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module2/ressources/jupyter.html
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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="#orgbc72472">Additional Jupyter resources or tricks</a> <li style="margin-bottom:0;"><a href="#orgeace9b7">Additional Jupyter resources or tricks</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org1be8a88">Tips and tricks</a></li> <li style="margin-bottom:0;"><a href="#org8c18a42">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#orga192b96">Running R and Python in the same notebook</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="#orgb30f3ee">Exporting a notebook</a></li> <li style="margin-bottom:0;"><a href="#org8a508ca">Exporting a notebook</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgd2ff654">Installing Jupyter on your own machine</a> <li style="margin-bottom:0;"><a href="#orgd693a15">Installing Jupyter on your own machine</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org23f8703">Installing jupyter</a></li> <li style="margin-bottom:0;"><a href="#orgb0a5241">Installing Jupyter</a></li>
<li style="margin-bottom:0;"><a href="#orge0aee6c">Exporting your notebooks with latex</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="#org4f61d38">Interesting extensions to improve notebook readability</a></li> <li style="margin-bottom:0;"><a href="#orgb1c52f4">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#org06844c1">Jupyter extensions/plugins</a>
<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="#org1b381cf">Interacting with GitLab and GitHub</a></li>
</ul>
</li>
</ul> </ul>
</li> </li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orgbc72472" class="outline-2"> <div id="outline-container-orgeace9b7" class="outline-2">
<h2 id="orgbc72472">Additional Jupyter resources or tricks</h2> <h2 id="orgeace9b7">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgbc72472"> <div class="outline-text-2" id="text-orgeace9b7">
</div> </div>
<div id="outline-container-org1be8a88" class="outline-3"> <div id="outline-container-org8c18a42" class="outline-3">
<h3 id="org1be8a88">Tips and tricks</h3> <h3 id="org8c18a42">Tips and tricks</h3>
<div class="outline-text-3" id="text-org1be8a88"> <div class="outline-text-3" id="text-org8c18a42">
<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
efficiency (note that this blog post is about two years old so some of efficiency (note that this blog post is about two years old so some of
the tricks may have been integrated in the default behavior of jupyter the tricks may have been integrated in the default behavior of Jupyter
now). now).
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orga192b96" class="outline-3"> <div id="outline-container-orgdc83801" class="outline-3">
<h3 id="orga192b96">Running R and Python in the same notebook</h3> <h3 id="orgdc83801">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orga192b96"> <div class="outline-text-3" id="text-orgdc83801">
<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.,
...@@ -88,9 +94,9 @@ plot(df) ...@@ -88,9 +94,9 @@ plot(df)
</ol> </ol>
</div> </div>
</div> </div>
<div id="outline-container-orgb30f3ee" class="outline-3"> <div id="outline-container-org8a508ca" class="outline-3">
<h3 id="orgb30f3ee">Exporting a notebook</h3> <h3 id="org8a508ca">Exporting a notebook</h3>
<div class="outline-text-3" id="text-orgb30f3ee"> <div class="outline-text-3" id="text-org8a508ca">
<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
...@@ -117,24 +123,29 @@ taste. ...@@ -117,24 +123,29 @@ taste.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgd2ff654" class="outline-2"> <div id="outline-container-orgd693a15" class="outline-2">
<h2 id="orgd2ff654">Installing Jupyter on your own machine</h2> <h2 id="orgd693a15">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-orgd2ff654"> <div class="outline-text-2" id="text-orgd693a15">
</div> </div>
<div id="outline-container-org23f8703" class="outline-3"> <div id="outline-container-orgb0a5241" class="outline-3">
<h3 id="org23f8703">Installing jupyter</h3> <h3 id="orgb0a5241">Installing Jupyter</h3>
<div class="outline-text-3" id="text-org23f8703"> <div class="outline-text-3" id="text-orgb0a5241">
<p>
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.
</p>
<p> <p>
Follow these instructions if you wish to have a similar Jupyter environment on you own machine. First, download and install the <a href="https://conda.io/miniconda.html">latest version of Miniconda</a>. We use
Miniconda version <code>4.5.4</code> and Python version <code>3.6</code> on our server.
</p> </p>
<p> <p>
First, download and install <a href="https://conda.io/miniconda.html">Miniconda latest version</a>. We use Miniconda version <code>4.5.4</code> and Python version <code>3.6</code> on our server .<br /> Miniconda is a light version of Anaconda, which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
Miniconda is a light version of Anaconda which includes Python, the Jupyter Notebook, and other commonly used packages for scientific computing and data science.
