Commit 5ce6b00b authored by Arnaud Legrand's avatar Arnaud Legrand

Regenerate HTML filesxs

parent e75d84f2
......@@ -4,26 +4,26 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org279375a">Syntaxe</a>
<li><a href="#orge7765d4">Syntaxe</a>
<ul>
<li><a href="#orgea0a250">Headers</a></li>
<li><a href="#org7b2e0c4">Emphasis</a></li>
<li><a href="#org68e8471">Lists</a>
<li><a href="#orgfa68a29">Headers</a></li>
<li><a href="#org8efa22f">Emphasis</a></li>
<li><a href="#orge264e14">Lists</a>
<ul>
<li><a href="#orgd550835">Unordered</a></li>
<li><a href="#org47754af">Ordered</a></li>
<li><a href="#org8aff08d">Unordered</a></li>
<li><a href="#org4acaa77">Ordered</a></li>
</ul>
</li>
<li><a href="#org1cdf055">Images</a></li>
<li><a href="#org22b813b">Links</a></li>
<li><a href="#org4b5671d">Blockquotes</a></li>
<li><a href="#org58b14cd">Inline code</a></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>
</ul>
</li>
<li><a href="#org17d57d0">Écrire des Maths</a>
<li><a href="#orgec971b4">Écrire des Maths</a>
<ul>
<li><a href="#org366dfa8">Lettres grecques</a></li>
<li><a href="#org59bccec">Operators</a></li>
<li><a href="#org71635d1">Lettres grecques</a></li>
<li><a href="#org08d8b82">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-org279375a" class="outline-2">
<h2 id="org279375a">Syntaxe</h2>
<div class="outline-text-2" id="text-org279375a">
<div id="outline-container-orge7765d4" class="outline-2">
<h2 id="orge7765d4">Syntaxe</h2>
<div class="outline-text-2" id="text-orge7765d4">
</div>
<div id="outline-container-orgea0a250" class="outline-3">
<h3 id="orgea0a250">Headers</h3>
<div class="outline-text-3" id="text-orgea0a250">
<div id="outline-container-orgfa68a29" class="outline-3">
<h3 id="orgfa68a29">Headers</h3>
<div class="outline-text-3" id="text-orgfa68a29">
<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-org7b2e0c4" class="outline-3">
<h3 id="org7b2e0c4">Emphasis</h3>
<div class="outline-text-3" id="text-org7b2e0c4">
<div id="outline-container-org8efa22f" class="outline-3">
<h3 id="org8efa22f">Emphasis</h3>
<div class="outline-text-3" id="text-org8efa22f">
<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-org68e8471" class="outline-3">
<h3 id="org68e8471">Lists</h3>
<div class="outline-text-3" id="text-org68e8471">
<div id="outline-container-orge264e14" class="outline-3">
<h3 id="orge264e14">Lists</h3>
<div class="outline-text-3" id="text-orge264e14">
</div>
<div id="outline-container-orgd550835" class="outline-4">
<h4 id="orgd550835">Unordered</h4>
<div class="outline-text-4" id="text-orgd550835">
<div id="outline-container-org8aff08d" class="outline-4">
<h4 id="org8aff08d">Unordered</h4>
<div class="outline-text-4" id="text-org8aff08d">
<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-org47754af" class="outline-4">
<h4 id="org47754af">Ordered</h4>
<div class="outline-text-4" id="text-org47754af">
<div id="outline-container-org4acaa77" class="outline-4">
<h4 id="org4acaa77">Ordered</h4>
<div class="outline-text-4" id="text-org4acaa77">
<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-org1cdf055" class="outline-3">
<h3 id="org1cdf055">Images</h3>
<div class="outline-text-3" id="text-org1cdf055">
<div id="outline-container-orgb7930f3" class="outline-3">
<h3 id="orgb7930f3">Images</h3>
<div class="outline-text-3" id="text-orgb7930f3">
<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-org22b813b" class="outline-3">
<h3 id="org22b813b">Links</h3>
<div class="outline-text-3" id="text-org22b813b">
<div id="outline-container-orgef25979" class="outline-3">
<h3 id="orgef25979">Links</h3>
<div class="outline-text-3" id="text-orgef25979">
<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-org4b5671d" class="outline-3">
<h3 id="org4b5671d">Blockquotes</h3>
<div class="outline-text-3" id="text-org4b5671d">
<div id="outline-container-org075cffa" class="outline-3">
<h3 id="org075cffa">Blockquotes</h3>
<div class="outline-text-3" id="text-org075cffa">
<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-org58b14cd" class="outline-3">
<h3 id="org58b14cd">Inline code</h3>
<div class="outline-text-3" id="text-org58b14cd">
<div id="outline-container-orgfd6d212" class="outline-3">
<h3 id="orgfd6d212">Inline code</h3>
<div class="outline-text-3" id="text-orgfd6d212">
<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-org17d57d0" class="outline-2">
<h2 id="org17d57d0">Écrire des Maths</h2>
<div class="outline-text-2" id="text-org17d57d0">
<div id="outline-container-orgec971b4" class="outline-2">
<h2 id="orgec971b4">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgec971b4">
<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-org366dfa8" class="outline-3">
<h3 id="org366dfa8">Lettres grecques</h3>
<div class="outline-text-3" id="text-org366dfa8">
<div id="outline-container-org71635d1" class="outline-3">
<h3 id="org71635d1">Lettres grecques</h3>
<div class="outline-text-3" id="text-org71635d1">
<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-org59bccec" class="outline-3">
<h3 id="org59bccec">Operators</h3>
<div id="outline-container-org08d8b82" class="outline-3">
<h3 id="org08d8b82">Operators</h3>
</div>
</div>
</div>
This diff is collapsed.
