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Commit 388ab714 authored by Arnaud Legrand's avatar Arnaud Legrand
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Benoit will take care of this (or not)

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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="#orgaa631f0">Interacting with gitlab</a></li> <li style="margin-bottom:0;"><a href="#org975cdde">Additional Jupyter resources or tricks</a>
<li style="margin-bottom:0;"><a href="#orgc0bede2">Additional Jupyter resources or tricks</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orga0a8c0a">Tips and tricks</a></li> <li style="margin-bottom:0;"><a href="#org27d1582">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#orgcc5df2c">Running R and Python in the same notebook</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="#org50f9d65">Exporting a notebook</a></li> <li style="margin-bottom:0;"><a href="#org6e2f783">Exporting a notebook</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org9ad15fe">Installing jupyter or jupyter hub on your own machine</a> <li style="margin-bottom:0;"><a href="#org75409e5">Installing Jupyter on your own machine</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3c82116">Installing jupyter</a></li> <li style="margin-bottom:0;"><a href="#org73474e0">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#org41613aa">Using R</a></li> <li style="margin-bottom:0;"><a href="#org5dcb2d4">Using R</a></li>
<li style="margin-bottom:0;"><a href="#orgeebc12b">Exporting your notebooks with latex</a></li> <li style="margin-bottom:0;"><a href="#org919a045">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#orgf4f33c6">Interacting with gitlab</a></li> <li style="margin-bottom:0;"><a href="#org3bdebfb">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#orgd30b2c8">Interesting extensions to improve notebook readability</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="#org883d82c">Installing jupyterhub</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>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orgaa631f0" class="outline-2"> <div id="outline-container-org975cdde" class="outline-2">
<h2 id="orgaa631f0">Interacting with gitlab</h2> <h2 id="org975cdde">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgaa631f0"> <div class="outline-text-2" id="text-org975cdde">
<blockquote>
<p>
This section needs some love.
</p>
</blockquote>
<p>
As you may have seen from the videos, we provide two buttons to sync
with gitlab. Indeed, even if you recover your files when you log back
into fun, the jupyter runs on a different machine than the gitlab
server and you need to commit your notebook every time you have made a
significant step. This is also the only way to really make it public
and to share your notebook with others.
</p>
</div>
</div>
<div id="outline-container-orgc0bede2" class="outline-2">
<h2 id="orgc0bede2">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgc0bede2">
</div> </div>
<div id="outline-container-orga0a8c0a" class="outline-3"> <div id="outline-container-org27d1582" class="outline-3">
<h3 id="orga0a8c0a">Tips and tricks</h3> <h3 id="org27d1582">Tips and tricks</h3>
<div class="outline-text-3" id="text-orga0a8c0a"> <div class="outline-text-3" id="text-org27d1582">
<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
...@@ -61,9 +41,9 @@ now). ...@@ -61,9 +41,9 @@ now).
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgcc5df2c" class="outline-3"> <div id="outline-container-org4f5f0e8" class="outline-3">
<h3 id="orgcc5df2c">Running R and Python in the same notebook</h3> <h3 id="org4f5f0e8">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orgcc5df2c"> <div class="outline-text-3" id="text-org4f5f0e8">
<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
...@@ -105,9 +85,9 @@ plot((df) ...@@ -105,9 +85,9 @@ plot((df)
</ol> </ol>
</div> </div>
</div> </div>
<div id="outline-container-org50f9d65" class="outline-3"> <div id="outline-container-org6e2f783" class="outline-3">
<h3 id="org50f9d65">Exporting a notebook</h3> <h3 id="org6e2f783">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org50f9d65"> <div class="outline-text-3" id="text-org6e2f783">
<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
...@@ -134,13 +114,13 @@ taste. ...@@ -134,13 +114,13 @@ taste.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org9ad15fe" class="outline-2"> <div id="outline-container-org75409e5" class="outline-2">
<h2 id="org9ad15fe">Installing jupyter or jupyter hub on your own machine</h2> <h2 id="org75409e5">Installing Jupyter on your own machine</h2>
<div class="outline-text-2" id="text-org9ad15fe"> <div class="outline-text-2" id="text-org75409e5">
</div> </div>
<div id="outline-container-org3c82116" class="outline-3"> <div id="outline-container-org73474e0" class="outline-3">
<h3 id="org3c82116">Installing jupyter</h3> <h3 id="org73474e0">Installing jupyter</h3>
<div class="outline-text-3" id="text-org3c82116"> <div class="outline-text-3" id="text-org73474e0">
<p> <p>
Here is what you should install: Here is what you should install:
</p> </p>
...@@ -171,16 +151,16 @@ The ipython notebook can then be run with the following command: ...@@ -171,16 +151,16 @@ The ipython notebook can then be run with the following command:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org41613aa" class="outline-3"> <div id="outline-container-org5dcb2d4" class="outline-3">
<h3 id="org41613aa">Using R</h3> <h3 id="org5dcb2d4">Using R</h3>
<div class="outline-text-3" id="text-org41613aa"> <div class="outline-text-3" id="text-org5dcb2d4">
<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 also want to have 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="#orgcc5df2c">Running R and Python in Alternatively, you can install <code>rpy2</code> (see the <a href="#org4f5f0e8">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">
...@@ -189,9 +169,9 @@ the same notebook</a> section). ...@@ -189,9 +169,9 @@ the same notebook</a> section).
