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module1/ressources/introduction_to_markdown.html
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......@@ -4,26 +4,26 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge7765d4">Syntaxe</a>
<li style="margin-bottom:0;"><a href="#org8de79b7">Syntaxe</a>
<ul>
<li><a href="#orgfa68a29">Headers</a></li>
<li><a href="#org8efa22f">Emphasis</a></li>
<li><a href="#orge264e14">Lists</a>
<li style="margin-bottom:0;"><a href="#orgd0cd01a">Headers</a></li>
<li style="margin-bottom:0;"><a href="#org0a02e8a">Emphasis</a></li>
<li style="margin-bottom:0;"><a href="#org5ba3da0">Lists</a>
<ul>
<li><a href="#org8aff08d">Unordered</a></li>
<li><a href="#org4acaa77">Ordered</a></li>
<li style="margin-bottom:0;"><a href="#orgf404e08">Unordered</a></li>
<li style="margin-bottom:0;"><a href="#orga07db10">Ordered</a></li>
</ul>
</li>
<li><a href="#orgb7930f3">Images</a></li>
<li><a href="#orgef25979">Links</a></li>
<li><a href="#org075cffa">Blockquotes</a></li>
<li><a href="#orgfd6d212">Inline code</a></li>
<li style="margin-bottom:0;"><a href="#orgea33b61">Images</a></li>
<li style="margin-bottom:0;"><a href="#org45306c5">Links</a></li>
<li style="margin-bottom:0;"><a href="#org8cf7f47">Blockquotes</a></li>
<li style="margin-bottom:0;"><a href="#org5cc4188">Inline code</a></li>
</ul>
</li>
<li><a href="#orgec971b4">Écrire des Maths</a>
<li style="margin-bottom:0;"><a href="#orgf5d12d0">Écrire des Maths</a>
<ul>
<li><a href="#org71635d1">Lettres grecques</a></li>
<li><a href="#org08d8b82">Operators</a></li>
<li style="margin-bottom:0;"><a href="#orgd3d090f">Lettres grecques</a></li>
<li style="margin-bottom:0;"><a href="#org4cbab17">Operators</a></li>
</ul>
</li>
</ul>
......@@ -34,13 +34,13 @@ Voici un aperçu rapide de la syntaxe Markdown repris d'une
<a href="https://guides.github.com/features/mastering-markdown/">présentation de Github</a> ainsi que de celles d'<a href="http://csrgxtu.github.io/2015/03/20/Writing-Mathematic-Fomulars-in-Markdown/">Archer Reilly</a> et de <a href="http://www.statpower.net/Content/310/R%20Stuff/SampleMarkdown.html">James
H. Steiger</a>.
</p>
<div id="outline-container-orge7765d4" class="outline-2">
<h2 id="orge7765d4">Syntaxe</h2>
<div class="outline-text-2" id="text-orge7765d4">
<div id="outline-container-org8de79b7" class="outline-2">
<h2 id="org8de79b7">Syntaxe</h2>
<div class="outline-text-2" id="text-org8de79b7">
</div>
<div id="outline-container-orgfa68a29" class="outline-3">
<h3 id="orgfa68a29">Headers</h3>
<div class="outline-text-3" id="text-orgfa68a29">
<div id="outline-container-orgd0cd01a" class="outline-3">
<h3 id="orgd0cd01a">Headers</h3>
<div class="outline-text-3" id="text-orgd0cd01a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
# This is an &lt;h1&gt; tag
## This is an &lt;h2&gt; tag
......@@ -49,9 +49,9 @@ H. Steiger</a>.
