deploy: a9e387a

Ziaeemehr · Aug 2, 2024 · 2bdfaf1 · 2bdfaf1
commit 2bdfaf1
Show file tree

Hide file tree

Showing 27 changed files with 4,020 additions and 0 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +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: ae5712abed9b5413629774078a318328
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
diff --git a/.nojekyll b/.nojekyll
diff --git a/_modules/index.html b/_modules/index.html
@@ -0,0 +1,80 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Overview: module code &#8212; netsci 0.1.dev1+ga9e387a documentation</title>
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=82a976d7" />
+    <link rel="stylesheet" type="text/css" href="../_static/nature.css?v=0f882399" />
+    <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
+    <script src="../_static/documentation_options.js?v=ee09313d"></script>
+    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">netsci 0.1.dev1+ga9e387a documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="netsci/analysis.html">netsci.analysis</a></li>
+<li><a href="netsci/plot.html">netsci.plot</a></li>
+<li><a href="netsci/utils.html">netsci.utils</a></li>
+</ul>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">netsci 0.1.dev1+ga9e387a documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+    &#169; Copyright 2024, Abolfazl Ziaeemehr.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    </div>
+  </body>
+</html>
diff --git a/_modules/netsci/analysis.html b/_modules/netsci/analysis.html
diff --git a/_modules/netsci/plot.html b/_modules/netsci/plot.html
@@ -0,0 +1,170 @@
+<!DOCTYPE html>
+
+<html lang="en" data-content_root="../../">
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>netsci.plot &#8212; netsci 0.1.dev1+ga9e387a documentation</title>
+    <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=82a976d7" />
+    <link rel="stylesheet" type="text/css" href="../../_static/nature.css?v=0f882399" />
+    <link rel="stylesheet" type="text/css" href="../../_static/graphviz.css?v=fd3f3429" />
+    <script src="../../_static/documentation_options.js?v=ee09313d"></script>
+    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <link rel="index" title="Index" href="../../genindex.html" />
+    <link rel="search" title="Search" href="../../search.html" /> 
+  </head><body>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">netsci 0.1.dev1+ga9e387a documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" accesskey="U">Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">netsci.plot</a></li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+
+  <h1>Source code for netsci.plot</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">itertools</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">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+
+
+
+<div class="viewcode-block" id="plot_graph">
+<a class="viewcode-back" href="../../index.html#netsci.plot.plot_graph">[docs]</a>
+<span class="k">def</span> <span class="nf">plot_graph</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">    Plots a NetworkX graph with customizable options.</span>
+
+<span class="sd">    Parameters</span>
+<span class="sd">    ----------</span>
+<span class="sd">    G : NetworkX graph</span>
+<span class="sd">        A NetworkX graph object (e.g., nx.Graph, nx.DiGraph).</span>
+<span class="sd">    **kwargs : keyword arguments</span>
+<span class="sd">        Additional keyword arguments to customize the plot. These can include:</span>
+<span class="sd">        </span>
+<span class="sd">        node_color : str or list, optional</span>
+<span class="sd">            Color of the nodes (can be a single color or a list of colors).</span>
+<span class="sd">        node_size : int or list, optional</span>
+<span class="sd">            Size of the nodes (single value or list of sizes).</span>
+<span class="sd">        edge_color : str or list, optional</span>
+<span class="sd">            Color of the edges (can be a single color or a list of colors).</span>
+<span class="sd">        width : float, optional</span>
+<span class="sd">            Width of the edges.</span>
+<span class="sd">        with_labels : bool, optional</span>
+<span class="sd">            Whether to draw node labels or not.</span>
+<span class="sd">        font_size : int, optional</span>
+<span class="sd">            Size of the font for node labels.</span>
+<span class="sd">        font_color : str, optional</span>
+<span class="sd">            Color of the font for node labels.</span>
+<span class="sd">        title : str, optional</span>
+<span class="sd">            Title of the plot.</span>
+<span class="sd">        seed : int, optional</span>
+<span class="sd">            Seed for the random layout algorithm.</span>
+<span class="sd">        figsize : tuple, optional</span>
+<span class="sd">            Size of the figure.</span>
+
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="c1"># Extracting optional arguments</span>
+    <span class="n">node_color</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;node_color&quot;</span><span class="p">,</span> <span class="s2">&quot;lightblue&quot;</span><span class="p">)</span>
+    <span class="n">node_size</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;node_size&quot;</span><span class="p">,</span> <span class="mi">300</span><span class="p">)</span>
