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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0125a5d">Installing emacs, org-mode, ess, and auctex.</a>
<li style="margin-bottom:0;"><a href="#orge175e93">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgd0985c0">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org802a903">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org947a24e">Windows</a></li>
<li style="margin-bottom:0;"><a href="#org7e10563">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orgc35d341">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#orge9f89e6">Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgf9c74de">A simple "<i>reproducible research</i>" emacs configuration</a>
<li style="margin-bottom:0;"><a href="#orgcb2ceeb">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8231f7a">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org5c0abc0">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org3eb73fd">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org6043aac">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org456398a">Step 4: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#org45b7ef8">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#orgb252f52">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org5f181b6">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org1c768ac">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#orgfd8520c">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org578a4a4">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#orgce9f641">Emacs Tips and tricks</a>
<li style="margin-bottom:0;"><a href="#org62d8122">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org6e1e28d">Emacs Tips and tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orge3bb1b2">Cheat-sheets</a>
<li style="margin-bottom:0;"><a href="#orgbb3b0f2">Cheat-sheets</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0a30ece">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org0389dfc">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#orga7cf047">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#orga3d7d1f">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgc9149b2">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org8ddb11d">Additional useful emacs packages</a>
<li style="margin-bottom:0;"><a href="#org5711421">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org194e358">Additional useful emacs packages</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orge154c83">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org77f5398">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orgccdd44f">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org661ca19">Magit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgb4f2246">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#org2fde45b">Other resources</a></li>
</ul>
</li>
</ul>
......@@ -57,13 +57,13 @@ the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/
The next section provides information on how to install emacs.
</p>
<div id="outline-container-org0125a5d" class="outline-2">
<h2 id="org0125a5d">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org0125a5d">
<div id="outline-container-orge175e93" class="outline-2">
<h2 id="orge175e93">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orge175e93">
</div>
<div id="outline-container-orgd0985c0" class="outline-3">
<h3 id="orgd0985c0">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-orgd0985c0">
<div id="outline-container-org7e10563" class="outline-3">
<h3 id="org7e10563">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org7e10563">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -125,9 +125,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org802a903" class="outline-3">
<h3 id="org802a903">Mac OS X</h3>
<div class="outline-text-3" id="text-org802a903">
<div id="outline-container-orgc35d341" class="outline-3">
<h3 id="orgc35d341">Mac OS X</h3>
<div class="outline-text-3" id="text-orgc35d341">
<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>:
......@@ -160,9 +160,9 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org947a24e" class="outline-3">
<h3 id="org947a24e">Windows</h3>
<div class="outline-text-3" id="text-org947a24e">
<div id="outline-container-orge9f89e6" class="outline-3">
<h3 id="orge9f89e6">Windows</h3>
<div class="outline-text-3" id="text-orge9f89e6">
<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
......@@ -176,9 +176,9 @@ versions:
</div>
</div>
</div>
<div id="outline-container-orgf9c74de" class="outline-2">
<h2 id="orgf9c74de">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-orgf9c74de">
<div id="outline-container-orgcb2ceeb" class="outline-2">
<h2 id="orgcb2ceeb">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-orgcb2ceeb">
<p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Mise en place
Emacs/Orgmode"</i> in French). Watching it before following the
......@@ -197,9 +197,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-org8231f7a" class="outline-3">
<h3 id="org8231f7a">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org8231f7a">
<div id="outline-container-org45b7ef8" class="outline-3">
<h3 id="org45b7ef8">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org45b7ef8">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -220,9 +220,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-org5c0abc0" class="outline-3">
<h3 id="org5c0abc0">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-org5c0abc0">
<div id="outline-container-orgb252f52" class="outline-3">
<h3 id="orgb252f52">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-orgb252f52">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -239,9 +239,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-org3eb73fd" class="outline-3">
<h3 id="org3eb73fd">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org3eb73fd">
<div id="outline-container-org5f181b6" class="outline-3">
<h3 id="org5f181b6">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org5f181b6">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -253,9 +253,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org6043aac" class="outline-3">
<h3 id="org6043aac">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org6043aac">
<div id="outline-container-org1c768ac" class="outline-3">
<h3 id="org1c768ac">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org1c768ac">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -286,9 +286,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p>
</div>
</div>
<div id="outline-container-org456398a" class="outline-3">
<h3 id="org456398a">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-org456398a">
<div id="outline-container-orgfd8520c" class="outline-3">
<h3 id="orgfd8520c">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-orgfd8520c">
<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
......@@ -299,9 +299,9 @@ forums.
