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module1/ressources/introduction_to_markdown.html
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...@@ -4,26 +4,26 @@ ...@@ -4,26 +4,26 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#orge7765d4">Syntaxe</a> <li style="margin-bottom:0;"><a href="#org8de79b7">Syntaxe</a>
<ul> <ul>
<li><a href="#orgfa68a29">Headers</a></li> <li style="margin-bottom:0;"><a href="#orgd0cd01a">Headers</a></li>
<li><a href="#org8efa22f">Emphasis</a></li> <li style="margin-bottom:0;"><a href="#org0a02e8a">Emphasis</a></li>
<li><a href="#orge264e14">Lists</a> <li style="margin-bottom:0;"><a href="#org5ba3da0">Lists</a>
<ul> <ul>
<li><a href="#org8aff08d">Unordered</a></li> <li style="margin-bottom:0;"><a href="#orgf404e08">Unordered</a></li>
<li><a href="#org4acaa77">Ordered</a></li> <li style="margin-bottom:0;"><a href="#orga07db10">Ordered</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgb7930f3">Images</a></li> <li style="margin-bottom:0;"><a href="#orgea33b61">Images</a></li>
<li><a href="#orgef25979">Links</a></li> <li style="margin-bottom:0;"><a href="#org45306c5">Links</a></li>
<li><a href="#org075cffa">Blockquotes</a></li> <li style="margin-bottom:0;"><a href="#org8cf7f47">Blockquotes</a></li>
<li><a href="#orgfd6d212">Inline code</a></li> <li style="margin-bottom:0;"><a href="#org5cc4188">Inline code</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgec971b4">Écrire des Maths</a> <li style="margin-bottom:0;"><a href="#orgf5d12d0">Écrire des Maths</a>
<ul> <ul>
<li><a href="#org71635d1">Lettres grecques</a></li> <li style="margin-bottom:0;"><a href="#orgd3d090f">Lettres grecques</a></li>
<li><a href="#org08d8b82">Operators</a></li> <li style="margin-bottom:0;"><a href="#org4cbab17">Operators</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
...@@ -34,13 +34,13 @@ Voici un aperçu rapide de la syntaxe Markdown repris d'une ...@@ -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 <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>. H. Steiger</a>.
</p> </p>
<div id="outline-container-orge7765d4" class="outline-2"> <div id="outline-container-org8de79b7" class="outline-2">
<h2 id="orge7765d4">Syntaxe</h2> <h2 id="org8de79b7">Syntaxe</h2>
<div class="outline-text-2" id="text-orge7765d4"> <div class="outline-text-2" id="text-org8de79b7">
</div> </div>
<div id="outline-container-orgfa68a29" class="outline-3"> <div id="outline-container-orgd0cd01a" class="outline-3">
<h3 id="orgfa68a29">Headers</h3> <h3 id="orgd0cd01a">Headers</h3>
<div class="outline-text-3" id="text-orgfa68a29"> <div class="outline-text-3" id="text-orgd0cd01a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
# This is an &lt;h1&gt; tag # This is an &lt;h1&gt; tag
## This is an &lt;h2&gt; tag ## This is an &lt;h2&gt; tag
...@@ -49,9 +49,9 @@ H. Steiger</a>. ...@@ -49,9 +49,9 @@ H. Steiger</a>.
</div> </div>
</div> </div>
<div id="outline-container-org8efa22f" class="outline-3"> <div id="outline-container-org0a02e8a" class="outline-3">
<h3 id="org8efa22f">Emphasis</h3> <h3 id="org0a02e8a">Emphasis</h3>
<div class="outline-text-3" id="text-org8efa22f"> <div class="outline-text-3" id="text-org0a02e8a">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
*This text will be italic* *This text will be italic*
_This will also be italic_ _This will also be italic_
...@@ -64,13 +64,13 @@ _You **can** combine them_ ...@@ -64,13 +64,13 @@ _You **can** combine them_
</div> </div>
</div> </div>
<div id="outline-container-orge264e14" class="outline-3"> <div id="outline-container-org5ba3da0" class="outline-3">
<h3 id="orge264e14">Lists</h3> <h3 id="org5ba3da0">Lists</h3>
<div class="outline-text-3" id="text-orge264e14"> <div class="outline-text-3" id="text-org5ba3da0">
</div> </div>
<div id="outline-container-org8aff08d" class="outline-4"> <div id="outline-container-orgf404e08" class="outline-4">
<h4 id="org8aff08d">Unordered</h4> <h4 id="orgf404e08">Unordered</h4>
<div class="outline-text-4" id="text-org8aff08d"> <div class="outline-text-4" id="text-orgf404e08">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
* Item 1 * Item 1
* Item 2 * Item 2
...@@ -79,9 +79,9 @@ _You **can** combine them_ ...@@ -79,9 +79,9 @@ _You **can** combine them_
</pre> </pre>
</div> </div>
</div> </div>
<div id="outline-container-org4acaa77" class="outline-4"> <div id="outline-container-orga07db10" class="outline-4">
<h4 id="org4acaa77">Ordered</h4> <h4 id="orga07db10">Ordered</h4>
<div class="outline-text-4" id="text-org4acaa77"> <div class="outline-text-4" id="text-orga07db10">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
1. Item 1 1. Item 1
1. Item 2 1. Item 2
...@@ -92,27 +92,27 @@ _You **can** combine them_ ...@@ -92,27 +92,27 @@ _You **can** combine them_
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgb7930f3" class="outline-3"> <div id="outline-container-orgea33b61" class="outline-3">
<h3 id="orgb7930f3">Images</h3> <h3 id="orgea33b61">Images</h3>
<div class="outline-text-3" id="text-orgb7930f3"> <div class="outline-text-3" id="text-orgea33b61">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
![GitHub Logo](/images/logo.png) ![GitHub Logo](/images/logo.png)
Format: ![Alt Text](url) Format: ![Alt Text](url)
</pre> </pre>
</div> </div>
</div> </div>
<div id="outline-container-orgef25979" class="outline-3"> <div id="outline-container-org45306c5" class="outline-3">
<h3 id="orgef25979">Links</h3> <h3 id="org45306c5">Links</h3>
<div class="outline-text-3" id="text-orgef25979"> <div class="outline-text-3" id="text-org45306c5">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
http://github.com - automatic! http://github.com - automatic!
