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Jupyter resources completed

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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="#org975cdde">Additional Jupyter resources or tricks</a> <li style="margin-bottom:0;"><a href="#org8ad7af5">Additional Jupyter resources or tricks</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org27d1582">Tips and tricks</a></li> <li style="margin-bottom:0;"><a href="#org22d89f4">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#org4f5f0e8">Running R and Python in the same notebook</a></li> <li style="margin-bottom:0;"><a href="#org0420686">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org6e2f783">Exporting a notebook</a></li> <li style="margin-bottom:0;"><a href="#org468b24f">Exporting a notebook</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org75409e5">Installing Jupyter on your own machine</a> <li style="margin-bottom:0;"><a href="#org2c7ad73">Installing Jupyter on your own machine</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org73474e0">Installing jupyter</a></li> <li style="margin-bottom:0;"><a href="#orgb4b3874">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#org5dcb2d4">Using R</a></li> <li style="margin-bottom:0;"><a href="#orgf5ae3b1">Using R</a></li>
<li style="margin-bottom:0;"><a href="#org919a045">Exporting your notebooks with latex</a></li> <li style="margin-bottom:0;"><a href="#orgf90bf40">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#org3bdebfb">Interacting with gitlab</a></li> <li style="margin-bottom:0;"><a href="#org77f31cb">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#orgee218a0">Interesting extensions to improve notebook readability</a></li> <li style="margin-bottom:0;"><a href="#org0c2d49c">Interesting extensions to improve notebook readability</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org4ee7491">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></a></li> <li style="margin-bottom:0;"><a href="#orgacebcf9">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></a></li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org975cdde" class="outline-2"> <div id="outline-container-org8ad7af5" class="outline-2">
<h2 id="org975cdde">Additional Jupyter resources or tricks</h2> <h2 id="org8ad7af5">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org975cdde"> <div class="outline-text-2" id="text-org8ad7af5">
</div> </div>
<div id="outline-container-org27d1582" class="outline-3"> <div id="outline-container-org22d89f4" class="outline-3">
<h3 id="org27d1582">Tips and tricks</h3> <h3 id="org22d89f4">Tips and tricks</h3>
<div class="outline-text-3" id="text-org27d1582"> <div class="outline-text-3" id="text-org22d89f4">
<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
...@@ -41,9 +41,9 @@ now). ...@@ -41,9 +41,9 @@ now).
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org4f5f0e8" class="outline-3"> <div id="outline-container-org0420686" class="outline-3">
<h3 id="org4f5f0e8">Running R and Python in the same notebook</h3> <h3 id="org0420686">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org4f5f0e8"> <div class="outline-text-3" id="text-org0420686">
<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>. An installed the <code>python3-rpy2</code> debian package with <code>apt-get install</code>. An
...@@ -74,20 +74,20 @@ summary(cars) ...@@ -74,20 +74,20 @@ summary(cars)
</pre> </pre>
</div> </div>
<p> <p>
Python objects can then even be passed to R as follows (assuming df Python objects can then even be passed to R as follows (assuming <code>df</code>
is a pandas dataframe: is a pandas dataframe):
</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 -i df <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%%R -i df
plot((df) plot(df)
</pre> </pre>
</div></li> </div></li>
</ol> </ol>
</div> </div>
</div> </div>
<div id="outline-container-org6e2f783" class="outline-3"> <div id="outline-container-org468b24f" class="outline-3">
<h3 id="org6e2f783">Exporting a notebook</h3> <h3 id="org468b24f">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org6e2f783"> <div class="outline-text-3" id="text-org468b24f">
<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
...@@ -114,13 +114,13 @@ taste. ...@@ -114,13 +114,13 @@ taste.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org75409e5" class="outline-2"> <div id="outline-container-org2c7ad73" class="outline-2">
<h2 id="org75409e5">Installing Jupyter on your own machine</h2> <h2 id="org2c7ad73">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-org75409e5"> <div class="outline-text-2" id="text-org2c7ad73">
</div> </div>
<div id="outline-container-org73474e0" class="outline-3"> <div id="outline-container-orgb4b3874" class="outline-3">
<h3 id="org73474e0">Installing jupyter</h3> <h3 id="orgb4b3874">Installing jupyter</h3>
<div class="outline-text-3" id="text-org73474e0"> <div class="outline-text-3" id="text-orgb4b3874">
<p> <p>
Here is what you should install: Here is what you should install:
</p> </p>
...@@ -151,16 +151,15 @@ The ipython notebook can then be run with the following command: ...@@ -151,16 +151,15 @@ The ipython notebook can then be run with the following command:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org5dcb2d4" class="outline-3"> <div id="outline-container-orgf5ae3b1" class="outline-3">
<h3 id="org5dcb2d4">Using R</h3> <h3 id="orgf5ae3b1">Using R</h3>
<div class="outline-text-3" id="text-org5dcb2d4"> <div class="outline-text-3" id="text-orgf5ae3b1">
<p> <p>
If you also want to have the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these If you want to use the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these instructions</a>.
instructions</a>.