</div>
</div>
<div id="outline-container-org8efa22f" class="outline-3">
<h3 id="org8efa22f">Emphasis</h3>
<div class="outline-text-3" id="text-org8efa22f">
<div id="outline-container-org0a02e8a" class="outline-3">
<h3 id="org0a02e8a">Emphasis</h3>
<div class="outline-text-3" id="text-org0a02e8a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
*This text will be italic*
_This will also be italic_
......@@ -64,13 +64,13 @@ _You **can** combine them_
</div>
</div>
<div id="outline-container-orge264e14" class="outline-3">
<h3 id="orge264e14">Lists</h3>
<div class="outline-text-3" id="text-orge264e14">
<div id="outline-container-org5ba3da0" class="outline-3">
<h3 id="org5ba3da0">Lists</h3>
<div class="outline-text-3" id="text-org5ba3da0">
</div>
<div id="outline-container-org8aff08d" class="outline-4">
<h4 id="org8aff08d">Unordered</h4>
<div class="outline-text-4" id="text-org8aff08d">
<div id="outline-container-orgf404e08" class="outline-4">
<h4 id="orgf404e08">Unordered</h4>
<div class="outline-text-4" id="text-orgf404e08">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
* Item 1
* Item 2
......@@ -79,9 +79,9 @@ _You **can** combine them_
</pre>
</div>
</div>
<div id="outline-container-org4acaa77" class="outline-4">
<h4 id="org4acaa77">Ordered</h4>
<div class="outline-text-4" id="text-org4acaa77">
<div id="outline-container-orga07db10" class="outline-4">
<h4 id="orga07db10">Ordered</h4>
<div class="outline-text-4" id="text-orga07db10">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
1. Item 1
1. Item 2
......@@ -92,27 +92,27 @@ _You **can** combine them_
</div>
</div>
</div>
<div id="outline-container-orgb7930f3" class="outline-3">
<h3 id="orgb7930f3">Images</h3>
<div class="outline-text-3" id="text-orgb7930f3">
<div id="outline-container-orgea33b61" class="outline-3">
<h3 id="orgea33b61">Images</h3>
<div class="outline-text-3" id="text-orgea33b61">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
![GitHub Logo](/images/logo.png)
Format: ![Alt Text](url)
</pre>
</div>
</div>
<div id="outline-container-orgef25979" class="outline-3">
<h3 id="orgef25979">Links</h3>
<div class="outline-text-3" id="text-orgef25979">
<div id="outline-container-org45306c5" class="outline-3">
<h3 id="org45306c5">Links</h3>
<div class="outline-text-3" id="text-org45306c5">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
http://github.com - automatic!
[GitHub](http://github.com)
</pre>
</div>
</div>
<div id="outline-container-org075cffa" class="outline-3">
<h3 id="org075cffa">Blockquotes</h3>
<div class="outline-text-3" id="text-org075cffa">
<div id="outline-container-org8cf7f47" class="outline-3">
<h3 id="org8cf7f47">Blockquotes</h3>
<div class="outline-text-3" id="text-org8cf7f47">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
As Kanye West said:
......@@ -121,9 +121,9 @@ As Kanye West said:
</pre>
</div>
</div>
<div id="outline-container-orgfd6d212" class="outline-3">
<h3 id="orgfd6d212">Inline code</h3>
<div class="outline-text-3" id="text-orgfd6d212">
<div id="outline-container-org5cc4188" class="outline-3">
<h3 id="org5cc4188">Inline code</h3>
<div class="outline-text-3" id="text-org5cc4188">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
I think you should use an
`&lt;addr&gt;` element here instead.
......@@ -131,9 +131,9 @@ I think you should use an
</div>
</div>
</div>
<div id="outline-container-orgec971b4" class="outline-2">
<h2 id="orgec971b4">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgec971b4">
<div id="outline-container-orgf5d12d0" class="outline-2">
<h2 id="orgf5d12d0">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgf5d12d0">
<p>
Equations can be formatted <b>inline</b> or as <b>displayed formulas</b>. In the
latter case, they are centered and set off from the main text. In the
......@@ -177,9 +177,9 @@ This summation expression is in display form.
</p>
</div>
<div id="outline-container-org71635d1" class="outline-3">
<h3 id="org71635d1">Lettres grecques</h3>
<div class="outline-text-3" id="text-org71635d1">
<div id="outline-container-orgd3d090f" class="outline-3">
<h3 id="orgd3d090f">Lettres grecques</h3>
<div class="outline-text-3" id="text-orgd3d090f">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
......@@ -223,8 +223,8 @@ This summation expression is in display form.
