prefntext
-    \rule\z@\footnotesep\ignorespaces
-}%
-\def\FNH@endfntext {%
-    \@finalstrut\strutbox
-    \FNH@postfntext
-    \FNH@endnote
-    \egroup
-  \begingroup
-    \let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo
-    \FNH@endfntext@fntext {\unvbox\z@}%
-  \endgroup
-}%
-\AtBeginDocument{%
-   \let\FNH@@makefntext\@makefntext
-   \ifx\@makefntextFB\@undefined
-   \expandafter\@gobble\else\expandafter\@firstofone\fi
-   {\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else
-                         \let\FNH@@makefntext\@makefntextORI\fi}%
-   \expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}%
-               \FNH@@@1.2!3?4,\FNH@@@\relax
-}%
-\long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{%
-    \ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi
-    \FNH@bad@makefntext@alert
-    {\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}%
-}%
-\def\FNH@check@b #1\relax{%
-    \expandafter\expandafter\expandafter\FNH@check@c
-    \expandafter\meaning\expandafter\FNH@prefntext
-    \meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax
-}%
-\def\FNH@check@c #11.2!3?4,#2#3\relax{%
-    \ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert
-}%
-% slight reformulation for Sphinx
-\def\FNH@bad@makefntext@alert{%
-  \PackageWarningNoLine{footnotehyper-sphinx}%
-    {Footnotes will be sub-optimal, sorry. This is due to the document class or^^J
-  some package modifying macro \string\@makefntext.^^J
-  You can try to report this incompatibility at^^J
-  https://github.com/sphinx-doc/sphinx with this info:}%
-    \typeout{\meaning\@makefntext}%
-    \let\FNH@prefntext\@empty\let\FNH@postfntext\@empty
-}%
-% this macro from original footnote.sty is not used anymore by Sphinx
-% but for simplicity sake let's just keep it as is
-\def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%]
-\def\FNH@msne@i #1{%
-  \expandafter\let\csname FNH$#1\expandafter\endcsname %$
-                  \csname #1\endcsname
-  \expandafter\let\csname endFNH$#1\expandafter\endcsname %$
-                  \csname end#1\endcsname
-  \FNH@msne@ii[#1]{FNH$#1}%$
-}%
-\def\FNH@msne@ii[#1]#2{%
-  \expandafter\edef\csname#1\endcsname{%
-    \noexpand\savenotes
-    \expandafter\noexpand\csname#2\endcsname
-  }%
-  \expandafter\edef\csname end#1\endcsname{%
-    \expandafter\noexpand\csname end#2\endcsname
-    \noexpand\expandafter
-    \noexpand\spewnotes
-    \noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi
-  }%
-}%
-% end of footnotehyper 2017/02/16 v0.99
-% some extras for Sphinx :
-% \sphinxfootnotemark: usable in section titles and silently removed from TOCs.
-\def\sphinxfootnotemark [#1]%
-   {\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote
-                             \protect\footnotemark[#1]\fi}%
-\AtBeginDocument{%
-   % let hyperref less complain
-   \pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}%
-   % to obtain hyperlinked footnotes in longtable environment we must replace
-   % hyperref's patch of longtable's patch of \@footnotetext by our own
-   \let\LT@p@ftntext\FNH@hyper@fntext
-   % this *requires* longtable to be used always wrapped in savenotes environment
-}%
-\endinput
-%%
-%% End of file `footnotehyper-sphinx.sty'.