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<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0fbdfa9">Installing emacs, org-mode, ess, and auctex.</a> <li style="margin-bottom:0;"><a href="#org0125a5d">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org4a4ee20">Linux (Debian, Ubuntu)</a></li> <li style="margin-bottom:0;"><a href="#orgd0985c0">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org101dae2">Mac OS X</a></li> <li style="margin-bottom:0;"><a href="#org802a903">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org048091d">Windows</a></li> <li style="margin-bottom:0;"><a href="#org947a24e">Windows</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgccaf2ff">A simple "<i>reproducible research</i>" emacs configuration</a> <li style="margin-bottom:0;"><a href="#orgf9c74de">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org59fef98">Step 0: Backup and download our configuration</a></li> <li style="margin-bottom:0;"><a href="#org8231f7a">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org19679a8">Step 1: Prepare your journal</a></li> <li style="margin-bottom:0;"><a href="#org5c0abc0">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org3142fb4">Step 2: Set up Emacs configuration</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="#org9657e1f">Step 3: Check whether the installation is working or not</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="#org26b639c">Step 4: Open and play with your journal:</a></li> <li style="margin-bottom:0;"><a href="#org456398a">Step 4: Open and play with your journal:</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgf2f9128">A stub of replicable article</a></li> <li style="margin-bottom:0;"><a href="#org578a4a4">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#orge35ff2f">Emacs Tips and tricks</a> <li style="margin-bottom:0;"><a href="#orgce9f641">Emacs Tips and tricks</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgd3ea437">Cheat-sheets</a> <li style="margin-bottom:0;"><a href="#orge3bb1b2">Cheat-sheets</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgef979b2">Emacs</a></li> <li style="margin-bottom:0;"><a href="#org0a30ece">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#orge1bce05">Org-mode</a></li> <li style="margin-bottom:0;"><a href="#org0389dfc">Org-mode</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org151e7c0">Video tutorials</a></li> <li style="margin-bottom:0;"><a href="#orgc9149b2">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org29b5af4">Additional useful emacs packages</a> <li style="margin-bottom:0;"><a href="#org8ddb11d">Additional useful emacs packages</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb61c58f">Company-mode</a></li> <li style="margin-bottom:0;"><a href="#orge154c83">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org74978d6">Magit</a></li> <li style="margin-bottom:0;"><a href="#org77f5398">Magit</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org425cf50">Other resources</a></li> <li style="margin-bottom:0;"><a href="#orgb4f2246">Other resources</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
...@@ -45,24 +45,25 @@ ...@@ -45,24 +45,25 @@
<p> <p>
<b>Disclaimer:</b> The two sections <span class="underline">A simple "<i>reproducible research</i>" emacs <b>Disclaimer:</b> The two sections <span class="underline">A simple "<i>reproducible research</i>" emacs
configuration</span> and <span class="underline">A stub of replicable article</span> explain how to set up configuration</span> and <span class="underline">A stub of replicable article</span> explain how to set up
emacs/org-mode for this MOOC. <b>These sections are illustrated in two emacs/org-mode for this MOOC. These are very important sections in the
out of the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">three video tutorials of this sequence</a>, and</b> <b>which you context of this MOOC. <b>These sections are illustrated in two
out of the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">three video tutorials of this sequence</a>, and</b> <b>which you
really should follow carefully</b>. <b>Otherwise, you may have trouble doing really should follow carefully</b>. <b>Otherwise, you may have trouble doing
the exercises later on</b>. Likewise, I strongly encourage you to watch the exercises later on</b>. Likewise, I strongly encourage you to watch
the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">"emacs and git" video tutorial available at the same place</a>. the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">"emacs and git" video tutorial available at the same place</a>.
</p> </p>
<p> <p>
The next section provides information on how to install emacs. The next section provides information on how to install emacs.
