Merge pull request #69 from pnnl/develop

Develop

docs/build/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 96469606dd28c6a046e9b1d637a7aa64
+config: 580a8748e0d0b3613c35d39d96ee687c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_modules/algorithms/contagion/animation.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.contagion.animation &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.contagion.animation &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 
@@ -268,7 +268,7 @@ <h1>Source code for algorithms.contagion.animation</h1><div class="highlight"><p
         <span class="p">}</span>
 
         <span class="c1"># draw hypergraph</span>
-        <span class="n">hnx</span><span class="o">.</span><span class="n">drawing</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span>
+        <span class="n">hnx</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span>
             <span class="n">H</span><span class="p">,</span>
             <span class="n">node_radius</span><span class="o">=</span><span class="n">node_radius</span><span class="p">,</span>
             <span class="n">nodes_kwargs</span><span class="o">=</span><span class="n">nodeStyle</span><span class="p">,</span>

docs/build/_modules/algorithms/contagion/epidemics.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.contagion.epidemics &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.contagion.epidemics &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/algorithms/generative_models.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.generative_models &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.generative_models &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/algorithms/homology_mod2.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.homology_mod2 &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.homology_mod2 &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/algorithms/laplacians_clustering.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.laplacians_clustering &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.laplacians_clustering &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/algorithms/s_centrality_measures.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.s_centrality_measures &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.s_centrality_measures &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/classes/entity.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>classes.entity &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>classes.entity &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/classes/hypergraph.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>classes.hypergraph &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>classes.hypergraph &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 
@@ -854,34 +854,25 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">isstatic</span><span class="p">:</span>
             <span class="n">ndx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_id</span><span class="p">(</span><span class="n">node</span><span class="p">)</span>
-            <span class="c1">#             if s == 1:</span>
-            <span class="c1">#                 return np.sum(self.edges.data.T[1] == ndx)</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">nwhy</span><span class="p">:</span>
+            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">nwhy</span><span class="p">:</span>                
                 <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">degree</span><span class="p">(</span><span class="n">ndx</span><span class="p">,</span> <span class="n">min_size</span><span class="o">=</span><span class="n">s</span><span class="p">,</span> <span class="n">max_size</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-
             <span class="k">else</span><span class="p">:</span>
-                <span class="k">if</span> <span class="n">max_size</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-                    <span class="n">ids</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span>
-                        <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edge_size_dist</span><span class="p">())</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">max_size</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
-                    <span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
-                <span class="k">else</span><span class="p">:</span>
-                    <span class="n">ids</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edge_size_dist</span><span class="p">())</span> <span class="o">&gt;=</span> <span class="n">s</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
-                <span class="n">imat</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">incidence_matrix</span><span class="p">()</span>
-                <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">imat</span><span class="p">[</span><span class="n">ndx</span><span class="p">,</span> <span class="n">ids</span><span class="p">])</span>
+                <span class="n">memberships</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="o">.</span><span class="n">memberships</span><span class="p">[</span><span class="n">node</span><span class="p">])</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">memberships</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">nodes</span><span class="p">[</span><span class="n">node</span><span class="p">]</span><span class="o">.</span><span class="n">memberships</span><span class="p">)</span>
-            <span class="k">if</span> <span class="n">max_size</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</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">e</span>
-                        <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">memberships</span>
-                        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">e</span><span class="p">])</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">max_size</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
-                    <span class="p">)</span>
+                                  
+        <span class="k">if</span> <span class="n">max_size</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</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">e</span>
+                    <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">memberships</span>
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">e</span><span class="p">])</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">s</span><span class="p">,</span> <span class="n">max_size</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
                 <span class="p">)</span>
-            <span class="k">elif</span> <span class="n">s</span> <span class="o">&gt;</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="nb">set</span><span class="p">(</span><span class="n">e</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">memberships</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">e</span><span class="p">])</span> <span class="o">&gt;=</span> <span class="n">s</span><span class="p">))</span>
-            <span class="k">else</span><span class="p">:</span>
-                <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">memberships</span><span class="p">)</span></div>
+            <span class="p">)</span>
+        <span class="k">elif</span> <span class="n">s</span> <span class="o">&gt;</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="nb">set</span><span class="p">(</span><span class="n">e</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">memberships</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">e</span><span class="p">])</span> <span class="o">&gt;=</span> <span class="n">s</span><span class="p">))</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="n">memberships</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="Hypergraph.size"><a class="viewcode-back" href="../../classes/classes.html#classes.hypergraph.Hypergraph.size">[docs]</a>    <span class="k">def</span> <span class="nf">size</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">edge</span><span class="p">,</span> <span class="n">nodeset</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
@@ -902,6 +893,7 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
             <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">nodeset</span><span class="p">)</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="bp">self</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="k">else</span><span class="p">:</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">nwhy</span><span class="p">:</span>
+                <span class="n">edx</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_id</span><span class="p">(</span><span class="n">edge</span><span class="p">,</span><span class="n">edges</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
                 <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">g</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">edx</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="k">return</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="n">edge</span><span class="p">])</span></div>

docs/build/_modules/classes/staticentity.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>classes.staticentity &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>classes.staticentity &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/drawing/rubber_band.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>drawing.rubber_band &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>drawing.rubber_band &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/drawing/two_column.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>drawing.two_column &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>drawing.two_column &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/drawing/util.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>drawing.util &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>drawing.util &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/index.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Overview: module code &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Overview: module code &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_modules/reports/descriptive_stats.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>reports.descriptive_stats &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>reports.descriptive_stats &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.1.2',
+    VERSION: '1.1.3',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/build/algorithms/algorithms.contagion.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms.contagion package &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms.contagion package &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/algorithms/algorithms.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms package &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms package &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/algorithms/modules.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>algorithms &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>algorithms &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/classes/classes.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>classes package &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>classes package &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/classes/modules.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>classes &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>classes &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/core.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>HyperNetX Packages &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>HyperNetX Packages &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/drawing/drawing.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>drawing package &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>drawing package &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/drawing/modules.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>drawing &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>drawing &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/genindex.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Index &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Index &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/glossary.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Glossary of HNX terms &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Glossary of HNX terms &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/home.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>HyperNetX (HNX) &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>HyperNetX (HNX) &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/index.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>HyperNetX (HNX) &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>HyperNetX (HNX) &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/install.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Installing HyperNetX &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Installing HyperNetX &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/license.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>License &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>License &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/nwhy.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>NWHy &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>NWHy &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/overview/index.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Overview &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Overview &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/publications.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Publications &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Publications &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/py-modindex.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Python Module Index &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>Python Module Index &mdash; HyperNetX 1.1.3 documentation</title>
 
 
 

docs/build/reports/modules.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>reports &mdash; HyperNetX 1.1.2 documentation</title>
+  <title>reports &mdash; HyperNetX 1.1.3 documentation</title>