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgeebc12b" class="outline-3"> <div id="outline-container-org919a045" class="outline-3">
<h3 id="orgeebc12b">Exporting your notebooks with latex</h3> <h3 id="org919a045">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgeebc12b"> <div class="outline-text-3" id="text-org919a045">
<p> <p>
Here is what I had to install to make sure the notebook export via Here is what I had to install to make sure the notebook export via
latex works: latex works:
...@@ -203,9 +183,9 @@ sudo apt-get install texlive-xetex ...@@ -203,9 +183,9 @@ sudo apt-get install texlive-xetex
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgf4f33c6" class="outline-3"> <div id="outline-container-org3bdebfb" class="outline-3">
<h3 id="orgf4f33c6">Interacting with gitlab</h3> <h3 id="org3bdebfb">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgf4f33c6"> <div class="outline-text-3" id="text-org3bdebfb">
<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>:
...@@ -217,9 +197,9 @@ jupyter nbextension enable nb-git ...@@ -217,9 +197,9 @@ jupyter nbextension enable nb-git
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgd30b2c8" class="outline-3"> <div id="outline-container-orgee218a0" class="outline-3">
<h3 id="orgd30b2c8">Interesting extensions to improve notebook readability</h3> <h3 id="orgee218a0">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgd30b2c8"> <div class="outline-text-3" id="text-orgee218a0">
<p> <p>
Here are two interesting extensions that can improve readability: Here are two interesting extensions that can improve readability:
</p> </p>
...@@ -245,9 +225,10 @@ jupyter-serverextension enable --py hide_code ...@@ -245,9 +225,10 @@ jupyter-serverextension enable --py hide_code
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org883d82c" class="outline-3"> </div>
<h3 id="org883d82c">Installing jupyterhub</h3> <div id="outline-container-org4ee7491" class="outline-2">
<div class="outline-text-3" id="text-org883d82c"> <h2 id="org4ee7491">Installing JupyterHub&#xa0;&#xa0;&#xa0;<span class="tag"><span class="Benoit">Benoit</span></span></h2>
<div class="outline-text-2" id="text-org4ee7491">
<blockquote> <blockquote>
<p> <p>
Benoit may give a few hints on this. Benoit may give a few hints on this.
...@@ -256,4 +237,3 @@ Benoit may give a few hints on this. ...@@ -256,4 +237,3 @@ Benoit may give a few hints on this.
</div> </div>
</div> </div>
</div> </div>
</div>
module2/ressources/jupyter.org
View file @ 388ab714
...@@ -4,18 +4,8 @@ ...@@ -4,18 +4,8 @@
#+DATE: June, 2018 #+DATE: June, 2018
#+STARTUP: overview indent #+STARTUP: overview indent
#+OPTIONS: num:nil toc:t #+OPTIONS: num:nil toc:t
#+PROPERTY: header-args :eval never-export
* Interacting with gitlab
#+BEGIN_QUOTE
This section needs some love.
#+END_QUOTE
As you may have seen from the videos, we provide two buttons to sync
with gitlab. Indeed, even if you recover your files when you log back
into fun, the jupyter runs on a different machine than the gitlab
server and you need to commit your notebook every time you have made a
significant step. This is also the only way to really make it public
and to share your notebook with others.
* Additional Jupyter resources or tricks * Additional Jupyter resources or tricks
** Tips and tricks ** Tips and tricks
The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it
...@@ -64,7 +54,7 @@ Instead of going directly through LaTeX and playing too much with the ...@@ -64,7 +54,7 @@ Instead of going directly through LaTeX and playing too much with the
nbconvert exporter, an other option consists in exporting to Markdown nbconvert exporter, an other option consists in exporting to Markdown
and playing with [[https://pandoc.org/][pandoc]]. Both approaches work, it's rather a matter of and playing with [[https://pandoc.org/][pandoc]]. Both approaches work, it's rather a matter of
taste. taste.
* Installing jupyter or jupyter hub on your own machine * Installing Jupyter on your own machine
** Installing jupyter ** Installing jupyter
Here is what you should install: Here is what you should install:
#+begin_src shell :results output :exports both #+begin_src shell :results output :exports both
...@@ -120,7 +110,7 @@ Here are two interesting extensions that can improve readability: ...@@ -120,7 +110,7 @@ Here are two interesting extensions that can improve readability:
jupyter-nbextension enable --py hide_code jupyter-nbextension enable --py hide_code
jupyter-serverextension enable --py hide_code jupyter-serverextension enable --py hide_code
#+end_src #+end_src
** Installing jupyterhub * Installing JupyterHub :Benoit:
#+BEGIN_QUOTE #+BEGIN_QUOTE
Benoit may give a few hints on this. Benoit may give a few hints on this.
#+END_QUOTE #+END_QUOTE
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