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<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgeace9b7">Additional Jupyter resources or tricks</a> <li style="margin-bottom:0;"><a href="#org974f69e">Additional Jupyter resources or tricks</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8c18a42">Tips and tricks</a></li> <li style="margin-bottom:0;"><a href="#orgff5515e">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#orgdc83801">Running R and Python in the same notebook</a></li> <li style="margin-bottom:0;"><a href="#orgc5ef309">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org8a508ca">Exporting a notebook</a></li> <li style="margin-bottom:0;"><a href="#orgb6f8685">Exporting a notebook</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgd693a15">Installing Jupyter on your own machine</a> <li style="margin-bottom:0;"><a href="#orge73aaac">Installing Jupyter on your own machine</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb0a5241">Installing Jupyter</a></li> <li style="margin-bottom:0;"><a href="#orgc837a03">Installing Jupyter</a></li>
<li style="margin-bottom:0;"><a href="#org6c5cc92">Side note about Jupyter, JupyterLab, JupyterHub, &#x2026;</a></li> <li style="margin-bottom:0;"><a href="#orgbafde52">Side note about Jupyter, JupyterLab, JupyterHub, &#x2026;</a></li>
<li style="margin-bottom:0;"><a href="#orgb1c52f4">Exporting your notebooks with latex</a></li> <li style="margin-bottom:0;"><a href="#orga906562">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#org06844c1">Jupyter extensions/plugins</a> <li style="margin-bottom:0;"><a href="#org11225f1">Jupyter extensions/plugins</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0bf2e9c">Improving notebook readability</a></li> <li style="margin-bottom:0;"><a href="#orgd0bb8e3">Improving notebook readability</a></li>
<li style="margin-bottom:0;"><a href="#org1b381cf">Interacting with GitLab and GitHub</a></li> <li style="margin-bottom:0;"><a href="#orgfb9dba8">Interacting with GitLab and GitHub</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
...@@ -28,13 +28,13 @@ ...@@ -28,13 +28,13 @@
</div> </div>
</div> </div>
<div id="outline-container-orgeace9b7" class="outline-2"> <div id="outline-container-org974f69e" class="outline-2">
<h2 id="orgeace9b7">Additional Jupyter resources or tricks</h2> <h2 id="org974f69e">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgeace9b7"> <div class="outline-text-2" id="text-org974f69e">
</div> </div>
<div id="outline-container-org8c18a42" class="outline-3"> <div id="outline-container-orgff5515e" class="outline-3">
<h3 id="org8c18a42">Tips and tricks</h3> <h3 id="orgff5515e">Tips and tricks</h3>
<div class="outline-text-3" id="text-org8c18a42"> <div class="outline-text-3" id="text-orgff5515e">
<p> <p>
The following <a href="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it 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 illustrates many <code>Ipython magic</code> commands) that should improve your
...@@ -44,9 +44,9 @@ now). ...@@ -44,9 +44,9 @@ now).
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgdc83801" class="outline-3"> <div id="outline-container-orgc5ef309" class="outline-3">
<h3 id="orgdc83801">Running R and Python in the same notebook</h3> <h3 id="orgc5ef309">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orgdc83801"> <div class="outline-text-3" id="text-orgc5ef309">
<p> <p>
The best solution to this is to install rpy2. On my machine, I have 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., installed the <code>python3-rpy2</code> debian package with <code>apt-get install</code>. E.g.,
...@@ -56,8 +56,8 @@ installed the <code>python3-rpy2</code> debian package with <code>apt-get instal ...@@ -56,8 +56,8 @@ installed the <code>python3-rpy2</code> debian package with <code>apt-get instal
</pre> </pre>
</div> </div>
<p> <p>
An other (not really recommanded) alternative consists in going An other (not really recommended if the first one is available)
through the python package manager with alternative consists in going through the python package manager with
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">pip3 install rpy2 <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">pip3 install rpy2
...@@ -78,7 +78,7 @@ Loading <code>rpy2</code>: ...@@ -78,7 +78,7 @@ Loading <code>rpy2</code>:
Using the <code>%R</code> Ipython magic: Using the <code>%R</code> Ipython magic:
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%R <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%%R
summary(cars) summary(cars)
</pre> </pre>
</div> </div>
...@@ -92,11 +92,16 @@ plot(df) ...@@ -92,11 +92,16 @@ plot(df)
</pre> </pre>
</div></li> </div></li>
</ol> </ol>
<p>
Note that this <code>%%R</code> notation allows you to use R for the whole cell but
an other possibility is to use <code>%R</code> to have a single line of R within a
python cell.
