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<!DOCTYPE html>
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<title>Installation and Getting Started — Cortix 0.1.0 documentation</title>
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<div class="section" id="installation-and-getting-started">
<h1>Installation and Getting Started<a class="headerlink" href="#installation-and-getting-started" title="Permalink to this headline">¶</a></h1>
<p><strong>Pythons</strong>: Python 3.4, 3.5, 3.6, 3.7</p>
<p><strong>Platforms</strong>: Linux/Unix (inluding macOS)</p>
<p><strong>PyPI package name</strong>: <a class="reference external" href="https://pypi.org/project/cortix/">cortix</a></p>
<dl class="simple">
<dt><strong>Dependencies</strong>:</dt><dd><ul class="simple">
<li><p><a class="reference external" href="https://mpi4py.readthedocs.io/en/stable/">mpi4py</a></p></li>
<li><p><a class="reference external" href="https://pandas.pydata.org/">pandas</a></p></li>
<li><p><a class="reference external" href="https://networkx.github.io/">networkx</a></p></li>
<li><p><a class="reference external" href="https://matplotlib.org/">matplotlib</a></p></li>
<li><p><a class="reference external" href="https://www.numpy.org/">numpy</a></p></li>
<li><p><a class="reference external" href="https://www.scipy.org/">scipy</a></p></li>
<li><p><a class="reference external" href="https://www.pytest.org/">pytest</a></p></li>
</ul>
</dd>
</dl>
<p><strong>Documentation as PDF</strong>: <a class="reference external" href="https://dpploy.github.io/cortix/Cortix.pdf">download latest</a></p>
<div class="section" id="install-cortix">
<h2>Install <code class="docutils literal notranslate"><span class="pre">cortix</span></code><a class="headerlink" href="#install-cortix" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="stable-release-via-pypi">
<h2>Stable Release (via PyPi)<a class="headerlink" href="#stable-release-via-pypi" title="Permalink to this headline">¶</a></h2>
<ol class="arabic">
<li><p>Run the following command in your command line:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">--</span><span class="n">user</span> <span class="n">cortix</span>
</pre></div>
</div>
</li>
</ol>
</div>
<div class="section" id="development-version-from-source">
<h2>Development Version (from source)<a class="headerlink" href="#development-version-from-source" title="Permalink to this headline">¶</a></h2>
<ol class="arabic">
<li><p>Clone the repository:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ git clone https://github.com/dpploy/cortix.git
</pre></div>
</div>
</li>
<li><p>Install the required dependencies listed in <cite>requirements.txt</cite>:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ pip install --user -r cortix/requirements.txt
</pre></div>
</div>
</li>
<li><p>Add <cite>cortix</cite>’s parent path to the <cite>PYTHONPATH</cite> environment variable:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ export PYTHONPATH=$PYTHONPATH:/path/to/dir/containing/cortix
</pre></div>
</div>
</li>
</ol>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The path above is NOT the path to <code class="docutils literal notranslate"><span class="pre">cortix</span></code> itself, but rather the
path to <code class="docutils literal notranslate"><span class="pre">cortix</span></code>’s parent directory. That is, if <code class="docutils literal notranslate"><span class="pre">cortix</span></code> exists in
<code class="docutils literal notranslate"><span class="pre">/some/path/cortix</span></code>, be sure to add <code class="docutils literal notranslate"><span class="pre">/some/path</span></code> to your <code class="docutils literal notranslate"><span class="pre">PYTHONPATH</span></code>.
You may want to add this line to your <code class="docutils literal notranslate"><span class="pre">.bashrc</span></code> in order for it
to be persistent</p>
</div>
</div>
<div class="section" id="testing-your-install">
<h2>Testing your install<a class="headerlink" href="#testing-your-install" title="Permalink to this headline">¶</a></h2>
<p>To test your Cortix install, run the droplet example from the python shell:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">>></span> <span class="kn">from</span> <span class="nn">cortix.examples.console_run</span> <span class="k">import</span> <span class="n">droplet_run</span> <span class="k">as</span> <span class="n">droplet</span>
<span class="o">>></span> <span class="n">droplet</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
</pre></div>
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<a href="https://github.com/dpploy/cortix"><img src="https://cortix.org/logo.jpg" alt="Cortix" style="border:none;"></a>
<h3>About Cortix</h3>
<p>
Cortix is a Python library for network modeling and HPC simulation.
</p>
<p>
Cortix Group <br>
c/o <a href="https://www.uml.edu/innovation-hub">UMass Innovation Hub</a> <br>
110 Canal St., 3rd Floor <br>
Lower, MA 01852
</p>
<p>
<a href="https://www.uml.edu/Engineering/Chemical/faculty/de-Almeida-Valmor.aspx">Prof. V. F. de Almeida, Ph.D.</a></br>
Group Leader <br>
<a href="https://www.uml.edu/Engineering/Chemical">Dept. of Chemical Engineering (Nuclear Program)</a></br>
<a href="https://www.uml.edu/">UMass Lowell</a><br>
</p>
<!---->
<h3><a href="index.html">Table of Contents</a></h3>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="#">Install</a></li>
<li><a href="contents.html">On-line Documentation</a></li>
<li><a href="https://dpploy.github.io/cortix/Cortix.pdf">PDF Documentation</a></li>
<li><a href="license.html">License</a></li>
</ul>
<h3>Cortix Links</h3>
<ul>
<li><a href="https://mybinder.org/v2/gh/dpploy/cortix-nb/master">Run examples: Binder</a></li>
<li><a href="https://nbviewer.jupyter.org/github/dpploy/cortix-nb/tree/master/">View examples: NBViewer</a></li>
<li><a href="https://github.com/dpploy/cortix-nb">Examples repo: GitHub</a></li>
<li><a href="https://pypi.org/project/cortix/">PyPI install</a></li>
<li><a href="https://github.com/dpploy/cortix">GitHub repo</a></li>
<li><a href="https://github.com/dpploy/cortix/issues">Issue Tracker</a></li>
</ul>
<h3>HPC Resources</h3>
<ul>
<li><a href="https://hpc.inl.gov/SitePages/Home.aspx">Idaho National Laboratory HPC</a></li>
<li><a href="http://wiki.umassrc.org/wiki/index.php/Main_Page">UMass Green HPC Cluster </a></li>
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