</p> </p>
<div id="outline-container-org0fbdfa9" class="outline-2"> <div id="outline-container-org0125a5d" class="outline-2">
<h2 id="org0fbdfa9">Installing emacs, org-mode, ess, and auctex.</h2> <h2 id="org0125a5d">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org0fbdfa9"> <div class="outline-text-2" id="text-org0125a5d">
</div> </div>
<div id="outline-container-org4a4ee20" class="outline-3"> <div id="outline-container-orgd0985c0" class="outline-3">
<h3 id="org4a4ee20">Linux (Debian, Ubuntu)</h3> <h3 id="orgd0985c0">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org4a4ee20"> <div class="outline-text-3" id="text-orgd0985c0">
<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
...@@ -124,9 +125,9 @@ which is now deprecated. ...@@ -124,9 +125,9 @@ which is now deprecated.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org101dae2" class="outline-3"> <div id="outline-container-org802a903" class="outline-3">
<h3 id="org101dae2">Mac OS X</h3> <h3 id="org802a903">Mac OS X</h3>
<div class="outline-text-3" id="text-org101dae2"> <div class="outline-text-3" id="text-org802a903">
<ul class="org-ul"> <ul class="org-ul">
<li style="margin-bottom:0;"><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>:
...@@ -159,9 +160,9 @@ brew install wget ...@@ -159,9 +160,9 @@ brew install wget
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org048091d" class="outline-3"> <div id="outline-container-org947a24e" class="outline-3">
<h3 id="org048091d">Windows</h3> <h3 id="org947a24e">Windows</h3>
<div class="outline-text-3" id="text-org048091d"> <div class="outline-text-3" id="text-org947a24e">
<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
...@@ -175,12 +176,13 @@ versions: ...@@ -175,12 +176,13 @@ versions:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgccaf2ff" class="outline-2"> <div id="outline-container-orgf9c74de" class="outline-2">
<h2 id="orgccaf2ff">A simple "<i>reproducible research</i>" emacs configuration</h2> <h2 id="orgf9c74de">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-orgccaf2ff"> <div class="outline-text-2" id="text-orgf9c74de">
<p> <p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">video tutorial</a> (in French). Watching 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
it before following the instructions given in this section may help. Emacs/Orgmode"</i> in French). Watching it before following the
instructions given in this section may help.
</p> </p>
<p> <p>
...@@ -195,9 +197,9 @@ adding a few org-mode specific configurations. ...@@ -195,9 +197,9 @@ adding a few org-mode specific configurations.
</p> </p>
</div> </div>
<div id="outline-container-org59fef98" class="outline-3"> <div id="outline-container-org8231f7a" class="outline-3">
<h3 id="org59fef98">Step 0: Backup and download our configuration</h3> <h3 id="org8231f7a">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org59fef98"> <div class="outline-text-3" id="text-org8231f7a">
<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
...@@ -218,9 +220,9 @@ rr_org/journal.org ...@@ -218,9 +220,9 @@ rr_org/journal.org
</div> </div>
</div> </div>
<div id="outline-container-org19679a8" class="outline-3"> <div id="outline-container-org5c0abc0" class="outline-3">
<h3 id="org19679a8">Step 1: Prepare your journal</h3> <h3 id="org5c0abc0">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-org19679a8"> <div class="outline-text-3" id="text-org5c0abc0">
<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>
...@@ -237,9 +239,9 @@ should give a try. ...@@ -237,9 +239,9 @@ should give a try.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org3142fb4" class="outline-3"> <div id="outline-container-org3eb73fd" class="outline-3">
<h3 id="org3142fb4">Step 2: Set up Emacs configuration</h3> <h3 id="org3eb73fd">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org3142fb4"> <div class="outline-text-3" id="text-org3eb73fd">
<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>
...@@ -251,9 +253,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code ...@@ -251,9 +253,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org9657e1f" class="outline-3"> <div id="outline-container-org6043aac" class="outline-3">
<h3 id="org9657e1f">Step 3: Check whether the installation is working or not</h3> <h3 id="org6043aac">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org9657e1f"> <div class="outline-text-3" id="text-org6043aac">
<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:
...@@ -284,9 +286,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning ...@@ -284,9 +286,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org26b639c" class="outline-3"> <div id="outline-container-org456398a" class="outline-3">
<h3 id="org26b639c">Step 4: Open and play with your journal:</h3> <h3 id="org456398a">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-org26b639c"> <div class="outline-text-3" id="text-org456398a">
<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
...@@ -297,12 +299,13 @@ forums. ...@@ -297,12 +299,13 @@ forums.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgf2f9128" class="outline-2"> <div id="outline-container-org578a4a4" class="outline-2">
<h2 id="orgf2f9128">A stub of replicable article</h2> <h2 id="org578a4a4">A stub of replicable article</h2>
<div class="outline-text-2" id="text-orgf2f9128"> <div class="outline-text-2" id="text-org578a4a4">
<p> <p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">video tutorial</a> (in French). Watching 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
it before following the instructions given in this section may help. réplicable avec Emacs/Orgmode"</i> in French). Watching it before
following the instructions given in this section may help.
