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module1/ressources/introduction_to_markdown.html
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......@@ -3,27 +3,27 @@
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li style="margin-bottom:0;"><a href="#org8de79b7">Syntaxe</a>
<ul>
<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 style="margin-bottom:0;"><a href="#orgf404e08">Unordered</a></li>
<li style="margin-bottom:0;"><a href="#orga07db10">Ordered</a></li>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgf6eedf1">Syntaxe</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org73f8334">Headers</a></li>
<li style="margin-bottom:0;"><a href="#orge859927">Emphasis</a></li>
<li style="margin-bottom:0;"><a href="#orgd9ebabe">Lists</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org82bce14">Unordered</a></li>
<li style="margin-bottom:0;"><a href="#orgc3305db">Ordered</a></li>
</ul>
</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>
<li style="margin-bottom:0;"><a href="#orgcf2594b">Images</a></li>
<li style="margin-bottom:0;"><a href="#org12709c1">Links</a></li>
<li style="margin-bottom:0;"><a href="#org36f0088">Blockquotes</a></li>
<li style="margin-bottom:0;"><a href="#org4178eea">Inline code</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgf5d12d0">Écrire des Maths</a>
<ul>
<li style="margin-bottom:0;"><a href="#orgd3d090f">Lettres grecques</a></li>
<li style="margin-bottom:0;"><a href="#org4cbab17">Operators</a></li>
<li style="margin-bottom:0;"><a href="#orgdd8366e">Écrire des Maths</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgce6558c">Lettres grecques</a></li>
<li style="margin-bottom:0;"><a href="#orgad06742">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-org8de79b7" class="outline-2">
<h2 id="org8de79b7">Syntaxe</h2>
<div class="outline-text-2" id="text-org8de79b7">
<div id="outline-container-orgf6eedf1" class="outline-2">
<h2 id="orgf6eedf1">Syntaxe</h2>
<div class="outline-text-2" id="text-orgf6eedf1">
</div>
<div id="outline-container-orgd0cd01a" class="outline-3">
<h3 id="orgd0cd01a">Headers</h3>
<div class="outline-text-3" id="text-orgd0cd01a">
<div id="outline-container-org73f8334" class="outline-3">
<h3 id="org73f8334">Headers</h3>
<div class="outline-text-3" id="text-org73f8334">
<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-org0a02e8a" class="outline-3">
<h3 id="org0a02e8a">Emphasis</h3>
<div class="outline-text-3" id="text-org0a02e8a">
<div id="outline-container-orge859927" class="outline-3">
<h3 id="orge859927">Emphasis</h3>
<div class="outline-text-3" id="text-orge859927">
<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-org5ba3da0" class="outline-3">
<h3 id="org5ba3da0">Lists</h3>
<div class="outline-text-3" id="text-org5ba3da0">
<div id="outline-container-orgd9ebabe" class="outline-3">
<h3 id="orgd9ebabe">Lists</h3>
<div class="outline-text-3" id="text-orgd9ebabe">
</div>
<div id="outline-container-orgf404e08" class="outline-4">
<h4 id="orgf404e08">Unordered</h4>
<div class="outline-text-4" id="text-orgf404e08">
<div id="outline-container-org82bce14" class="outline-4">
<h4 id="org82bce14">Unordered</h4>
<div class="outline-text-4" id="text-org82bce14">
<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-orga07db10" class="outline-4">
<h4 id="orga07db10">Ordered</h4>
<div class="outline-text-4" id="text-orga07db10">
<div id="outline-container-orgc3305db" class="outline-4">
<h4 id="orgc3305db">Ordered</h4>
<div class="outline-text-4" id="text-orgc3305db">
<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-orgea33b61" class="outline-3">
<h3 id="orgea33b61">Images</h3>
<div class="outline-text-3" id="text-orgea33b61">
<div id="outline-container-orgcf2594b" class="outline-3">
<h3 id="orgcf2594b">Images</h3>
<div class="outline-text-3" id="text-orgcf2594b">
<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-org45306c5" class="outline-3">
<h3 id="org45306c5">Links</h3>
<div class="outline-text-3" id="text-org45306c5">
<div id="outline-container-org12709c1" class="outline-3">
<h3 id="org12709c1">Links</h3>
<div class="outline-text-3" id="text-org12709c1">
<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-org8cf7f47" class="outline-3">
<h3 id="org8cf7f47">Blockquotes</h3>
<div class="outline-text-3" id="text-org8cf7f47">
<div id="outline-container-org36f0088" class="outline-3">
<h3 id="org36f0088">Blockquotes</h3>
<div class="outline-text-3" id="text-org36f0088">
<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-org5cc4188" class="outline-3">