[GitHub](http://github.com) [GitHub](http://github.com)
</pre> </pre>
</div> </div>
</div> </div>
<div id="outline-container-org075cffa" class="outline-3"> <div id="outline-container-org8cf7f47" class="outline-3">
<h3 id="org075cffa">Blockquotes</h3> <h3 id="org8cf7f47">Blockquotes</h3>
<div class="outline-text-3" id="text-org075cffa"> <div class="outline-text-3" id="text-org8cf7f47">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
As Kanye West said: As Kanye West said:
...@@ -121,9 +121,9 @@ As Kanye West said: ...@@ -121,9 +121,9 @@ As Kanye West said:
</pre> </pre>
</div> </div>
</div> </div>
<div id="outline-container-orgfd6d212" class="outline-3"> <div id="outline-container-org5cc4188" class="outline-3">
<h3 id="orgfd6d212">Inline code</h3> <h3 id="org5cc4188">Inline code</h3>
<div class="outline-text-3" id="text-orgfd6d212"> <div class="outline-text-3" id="text-org5cc4188">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example"> <pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
I think you should use an I think you should use an
`&lt;addr&gt;` element here instead. `&lt;addr&gt;` element here instead.
...@@ -131,9 +131,9 @@ I think you should use an ...@@ -131,9 +131,9 @@ I think you should use an
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgec971b4" class="outline-2"> <div id="outline-container-orgf5d12d0" class="outline-2">
<h2 id="orgec971b4">Écrire des Maths</h2> <h2 id="orgf5d12d0">Écrire des Maths</h2>
<div class="outline-text-2" id="text-orgec971b4"> <div class="outline-text-2" id="text-orgf5d12d0">
<p> <p>
Equations can be formatted <b>inline</b> or as <b>displayed formulas</b>. In the 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 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. ...@@ -177,9 +177,9 @@ This summation expression is in display form.
</p> </p>
</div> </div>
<div id="outline-container-org71635d1" class="outline-3"> <div id="outline-container-orgd3d090f" class="outline-3">
<h3 id="org71635d1">Lettres grecques</h3> <h3 id="orgd3d090f">Lettres grecques</h3>
<div class="outline-text-3" id="text-org71635d1"> <div class="outline-text-3" id="text-orgd3d090f">
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
...@@ -223,8 +223,8 @@ This summation expression is in display form. ...@@ -223,8 +223,8 @@ This summation expression is in display form.
</table> </table>
</div> </div>
</div> </div>
<div id="outline-container-org08d8b82" class="outline-3"> <div id="outline-container-org4cbab17" class="outline-3">
<h3 id="org08d8b82">Operators</h3> <h3 id="org4cbab17">Operators</h3>
</div> </div>
</div> </div>
</div> </div>
module2/ressources/emacs_orgmode.html
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...@@ -4,64 +4,64 @@ ...@@ -4,64 +4,64 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org9fae67d">Installing emacs, org-mode, ess, and auctex.</a> <li style="margin-bottom:0;"><a href="#orgf0788f0">Installing emacs, org-mode, ess, and auctex.</a>
<ul> <ul>
<li><a href="#org7e26f43">OS-specific installation procedure</a> <li style="margin-bottom:0;"><a href="#org8412fbd">OS-specific installation procedure</a>
<ul> <ul>
<li><a href="#orga1850db">Linux (Debian, Ubuntu)</a></li> <li style="margin-bottom:0;"><a href="#org6c162ce">Linux (Debian, Ubuntu)</a></li>
<li><a href="#org7e15d03">Mac OS X</a></li> <li style="margin-bottom:0;"><a href="#org61fb10d">Mac OS X</a></li>
<li><a href="#org2955a3d">Windows</a></li> <li style="margin-bottom:0;"><a href="#org6345a15">Windows</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org796e741">A simple "<i>reproducible research</i>" emacs configuration</a> <li style="margin-bottom:0;"><a href="#org39100b1">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul> <ul>
<li><a href="#orgc87137c">Step 0: Backup and download our configuration</a></li> <li style="margin-bottom:0;"><a href="#orgead59ff">Step 0: Backup and download our configuration</a></li>
<li><a href="#org0433a0a">Step 1: Prepare your journal</a></li> <li style="margin-bottom:0;"><a href="#org45cc743">Step 1: Prepare your journal</a></li>
<li><a href="#orgaf628c4">Step 2: Set up Emacs configuration</a></li> <li style="margin-bottom:0;"><a href="#org12df21d">Step 2: Set up Emacs configuration</a></li>
<li><a href="#org76a0967">Step 3: Check whether the installation is working or not</a></li> <li style="margin-bottom:0;"><a href="#org1fbd541">Step 3: Check whether the installation is working or not</a></li>
<li><a href="#org1b44bc8">Step 4: Open and play with your journal:</a></li> <li style="margin-bottom:0;"><a href="#org528bb3d">Step 4: Open and play with your journal:</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</li> </li>
<li><a href="#org5233724">Emacs Tips and tricks</a> <li style="margin-bottom:0;"><a href="#orgf3207a2">Emacs Tips and tricks</a>
<ul> <ul>
<li><a href="#orgcf5a5b2">Cheat-sheets</a> <li style="margin-bottom:0;"><a href="#org63f18b5">Cheat-sheets</a>
<ul> <ul>
<li><a href="#orgcb4078f">Emacs</a></li> <li style="margin-bottom:0;"><a href="#org22fe63d">Emacs</a></li>
<li><a href="#orgde1963f">Org-mode</a></li> <li style="margin-bottom:0;"><a href="#org4d46779">Org-mode</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgc2d812a">Video tutorials</a></li> <li style="margin-bottom:0;"><a href="#orgefcfd8e">Video tutorials</a></li>
<li><a href="#org6c3b81d">Additional useful emacs packages</a> <li style="margin-bottom:0;"><a href="#org4a1463b">Additional useful emacs packages</a>
<ul> <ul>
<li><a href="#org2b1ba15">Company-mode</a></li> <li style="margin-bottom:0;"><a href="#orgf784a61">Company-mode</a></li>
<li><a href="#org5a154db">Magit</a></li> <li style="margin-bottom:0;"><a href="#org57b6a55">Magit</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org00ecde8">Other resources</a></li> <li style="margin-bottom:0;"><a href="#org84da85a">Other resources</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org0e133ea">A replicable article</a> <li style="margin-bottom:0;"><a href="#org1a26eb1">A replicable article</a>
