Merge pull request #16 from pnnl/develop

Develop

.gitignore

@@ -1,4 +1,6 @@
 .DS_Store
 gitmerge.sh
 dist
-hypernetx.egg-info
+hypernetx.egg-info
+logfiles/
+stashmerge.sh

DISCLAIMER.txt

@@ -0,0 +1,22 @@
+This material was prepared as an account of work sponsored by an agency of the
+United States Government.  Neither the United States Government nor the United
+States Department of Energy, nor Battelle, nor any of their employees, nor any
+jurisdiction or organization that has cooperated in the development of these
+materials, makes any warranty, express or implied, or assumes any legal
+liability or responsibility for the accuracy, completeness, or usefulness or
+any information, apparatus, product, software, or process disclosed, or
+represents that its use would not infringe privately owned rights.
+
+Reference herein to any specific commercial product, process, or service by
+trade name, trademark, manufacturer, or otherwise does not necessarily
+constitute or imply its endorsement, recommendation, or favoring by the United
+States Government or any agency thereof, or Battelle Memorial Institute. The
+views and opinions of authors expressed herein do not necessarily state or
+reflect those of the United States Government or any agency thereof.
+
+		 PACIFIC NORTHWEST NATIONAL LABORATORY
+			      operated by
+				BATTELLE
+				for the
+		   UNITED STATES DEPARTMENT OF ENERGY
+		    under Contract DE-AC05-76RL01830

README.md

@@ -98,8 +98,4 @@ License
 
 Released under the 3-Clause BSD license (see License.rst)
 
-Notice
-------
-This material was prepared as an account of work sponsored by an agency of the United States Government.  Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.
-Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
 

README.rst

@@ -99,9 +99,5 @@ License
 
 Released under the 3-Clause BSD license (see :ref:`license`)
 
-Notice
-------
-This material was prepared as an account of work sponsored by an agency of the United States Government.  Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights.
-Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
 
 

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: ada116df8ac3aed05d3fffeba82a4a72
+config: c8e13f7db8cf9bc74590b2bdc1fee533
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_modules/classes/entity.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes.entity &mdash; HyperNetX 0.2.0 documentation</title>
+  <title>classes.entity &mdash; HyperNetX 0.2.5 documentation</title>
 
 
 
@@ -1187,7 +1187,7 @@ <h1>Source code for classes.entity</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2018 Battelle Memorial Institute.
+        &copy; Copyright 2018 Battelle Memorial Institute
 
     </p>
   </div>
@@ -1206,22 +1206,15 @@ <h1>Source code for classes.entity</h1><div class="highlight"><pre>
 
 
 
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../../',
-            VERSION:'0.2.0',
-            LANGUAGE:'None',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true,
-            SOURCELINK_SUFFIX: '.txt'
-        };
-    </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 type="text/javascript" src="../../_static/copybutton.js"></script>
-      <script 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" 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 type="text/javascript" src="../../_static/copybutton.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>
+
 
 
 

docs/build/_modules/classes/hypergraph.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>classes.hypergraph &mdash; HyperNetX 0.2.0 documentation</title>
+  <title>classes.hypergraph &mdash; HyperNetX 0.2.5 documentation</title>
 
 
 
@@ -1079,13 +1079,13 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
 
 <div class="viewcode-block" id="Hypergraph.restrict_to_nodes"><a class="viewcode-back" href="../../classes/classes.html#classes.hypergraph.Hypergraph.restrict_to_nodes">[docs]</a>	<span class="k">def</span> <span class="nf">restrict_to_nodes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">nodeset</span><span class="p">,</span><span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 		<span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">		Constructs a new hypergraph by restricint the edges in hypergraph to</span>
-<span class="sd">		the nodes in nodesetdes restricted to what is in nodeset.</span>
+<span class="sd">		Constructs a new hypergraph by restricting the edges in the hypergraph to</span>
+<span class="sd">		the nodes referenced by nodeset.</span>
 
 <span class="sd">		Parameters</span>
 <span class="sd">		----------</span>
-<span class="sd">		nodeset: iterable of hashables or Entities</span>
-<span class="sd">			A subset of elements of the hypergraph nodes</span>
+<span class="sd">		nodeset: iterable of hashables</span>
+<span class="sd">			References a subset of elements of self.nodes</span>
 
 <span class="sd">		name: string, optional, default: None</span>
 
@@ -1100,9 +1100,9 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
 		<span class="n">newedgeset</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
 		<span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">memberships</span><span class="p">:</span>
 			<span class="k">if</span> <span class="n">e</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">edges</span><span class="p">:</span>
-				<span class="n">newe</span> <span class="o">=</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">.</span><span class="n">restrict_to</span><span class="p">(</span><span class="n">nodeset</span><span class="p">,</span><span class="n">e</span><span class="p">)</span>
-				<span class="k">if</span> <span class="ow">not</span> <span class="n">newe</span><span class="o">.</span><span class="n">is_empty</span><span class="p">:</span>
-					<span class="n">newedgeset</span><span class="p">[</span><span class="n">e</span><span class="p">]</span> <span class="o">=</span> <span class="n">newe</span>
+				<span class="n">temp</span> <span class="o">=</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">.</span><span class="n">uidset</span><span class="o">.</span><span class="n">intersection</span><span class="p">(</span><span class="n">nodeset</span><span class="p">)</span>
+				<span class="k">if</span> <span class="n">temp</span><span class="p">:</span>
+					<span class="n">newedgeset</span><span class="p">[</span><span class="n">e</span><span class="p">]</span> <span class="o">=</span> <span class="n">Entity</span><span class="p">(</span><span class="n">e</span><span class="p">,</span><span class="n">temp</span><span class="p">,</span><span class="o">**</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">.</span><span class="n">properties</span><span class="p">)</span>
 		<span class="k">return</span> <span class="n">Hypergraph</span><span class="p">(</span><span class="n">newedgeset</span><span class="p">,</span><span class="n">name</span><span class="p">)</span> </div>
 