<h3 id="org5cc4188">Inline code</h3>
<div class="outline-text-3" id="text-org5cc4188">
<div id="outline-container-org4178eea" class="outline-3">
<h3 id="org4178eea">Inline code</h3>
<div class="outline-text-3" id="text-org4178eea">
<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-orgf5d12d0" class="outline-2">
<h2 id="orgf5d12d0">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgf5d12d0">
<div id="outline-container-orgdd8366e" class="outline-2">
<h2 id="orgdd8366e">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgdd8366e">
<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-orgd3d090f" class="outline-3">
<h3 id="orgd3d090f">Lettres grecques</h3>
<div class="outline-text-3" id="text-orgd3d090f">
<div id="outline-container-orgce6558c" class="outline-3">
<h3 id="orgce6558c">Lettres grecques</h3>
<div class="outline-text-3" id="text-orgce6558c">
<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-org4cbab17" class="outline-3">
<h3 id="org4cbab17">Operators</h3>
<div id="outline-container-orgad06742" class="outline-3">
<h3 id="orgad06742">Operators</h3>
</div>
</div>
</div>
module2/ressources/emacs_orgmode.html
View file @ 91dec995
......@@ -3,65 +3,65 @@
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li style="margin-bottom:0;"><a href="#orgf0788f0">Installing emacs, org-mode, ess, and auctex.</a>
<ul>
<li style="margin-bottom:0;"><a href="#org8412fbd">OS-specific installation procedure</a>
<ul>
<li style="margin-bottom:0;"><a href="#org6c162ce">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org61fb10d">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org6345a15">Windows</a></li>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgdc09806">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb3c62fd">OS-specific installation procedure</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org235f5db">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org601b552">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#orgeb7cce9">Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org39100b1">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul>
<li style="margin-bottom:0;"><a href="#orgead59ff">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org45cc743">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org12df21d">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org1fbd541">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org528bb3d">Step 4: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#org927f811">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgf5e3e23">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org793f930">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org09a3dc2">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org1484860">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org01379a1">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgf3207a2">Emacs Tips and tricks</a>
<ul>
<li style="margin-bottom:0;"><a href="#org63f18b5">Cheat-sheets</a>
<ul>
<li style="margin-bottom:0;"><a href="#org22fe63d">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org4d46779">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#orgd96cc54">Emacs Tips and tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org7b80429">Cheat-sheets</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgc60a5a4">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org12dfdcf">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgefcfd8e">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org4a1463b">Additional useful emacs packages</a>
<ul>
<li style="margin-bottom:0;"><a href="#orgf784a61">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org57b6a55">Magit</a></li>
<li style="margin-bottom:0;"><a href="#org37ba57d">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org9c09e0f">Additional useful emacs packages</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org540b4bf">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org22d5f9b">Magit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org84da85a">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#org8e569d2">Other resources</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org1a26eb1">A replicable article</a>
<ul>
<li style="margin-bottom:0;"><a href="#org33696b8">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org134c336">A replicable article</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org4f6d44d">A stub of replicable article</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgf0788f0" class="outline-2">