</p>
</div> </div>
</div> </div>
<div id="outline-container-org8a508ca" class="outline-3"> <div id="outline-container-orgb6f8685" class="outline-3">
<h3 id="org8a508ca">Exporting a notebook</h3> <h3 id="orgb6f8685">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org8a508ca"> <div class="outline-text-3" id="text-orgb6f8685">
<p> <p>
Obviously, you can convert to html or pdf using the using the <code>File &gt; 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 Download as &gt; HTML</code> (or <code>PDF</code>) menu option. This can also be done from
...@@ -109,27 +114,27 @@ the command line with the following command: ...@@ -109,27 +114,27 @@ the command line with the following command:
</div> </div>
<p> <p>
If you want to use a specific style, then the nbconvert exporter If you want to use a specific style, then the <code>nbconvert</code> exporter
should be customised. This is discussed and demoed <a href="http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html">here</a>. We encourage should be customized. This is discussed and demoed <a href="http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html">here</a>. We encourage
you to simply read the <a href="https://nbconvert.readthedocs.io/en/latest/">doc of nbconvert</a>. you to simply read the <a href="https://nbconvert.readthedocs.io/en/latest/">doc of nbconvert</a>.
</p> </p>
<p> <p>
Instead of going directly through LaTeX and playing too much with the Instead of going directly through LaTeX and playing too much with the
nbconvert exporter, an other option consists in exporting to Markdown <code>nbconvert</code> exporter, an other option consists in exporting to Markdown
and playing with <a href="https://pandoc.org/">pandoc</a>. Both approaches work, it's rather a matter of and playing with <a href="https://pandoc.org/">pandoc</a>. Both approaches work, it's rather a matter of
taste. taste.
</p> </p>
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgd693a15" class="outline-2"> <div id="outline-container-orge73aaac" class="outline-2">
<h2 id="orgd693a15">Installing Jupyter on your own machine</h2> <h2 id="orge73aaac">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-orgd693a15"> <div class="outline-text-2" id="text-orge73aaac">
</div> </div>
<div id="outline-container-orgb0a5241" class="outline-3"> <div id="outline-container-orgc837a03" class="outline-3">
<h3 id="orgb0a5241">Installing Jupyter</h3> <h3 id="orgc837a03">Installing Jupyter</h3>
<div class="outline-text-3" id="text-orgb0a5241"> <div class="outline-text-3" id="text-orgc837a03">
<p> <p>
Follow these instructions if you wish to have a Jupyter environment on Follow these instructions if you wish to have a Jupyter environment on
your own machine similar to the one we set up for this MOOC. your own machine similar to the one we set up for this MOOC.