</p> </p>
<p> <p>
Alternatively, you can install <code>rpy2</code> (see the <a href="#org4f5f0e8">Running R and Python in Alternatively, you can install <code>rpy2</code> (see the <a href="#org0420686">Running R and Python in
the same notebook</a> section). the same notebook</a> section).
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -169,12 +168,12 @@ the same notebook</a> section). ...@@ -169,12 +168,12 @@ the same notebook</a> section).
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org919a045" class="outline-3"> <div id="outline-container-orgf90bf40" class="outline-3">
<h3 id="org919a045">Exporting your notebooks with latex</h3> <h3 id="orgf90bf40">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-org919a045"> <div class="outline-text-3" id="text-orgf90bf40">
<p> <p>
Here is what I had to install to make sure the notebook export via Here is what I had to install on my recent debian machine to make sure
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 wkhtmltopdf
...@@ -183,9 +182,9 @@ sudo apt-get install texlive-xetex ...@@ -183,9 +182,9 @@ sudo apt-get install texlive-xetex
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org3bdebfb" class="outline-3"> <div id="outline-container-org77f31cb" class="outline-3">
<h3 id="org3bdebfb">Interacting with gitlab</h3> <h3 id="org77f31cb">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-org3bdebfb"> <div class="outline-text-3" id="text-org77f31cb">
<p> <p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>: notebooks</a>:
...@@ -197,9 +196,9 @@ jupyter nbextension enable nb-git ...@@ -197,9 +196,9 @@ jupyter nbextension enable nb-git
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgee218a0" class="outline-3"> <div id="outline-container-org0c2d49c" class="outline-3">
<h3 id="orgee218a0">Interesting extensions to improve notebook readability</h3> <h3 id="org0c2d49c">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgee218a0"> <div class="outline-text-3" id="text-org0c2d49c">
<p> <p>
Here are two interesting extensions that can improve readability: Here are two interesting extensions that can improve readability:
</p> </p>
...@@ -226,9 +225,9 @@ jupyter-serverextension enable --py hide_code ...@@ -226,9 +225,9 @@ jupyter-serverextension enable --py hide_code
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org4ee7491" class="outline-2"> <div id="outline-container-orgacebcf9" class="outline-2">
<h2 id="org4ee7491">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></h2> <h2 id="orgacebcf9">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></h2>
<div class="outline-text-2" id="text-org4ee7491"> <div class="outline-text-2" id="text-orgacebcf9">
<blockquote> <blockquote>
<p> <p>
Benoit may give a few hints on this. Benoit may give a few hints on this.
......
module2/ressources/jupyter.org
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...@@ -31,11 +31,11 @@ Then you'll be able to use both languages in the same notebook by: ...@@ -31,11 +31,11 @@ Then you'll be able to use both languages in the same notebook by:
%R %R
summary(cars) summary(cars)
#+end_src #+end_src
Python objects can then even be passed to R as follows (assuming df Python objects can then even be passed to R as follows (assuming =df=
is a pandas dataframe: is a pandas dataframe):
#+begin_src python :results output :exports both #+begin_src python :results output :exports both
%%R -i df %%R -i df
plot((df) plot(df)
#+end_src #+end_src
** Exporting a notebook ** Exporting a notebook
Obviously, you can convert to html or pdf using the using the =File > Obviously, you can convert to html or pdf using the using the =File >
...@@ -74,8 +74,7 @@ The ipython notebook can then be run with the following command: ...@@ -74,8 +74,7 @@ The ipython notebook can then be run with the following command:
jupyter-notebook jupyter-notebook
#+end_src #+end_src
** Using R ** Using R
If you also want to have the R kernel in jupyter, follow [[https://github.com/IRkernel/IRkernel#installation][these If you want to use the R kernel in jupyter, follow [[https://github.com/IRkernel/IRkernel#installation][these instructions]].
instructions]].
Alternatively, you can install =rpy2= (see the [[*Running R and Python in the same notebook][Running R and Python in Alternatively, you can install =rpy2= (see the [[*Running R and Python in the same notebook][Running R and Python in
the same notebook]] section). the same notebook]] section).
...@@ -83,8 +82,8 @@ the same notebook]] section). ...@@ -83,8 +82,8 @@ the same notebook]] section).
sudo apt-get python3-rpy2 sudo apt-get python3-rpy2
#+end_src #+end_src
** Exporting your notebooks with latex ** Exporting your notebooks with latex
Here is what I had to install to make sure the notebook export via Here is what I had to install on my recent debian machine to make sure
latex works: the notebook export via latex works:
#+begin_src shell :results output :exports both #+begin_src shell :results output :exports both
sudo apt-get install wkhtmltopdf sudo apt-get install wkhtmltopdf
sudo apt-get install texlive-xetex sudo apt-get install texlive-xetex
......
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