<h2 id="orgf0788f0">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orgf0788f0">
<div id="outline-container-orgdc09806" class="outline-2">
<h2 id="orgdc09806">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orgdc09806">
</div>
<div id="outline-container-org8412fbd" class="outline-3">
<h3 id="org8412fbd">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-org8412fbd">
<div id="outline-container-orgb3c62fd" class="outline-3">
<h3 id="orgb3c62fd">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-orgb3c62fd">
</div>
<div id="outline-container-org6c162ce" class="outline-4">
<h4 id="org6c162ce">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-org6c162ce">
<div id="outline-container-org235f5db" class="outline-4">
<h4 id="org235f5db">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-org235f5db">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -123,9 +123,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org61fb10d" class="outline-4">
<h4 id="org61fb10d">Mac OS X</h4>
<div class="outline-text-4" id="text-org61fb10d">
<div id="outline-container-org601b552" class="outline-4">
<h4 id="org601b552">Mac OS X</h4>
<div class="outline-text-4" id="text-org601b552">
<ul class="org-ul">
<li style="margin-bottom:0;"><p>
<b>Option 1</b>: Install the <code>.dmg</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
......@@ -158,9 +158,9 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org6345a15" class="outline-4">
<h4 id="org6345a15">Windows</h4>
<div class="outline-text-4" id="text-org6345a15">
<div id="outline-container-orgeb7cce9" class="outline-4">
<h4 id="orgeb7cce9">Windows</h4>
<div class="outline-text-4" id="text-orgeb7cce9">
<p>
Install the <code>.exe</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.github.io/emacs-modified-windows/">https://vigou3.github.io/emacs-modified-windows/</a>. It ships with recent
......@@ -174,9 +174,9 @@ versions:
</div>
</div>
</div>
<div id="outline-container-org39100b1" class="outline-3">
<h3 id="org39100b1">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org39100b1">
<div id="outline-container-org927f811" class="outline-3">
<h3 id="org927f811">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org927f811">
<p>
Emacs comes with very basic default configuration and it appears like
everyone has its own taste. You will for example find <a href="https://www.emacswiki.org/emacs/StarterKits">here</a> several
......@@ -189,9 +189,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-orgead59ff" class="outline-4">
<h4 id="orgead59ff">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgead59ff">
<div id="outline-container-orgf5e3e23" class="outline-4">
<h4 id="orgf5e3e23">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgf5e3e23">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -212,9 +212,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-org45cc743" class="outline-4">
<h4 id="org45cc743">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org45cc743">
<div id="outline-container-org793f930" class="outline-4">
<h4 id="org793f930">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org793f930">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -231,9 +231,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-org12df21d" class="outline-4">
<h4 id="org12df21d">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-org12df21d">
<div id="outline-container-org09a3dc2" class="outline-4">
<h4 id="org09a3dc2">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-org09a3dc2">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -245,9 +245,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org1fbd541" class="outline-4">
<h4 id="org1fbd541">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org1fbd541">
<div id="outline-container-org1484860" class="outline-4">
<h4 id="org1484860">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org1484860">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -278,9 +278,9 @@ is demonstrated in the <a href="rr_org/journal.html#MissingReference">first entr
</p>
</div>
</div>
<div id="outline-container-org528bb3d" class="outline-4">
<h4 id="org528bb3d">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org528bb3d">
<div id="outline-container-org01379a1" class="outline-4">
<h4 id="org01379a1">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org01379a1">
<p>
In step 1, you were told to create an journal in
<code>~org/journal.org</code>. First you probably want to make sure this file is
......@@ -292,22 +292,22 @@ forums.
