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ouaelesi merged 1 commit into from
Jan 17, 2026
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fix. read the docs #9

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2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
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# 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: 0c6cb496db24d1d9f60d1aa1f06bb5d2
config: 42e6c4ce09f75e9867b1c2894d0ba5b5
tags: 645f666f9bcd5a90fca523b33c5a78b7
50 changes: 28 additions & 22 deletions docs/build/html/Documentation.html
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<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Documentation &mdash; MEDfl 0.1.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/dark_mode_css/general.css" type="text/css" />
<link rel="stylesheet" href="_static/dark_mode_css/dark.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/css/theme.css" />
<link rel="stylesheet" type="text/css" href="_static/custom.css" />
<link rel="stylesheet" type="text/css" href="_static/css/custom.css" />
<link rel="stylesheet" type="text/css" href="_static/dark_mode_css/general.css" />
<link rel="stylesheet" type="text/css" href="_static/dark_mode_css/dark.css" />


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<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
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<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Configuration File" href="configuration_file.html" />
<link rel="next" title="Introduction" href="simulation_tutorials.html" />
<link rel="prev" title="Installation" href="Installation.html" />
</head>

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<a href="index.html">

<img src="_static/MEDomics.png" class="logo" alt="Logo"/>
<img src="_static/medfl_logo.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
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</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="Installation.html">Installation</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration File</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
<p class="caption" role="heading"><span class="caption-text">Simulation Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#database-management">Database management</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#netmanager">NetManager</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#transfer-learning">Transfer Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#learning-manager">Learning Manager</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#learning-results">Learning Results</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#model-choice">Model choice</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials_complete.html">MEDfl Complete Tutorial (Simulation)</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">🌍 Real-World Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#database-management">Database management</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#netmanager">NetManager</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#transfer-learning">Transfer Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-manager">Learning Manager</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-results">Learning Results</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#model-choice">Model choice</a></li>
<li class="toctree-l1"><a class="reference internal" href="rw_tutorial_complete.html">Real-world Federated Learning Tutorial</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<p class="caption" role="heading"><span class="caption-text">Contents</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules.html">MEDfl</a></li>
</ul>
Expand Down Expand Up @@ -115,7 +121,7 @@ <h1>Documentation<a class="headerlink" href="#documentation" title="Permalink to
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="Installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="configuration_file.html" class="btn btn-neutral float-right" title="Configuration File" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
<a href="simulation_tutorials.html" class="btn btn-neutral float-right" title="Introduction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>

<hr/>
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95 changes: 57 additions & 38 deletions docs/build/html/Installation.html
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<!DOCTYPE html>
<html class="writer-html5" lang="en" >
<html class="writer-html5" lang="en">
<head>
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
<meta charset="utf-8" /><meta name="generator" content="Docutils 0.19: https://docutils.sourceforge.io/" />

<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Installation &mdash; MEDfl 0.1.0 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/dark_mode_css/general.css" type="text/css" />
<link rel="stylesheet" href="_static/dark_mode_css/dark.css" type="text/css" />
<link rel="stylesheet" type="text/css" href="_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="_static/css/theme.css" />
<link rel="stylesheet" type="text/css" href="_static/custom.css" />
<link rel="stylesheet" type="text/css" href="_static/css/custom.css" />
<link rel="stylesheet" type="text/css" href="_static/dark_mode_css/general.css" />
<link rel="stylesheet" type="text/css" href="_static/dark_mode_css/dark.css" />


<!--[if lt IE 9]>
<script src="_static/js/html5shiv.min.js"></script>
<![endif]-->
Expand All @@ -27,7 +29,7 @@
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Documentation" href="Documentation.html" />
<link rel="prev" title="Welcome to the MEDfl documentation!" href="index.html" />
<link rel="prev" title="Welcome to the MEDfl Documentation" href="index.html" />
</head>

<body class="wy-body-for-nav">
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<a href="index.html">