<ul> <ul>
<li><a href="#orgf3a84c7">A stub of replicable article</a></li> <li style="margin-bottom:0;"><a href="#org33696b8">A stub of replicable article</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org9fae67d" class="outline-2"> <div id="outline-container-orgf0788f0" class="outline-2">
<h2 id="org9fae67d">Installing emacs, org-mode, ess, and auctex.</h2> <h2 id="orgf0788f0">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org9fae67d"> <div class="outline-text-2" id="text-orgf0788f0">
</div> </div>
<div id="outline-container-org7e26f43" class="outline-3"> <div id="outline-container-org8412fbd" class="outline-3">
<h3 id="org7e26f43">OS-specific installation procedure</h3> <h3 id="org8412fbd">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-org7e26f43"> <div class="outline-text-3" id="text-org8412fbd">
</div> </div>
<div id="outline-container-orga1850db" class="outline-4"> <div id="outline-container-org6c162ce" class="outline-4">
<h4 id="orga1850db">Linux (Debian, Ubuntu)</h4> <h4 id="org6c162ce">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-orga1850db"> <div class="outline-text-4" id="text-org6c162ce">
<p> <p>
We provide here only instructions for debian-based distributions. Feel We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information free to contribute to this document to provide up-to-date information
...@@ -73,9 +73,9 @@ Today, the stable versions of the most common distributions provide ...@@ -73,9 +73,9 @@ Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode: recent enough versions of emacs and org-mode:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/emacs25">emacs 25.1</a> and <a href="https://packages.debian.org/stretch/org-mode">org-mode 9.0.3</a></li> <li style="margin-bottom:0;">Debian (stretch) ships with <a href="https://packages.debian.org/stretch/emacs25">emacs 25.1</a> and <a href="https://packages.debian.org/stretch/org-mode">org-mode 9.0.3</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/bionic/org-mode">org-mode 9.1.6</a></li> <li style="margin-bottom:0;">Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/bionic/org-mode">org-mode 9.1.6</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/artful/org-mode">org-mode 9.0.9</a></li> <li style="margin-bottom:0;">Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/artful/org-mode">org-mode 9.0.9</a></li>
</ul> </ul>
<p> <p>
If your distribution is older than this, well, it may be a good time If your distribution is older than this, well, it may be a good time
...@@ -123,26 +123,26 @@ which is now deprecated. ...@@ -123,26 +123,26 @@ which is now deprecated.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org7e15d03" class="outline-4"> <div id="outline-container-org61fb10d" class="outline-4">
<h4 id="org7e15d03">Mac OS X</h4> <h4 id="org61fb10d">Mac OS X</h4>
<div class="outline-text-4" id="text-org7e15d03"> <div class="outline-text-4" id="text-org61fb10d">
<ul class="org-ul"> <ul class="org-ul">
<li><p> <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>: <b>Option 1</b>: Install the <code>.dmg</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.github.io/emacs-modified-macos/">https://vigou3.github.io/emacs-modified-macos/</a>. It ships with recent <a href="https://vigou3.github.io/emacs-modified-macos/">https://vigou3.github.io/emacs-modified-macos/</a>. It ships with recent
versions: versions:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li>Emacs 26.1</li> <li style="margin-bottom:0;">Emacs 26.1</li>
<li>Org-mode 9.1.13</li> <li style="margin-bottom:0;">Org-mode 9.1.13</li>
<li>ESS 17.11</li> <li style="margin-bottom:0;">ESS 17.11</li>
</ul> </ul>
<p> <p>
In that case you may have several versions of emacs installed on In that case you may have several versions of emacs installed on
your machine and launching emacs from a terminal may not run the one your machine and launching emacs from a terminal may not run the one
you just installed. If anyone know how to get rid of this&#x2026; you just installed. If anyone know how to get rid of this&#x2026;
</p></li> </p></li>
<li><p> <li style="margin-bottom:0;"><p>
<b>Option 2</b>: If you already use <code>brew</code>, simply do the following <b>Option 2</b>: If you already use <code>brew</code>, simply do the following
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -158,25 +158,25 @@ brew install wget ...@@ -158,25 +158,25 @@ brew install wget
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org2955a3d" class="outline-4"> <div id="outline-container-org6345a15" class="outline-4">
<h4 id="org2955a3d">Windows</h4> <h4 id="org6345a15">Windows</h4>
<div class="outline-text-4" id="text-org2955a3d"> <div class="outline-text-4" id="text-org6345a15">
<p> <p>
Install the <code>.exe</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>: 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 <a href="https://vigou3.github.io/emacs-modified-windows/">https://vigou3.github.io/emacs-modified-windows/</a>. It ships with recent
versions: versions:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li>Emacs 26.1</li> <li style="margin-bottom:0;">Emacs 26.1</li>
<li>Org-mode 9.1.13</li> <li style="margin-bottom:0;">Org-mode 9.1.13</li>
<li>ESS 17.11</li> <li style="margin-bottom:0;">ESS 17.11</li>
</ul> </ul>
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org796e741" class="outline-3"> <div id="outline-container-org39100b1" class="outline-3">
<h3 id="org796e741">A simple "<i>reproducible research</i>" emacs configuration</h3> <h3 id="org39100b1">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org796e741"> <div class="outline-text-3" id="text-org39100b1">
<p> <p>
Emacs comes with very basic default configuration and it appears like 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 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. ...@@ -189,9 +189,9 @@ adding a few org-mode specific configurations.