</div>
</div>
</div>
<div id="outline-container-org578a4a4" class="outline-2">
<h2 id="org578a4a4">A stub of replicable article</h2>
<div class="outline-text-2" id="text-org578a4a4">
<div id="outline-container-org62d8122" class="outline-2">
<h2 id="org62d8122">A stub of replicable article</h2>
<div class="outline-text-2" id="text-org62d8122">
<p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Écrire un article
réplicable avec Emacs/Orgmode"</i> in French). Watching it before
......@@ -318,13 +318,13 @@ source (<a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-re
</p>
<p>
Download the following <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz">archive</a>, uncompress it and simply <code>make</code> to generate the
Download the following <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz">archive</a>, uncompress it and simply <code>make</code> to generate the
article. You should then be able to open the <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf">resulting article</a>. This
is summarized in the following command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">wget --no-check-certificate -O replicable.tgz https://github.com/alegrand/RR_webinars/raw/master/1_replicable_article_laboratory_notebook/replicable/replicable.tgz <span style="font-weight: bold; font-style: italic;">### </span><span style="font-weight: bold; font-style: italic;">Fix the broken URL</span>
tar zxf replicable.tgz; <span style="font-weight: bold;">cd</span> replicable; make ; evince article.pdf
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">wget --no-check-certificate -O replicable_article.tgz https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz
tar zxf replicable_article.tgz; <span style="font-weight: bold;">cd</span> replicable_article; make ; evince article.pdf
</pre>
</div>
......@@ -365,22 +365,22 @@ chunk of code when exporting.
</div>
</div>
<div id="outline-container-orgce9f641" class="outline-2">
<h2 id="orgce9f641">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orgce9f641">
<div id="outline-container-org6e1e28d" class="outline-2">
<h2 id="org6e1e28d">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org6e1e28d">
</div>
<div id="outline-container-orge3bb1b2" class="outline-3">
<h3 id="orge3bb1b2">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orge3bb1b2">
<div id="outline-container-orgbb3b0f2" class="outline-3">
<h3 id="orgbb3b0f2">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgbb3b0f2">
<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-org0a30ece" class="outline-4">
<h4 id="org0a30ece">Emacs</h4>
<div class="outline-text-4" id="text-org0a30ece">
<div id="outline-container-orga7cf047" class="outline-4">
<h4 id="orga7cf047">Emacs</h4>
<div class="outline-text-4" id="text-orga7cf047">
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">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>
......@@ -389,9 +389,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-org0389dfc" class="outline-4">
<h4 id="org0389dfc">Org-mode</h4>
<div class="outline-text-4" id="text-org0389dfc">
<div id="outline-container-orga3d7d1f" class="outline-4">
<h4 id="orga3d7d1f">Org-mode</h4>
<div class="outline-text-4" id="text-orga3d7d1f">
<ul class="org-ul">
<li style="margin-bottom:0;"><a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org">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>
......@@ -400,22 +400,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-orgc9149b2" class="outline-3">
<h3 id="orgc9149b2">Video tutorials</h3>
<div class="outline-text-3" id="text-orgc9149b2">
<div id="outline-container-org5711421" class="outline-3">
<h3 id="org5711421">Video tutorials</h3>
<div class="outline-text-3" id="text-org5711421">
<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-org8ddb11d" class="outline-3">
<h3 id="org8ddb11d">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org8ddb11d">
<div id="outline-container-org194e358" class="outline-3">
<h3 id="org194e358">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org194e358">
</div>
<div id="outline-container-orge154c83" class="outline-4">
<h4 id="orge154c83">Company-mode</h4>
<div class="outline-text-4" id="text-orge154c83">
<div id="outline-container-orgccdd44f" class="outline-4">
<h4 id="orgccdd44f">Company-mode</h4>
<div class="outline-text-4" id="text-orgccdd44f">
<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
......@@ -424,9 +424,9 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode.
</p>
</div>
</div>
<div id="outline-container-org77f5398" class="outline-4">
<h4 id="org77f5398">Magit</h4>
<div class="outline-text-4" id="text-org77f5398">
<div id="outline-container-org661ca19" class="outline-4">
<h4 id="org661ca19">Magit</h4>
<div class="outline-text-4" id="text-org661ca19">
<p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Utilisation
......@@ -444,9 +444,9 @@ invoke magit by using <code>C-x g</code>.
</div>
</div>
</div>
<div id="outline-container-orgb4f2246" class="outline-3">
<h3 id="orgb4f2246">Other resources</h3>
<div class="outline-text-3" id="text-orgb4f2246">
<div id="outline-container-org2fde45b" class="outline-3">
<h3 id="org2fde45b">Other resources</h3>
<div class="outline-text-3" id="text-org2fde45b">
<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>
......
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