......@@ -4,31 +4,31 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orga526517">Interacting with gitlab</a></li>
<li><a href="#orgc2f491d">Additional Jupyter resources or tricks</a>
<li><a href="#org877f03b">Interacting with gitlab</a></li>
<li><a href="#org16a59c6">Additional Jupyter resources or tricks</a>
<ul>
<li><a href="#org8e565a9">Tips and tricks</a></li>
<li><a href="#org4cdc7d0">Running R and Python in the same notebook</a></li>
<li><a href="#org903f8bb">Exporting a notebook</a></li>
<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>
</ul>
</li>
<li><a href="#orgc7fa362">Installing jupyter or jupyter hub on your own machine</a>
<li><a href="#org3bb44ad">Installing jupyter or jupyter hub on your own machine</a>
<ul>
<li><a href="#org7a1f8ea">Installing jupyter</a></li>
<li><a href="#orgce00981">Using R</a></li>
<li><a href="#orgb434d6b">Exporting your notebooks with latex</a></li>
<li><a href="#org2f9a28e">Interacting with gitlab</a></li>
<li><a href="#org0c89d5b">Interesting extensions to improve notebook readability</a></li>
<li><a href="#org04fd4d3">Installing jupyterhub</a></li>
<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>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orga526517" class="outline-2">
<h2 id="orga526517">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-orga526517">
<div id="outline-container-org877f03b" class="outline-2">
<h2 id="org877f03b">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-org877f03b">
<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-orgc2f491d" class="outline-2">
<h2 id="orgc2f491d">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-orgc2f491d">
<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>
<div id="outline-container-org8e565a9" class="outline-3">
<h3 id="org8e565a9">Tips and tricks</h3>
<div class="outline-text-3" id="text-org8e565a9">
<div id="outline-container-org21ed683" class="outline-3">
<h3 id="org21ed683">Tips and tricks</h3>
<div class="outline-text-3" id="text-org21ed683">
<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-org4cdc7d0" class="outline-3">
<h3 id="org4cdc7d0">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org4cdc7d0">
<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">
<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
......@@ -105,9 +105,9 @@ plot((df)
</ol>
</div>
</div>
<div id="outline-container-org903f8bb" class="outline-3">
<h3 id="org903f8bb">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org903f8bb">
<div id="outline-container-orgff572f3" class="outline-3">
<h3 id="orgff572f3">Exporting a notebook</h3>
<div class="outline-text-3" id="text-orgff572f3">
<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-orgc7fa362" class="outline-2">
<h2 id="orgc7fa362">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-orgc7fa362">
<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>
<div id="outline-container-org7a1f8ea" class="outline-3">
<h3 id="org7a1f8ea">Installing jupyter</h3>
<div class="outline-text-3" id="text-org7a1f8ea">
<div id="outline-container-org7acfd0d" class="outline-3">
<h3 id="org7acfd0d">Installing jupyter</h3>
<div class="outline-text-3" id="text-org7acfd0d">
<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-orgce00981" class="outline-3">
<h3 id="orgce00981">Using R</h3>
<div class="outline-text-3" id="text-orgce00981">
<div id="outline-container-org4236b75" class="outline-3">
<h3 id="org4236b75">Using R</h3>
<div class="outline-text-3" id="text-org4236b75">
<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="#org4cdc7d0">Running R and Python in
Alternatively, you can install <code>rpy2</code> (see the <a href="#org81cf6e7">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-orgb434d6b" class="outline-3">
<h3 id="orgb434d6b">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgb434d6b">
<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">
<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-org2f9a28e" class="outline-3">
<h3 id="org2f9a28e">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-org2f9a28e">
<div id="outline-container-orgd9a7f1c" class="outline-3">
<h3 id="orgd9a7f1c">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgd9a7f1c">
<p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>:
......@@ -217,9 +217,9 @@ jupyter nbextension enable nb-git
</div>
</div>
</div>
<div id="outline-container-org0c89d5b" class="outline-3">
<h3 id="org0c89d5b">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-org0c89d5b">
<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">
<p>
Here are two interesting extensions that can improve readability:
</p>
......@@ -245,9 +245,9 @@ jupyter-serverextension enable --py hide_code
</ul>
</div>
</div>
<div id="outline-container-org04fd4d3" class="outline-3">
<h3 id="org04fd4d3">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org04fd4d3">
<div id="outline-container-orgff424ae" class="outline-3">
<h3 id="orgff424ae">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-orgff424ae">
<blockquote>
<p>
Benoit may give a few hints on this.