</p> </p>
</div> </div>
<div id="outline-container-orgc87137c" class="outline-4"> <div id="outline-container-orgead59ff" class="outline-4">
<h4 id="orgc87137c">Step 0: Backup and download our configuration</h4> <h4 id="orgead59ff">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgc87137c"> <div class="outline-text-4" id="text-orgead59ff">
<p> <p>
The procedure we propose will wipe your already existing custom emacs The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make configuration if you already have one. <b>You should thus beforehand make
...@@ -212,9 +212,9 @@ rr_org/journal.org ...@@ -212,9 +212,9 @@ rr_org/journal.org
</div> </div>
</div> </div>
<div id="outline-container-org0433a0a" class="outline-4"> <div id="outline-container-org45cc743" class="outline-4">
<h4 id="org0433a0a">Step 1: Prepare your journal</h4> <h4 id="org45cc743">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org0433a0a"> <div class="outline-text-4" id="text-org45cc743">
<p> <p>
Create an <code>org/</code> directory in the top of your home: Create an <code>org/</code> directory in the top of your home:
</p> </p>
...@@ -231,9 +231,9 @@ should give a try. ...@@ -231,9 +231,9 @@ should give a try.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgaf628c4" class="outline-4"> <div id="outline-container-org12df21d" class="outline-4">
<h4 id="orgaf628c4">Step 2: Set up Emacs configuration</h4> <h4 id="org12df21d">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-orgaf628c4"> <div class="outline-text-4" id="text-org12df21d">
<p> <p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory. Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p> </p>
...@@ -245,9 +245,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code ...@@ -245,9 +245,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org76a0967" class="outline-4"> <div id="outline-container-org1fbd541" class="outline-4">
<h4 id="org76a0967">Step 3: Check whether the installation is working or not</h4> <h4 id="org1fbd541">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org76a0967"> <div class="outline-text-4" id="text-org1fbd541">
<p> <p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file: following lines in this file:
...@@ -278,9 +278,9 @@ is demonstrated in the <a href="rr_org/journal.html#MissingReference">first entr ...@@ -278,9 +278,9 @@ is demonstrated in the <a href="rr_org/journal.html#MissingReference">first entr
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org1b44bc8" class="outline-4"> <div id="outline-container-org528bb3d" class="outline-4">
<h4 id="org1b44bc8">Step 4: Open and play with your journal:</h4> <h4 id="org528bb3d">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org1b44bc8"> <div class="outline-text-4" id="text-org528bb3d">
<p> <p>
In step 1, you were told to create an journal in 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 <code>~org/journal.org</code>. First you probably want to make sure this file is
...@@ -292,57 +292,57 @@ forums. ...@@ -292,57 +292,57 @@ forums.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org5233724" class="outline-2"> <div id="outline-container-orgf3207a2" class="outline-2">
<h2 id="org5233724">Emacs Tips and tricks</h2> <h2 id="orgf3207a2">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org5233724"> <div class="outline-text-2" id="text-orgf3207a2">
</div> </div>
<div id="outline-container-orgcf5a5b2" class="outline-3"> <div id="outline-container-org63f18b5" class="outline-3">
<h3 id="orgcf5a5b2">Cheat-sheets</h3> <h3 id="org63f18b5">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgcf5a5b2"> <div class="outline-text-3" id="text-org63f18b5">
<p> <p>
Learning emacs and org-mode can be difficult as there is an inordinate Learning emacs and org-mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps: cheat-sheats. Here is a selection in case it helps:
</p> </p>
</div> </div>
<div id="outline-container-orgcb4078f" class="outline-4"> <div id="outline-container-org22fe63d" class="outline-4">
<h4 id="orgcb4078f">Emacs</h4> <h4 id="org22fe63d">Emacs</h4>
<div class="outline-text-4" id="text-orgcb4078f"> <div class="outline-text-4" id="text-org22fe63d">
<ul class="org-ul"> <ul class="org-ul">
<li><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="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</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>
<li>Two graphical cheat-sheats by Sacha Hua on <a href="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on <li style="margin-bottom:0;">Two graphical cheat-sheats by Sacha Hua on <a href="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on
<a href="http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png">how to learn emacs shortcuts</a>.</li> <a href="http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png">how to learn emacs shortcuts</a>.</li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orgde1963f" class="outline-4"> <div id="outline-container-org4d46779" class="outline-4">
<h4 id="orgde1963f">Org-mode</h4> <h4 id="org4d46779">Org-mode</h4>
<div class="outline-text-4" id="text-orgde1963f"> <div class="outline-text-4" id="text-org4d46779">
<ul class="org-ul"> <ul class="org-ul">
<li><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="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li> <li style="margin-bottom:0;"><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<li><a href="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <a href="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li> <li style="margin-bottom:0;"><a href="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <a href="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li>
</ul> </ul>
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgc2d812a" class="outline-3"> <div id="outline-container-orgefcfd8e" class="outline-3">