+    <span class="n">edge_color</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;edge_color&quot;</span><span class="p">,</span> <span class="s2">&quot;black&quot;</span><span class="p">)</span>
+    <span class="n">width</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;width&quot;</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
+    <span class="n">with_labels</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;with_labels&quot;</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+    <span class="n">font_size</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;font_size&quot;</span><span class="p">,</span> <span class="mi">12</span><span class="p">)</span>
+    <span class="n">font_color</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;font_color&quot;</span><span class="p">,</span> <span class="s2">&quot;black&quot;</span><span class="p">)</span>
+    <span class="n">title</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;title&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">seed</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seed&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">edge_labels</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;edge_labels&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+    <span class="n">figsize</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;figsize&quot;</span><span class="p">,</span> <span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">4</span><span class="p">))</span>
+
+    <span class="k">if</span> <span class="s2">&quot;figsize&quot;</span> <span class="ow">in</span> <span class="n">kwargs</span><span class="p">:</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="n">figsize</span><span class="p">)</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">axis</span><span class="p">(</span><span class="s2">&quot;off&quot;</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">seed</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span>  <span class="c1"># Set the random seed for reproducibility</span>
+
+    <span class="c1"># Position nodes using a layout algorithm</span>
+    <span class="n">pos</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">spring_layout</span><span class="p">(</span>
+        <span class="n">G</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="n">seed</span>
+    <span class="p">)</span>  <span class="c1"># You can choose other layouts like nx.circular_layout(G) or nx.kamada_kaway_layout(G)</span>
+
+    <span class="c1"># Draw the network</span>
+    <span class="n">nx</span><span class="o">.</span><span class="n">draw</span><span class="p">(</span>
+        <span class="n">G</span><span class="p">,</span>
+        <span class="n">pos</span><span class="p">,</span>
+        <span class="n">node_color</span><span class="o">=</span><span class="n">node_color</span><span class="p">,</span>
+        <span class="n">node_size</span><span class="o">=</span><span class="n">node_size</span><span class="p">,</span>
+        <span class="n">edge_color</span><span class="o">=</span><span class="n">edge_color</span><span class="p">,</span>
+        <span class="n">width</span><span class="o">=</span><span class="n">width</span><span class="p">,</span>
+        <span class="n">with_labels</span><span class="o">=</span><span class="n">with_labels</span><span class="p">,</span>
+        <span class="n">font_size</span><span class="o">=</span><span class="n">font_size</span><span class="p">,</span>
+        <span class="n">font_color</span><span class="o">=</span><span class="n">font_color</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="k">if</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>
+        <span class="n">nx</span><span class="o">.</span><span class="n">draw_networkx_edge_labels</span><span class="p">(</span><span class="n">G</span><span class="p">,</span> <span class="n">pos</span><span class="p">,</span> <span class="n">edge_labels</span><span class="o">=</span><span class="n">edge_labels</span><span class="p">)</span>
+
+    <span class="c1"># Set the plot title</span>
+    <span class="k">if</span> <span class="n">title</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="n">title</span><span class="p">)</span></div>
+
+
+    <span class="c1"># Show the plot</span>
+    <span class="c1"># plt.show()</span>
+</pre></div>
+
+            <div class="clearer"></div>
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
+        <div class="sphinxsidebarwrapper">
+<search id="searchbox" style="display: none" role="search">
+  <h3 id="searchlabel">Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="../../search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="Related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="../../genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="../../py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="nav-item nav-item-0"><a href="../../index.html">netsci 0.1.dev1+ga9e387a documentation</a> &#187;</li>
+          <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">netsci.plot</a></li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+    &#169; Copyright 2024, Abolfazl Ziaeemehr.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    </div>
+  </body>
+</html>