</table>
</div>
</div>
<div id="outline-container-org08d8b82" class="outline-3">
<h3 id="org08d8b82">Operators</h3>
<div id="outline-container-org4cbab17" class="outline-3">
<h3 id="org4cbab17">Operators</h3>
</div>
</div>
</div>
module2/ressources/emacs_orgmode.html
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module2/ressources/jupyter.html
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......@@ -4,31 +4,31 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org877f03b">Interacting with gitlab</a></li>
<li><a href="#org16a59c6">Additional Jupyter resources or tricks</a>
<li style="margin-bottom:0;"><a href="#orgc72397d">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org186a10f">Additional Jupyter resources or tricks</a>
<ul>
<li><a href="#org21ed683">Tips and tricks</a></li>
<li><a href="#org81cf6e7">Running R and Python in the same notebook</a></li>
<li><a href="#orgff572f3">Exporting a notebook</a></li>
<li style="margin-bottom:0;"><a href="#org9d17f16">Tips and tricks</a></li>
<li style="margin-bottom:0;"><a href="#org3c5eb3e">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org656a59e">Exporting a notebook</a></li>
</ul>
</li>
<li><a href="#org3bb44ad">Installing jupyter or jupyter hub on your own machine</a>
<li style="margin-bottom:0;"><a href="#org2b24a9c">Installing jupyter or jupyter hub on your own machine</a>
<ul>
<li><a href="#org7acfd0d">Installing jupyter</a></li>
<li><a href="#org4236b75">Using R</a></li>
<li><a href="#org04ec93e">Exporting your notebooks with latex</a></li>
<li><a href="#orgd9a7f1c">Interacting with gitlab</a></li>
<li><a href="#orgad4d4c4">Interesting extensions to improve notebook readability</a></li>
<li><a href="#orgff424ae">Installing jupyterhub</a></li>
<li style="margin-bottom:0;"><a href="#orgfe13c9b">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#orgaeb7a97">Using R</a></li>
<li style="margin-bottom:0;"><a href="#orgbf7d110">Exporting your notebooks with latex</a></li>
<li style="margin-bottom:0;"><a href="#orgff388aa">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org77fb4ca">Interesting extensions to improve notebook readability</a></li>
<li style="margin-bottom:0;"><a href="#org364ee89">Installing jupyterhub</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org877f03b" class="outline-2">
<h2 id="org877f03b">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-org877f03b">
<div id="outline-container-orgc72397d" class="outline-2">
<h2 id="orgc72397d">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-orgc72397d">
<blockquote>
<p>
This section needs some love.
......@@ -45,13 +45,13 @@ and to share your notebook with others.
</p>
</div>
</div>
<div id="outline-container-org16a59c6" class="outline-2">
<h2 id="org16a59c6">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org16a59c6">
<div id="outline-container-org186a10f" class="outline-2">
<h2 id="org186a10f">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org186a10f">
</div>
<div id="outline-container-org21ed683" class="outline-3">
<h3 id="org21ed683">Tips and tricks</h3>
<div class="outline-text-3" id="text-org21ed683">
<div id="outline-container-org9d17f16" class="outline-3">
<h3 id="org9d17f16">Tips and tricks</h3>
<div class="outline-text-3" id="text-org9d17f16">
<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
......@@ -61,9 +61,9 @@ now).
</p>
</div>
</div>
<div id="outline-container-org81cf6e7" class="outline-3">
<h3 id="org81cf6e7">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org81cf6e7">
<div id="outline-container-org3c5eb3e" class="outline-3">
<h3 id="org3c5eb3e">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org3c5eb3e">
<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>. An
......@@ -78,14 +78,14 @@ with
Then you'll be able to use both languages in the same notebook by:
</p>
<ol class="org-ol">
<li><p>
<li style="margin-bottom:0;"><p>
Loading <code>rpy2</code>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%load_ext rpy2.ipython
</pre>
</div></li>
<li><p>
<li style="margin-bottom:0;"><p>
Using the <code>%R</code> Ipython magic:
</p>
<div class="org-src-container">
......@@ -105,9 +105,9 @@ plot((df)
</ol>
</div>
</div>
<div id="outline-container-orgff572f3" class="outline-3">
<h3 id="orgff572f3">Exporting a notebook</h3>
<div class="outline-text-3" id="text-orgff572f3">
<div id="outline-container-org656a59e" class="outline-3">
<h3 id="org656a59e">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org656a59e">
<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
......@@ -134,13 +134,13 @@ taste.