</div>
</div>
</div>
<div id="outline-container-orgf3207a2" class="outline-2">
<h2 id="orgf3207a2">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orgf3207a2">
<div id="outline-container-orgd96cc54" class="outline-2">
<h2 id="orgd96cc54">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orgd96cc54">
</div>
<div id="outline-container-org63f18b5" class="outline-3">
<h3 id="org63f18b5">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org63f18b5">
<div id="outline-container-org7b80429" class="outline-3">
<h3 id="org7b80429">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org7b80429">
<p>
Learning emacs and org-mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps:
</p>
</div>
<div id="outline-container-org22fe63d" class="outline-4">
<h4 id="org22fe63d">Emacs</h4>
<div class="outline-text-4" id="text-org22fe63d">
<div id="outline-container-orgc60a5a4" class="outline-4">
<h4 id="orgc60a5a4">Emacs</h4>
<div class="outline-text-4" id="text-orgc60a5a4">
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<li style="margin-bottom:0;"><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
......@@ -316,9 +316,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-org4d46779" class="outline-4">
<h4 id="org4d46779">Org-mode</h4>
<div class="outline-text-4" id="text-org4d46779">
<div id="outline-container-org12dfdcf" class="outline-4">
<h4 id="org12dfdcf">Org-mode</h4>
<div class="outline-text-4" id="text-org12dfdcf">
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<li style="margin-bottom:0;"><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
......@@ -327,22 +327,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-orgefcfd8e" class="outline-3">
<h3 id="orgefcfd8e">Video tutorials</h3>
<div class="outline-text-3" id="text-orgefcfd8e">
<div id="outline-container-org37ba57d" class="outline-3">
<h3 id="org37ba57d">Video tutorials</h3>
<div class="outline-text-3" id="text-org37ba57d">
<p>
For those of you who prefer video explanations, here is a <a href="https://www.youtube.com/playlist?list=PL9KxKa8NpFxIcNQa9js7dQQIHc81b0-Xg">Youtube
channel with many step by step emacs tutorials</a>.
</p>
</div>
</div>
<div id="outline-container-org4a1463b" class="outline-3">
<h3 id="org4a1463b">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org4a1463b">
<div id="outline-container-org9c09e0f" class="outline-3">
<h3 id="org9c09e0f">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org9c09e0f">
</div>
<div id="outline-container-orgf784a61" class="outline-4">
<h4 id="orgf784a61">Company-mode</h4>
<div class="outline-text-4" id="text-orgf784a61">
<div id="outline-container-org540b4bf" class="outline-4">
<h4 id="org540b4bf">Company-mode</h4>
<div class="outline-text-4" id="text-org540b4bf">
<p>
<a href="http://company-mode.github.io/">Company-mode</a> is a text completion framework for Emacs. It allows to
have smart completion in emacs for the most common languages. If you
......@@ -351,9 +351,9 @@ official webpage: <a href="http://company-mode.github.io/">http://company-mode.g
</p>
</div>
</div>
<div id="outline-container-org57b6a55" class="outline-4">
<h4 id="org57b6a55">Magit</h4>
<div class="outline-text-4" id="text-org57b6a55">
<div id="outline-container-org22d5f9b" class="outline-4">
<h4 id="org22d5f9b">Magit</h4>
<div class="outline-text-4" id="text-org22d5f9b">
<p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. It is very powerfull and we use
it on a daily basis but you should definitely understand what git does
......@@ -364,9 +364,9 @@ you should follow the instructions from here:
</div>
</div>
</div>
<div id="outline-container-org84da85a" class="outline-3">
<h3 id="org84da85a">Other resources</h3>
<div class="outline-text-3" id="text-org84da85a">
<div id="outline-container-org8e569d2" class="outline-3">
<h3 id="org8e569d2">Other resources</h3>
<div class="outline-text-3" id="text-org8e569d2">
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li>
<li style="margin-bottom:0;"><a href="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
......@@ -374,13 +374,13 @@ you should follow the instructions from here:
</div>
</div>
</div>
<div id="outline-container-org1a26eb1" class="outline-2">
<h2 id="org1a26eb1">A replicable article</h2>
<div class="outline-text-2" id="text-org1a26eb1">
<div id="outline-container-org134c336" class="outline-2">
<h2 id="org134c336">A replicable article</h2>
<div class="outline-text-2" id="text-org134c336">
</div>
<div id="outline-container-org33696b8" class="outline-3">
<h3 id="org33696b8">A stub of replicable article</h3>
<div class="outline-text-3" id="text-org33696b8">
<div id="outline-container-org4f6d44d" class="outline-3">
<h3 id="org4f6d44d">A stub of replicable article</h3>
<div class="outline-text-3" id="text-org4f6d44d">
<p>
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands <code>R</code> and <code>pdflatex</code>, you will not be
......