<img src="_static/MEDomics.png" class="logo" alt="Logo"/>
<img src="_static/medfl_logo.png" class="logo" alt="Logo"/>
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
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</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#python-installation">Python installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#package-installation">Package Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#mysql-db-configuration">MySQL DB Configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="#python-requirements">Python Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#package-installation-for-users">Package Installation (For Users)</a></li>
<li class="toctree-l2"><a class="reference internal" href="#package-installation-for-contributors">Package Installation (For Contributors)</a></li>
<li class="toctree-l2"><a class="reference internal" href="#database-configuration">Database Configuration</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="Documentation.html">Documentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="configuration_file.html">Configuration File</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
<p class="caption" role="heading"><span class="caption-text">Simulation Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#database-management">Database management</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#netmanager">NetManager</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#transfer-learning">Transfer Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-manager">Learning Manager</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#learning-results">Learning Results</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials.html#model-choice">Model choice</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#database-management">Database management</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#netmanager">NetManager</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#transfer-learning">Transfer Learning</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#learning-manager">Learning Manager</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#learning-results">Learning Results</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials.html#model-choice">Model choice</a></li>
<li class="toctree-l1"><a class="reference internal" href="simulation_tutorials_complete.html">MEDfl Complete Tutorial (Simulation)</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
<p class="caption" role="heading"><span class="caption-text">🌍 Real-World Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="rw_tutorial_complete.html">Real-world Federated Learning Tutorial</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Contents</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="modules.html">MEDfl</a></li>
</ul>
Expand Down Expand Up @@ -102,34 +109,46 @@

<section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h1>
<section id="python-installation">
<h2>Python installation<a class="headerlink" href="#python-installation" title="Permalink to this heading"></a></h2>
<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>
It also requires MySQL database</p>
<section id="python-requirements">
<h2>Python Requirements<a class="headerlink" href="#python-requirements" title="Permalink to this heading"></a></h2>
<p>The MEDfl package requires <strong>Python 3.9+</strong>.
If you do not have Python installed on your machine, you can download it from:
<a class="reference external" href="https://www.python.org/downloads/">Python</a></p>
<p>MEDfl uses <strong>SQLite</strong> as its default database engine.
SQLite requires <strong>no setup and no configuration</strong> — it works automatically using a local <cite>.db</cite> file generated by MEDfl.</p>
</section>
<section id="package-installation">
<h2>Package Installation<a class="headerlink" href="#package-installation" title="Permalink to this heading"></a></h2>
<p>For now, you can install the <code class="docutils literal notranslate"><span class="pre">MEDfl</span></code> package as follows:</p>
<section id="package-installation-for-users">
<h2>Package Installation (For Users)<a class="headerlink" href="#package-installation-for-users" title="Permalink to this heading"></a></h2>
<p>If you simply want to <strong>use MEDfl</strong>, you can install the package directly from PyPI:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>MEDfl
</pre></div>
</div>
<p>This installs the latest stable release and allows you to start using MEDfl immediately.</p>
</section>
<section id="package-installation-for-contributors">
<h2>Package Installation (For Contributors)<a class="headerlink" href="#package-installation-for-contributors" title="Permalink to this heading"></a></h2>
<p>If you want to <strong>collaborate</strong>, contribute, or modify the MEDfl source code, install it from GitHub in editable mode:</p>
<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
<span class="nb">cd</span><span class="w"> </span>MEDfl
pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.
</pre></div>
</div>
<p>This setup allows you to modify the package locally while testing new features.</p>
</section>
<section id="mysql-db-configuration">
<h2>MySQL DB Configuration<a class="headerlink" href="#mysql-db-configuration" title="Permalink to this heading"></a></h2>
<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>
<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
</pre></div>
</div>
<section id="database-configuration">
<h2>Database Configuration<a class="headerlink" href="#database-configuration" title="Permalink to this heading"></a></h2>
<p>No database configuration is required.</p>
<p>MEDfl uses <strong>SQLite</strong>, a lightweight and reliable file-based database system.
A local <cite>.db</cite> file is created automatically when you initialize the MEDfl environment or use any functionality requiring storage.
No external server, setup script, or credentials are needed.</p>
</section>
</section>


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