</div>
</div>
</div>
<div id="outline-container-org3bb44ad" class="outline-2">
<h2 id="org3bb44ad">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org3bb44ad">
<div id="outline-container-org2b24a9c" class="outline-2">
<h2 id="org2b24a9c">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org2b24a9c">
</div>
<div id="outline-container-org7acfd0d" class="outline-3">
<h3 id="org7acfd0d">Installing jupyter</h3>
<div class="outline-text-3" id="text-org7acfd0d">
<div id="outline-container-orgfe13c9b" class="outline-3">
<h3 id="orgfe13c9b">Installing jupyter</h3>
<div class="outline-text-3" id="text-orgfe13c9b">
<p>
Here is what you should install:
</p>
......@@ -171,16 +171,16 @@ The ipython notebook can then be run with the following command:
</div>
</div>
</div>
<div id="outline-container-org4236b75" class="outline-3">
<h3 id="org4236b75">Using R</h3>
<div class="outline-text-3" id="text-org4236b75">
<div id="outline-container-orgaeb7a97" class="outline-3">
<h3 id="orgaeb7a97">Using R</h3>
<div class="outline-text-3" id="text-orgaeb7a97">
<p>
If you also want to have the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these
instructions</a>.
</p>
<p>
Alternatively, you can install <code>rpy2</code> (see the <a href="#org81cf6e7">Running R and Python in
Alternatively, you can install <code>rpy2</code> (see the <a href="#org3c5eb3e">Running R and Python in
the same notebook</a> section).
</p>
<div class="org-src-container">
......@@ -189,9 +189,9 @@ the same notebook</a> section).
</div>
</div>
</div>
<div id="outline-container-org04ec93e" class="outline-3">
<h3 id="org04ec93e">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-org04ec93e">
<div id="outline-container-orgbf7d110" class="outline-3">
<h3 id="orgbf7d110">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgbf7d110">
<p>
Here is what I had to install to make sure the notebook export via
latex works:
......@@ -203,9 +203,9 @@ sudo apt-get install texlive-xetex
</div>
</div>
</div>
<div id="outline-container-orgd9a7f1c" class="outline-3">
<h3 id="orgd9a7f1c">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgd9a7f1c">
<div id="outline-container-orgff388aa" class="outline-3">
<h3 id="orgff388aa">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgff388aa">
<p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>:
......@@ -217,14 +217,14 @@ jupyter nbextension enable nb-git
</div>
</div>
</div>
<div id="outline-container-orgad4d4c4" class="outline-3">
<h3 id="orgad4d4c4">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgad4d4c4">
<div id="outline-container-org77fb4ca" class="outline-3">
<h3 id="org77fb4ca">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-org77fb4ca">
<p>
Here are two interesting extensions that can improve readability:
</p>
<ul class="org-ul">
<li><p>
<li style="margin-bottom:0;"><p>
<a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a>
</p>
<div class="org-src-container">
......@@ -232,7 +232,7 @@ Here are two interesting extensions that can improve readability:
<span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">jupyter contrib nbextension install --user # not done yet</span>
</pre>
</div></li>
<li><p>
<li style="margin-bottom:0;"><p>
<a href="https://github.com/kirbs-/hide_code">Hiding code</a>
</p>
<div class="org-src-container">
......@@ -245,9 +245,9 @@ jupyter-serverextension enable --py hide_code
</ul>
</div>
</div>
<div id="outline-container-orgff424ae" class="outline-3">
<h3 id="orgff424ae">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-orgff424ae">
<div id="outline-container-org364ee89" class="outline-3">
<h3 id="org364ee89">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org364ee89">
<blockquote>
<p>
Benoit may give a few hints on this.
......
module2/ressources/rstudio.html
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