......
......@@ -4,36 +4,36 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org54d034a">Installing Rstudio</a>
<li><a href="#org937177d">Installing Rstudio</a>
<ul>
<li><a href="#org8769ef8">Linux (debian, ubuntu)</a>
<li><a href="#org8f48c7c">Linux (debian, ubuntu)</a>
<ul>
<li><a href="#org2be7be7">Installing R</a></li>
<li><a href="#orgb3b8562">Installing rstudio</a></li>
<li><a href="#orge26d961">Installing R</a></li>
<li><a href="#org8956720">Installing rstudio</a></li>
</ul>
</li>
<li><a href="#org4d687e8">Mac OSX and Windows</a></li>
<li><a href="#org8770e8d">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#org23609ff">Installing Git</a>
<li><a href="#orgc5c6960">Installing Git</a>
<ul>
<li><a href="#org3205f63">Linux (debian, ubuntu)</a></li>
<li><a href="#org825283e">Mac OSX and Windows</a></li>
<li><a href="#org5b86b8a">Linux (debian, ubuntu)</a></li>
<li><a href="#org18d42c3">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#orgf165b77">Rstudio and git/github/gitlab</a></li>
<li><a href="#org7da9c23">Cheat Sheets</a></li>
<li><a href="#org2392c30">Rstudio and git/github/gitlab</a></li>
<li><a href="#org40217fe">Cheat Sheets</a></li>
</ul>
</div>
</div>
<div id="outline-container-org54d034a" class="outline-2">
<h2 id="org54d034a">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org54d034a">
<div id="outline-container-org937177d" class="outline-2">
<h2 id="org937177d">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org937177d">
</div>
<div id="outline-container-org8769ef8" class="outline-3">
<h3 id="org8769ef8">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8769ef8">
<div id="outline-container-org8f48c7c" class="outline-3">
<h3 id="org8f48c7c">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8f48c7c">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -55,9 +55,9 @@ for upgrading&#x2026;
</p>
</div>
<div id="outline-container-org2be7be7" class="outline-4">
<h4 id="org2be7be7">Installing R</h4>
<div class="outline-text-4" id="text-org2be7be7">
<div id="outline-container-orge26d961" class="outline-4">
<h4 id="orge26d961">Installing R</h4>
<div class="outline-text-4" id="text-orge26d961">
<p>
Beforehand, you need to install the R language and convenient packages
by running (as root):
......@@ -90,9 +90,9 @@ to run (as root):
</div>
</div>
<div id="outline-container-orgb3b8562" class="outline-4">
<h4 id="orgb3b8562">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgb3b8562">
<div id="outline-container-org8956720" class="outline-4">
<h4 id="org8956720">Installing rstudio</h4>
<div class="outline-text-4" id="text-org8956720">
<p>
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the <a href="https://www.rstudio.com/products/rstudio/download/#download">Rstudio webpage</a>
......@@ -110,9 +110,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo
</div>
</div>
</div>
<div id="outline-container-org4d687e8" class="outline-3">
<h3 id="org4d687e8">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org4d687e8">
<div id="outline-container-org8770e8d" class="outline-3">
<h3 id="org8770e8d">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org8770e8d">
<blockquote>
<p>
Some instructions on installing R and knitr must be missing. This
......@@ -136,13 +136,13 @@ install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</div>
</div>
</div>
<div id="outline-container-org23609ff" class="outline-2">
<h2 id="org23609ff">Installing Git</h2>
<div class="outline-text-2" id="text-org23609ff">
<div id="outline-container-orgc5c6960" class="outline-2">
<h2 id="orgc5c6960">Installing Git</h2>
<div class="outline-text-2" id="text-orgc5c6960">
</div>
<div id="outline-container-org3205f63" class="outline-3">
<h3 id="org3205f63">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org3205f63">
<div id="outline-container-org5b86b8a" class="outline-3">
<h3 id="org5b86b8a">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org5b86b8a">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -158,9 +158,9 @@ Run (as root):
</div>
</div>
</div>
<div id="outline-container-org825283e" class="outline-3">
<h3 id="org825283e">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org825283e">
<div id="outline-container-org18d42c3" class="outline-3">
<h3 id="org18d42c3">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org18d42c3">
<ul class="org-ul">
<li>Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li>Optional Git clients (should not be needed if you work within
......@@ -180,9 +180,9 @@ Rstudio):
</div>
</div>
</div>
<div id="outline-container-orgf165b77" class="outline-2">
<h2 id="orgf165b77">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-orgf165b77">
<div id="outline-container-org2392c30" class="outline-2">
<h2 id="org2392c30">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-org2392c30">
<blockquote>
<p>
We may want to redo a screencast in French for this
......@@ -203,9 +203,9 @@ Alternatively, we can point to:
</ul>
</div>
</div>
<div id="outline-container-org7da9c23" class="outline-2">
<h2 id="org7da9c23">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org7da9c23">
<div id="outline-container-org40217fe" class="outline-2">
<h2 id="org40217fe">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org40217fe">
<p>
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the <a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheets webpage</a>. In particular
......
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