<h3 id="orgc2d812a">Video tutorials</h3> <h3 id="orgefcfd8e">Video tutorials</h3>
<div class="outline-text-3" id="text-orgc2d812a"> <div class="outline-text-3" id="text-orgefcfd8e">
<p> <p>
For those of you who prefer video explanations, here is a <a href="https://www.youtube.com/playlist?list=PL9KxKa8NpFxIcNQa9js7dQQIHc81b0-Xg">Youtube 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>. channel with many step by step emacs tutorials</a>.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org6c3b81d" class="outline-3"> <div id="outline-container-org4a1463b" class="outline-3">
<h3 id="org6c3b81d">Additional useful emacs packages</h3> <h3 id="org4a1463b">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org6c3b81d"> <div class="outline-text-3" id="text-org4a1463b">
</div> </div>
<div id="outline-container-org2b1ba15" class="outline-4"> <div id="outline-container-orgf784a61" class="outline-4">
<h4 id="org2b1ba15">Company-mode</h4> <h4 id="orgf784a61">Company-mode</h4>
<div class="outline-text-4" id="text-org2b1ba15"> <div class="outline-text-4" id="text-orgf784a61">
<p> <p>
<a href="http://company-mode.github.io/">Company-mode</a> is a text completion framework for Emacs. It allows to <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 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 ...@@ -351,9 +351,9 @@ official webpage: <a href="http://company-mode.github.io/">http://company-mode.g
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org5a154db" class="outline-4"> <div id="outline-container-org57b6a55" class="outline-4">
<h4 id="org5a154db">Magit</h4> <h4 id="org57b6a55">Magit</h4>
<div class="outline-text-4" id="text-org5a154db"> <div class="outline-text-4" id="text-org57b6a55">
<p> <p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. It is very powerfull and we use <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 it on a daily basis but you should definitely understand what git does
...@@ -364,23 +364,23 @@ you should follow the instructions from here: ...@@ -364,23 +364,23 @@ you should follow the instructions from here:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org00ecde8" class="outline-3"> <div id="outline-container-org84da85a" class="outline-3">
<h3 id="org00ecde8">Other resources</h3> <h3 id="org84da85a">Other resources</h3>
<div class="outline-text-3" id="text-org00ecde8"> <div class="outline-text-3" id="text-org84da85a">
<ul class="org-ul"> <ul class="org-ul">
<li><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li> <li style="margin-bottom:0;"><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li>
<li><a href="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</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>
</ul> </ul>
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org0e133ea" class="outline-2"> <div id="outline-container-org1a26eb1" class="outline-2">
<h2 id="org0e133ea">A replicable article</h2> <h2 id="org1a26eb1">A replicable article</h2>
<div class="outline-text-2" id="text-org0e133ea"> <div class="outline-text-2" id="text-org1a26eb1">
</div> </div>
<div id="outline-container-orgf3a84c7" class="outline-3"> <div id="outline-container-org33696b8" class="outline-3">
<h3 id="orgf3a84c7">A stub of replicable article</h3> <h3 id="org33696b8">A stub of replicable article</h3>
<div class="outline-text-3" id="text-orgf3a84c7"> <div class="outline-text-3" id="text-org33696b8">
<p> <p>
Remember, you need a working LaTeX and R environment. If you can't 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 open a terminal and run the commands <code>R</code> and <code>pdflatex</code>, you will not be
......
module2/ressources/jupyter.html
View file @ 1b527eda
...@@ -4,31 +4,31 @@ ...@@ -4,31 +4,31 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org877f03b">Interacting with gitlab</a></li> <li style="margin-bottom:0;"><a href="#orgc72397d">Interacting with gitlab</a></li>
<li><a href="#org16a59c6">Additional Jupyter resources or tricks</a> <li style="margin-bottom:0;"><a href="#org186a10f">Additional Jupyter resources or tricks</a>
<ul> <ul>
<li><a href="#org21ed683">Tips and tricks</a></li> <li style="margin-bottom:0;"><a href="#org9d17f16">Tips and tricks</a></li>
<li><a href="#org81cf6e7">Running R and Python in the same notebook</a></li> <li style="margin-bottom:0;"><a href="#org3c5eb3e">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="#org656a59e">Exporting a notebook</a></li>
</ul> </ul>
</li> </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> <ul>
<li><a href="#org7acfd0d">Installing jupyter</a></li> <li style="margin-bottom:0;"><a href="#orgfe13c9b">Installing jupyter</a></li>
<li><a href="#org4236b75">Using R</a></li> <li style="margin-bottom:0;"><a href="#orgaeb7a97">Using R</a></li>
<li><a href="#org04ec93e">Exporting your notebooks with latex</a></li> <li style="margin-bottom:0;"><a href="#orgbf7d110">Exporting your notebooks with latex</a></li>
<li><a href="#orgd9a7f1c">Interacting with gitlab</a></li> <li style="margin-bottom:0;"><a href="#orgff388aa">Interacting with gitlab</a></li>
<li><a href="#orgad4d4c4">Interesting extensions to improve notebook readability</a></li> <li style="margin-bottom:0;"><a href="#org77fb4ca">Interesting extensions to improve notebook readability</a></li>
<li><a href="#orgff424ae">Installing jupyterhub</a></li> <li style="margin-bottom:0;"><a href="#org364ee89">Installing jupyterhub</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org877f03b" class="outline-2"> <div id="outline-container-orgc72397d" class="outline-2">
<h2 id="org877f03b">Interacting with gitlab</h2> <h2 id="orgc72397d">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-org877f03b"> <div class="outline-text-2" id="text-orgc72397d">
<blockquote> <blockquote>
<p> <p>
This section needs some love. This section needs some love.