module2/ressources/jupyter.html
View file @ 91dec995
......@@ -3,32 +3,32 @@
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<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 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 style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgaa631f0">Interacting with gitlab</a></li>
<li style="margin-bottom:0;"><a href="#orgc0bede2">Additional Jupyter resources or tricks</a>
<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="#orgcc5df2c">Running R and Python in the same notebook</a></li>
<li style="margin-bottom:0;"><a href="#org50f9d65">Exporting a notebook</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org2b24a9c">Installing jupyter or jupyter hub on your own machine</a>
<ul>
<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>
<li style="margin-bottom:0;"><a href="#org9ad15fe">Installing jupyter or jupyter hub on your own machine</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3c82116">Installing jupyter</a></li>
<li style="margin-bottom:0;"><a href="#org41613aa">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="#orgf4f33c6">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="#org883d82c">Installing jupyterhub</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgc72397d" class="outline-2">
<h2 id="orgc72397d">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-orgc72397d">
<div id="outline-container-orgaa631f0" class="outline-2">
<h2 id="orgaa631f0">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-orgaa631f0">
<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-org186a10f" class="outline-2">
<h2 id="org186a10f">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org186a10f">
<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 id="outline-container-org9d17f16" class="outline-3">
<h3 id="org9d17f16">Tips and tricks</h3>
<div class="outline-text-3" id="text-org9d17f16">
<div id="outline-container-orga0a8c0a" class="outline-3">
<h3 id="orga0a8c0a">Tips and tricks</h3>
<div class="outline-text-3" id="text-orga0a8c0a">
<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-org3c5eb3e" class="outline-3">
<h3 id="org3c5eb3e">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org3c5eb3e">
<div id="outline-container-orgcc5df2c" class="outline-3">
<h3 id="orgcc5df2c">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orgcc5df2c">
<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-org656a59e" class="outline-3">
<h3 id="org656a59e">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org656a59e">
<div id="outline-container-org50f9d65" class="outline-3">
<h3 id="org50f9d65">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org50f9d65">
<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-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 id="outline-container-org9ad15fe" class="outline-2">
<h2 id="org9ad15fe">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org9ad15fe">
</div>
<div id="outline-container-orgfe13c9b" class="outline-3">
<h3 id="orgfe13c9b">Installing jupyter</h3>
<div class="outline-text-3" id="text-orgfe13c9b">
<div id="outline-container-org3c82116" class="outline-3">
<h3 id="org3c82116">Installing jupyter</h3>
<div class="outline-text-3" id="text-org3c82116">
<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-orgaeb7a97" class="outline-3">
<h3 id="orgaeb7a97">Using R</h3>
<div class="outline-text-3" id="text-orgaeb7a97">
<div id="outline-container-org41613aa" class="outline-3">
<h3 id="org41613aa">Using R</h3>
<div class="outline-text-3" id="text-org41613aa">
<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="#org3c5eb3e">Running R and Python in
Alternatively, you can install <code>rpy2</code> (see the <a href="#orgcc5df2c">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-orgbf7d110" class="outline-3">
<h3 id="orgbf7d110">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgbf7d110">
<div id="outline-container-orgeebc12b" class="outline-3">
<h3 id="orgeebc12b">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-orgeebc12b">
<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-orgff388aa" class="outline-3">
<h3 id="orgff388aa">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgff388aa">
<div id="outline-container-orgf4f33c6" class="outline-3">
<h3 id="orgf4f33c6">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgf4f33c6">
<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-org77fb4ca" class="outline-3">
<h3 id="org77fb4ca">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-org77fb4ca">
<div id="outline-container-orgd30b2c8" class="outline-3">
<h3 id="orgd30b2c8">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgd30b2c8">
<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-org364ee89" class="outline-3">
<h3 id="org364ee89">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org364ee89">
<div id="outline-container-org883d82c" class="outline-3">
<h3 id="org883d82c">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org883d82c">
<blockquote>
<p>
Benoit may give a few hints on this.
