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Merge pull request #5 from MEDomicsLab/rw-version
integrate the features selection
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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 0c6cb496db24d1d9f60d1aa1f06bb5d2
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tags: 645f666f9bcd5a90fca523b33c5a78b7

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‎docs/build/html/Documentation.html‎

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<!DOCTYPE html>
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<html class="writer-html5" lang="en" >
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Documentation &mdash; MEDfl 0.1.0 documentation</title>
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<link rel="index" title="Index" href="genindex.html" />
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<p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
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<li class="toctree-l1"><a class="reference internal" href="Installation.html">Installation</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Documentation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration File</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#database-management">Database management</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#netmanager">NetManager</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#transfer-learning">Transfer Learning</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-manager">Learning Manager</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-results">Learning Results</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#model-choice">Model choice</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="modules.html">MEDfl</a></li>
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</ul>
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</div>
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</nav>
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<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
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<a href="index.html">MEDfl</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<section id="documentation">
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<h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading"></a></h1>
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<p>We used Sphinx to create the documentation for this project. You can generate and host it locally by compiling the documentation source code using:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>docs
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make<span class="w"> </span>clean
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make<span class="w"> </span>html
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</pre></div>
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</div>
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<p>Then open it locally using:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span><span class="w"> </span>_build/html
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python<span class="w"> </span>-m<span class="w"> </span>http.server
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</pre></div>
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<p>&#169; Copyright 2023, MEDomics consortium.</p>
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Installation &mdash; MEDfl 0.1.0 documentation</title>
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<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<link rel="stylesheet" href="_static/custom.css" type="text/css" />
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<script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
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<script src="_static/_sphinx_javascript_frameworks_compat.js"></script>
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<script src="_static/js/theme.js"></script>
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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="Documentation" href="Documentation.html" />
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<link rel="prev" title="Welcome to the MEDfl documentation!" href="index.html" />
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</head>
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<body class="wy-body-for-nav">
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<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
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<input type="hidden" name="check_keywords" value="yes" />
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<input type="hidden" name="area" value="default" />
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</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
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<p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#python-installation">Python installation</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#package-installation">Package Installation</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#mysql-db-configuration">MySQL DB Configuration</a></li>
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="Documentation.html">Documentation</a></li>
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<li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration File</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#database-management">Database management</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#netmanager">NetManager</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#transfer-learning">Transfer Learning</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-manager">Learning Manager</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-results">Learning Results</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials.html#model-choice">Model choice</a></li>
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</ul>
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<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="modules.html">MEDfl</a></li>
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</ul>
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<a href="_sources/Installation.rst.txt" rel="nofollow"> View page source</a>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<section id="installation">
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<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
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<section id="python-installation">
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<h2>Python installation<a class="headerlink" href="#python-installation" title="Permalink to this heading"></a></h2>
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<p>The MEDfl package requires <code class="docutils literal notranslate"><span class="pre">python</span> <span class="pre">3.9</span></code> or more to be run. If you don’t have it installed on your machine, check out the following link <a class="reference external" href="https://www.python.org/downloads/">Python</a>
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It also requires MySQL database</p>
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</section>
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<section id="package-installation">
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<h2>Package Installation<a class="headerlink" href="#package-installation" title="Permalink to this heading"></a></h2>
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<p>For now, you can install the <code class="docutils literal notranslate"><span class="pre">MEDfl</span></code> package as follows:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/MEDomics-UdeS/MEDfl.git
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<span class="nb">cd</span><span class="w"> </span>MEDfl
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pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.
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</pre></div>
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</div>
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</section>
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<section id="mysql-db-configuration">
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<h2>MySQL DB Configuration<a class="headerlink" href="#mysql-db-configuration" title="Permalink to this heading"></a></h2>
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<p>MEDfl requires a MySQL DB connection, and this is in order to allow users to work with their own tabular datasets. We have created a bash script to install and configure a MySQL DB with phpMyAdmin monitoring system. Run the following command, then change your credentials in the MEDfl/scripts/base.py file:</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>sudo<span class="w"> </span>bash<span class="w"> </span>MEDfl/scripts/setup_mysql.sh
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</pre></div>
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<p>&#169; Copyright 2023, MEDomics consortium.</p>
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Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
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