...@@ -45,13 +45,13 @@ and to share your notebook with others. ...@@ -45,13 +45,13 @@ and to share your notebook with others.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org16a59c6" class="outline-2"> <div id="outline-container-org186a10f" class="outline-2">
<h2 id="org16a59c6">Additional Jupyter resources or tricks</h2> <h2 id="org186a10f">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org16a59c6"> <div class="outline-text-2" id="text-org186a10f">
</div> </div>
<div id="outline-container-org21ed683" class="outline-3"> <div id="outline-container-org9d17f16" class="outline-3">
<h3 id="org21ed683">Tips and tricks</h3> <h3 id="org9d17f16">Tips and tricks</h3>
<div class="outline-text-3" id="text-org21ed683"> <div class="outline-text-3" id="text-org9d17f16">
<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 +61,9 @@ now). ...@@ -61,9 +61,9 @@ now).
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org81cf6e7" class="outline-3"> <div id="outline-container-org3c5eb3e" class="outline-3">
<h3 id="org81cf6e7">Running R and Python in the same notebook</h3> <h3 id="org3c5eb3e">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-org81cf6e7"> <div class="outline-text-3" id="text-org3c5eb3e">
<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
...@@ -78,14 +78,14 @@ with ...@@ -78,14 +78,14 @@ with
Then you'll be able to use both languages in the same notebook by: Then you'll be able to use both languages in the same notebook by:
</p> </p>
<ol class="org-ol"> <ol class="org-ol">
<li><p> <li style="margin-bottom:0;"><p>
Loading <code>rpy2</code>: Loading <code>rpy2</code>:
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%load_ext rpy2.ipython <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%load_ext rpy2.ipython
</pre> </pre>
</div></li> </div></li>
<li><p> <li style="margin-bottom:0;"><p>
Using the <code>%R</code> Ipython magic: Using the <code>%R</code> Ipython magic:
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -105,9 +105,9 @@ plot((df) ...@@ -105,9 +105,9 @@ plot((df)
</ol> </ol>
</div> </div>
</div> </div>
<div id="outline-container-orgff572f3" class="outline-3"> <div id="outline-container-org656a59e" class="outline-3">
<h3 id="orgff572f3">Exporting a notebook</h3> <h3 id="org656a59e">Exporting a notebook</h3>
<div class="outline-text-3" id="text-orgff572f3"> <div class="outline-text-3" id="text-org656a59e">
<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 +134,13 @@ taste. ...@@ -134,13 +134,13 @@ taste.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org3bb44ad" class="outline-2"> <div id="outline-container-org2b24a9c" class="outline-2">
<h2 id="org3bb44ad">Installing jupyter or jupyter hub on your own machine</h2> <h2 id="org2b24a9c">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org3bb44ad"> <div class="outline-text-2" id="text-org2b24a9c">
</div> </div>
<div id="outline-container-org7acfd0d" class="outline-3"> <div id="outline-container-orgfe13c9b" class="outline-3">
<h3 id="org7acfd0d">Installing jupyter</h3> <h3 id="orgfe13c9b">Installing jupyter</h3>
<div class="outline-text-3" id="text-org7acfd0d"> <div class="outline-text-3" id="text-orgfe13c9b">
<p> <p>
Here is what you should install: Here is what you should install:
</p> </p>
...@@ -171,16 +171,16 @@ The ipython notebook can then be run with the following command: ...@@ -171,16 +171,16 @@ The ipython notebook can then be run with the following command:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org4236b75" class="outline-3"> <div id="outline-container-orgaeb7a97" class="outline-3">
<h3 id="org4236b75">Using R</h3> <h3 id="orgaeb7a97">Using R</h3>
<div class="outline-text-3" id="text-org4236b75"> <div class="outline-text-3" id="text-orgaeb7a97">
<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="#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). the same notebook</a> section).
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -189,9 +189,9 @@ the same notebook</a> section). ...@@ -189,9 +189,9 @@ the same notebook</a> section).
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org04ec93e" class="outline-3"> <div id="outline-container-orgbf7d110" class="outline-3">
<h3 id="org04ec93e">Exporting your notebooks with latex</h3> <h3 id="orgbf7d110">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-org04ec93e"> <div class="outline-text-3" id="text-orgbf7d110">
<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 +203,9 @@ sudo apt-get install texlive-xetex ...@@ -203,9 +203,9 @@ sudo apt-get install texlive-xetex
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgd9a7f1c" class="outline-3"> <div id="outline-container-orgff388aa" class="outline-3">
<h3 id="orgd9a7f1c">Interacting with gitlab</h3> <h3 id="orgff388aa">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgd9a7f1c"> <div class="outline-text-3" id="text-orgff388aa">
<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>:
...@@ -217,14 +217,14 @@ jupyter nbextension enable nb-git ...@@ -217,14 +217,14 @@ jupyter nbextension enable nb-git
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgad4d4c4" class="outline-3"> <div id="outline-container-org77fb4ca" class="outline-3">
<h3 id="orgad4d4c4">Interesting extensions to improve notebook readability</h3> <h3 id="org77fb4ca">Interesting extensions to improve notebook readability</h3>
<div class="outline-text-3" id="text-orgad4d4c4"> <div class="outline-text-3" id="text-org77fb4ca">
<p> <p>
Here are two interesting extensions that can improve readability: Here are two interesting extensions that can improve readability:
</p> </p>
<ul class="org-ul"> <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> <a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a>
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -232,7 +232,7 @@ Here are two interesting extensions that can improve readability: ...@@ -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> <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> </pre>
</div></li> </div></li>
<li><p> <li style="margin-bottom:0;"><p>
<a href="https://github.com/kirbs-/hide_code">Hiding code</a> <a href="https://github.com/kirbs-/hide_code">Hiding code</a>
</p> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -245,9 +245,9 @@ jupyter-serverextension enable --py hide_code ...@@ -245,9 +245,9 @@ jupyter-serverextension enable --py hide_code
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orgff424ae" class="outline-3"> <div id="outline-container-org364ee89" class="outline-3">
<h3 id="orgff424ae">Installing jupyterhub</h3> <h3 id="org364ee89">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-orgff424ae"> <div class="outline-text-3" id="text-org364ee89">
<blockquote> <blockquote>
<p> <p>
Benoit may give a few hints on this. Benoit may give a few hints on this.
