Merge pull request #71 from pnnl/develop

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pnnl · Oct 29, 2021 · 02ef33a · 02ef33a
2 parents c390a3d + bcbb046
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diff --git a/docs/build/.buildinfo b/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: 580a8748e0d0b3613c35d39d96ee687c
+config: 38df5440d6c68b719b03372bcc1f1ddd
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/.doctrees/algorithms/algorithms.doctree b/docs/build/.doctrees/algorithms/algorithms.doctree
diff --git a/docs/build/.doctrees/classes/classes.doctree b/docs/build/.doctrees/classes/classes.doctree
diff --git a/docs/build/.doctrees/drawing/drawing.doctree b/docs/build/.doctrees/drawing/drawing.doctree
diff --git a/docs/build/.doctrees/environment.pickle b/docs/build/.doctrees/environment.pickle
diff --git a/docs/build/.doctrees/index.doctree b/docs/build/.doctrees/index.doctree
diff --git a/docs/build/.doctrees/modularity.doctree b/docs/build/.doctrees/modularity.doctree
diff --git a/docs/build/.doctrees/overview/index.doctree b/docs/build/.doctrees/overview/index.doctree
diff --git a/docs/build/_images/ModularityScreenShot.png b/docs/build/_images/ModularityScreenShot.png
diff --git a/docs/build/_modules/algorithms/contagion/animation.html b/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 1.1.3 documentation</title>
+  <title>algorithms.contagion.animation &mdash; HyperNetX 1.2 documentation</title>
 
 
 
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                1.1
+                1.2
               </div>
 
 
@@ -101,6 +101,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../core.html">HyperNetX Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../nwhy.html">NWHypergraph C++ Optimization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../widget.html">HyperNetX Visualization Widget</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../modularity.html">Algorithms: Modularity and Clustering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../publications.html">Publications</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../license.html">License</a></li>
 </ul>

diff --git a/docs/build/_modules/algorithms/contagion/epidemics.html b/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 1.1.3 documentation</title>
+  <title>algorithms.contagion.epidemics &mdash; HyperNetX 1.2 documentation</title>
 
 
 
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                1.1
+                1.2
               </div>
 
 
@@ -101,6 +101,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../core.html">HyperNetX Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../nwhy.html">NWHypergraph C++ Optimization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../widget.html">HyperNetX Visualization Widget</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../modularity.html">Algorithms: Modularity and Clustering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../publications.html">Publications</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../license.html">License</a></li>
 </ul>

diff --git a/docs/build/_modules/algorithms/generative_models.html b/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 1.1.3 documentation</title>
+  <title>algorithms.generative_models &mdash; HyperNetX 1.2 documentation</title>
 
 
 
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                1.1
+                1.2
               </div>
 
 
@@ -101,6 +101,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../core.html">HyperNetX Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../nwhy.html">NWHypergraph C++ Optimization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../widget.html">HyperNetX Visualization Widget</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modularity.html">Algorithms: Modularity and Clustering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../publications.html">Publications</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../license.html">License</a></li>
 </ul>
@@ -200,13 +201,15 @@ <h1>Source code for algorithms.generative_models</h1><div class="highlight"><pre
 <span class="sd">    -------</span>
 <span class="sd">    HyperNetX Hypergraph object</span>
 
+
 <span class="sd">    Example::</span>
+<span class="sd">    </span>
+<span class="sd">    &gt;&gt;&gt; import hypernetx.algorithms.generative_models as gm</span>
+<span class="sd">    &gt;&gt;&gt; n = 1000</span>
+<span class="sd">    &gt;&gt;&gt; m = n</span>
+<span class="sd">    &gt;&gt;&gt; p = 0.01</span>
+<span class="sd">    &gt;&gt;&gt; H = gm.erdos_renyi_hypergraph(n, m, p)</span>
 
-<span class="sd">        &gt;&gt;&gt; import hypernetx.algorithms.generative_models as gm</span>
-<span class="sd">        &gt;&gt;&gt; n = 1000</span>
-<span class="sd">        &gt;&gt;&gt; m = n</span>
-<span class="sd">        &gt;&gt;&gt; p = 0.01</span>
-<span class="sd">        &gt;&gt;&gt; H = gm.erdos_renyi_hypergraph(n, m, p)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="k">if</span> <span class="n">node_labels</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">edge_labels</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
@@ -254,12 +257,12 @@ <h1>Source code for algorithms.generative_models</h1><div class="highlight"><pre
 