...@@ -161,9 +166,9 @@ jupyter notebook ...@@ -161,9 +166,9 @@ jupyter notebook
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org6c5cc92" class="outline-3"> <div id="outline-container-orgbafde52" class="outline-3">
<h3 id="org6c5cc92">Side note about Jupyter, JupyterLab, JupyterHub, &#x2026;</h3> <h3 id="orgbafde52">Side note about Jupyter, JupyterLab, JupyterHub, &#x2026;</h3>
<div class="outline-text-3" id="text-org6c5cc92"> <div class="outline-text-3" id="text-orgbafde52">
<p> <p>
Note that Jupyter notebooks are only a small part of the picture and Note that Jupyter notebooks are only a small part of the picture and
that Jupyter is now part of a bigger project: <a href="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows that Jupyter is now part of a bigger project: <a href="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows
...@@ -175,9 +180,9 @@ cutting-edge Jupyter notebooks. ...@@ -175,9 +180,9 @@ cutting-edge Jupyter notebooks.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgb1c52f4" class="outline-3"> <div id="outline-container-orga906562" class="outline-3">
<h3 id="orgb1c52f4">Exporting your notebooks with latex</h3> <h3 id="orga906562">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgb1c52f4"> <div class="outline-text-3" id="text-orga906562">
<p> <p>
Here is what we had to install on our recent debian machine to make sure Here is what we had to install on our recent debian machine to make sure
the notebook export via latex works: the notebook export via latex works:
...@@ -189,13 +194,13 @@ the notebook export via latex works: ...@@ -189,13 +194,13 @@ the notebook export via latex works:
</div> </div>
</div> </div>
<div id="outline-container-org06844c1" class="outline-3"> <div id="outline-container-org11225f1" class="outline-3">
<h3 id="org06844c1">Jupyter extensions/plugins</h3> <h3 id="org11225f1">Jupyter extensions/plugins</h3>
<div class="outline-text-3" id="text-org06844c1"> <div class="outline-text-3" id="text-org11225f1">
</div> </div>
<div id="outline-container-org0bf2e9c" class="outline-4"> <div id="outline-container-orgd0bb8e3" class="outline-4">
<h4 id="org0bf2e9c">Improving notebook readability</h4> <h4 id="orgd0bb8e3">Improving notebook readability</h4>
<div class="outline-text-4" id="text-org0bf2e9c"> <div class="outline-text-4" id="text-orgd0bb8e3">
<p> <p>
Here are a few extensions that can ease your life: Here are a few extensions that can ease your life:
</p> </p>
...@@ -221,9 +226,9 @@ jupyter-serverextension enable --py hide_code ...@@ -221,9 +226,9 @@ jupyter-serverextension enable --py hide_code
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org1b381cf" class="outline-4"> <div id="outline-container-orgfb9dba8" class="outline-4">
<h4 id="org1b381cf">Interacting with GitLab and GitHub</h4> <h4 id="orgfb9dba8">Interacting with GitLab and GitHub</h4>
<div class="outline-text-4" id="text-org1b381cf"> <div class="outline-text-4" id="text-orgfb9dba8">
<p> <p>
To ease your experience, we added some pull/push buttons that allow To ease your experience, we added some pull/push buttons that allow
you to commit and sync with GitLab. This development was specific to you to commit and sync with GitLab. This development was specific to
...@@ -239,14 +244,14 @@ This being said, you may have noticed that Jupyter keeps a perfect ...@@ -239,14 +244,14 @@ This being said, you may have noticed that Jupyter keeps a perfect
track of the sequence in which cells have been run by updating the track of the sequence in which cells have been run by updating the
"output index". This is a very good property from the reproducibility "output index". This is a very good property from the reproducibility
point of view but depending on your usage, you may find it a bit point of view but depending on your usage, you may find it a bit
painful when commiting. Some people have thus developped <a href="https://gist.github.com/pbugnion/ea2797393033b54674af">specific git painful when committing. Some people have thus developed <a href="https://gist.github.com/pbugnion/ea2797393033b54674af">specific git
hooks</a> to ignore these numbers when comitting Jupyter notebooks. There hooks</a> to ignore these numbers when committing Jupyter notebooks. There
is a long an interesting discussion about various options on is a long an interesting discussion about various options on
<a href="https://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control">StackOverflow</a>. <a href="https://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control">StackOverflow</a>.
</p> </p>
<p> <p>
Last but not least, remembter that Jupyter notebooks are only a small Last but not least, remember that Jupyter notebooks are only a small
part of the picture and that Jupyter is now part of a bigger project: part of the picture and that Jupyter is now part of a bigger project:
<a href="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows you to mix various components (including <a href="https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906">JupyterLab</a>, which allows you to mix various components (including
notebooks) in your browser. A specific <a href="https://github.com/jupyterlab/jupyterlab-git">JupyterLab git plugin</a> has been notebooks) in your browser. A specific <a href="https://github.com/jupyterlab/jupyterlab-git">JupyterLab git plugin</a> has been
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