......
module2/ressources/rstudio.html
View file @ 1b527eda
...@@ -4,36 +4,36 @@ ...@@ -4,36 +4,36 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org937177d">Installing Rstudio</a> <li style="margin-bottom:0;"><a href="#org47ec510">Installing Rstudio</a>
<ul> <ul>
<li><a href="#org8f48c7c">Linux (debian, ubuntu)</a> <li style="margin-bottom:0;"><a href="#org366dd3d">Linux (debian, ubuntu)</a>
<ul> <ul>
<li><a href="#orge26d961">Installing R</a></li> <li style="margin-bottom:0;"><a href="#orgba71b69">Installing R</a></li>
<li><a href="#org8956720">Installing rstudio</a></li> <li style="margin-bottom:0;"><a href="#orgfe3a4ba">Installing rstudio</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org8770e8d">Mac OSX and Windows</a></li> <li style="margin-bottom:0;"><a href="#orgdf29b54">Mac OSX and Windows</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgc5c6960">Installing Git</a> <li style="margin-bottom:0;"><a href="#orgd30feb0">Installing Git</a>
<ul> <ul>
<li><a href="#org5b86b8a">Linux (debian, ubuntu)</a></li> <li style="margin-bottom:0;"><a href="#org02fa6c2">Linux (debian, ubuntu)</a></li>
<li><a href="#org18d42c3">Mac OSX and Windows</a></li> <li style="margin-bottom:0;"><a href="#org0611f52">Mac OSX and Windows</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org2392c30">Rstudio and git/github/gitlab</a></li> <li style="margin-bottom:0;"><a href="#orgabc8626">Rstudio and git/github/gitlab</a></li>
<li><a href="#org40217fe">Cheat Sheets</a></li> <li style="margin-bottom:0;"><a href="#org270116a">Cheat Sheets</a></li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org937177d" class="outline-2"> <div id="outline-container-org47ec510" class="outline-2">
<h2 id="org937177d">Installing Rstudio</h2> <h2 id="org47ec510">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org937177d"> <div class="outline-text-2" id="text-org47ec510">
</div> </div>
<div id="outline-container-org8f48c7c" class="outline-3"> <div id="outline-container-org366dd3d" class="outline-3">
<h3 id="org8f48c7c">Linux (debian, ubuntu)</h3> <h3 id="org366dd3d">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8f48c7c"> <div class="outline-text-3" id="text-org366dd3d">
<p> <p>
We provide here only instructions for debian-based distributions. Feel We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information free to contribute to this document to provide up-to-date information
...@@ -45,9 +45,9 @@ Today, the stable versions of the most common distributions provide ...@@ -45,9 +45,9 @@ Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode: recent enough versions of emacs and org-mode:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/r-base">R 3.3.3-1</a>, <a href="https://packages.debian.org/stretch/r-cran-knitr">knitr 1.15.1</a>, and <a href="https://packages.debian.org/stretch/r-cran-ggplot2">ggplot 2.2.1</a></li> <li style="margin-bottom:0;">Debian (stretch) ships with <a href="https://packages.debian.org/stretch/r-base">R 3.3.3-1</a>, <a href="https://packages.debian.org/stretch/r-cran-knitr">knitr 1.15.1</a>, and <a href="https://packages.debian.org/stretch/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/r-base">R 3.4.4</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-knitr">knitr 1.17</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-ggplot2">ggplot 2.2.1</a></li> <li style="margin-bottom:0;">Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/r-base">R 3.4.4</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-knitr">knitr 1.17</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/r-base">R 3.4.2</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-knitr">knitr 1.15</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-ggplot2">ggplot 2.2.1</a></li> <li style="margin-bottom:0;">Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/r-base">R 3.4.2</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-knitr">knitr 1.15</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-ggplot2">ggplot 2.2.1</a></li>
</ul> </ul>
<p> <p>
If your distribution is older than this, well, it may be a good time If your distribution is older than this, well, it may be a good time
...@@ -55,9 +55,9 @@ for upgrading&#x2026; ...@@ -55,9 +55,9 @@ for upgrading&#x2026;
</p> </p>
</div> </div>
<div id="outline-container-orge26d961" class="outline-4"> <div id="outline-container-orgba71b69" class="outline-4">
<h4 id="orge26d961">Installing R</h4> <h4 id="orgba71b69">Installing R</h4>
<div class="outline-text-4" id="text-orge26d961"> <div class="outline-text-4" id="text-orgba71b69">
<p> <p>
Beforehand, you need to install the R language and convenient packages Beforehand, you need to install the R language and convenient packages
by running (as root): by running (as root):
...@@ -90,9 +90,9 @@ to run (as root): ...@@ -90,9 +90,9 @@ to run (as root):
</div> </div>
</div> </div>
<div id="outline-container-org8956720" class="outline-4"> <div id="outline-container-orgfe3a4ba" class="outline-4">
<h4 id="org8956720">Installing rstudio</h4> <h4 id="orgfe3a4ba">Installing rstudio</h4>
<div class="outline-text-4" id="text-org8956720"> <div class="outline-text-4" id="text-orgfe3a4ba">
<p> <p>
Rstudio is unfortunately not packaged within debian so the easiest is 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> 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 ...@@ -110,9 +110,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org8770e8d" class="outline-3"> <div id="outline-container-orgdf29b54" class="outline-3">
<h3 id="org8770e8d">Mac OSX and Windows</h3> <h3 id="orgdf29b54">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org8770e8d"> <div class="outline-text-3" id="text-orgdf29b54">
<blockquote> <blockquote>
<p> <p>