 <div class="viewcode-block" id="Hypergraph.toplexes"><a class="viewcode-back" href="../../classes/classes.html#classes.hypergraph.Hypergraph.toplexes">[docs]</a>	<span class="k">def</span> <span class="nf">toplexes</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span><span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span><span class="n">collapse</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span><span class="n">use_reps</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span><span class="n">return_counts</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span> 
@@ -1639,7 +1639,7 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2018 Battelle Memorial Institute.
+        &copy; Copyright 2018 Battelle Memorial Institute
 
     </p>
   </div>
@@ -1658,22 +1658,15 @@ <h1>Source code for classes.hypergraph</h1><div class="highlight"><pre>
 
 
 
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../../',
-            VERSION:'0.2.0',
-            LANGUAGE:'None',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true,
-            SOURCELINK_SUFFIX: '.txt'
-        };
-    </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 type="text/javascript" src="../../_static/copybutton.js"></script>
-      <script 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" 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 type="text/javascript" src="../../_static/copybutton.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>
+
 
 
 

docs/build/_modules/drawing/rubber_band.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing.rubber_band &mdash; HyperNetX 0.2.0 documentation</title>
+  <title>drawing.rubber_band &mdash; HyperNetX 0.2.5 documentation</title>
 
 
 
@@ -590,6 +590,7 @@ <h1>Source code for drawing.rubber_band</h1><div class="highlight"><pre>
                                <span class="n">color</span><span class="o">=</span><span class="n">edges_kwargs</span><span class="p">[</span><span class="s1">&#39;edgecolors&#39;</span><span class="p">],</span>
                                <span class="n">backgroundcolor</span><span class="o">=</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="mi">1</span><span class="p">,</span> <span class="n">label_alpha</span><span class="p">),</span>
                                <span class="n">labels</span><span class="o">=</span><span class="n">labels</span><span class="p">,</span>
+                               <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span>
                                <span class="o">**</span><span class="n">edge_labels_kwargs</span>
                                <span class="p">)</span>
 
@@ -621,8 +622,8 @@ <h1>Source code for drawing.rubber_band</h1><div class="highlight"><pre>
     <span class="k">else</span><span class="p">:</span>
         <span class="n">ax</span><span class="o">.</span><span class="n">axis</span><span class="p">(</span><span class="s1">&#39;equal&#39;</span><span class="p">)</span>
 
-    <span class="n">plt</span><span class="o">.</span><span class="n">xticks</span><span class="p">([])</span>
-    <span class="n">plt</span><span class="o">.</span><span class="n">yticks</span><span class="p">([])</span></div>
+    <span class="n">ax</span><span class="o">.</span><span class="n">xaxis</span><span class="o">.</span><span class="n">set_ticks</span><span class="p">([])</span>
+    <span class="n">ax</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">set_ticks</span><span class="p">([])</span></div>
 
 </pre></div>
 
@@ -636,7 +637,7 @@ <h1>Source code for drawing.rubber_band</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2018 Battelle Memorial Institute.
+        &copy; Copyright 2018 Battelle Memorial Institute
 
     </p>
   </div>
@@ -655,22 +656,15 @@ <h1>Source code for drawing.rubber_band</h1><div class="highlight"><pre>
 
 
 
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../../',
-            VERSION:'0.2.0',
-            LANGUAGE:'None',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true,
-            SOURCELINK_SUFFIX: '.txt'
-        };
-    </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 type="text/javascript" src="../../_static/copybutton.js"></script>
-      <script 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" 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 type="text/javascript" src="../../_static/copybutton.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>
+
 
 
 

docs/build/_modules/drawing/two_column.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>drawing.two_column &mdash; HyperNetX 0.2.0 documentation</title>
+  <title>drawing.two_column &mdash; HyperNetX 0.2.5 documentation</title>
 
 
 
@@ -359,7 +359,7 @@ <h1>Source code for drawing.two_column</h1><div class="highlight"><pre>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2018 Battelle Memorial Institute.
+        &copy; Copyright 2018 Battelle Memorial Institute
 
     </p>
   </div>
@@ -378,22 +378,15 @@ <h1>Source code for drawing.two_column</h1><div class="highlight"><pre>
 
 
 
-    <script type="text/javascript">
-        var DOCUMENTATION_OPTIONS = {
-            URL_ROOT:'../../',
-            VERSION:'0.2.0',
-            LANGUAGE:'None',
-            COLLAPSE_INDEX:false,
-            FILE_SUFFIX:'.html',
-            HAS_SOURCE:  true,
-            SOURCELINK_SUFFIX: '.txt'
-        };
-    </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 type="text/javascript" src="../../_static/copybutton.js"></script>
-      <script 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" 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 type="text/javascript" src="../../_static/copybutton.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>
+