</p> </p>
<p> <p>
Then download the <a href="https://gist.github.com/brospars/4671d9013f0d99e1c961482dab533c57">mooc<sub>rr</sub> environment file</a> and create it using conda: Then download the <a href="https://gist.github.com/brospars/4671d9013f0d99e1c961482dab533c57">mooc<sub>rr</sub> environment file</a> and create the environment using conda:
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">conda env create -f environment.yml <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">conda env create -f environment.yml
...@@ -150,31 +161,47 @@ jupyter notebook ...@@ -150,31 +161,47 @@ jupyter notebook
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org6c5cc92" class="outline-3">
<div id="outline-container-orge0aee6c" class="outline-3"> <h3 id="org6c5cc92">Side note about Jupyter, JupyterLab, JupyterHub, &#x2026;</h3>
<h3 id="orge0aee6c">Exporting your notebooks with latex</h3> <div class="outline-text-3" id="text-org6c5cc92">
<div class="outline-text-3" id="text-orge0aee6c"> <p>
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
you to mix various components (including notebooks) in your
browser. In the context of this MOOC, our time frame was too short to
benefit from JupyterLab which was still under active development but
this is probably the best option now if you want to benefit from
cutting-edge Jupyter notebooks.
</p>
</div>
</div>
<div id="outline-container-orgb1c52f4" class="outline-3">
<h3 id="orgb1c52f4">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgb1c52f4">
<p> <p>
Here is what I had to install on my 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:
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get install wkhtmltopdf <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get install texlive-xetex wkhtmltopdf
sudo apt-get install texlive-xetex
</pre> </pre>
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org4f61d38" class="outline-3"> <div id="outline-container-org06844c1" class="outline-3">
<h3 id="org4f61d38">Interesting extensions to improve notebook readability</h3> <h3 id="org06844c1">Jupyter extensions/plugins</h3>
<div class="outline-text-3" id="text-org4f61d38"> <div class="outline-text-3" id="text-org06844c1">
</div>
<div id="outline-container-org0bf2e9c" class="outline-4">
<h4 id="org0bf2e9c">Improving notebook readability</h4>
<div class="outline-text-4" id="text-org0bf2e9c">
<p> <p>
Here are two interesting extensions that can improve readability: Here are a few extensions that can ease your life:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li style="margin-bottom:0;"><p> <li style="margin-bottom:0;"><p>
<a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a> <a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a> to improve readability when browsing the notebook.
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 install jupyter_contrib_nbextensions <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 install jupyter_contrib_nbextensions
...@@ -182,7 +209,7 @@ Here are two interesting extensions that can improve readability: ...@@ -182,7 +209,7 @@ Here are two interesting extensions that can improve readability:
</pre> </pre>
</div></li> </div></li>
<li style="margin-bottom:0;"><p> <li style="margin-bottom:0;"><p>
<a href="https://github.com/kirbs-/hide_code">Hiding code</a> <a href="https://github.com/kirbs-/hide_code">Hiding code</a> to improve readability when exporting.
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">sudo pip3 install hide_code <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">sudo pip3 install hide_code
...@@ -194,5 +221,39 @@ jupyter-serverextension enable --py hide_code ...@@ -194,5 +221,39 @@ jupyter-serverextension enable --py hide_code
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org1b381cf" class="outline-4">
<h4 id="org1b381cf">Interacting with GitLab and GitHub</h4>
<div class="outline-text-4" id="text-org1b381cf">
<p>
To ease your experience, we added some pull/push buttons that allow
you to commit and sync with GitLab. This development was specific to
the MOOC but inspired from a previous <a href="https://github.com/Lab41/sunny-side-up">proof of concept</a>. We have
recently discovered that someone else developed about at the same time
a <a href="https://github.com/sat28/githubcommit">rather generic version of this Jupyter plugin</a>. Otherwise, remember
that it is very easy to insert a shell cell in Jupyter in which you
can easily issue git commands. This is how we work most of the time.
</p>
<p>
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
"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
painful when commiting. Some people have thus developped <a href="https://gist.github.com/pbugnion/ea2797393033b54674af">specific git
hooks</a> to ignore these numbers when comitting Jupyter notebooks. There
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>.
</p>
<p>
Last but not least, remembter 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 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
developed to offer a nice version control experience.
</p>
</div>
</div>
</div>
</div> </div>
</div> </div>
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