Some instructions on installing R and knitr must be missing. This Some instructions on installing R and knitr must be missing. This
...@@ -136,13 +136,13 @@ install.packages(<span style="font-style: italic;">"ggplot2"</span>) ...@@ -136,13 +136,13 @@ install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgc5c6960" class="outline-2"> <div id="outline-container-orgd30feb0" class="outline-2">
<h2 id="orgc5c6960">Installing Git</h2> <h2 id="orgd30feb0">Installing Git</h2>
<div class="outline-text-2" id="text-orgc5c6960"> <div class="outline-text-2" id="text-orgd30feb0">
</div> </div>
<div id="outline-container-org5b86b8a" class="outline-3"> <div id="outline-container-org02fa6c2" class="outline-3">
<h3 id="org5b86b8a">Linux (debian, ubuntu)</h3> <h3 id="org02fa6c2">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org5b86b8a"> <div class="outline-text-3" id="text-org02fa6c2">
<p> <p>
We provide here only instructions for debian-based distributions. Feel We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information free to contribute to this document to provide up-to-date information
...@@ -158,16 +158,16 @@ Run (as root): ...@@ -158,16 +158,16 @@ Run (as root):
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org18d42c3" class="outline-3"> <div id="outline-container-org0611f52" class="outline-3">
<h3 id="org18d42c3">Mac OSX and Windows</h3> <h3 id="org0611f52">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org18d42c3"> <div class="outline-text-3" id="text-org0611f52">
<ul class="org-ul"> <ul class="org-ul">
<li>Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li> <li style="margin-bottom:0;">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 <li style="margin-bottom:0;">Optional Git clients (should not be needed if you work within
Rstudio): Rstudio):
<ul class="org-ul"> <ul class="org-ul">
<li><a href="https://www.sourcetreeapp.com/">SourceTree</a></li> <li style="margin-bottom:0;"><a href="https://www.sourcetreeapp.com/">SourceTree</a></li>
<li><p> <li style="margin-bottom:0;"><p>
<a href="https://desktop.github.com/">GitHub Desktop</a> <a href="https://desktop.github.com/">GitHub Desktop</a>
</p> </p>
<blockquote> <blockquote>
...@@ -180,16 +180,16 @@ Rstudio): ...@@ -180,16 +180,16 @@ Rstudio):
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org2392c30" class="outline-2"> <div id="outline-container-orgabc8626" class="outline-2">
<h2 id="org2392c30">Rstudio and git/github/gitlab</h2> <h2 id="orgabc8626">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-org2392c30"> <div class="outline-text-2" id="text-orgabc8626">
<blockquote> <blockquote>
<p> <p>
We may want to redo a screencast in French for this We may want to redo a screencast in French for this
</p> </p>
</blockquote> </blockquote>
<ul class="org-ul"> <ul class="org-ul">
<li><a href="https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/">This video on using git/githugb/gitlab from Rstudio</a> (starting at time 9:09)</li> <li style="margin-bottom:0;"><a href="https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/">This video on using git/githugb/gitlab from Rstudio</a> (starting at time 9:09)</li>
</ul> </ul>
<p> <p>
...@@ -197,26 +197,26 @@ Alternatively, we can point to: ...@@ -197,26 +197,26 @@ Alternatively, we can point to:
<a href="http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/">http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/</a> <a href="http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/">http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/</a>
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li>Part 1/item 2: Setup Git in RStudio</li> <li style="margin-bottom:0;">Part 1/item 2: Setup Git in RStudio</li>
<li>Part 2 (to adapt to gitlab)</li> <li style="margin-bottom:0;">Part 2 (to adapt to gitlab)</li>
<li>Part 3</li> <li style="margin-bottom:0;">Part 3</li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org40217fe" class="outline-2"> <div id="outline-container-org270116a" class="outline-2">
<h2 id="org40217fe">Cheat Sheets</h2> <h2 id="org270116a">Cheat Sheets</h2>
<div class="outline-text-2" id="text-org40217fe"> <div class="outline-text-2" id="text-org270116a">
<p> <p>
The Rstudio team has created a lot of good material and tutorials. You 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 should definitively look at the <a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheets webpage</a>. In particular
you want to have look at the ones on: you want to have look at the ones on:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">the Rstudio IDE</a>,</li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">the Rstudio IDE</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li>
<li>the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li> <li style="margin-bottom:0;">the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">data visualization with ggplot2</a>,</li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">data visualization with ggplot2</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">data transformation with dplyr</a></li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">data transformation with dplyr</a></li>
</ul> </ul>
<p> <p>
...@@ -224,10 +224,10 @@ In case it helps, here are some (sometimes outdated) French versions ...@@ -224,10 +224,10 @@ In case it helps, here are some (sometimes outdated) French versions
of these documents: of these documents:
</p> </p>
<ul class="org-ul"> <ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li> <li style="margin-bottom:0;"><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li>
<li><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li> <li style="margin-bottom:0;"><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li>
</ul> </ul>
</div> </div>
</div> </div>
......
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