......
module2/ressources/rstudio.html
View file @ 91dec995
......@@ -3,37 +3,37 @@
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li style="margin-bottom:0;"><a href="#org47ec510">Installing Rstudio</a>
<ul>
<li style="margin-bottom:0;"><a href="#org366dd3d">Linux (debian, ubuntu)</a>
<ul>
<li style="margin-bottom:0;"><a href="#orgba71b69">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgfe3a4ba">Installing rstudio</a></li>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org68a44ad">Installing Rstudio</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org75fa2dd">Linux (debian, ubuntu)</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb3ecfea">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgd6fe18e">Installing rstudio</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgdf29b54">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#org337678e">Mac OSX and Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgd30feb0">Installing Git</a>
<ul>
<li style="margin-bottom:0;"><a href="#org02fa6c2">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org0611f52">Mac OSX and Windows</a></li>
<li style="margin-bottom:0;"><a href="#org150ee9f">Installing Git</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org79b3b23">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org536eda4">Mac OSX and Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgabc8626">Rstudio and git/github/gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org270116a">Cheat Sheets</a></li>
<li style="margin-bottom:0;"><a href="#orgbb4bef3">Rstudio and git/github/gitlab</a></li>
<li style="margin-bottom:0;"><a href="#org81cf7bc">Cheat Sheets</a></li>
</ul>
</div>
</div>
<div id="outline-container-org47ec510" class="outline-2">
<h2 id="org47ec510">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org47ec510">
<div id="outline-container-org68a44ad" class="outline-2">
<h2 id="org68a44ad">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org68a44ad">
</div>
<div id="outline-container-org366dd3d" class="outline-3">
<h3 id="org366dd3d">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org366dd3d">
<div id="outline-container-org75fa2dd" class="outline-3">
<h3 id="org75fa2dd">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org75fa2dd">
<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-orgba71b69" class="outline-4">
<h4 id="orgba71b69">Installing R</h4>
<div class="outline-text-4" id="text-orgba71b69">
<div id="outline-container-orgb3ecfea" class="outline-4">
<h4 id="orgb3ecfea">Installing R</h4>
<div class="outline-text-4" id="text-orgb3ecfea">
<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-orgfe3a4ba" class="outline-4">
<h4 id="orgfe3a4ba">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgfe3a4ba">
<div id="outline-container-orgd6fe18e" class="outline-4">
<h4 id="orgd6fe18e">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgd6fe18e">
<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-orgdf29b54" class="outline-3">
<h3 id="orgdf29b54">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-orgdf29b54">
<div id="outline-container-org337678e" class="outline-3">
<h3 id="org337678e">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org337678e">
<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-orgd30feb0" class="outline-2">
<h2 id="orgd30feb0">Installing Git</h2>
<div class="outline-text-2" id="text-orgd30feb0">
<div id="outline-container-org150ee9f" class="outline-2">
<h2 id="org150ee9f">Installing Git</h2>
<div class="outline-text-2" id="text-org150ee9f">
</div>
<div id="outline-container-org02fa6c2" class="outline-3">
<h3 id="org02fa6c2">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org02fa6c2">
<div id="outline-container-org79b3b23" class="outline-3">
<h3 id="org79b3b23">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org79b3b23">
<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-org0611f52" class="outline-3">
<h3 id="org0611f52">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org0611f52">
<div id="outline-container-org536eda4" class="outline-3">
<h3 id="org536eda4">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org536eda4">
<ul class="org-ul">
<li style="margin-bottom:0;">Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li style="margin-bottom:0;">Optional Git clients (should not be needed if you work within
......@@ -180,9 +180,9 @@ Rstudio):
</div>
</div>
</div>
<div id="outline-container-orgabc8626" class="outline-2">
<h2 id="orgabc8626">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-orgabc8626">
<div id="outline-container-orgbb4bef3" class="outline-2">
<h2 id="orgbb4bef3">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-orgbb4bef3">
<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-org270116a" class="outline-2">
<h2 id="org270116a">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org270116a">
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<h2 id="org81cf7bc">Cheat Sheets</h2>
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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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