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mooc-rr-ressources
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module2/ressources/jupyter.html
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgacd419d">Additional Jupyter resources or tricks</a>
<li style="margin-bottom:0;"><a href="#org8a3ae34">Additional Jupyter resources or tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgc5dc2d3">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#org9541939">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org4455d02">Exporting a notebook</a></li>
<li style="margin-bottom:0;"><a href="#org15943e2">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#orgf113d02">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org2ba4a8a">Exporting a notebook</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orga99785c">Installing Jupyter on your own machine</a>
<li style="margin-bottom:0;"><a href="#org97a2d04">Installing Jupyter on your own machine</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org1bef8c0">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#orgd85230e">Using R</a></li>
<li style="margin-bottom:0;"><a href="#orge05b608">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#orgd9d1407">Interacting with GitLab</a></li>
<li style="margin-bottom:0;"><a href="#orgcdb47ae">Interesting extensions to improve notebook readability</a></li>
<li style="margin-bottom:0;"><a href="#org9e75391">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#orgf9ac059">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#org01b32de">Interesting extensions to improve notebook readability</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org70343f1">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></a></li>
</ul>
</div>
</div>
<div id="outline-container-orgacd419d" class="outline-2">
<h2 id="orgacd419d">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgacd419d">
<div id="outline-container-org8a3ae34" class="outline-2">
<h2 id="org8a3ae34">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org8a3ae34">
</div>
<div id="outline-container-orgc5dc2d3" class="outline-3">
<h3 id="orgc5dc2d3">Tips and tricks</h3>
<div class="outline-text-3" id="text-orgc5dc2d3">
<div id="outline-container-org15943e2" class="outline-3">
<h3 id="org15943e2">Tips and tricks</h3>
<div class="outline-text-3" id="text-org15943e2">
<p>
The following <a href="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it
illustrates many <code>Ipython magic</code> commands) that should improve your
......@@ -41,9 +38,9 @@ now).
</p>
</div>
</div>
<div id="outline-container-org9541939" class="outline-3">
<h3 id="org9541939">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org9541939">
<div id="outline-container-orgf113d02" class="outline-3">
<h3 id="orgf113d02">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orgf113d02">
<p>
The best solution to this is to install rpy2. On my machine, I have
installed the <code>python3-rpy2</code> debian package with <code>apt-get install</code>. E.g.,
......@@ -91,9 +88,9 @@ plot(df)
</ol>
</div>
</div>
<div id="outline-container-org4455d02" class="outline-3">
<h3 id="org4455d02">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org4455d02">
<div id="outline-container-org2ba4a8a" class="outline-3">
<h3 id="org2ba4a8a">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org2ba4a8a">
<p>
Obviously, you can convert to html or pdf using the using the <code>File &gt;
Download as &gt; HTML</code> (or <code>PDF</code>) menu option. This can also be done from
......@@ -120,63 +117,43 @@ taste.
</div>
</div>
</div>
<div id="outline-container-orga99785c" class="outline-2">
<h2 id="orga99785c">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-orga99785c">
<div id="outline-container-org97a2d04" class="outline-2">
<h2 id="org97a2d04">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-org97a2d04">
</div>
<div id="outline-container-org1bef8c0" class="outline-3">
<h3 id="org1bef8c0">Installing jupyter</h3>
<div class="outline-text-3" id="text-org1bef8c0">
<div id="outline-container-org9e75391" class="outline-3">
<h3 id="org9e75391">Installing jupyter</h3>
<div class="outline-text-3" id="text-org9e75391">
<p>
Here is what you should install:
Follow these instructions if you wish to have a similar Jupyter environment on you own machine.
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get install jupyter-notebook python3-pip python3-matplotlib python3-numpy
</pre>
</div>
<p>
On my machine, I got the version 5.4.1:
First, download and install <a href="https://www.anaconda.com/download/">Anaconda latest version</a>. We use Anaconda version <code>4.5.4</code> on our server .<br />
Anaconda includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter-notebook --version
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
5.4.1
</pre>
<p>
The ipython notebook can then be run with the following command:
Then download the <a href="https://gist.github.com/brospars/4671d9013f0d99e1c961482dab533c57">mooc<sub>rr</sub> environment file</a> and create it using conda:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter-notebook
</pre>
</div>
</div>
</div>
<div id="outline-container-orgd85230e" class="outline-3">
<h3 id="orgd85230e">Using R</h3>
<div class="outline-text-3" id="text-orgd85230e">
<p>
If you want to use the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these instructions</a>.
</p>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">conda env create -f environment.yml
<p>
Alternatively, you can install <code>rpy2</code> (see the <a href="#org9541939">Running R and Python in
the same notebook</a> section).
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get python3-rpy2
<span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">Windows activate the environment</span>
activate mooc_rr
<span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">Linux and MacOS activate the environment</span>
<span style="font-weight: bold;">source</span> activate mooc_rr
jupyter notebook
</pre>
</div>
</div>
</div>
<div id="outline-container-orge05b608" class="outline-3">
<h3 id="orge05b608">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orge05b608">
<div id="outline-container-orgf9ac059" class="outline-3">
<h3 id="orgf9ac059">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgf9ac059">
<p>
Here is what I had to install on my recent debian machine to make sure
the notebook export via latex works:
......@@ -188,23 +165,10 @@ sudo apt-get install texlive-xetex
</div>
</div>
</div>
<div id="outline-container-orgd9d1407" class="outline-3">
<h3 id="orgd9d1407">Interacting with GitLab</h3>
<div class="outline-text-3" id="text-orgd9d1407">
<p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter nbextension install https://raw.githubusercontent.com/brospars/nb-git/master/nb-git.js
jupyter nbextension enable nb-git
</pre>
</div>
</div>
</div>
<div id="outline-container-orgcdb47ae" class="outline-3">
<h3 id="orgcdb47ae">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgcdb47ae">
<div id="outline-container-org01b32de" class="outline-3">
<h3 id="org01b32de">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-org01b32de">
<p>
Here are two interesting extensions that can improve readability:
</p>
......@@ -231,14 +195,4 @@ jupyter-serverextension enable --py hide_code
</div>
</div>
</div>
<div id="outline-container-org70343f1" class="outline-2">
<h2 id="org70343f1">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></h2>
<div class="outline-text-2" id="text-org70343f1">
<blockquote>
<p>
Benoit may give a few hints on this.
</p>
</blockquote>
</div>
</div>
</div>
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