 <span class="sd">    Example::</span>
 
-<span class="sd">        &gt;&gt;&gt; import hypernetx.algorithms.generative_models as gm</span>
-<span class="sd">        &gt;&gt;&gt; import random</span>
-<span class="sd">        &gt;&gt;&gt; n = 100</span>
-<span class="sd">        &gt;&gt;&gt; k1 = {i : random.randint(1, 100) for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; k2 = {i : sorted(k1.values())[i] for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; H = gm.chung_lu_hypergraph(k1, k2)</span>
+<span class="sd">    &gt;&gt;&gt; import hypernetx.algorithms.generative_models as gm</span>
+<span class="sd">    &gt;&gt;&gt; import random</span>
+<span class="sd">    &gt;&gt;&gt; n = 100</span>
+<span class="sd">    &gt;&gt;&gt; k1 = {i : random.randint(1, 100) for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; k2 = {i : sorted(k1.values())[i] for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; H = gm.chung_lu_hypergraph(k1, k2)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="c1"># sort dictionary by degree in decreasing order</span>
@@ -337,13 +340,13 @@ <h1>Source code for algorithms.generative_models</h1><div class="highlight"><pre
 
 <span class="sd">    Example::</span>
 
-<span class="sd">        &gt;&gt;&gt; n = 100</span>
-<span class="sd">        &gt;&gt;&gt; k1 = {i : random.randint(1, 100) for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; k2 = {i : sorted(k1.values())[i] for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; g1 = {i : random.choice([0, 1]) for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; g2 = {i : random.choice([0, 1]) for i in range(n)}</span>
-<span class="sd">        &gt;&gt;&gt; omega = np.array([[100, 10], [10, 100]])</span>
-<span class="sd">        &gt;&gt;&gt; H = gm.dcsbm_hypergraph(k1, k2, g1, g2, omega)</span>
+<span class="sd">    &gt;&gt;&gt; n = 100</span>
+<span class="sd">    &gt;&gt;&gt; k1 = {i : random.randint(1, 100) for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; k2 = {i : sorted(k1.values())[i] for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; g1 = {i : random.choice([0, 1]) for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; g2 = {i : random.choice([0, 1]) for i in range(n)}</span>
+<span class="sd">    &gt;&gt;&gt; omega = np.array([[100, 10], [10, 100]])</span>
+<span class="sd">    &gt;&gt;&gt; H = gm.dcsbm_hypergraph(k1, k2, g1, g2, omega)</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="c1"># sort dictionary by degree in decreasing order</span>

diff --git a/docs/build/_modules/algorithms/homology_mod2.html b/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 1.1.3 documentation</title>
+  <title>algorithms.homology_mod2 &mdash; HyperNetX 1.2 documentation</title>
 
 
 
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                1.1
+                1.2
               </div>
 
 
@@ -101,6 +101,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../core.html">HyperNetX Packages</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../nwhy.html">NWHypergraph C++ Optimization</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../widget.html">HyperNetX Visualization Widget</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../modularity.html">Algorithms: Modularity and Clustering</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../publications.html">Publications</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../license.html">License</a></li>
 </ul>
@@ -930,7 +931,7 @@ <h1>Source code for algorithms.homology_mod2</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="homology_basis"><a class="viewcode-back" href="../../algorithms/algorithms.html#algorithms.homology_mod2.homology_basis">[docs]</a><span class="k">def</span> <span class="nf">homology_basis</span><span class="p">(</span><span class="n">bd</span><span class="p">,</span> <span class="n">k</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">boundary</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Compute a basis for the kth-simplicial homology group, $H_k$, defined by a</span>
-<span class="sd">    chain complex $C$ with boundary maps given by bd $= \{k:\partial_k$\}$</span>
+<span class="sd">    chain complex $C$ with boundary maps given by bd $= \{k:\partial_k \}$</span>
 
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>