</p> </p>
<p> <p>
...@@ -362,22 +365,22 @@ chunk of code when exporting. ...@@ -362,22 +365,22 @@ chunk of code when exporting.
</div> </div>
</div> </div>
<div id="outline-container-orge35ff2f" class="outline-2"> <div id="outline-container-orgce9f641" class="outline-2">
<h2 id="orge35ff2f">Emacs Tips and tricks</h2> <h2 id="orgce9f641">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orge35ff2f"> <div class="outline-text-2" id="text-orgce9f641">
</div> </div>
<div id="outline-container-orgd3ea437" class="outline-3"> <div id="outline-container-orge3bb1b2" class="outline-3">
<h3 id="orgd3ea437">Cheat-sheets</h3> <h3 id="orge3bb1b2">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgd3ea437"> <div class="outline-text-3" id="text-orge3bb1b2">
<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-orgef979b2" class="outline-4"> <div id="outline-container-org0a30ece" class="outline-4">
<h4 id="orgef979b2">Emacs</h4> <h4 id="org0a30ece">Emacs</h4>
<div class="outline-text-4" id="text-orgef979b2"> <div class="outline-text-4" id="text-org0a30ece">
<ul class="org-ul"> <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://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> <li style="margin-bottom:0;"><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
...@@ -386,9 +389,9 @@ cheat-sheats. Here is a selection in case it helps: ...@@ -386,9 +389,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-orge1bce05" class="outline-4"> <div id="outline-container-org0389dfc" class="outline-4">
<h4 id="orge1bce05">Org-mode</h4> <h4 id="org0389dfc">Org-mode</h4>
<div class="outline-text-4" id="text-orge1bce05"> <div class="outline-text-4" id="text-org0389dfc">
<ul class="org-ul"> <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://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> <li style="margin-bottom:0;"><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
...@@ -397,22 +400,22 @@ cheat-sheats. Here is a selection in case it helps: ...@@ -397,22 +400,22 @@ cheat-sheats. Here is a selection in case it helps:
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org151e7c0" class="outline-3"> <div id="outline-container-orgc9149b2" class="outline-3">
<h3 id="org151e7c0">Video tutorials</h3> <h3 id="orgc9149b2">Video tutorials</h3>
<div class="outline-text-3" id="text-org151e7c0"> <div class="outline-text-3" id="text-orgc9149b2">
<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-org29b5af4" class="outline-3"> <div id="outline-container-org8ddb11d" class="outline-3">
<h3 id="org29b5af4">Additional useful emacs packages</h3> <h3 id="org8ddb11d">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org29b5af4"> <div class="outline-text-3" id="text-org8ddb11d">
</div> </div>
<div id="outline-container-orgb61c58f" class="outline-4"> <div id="outline-container-orge154c83" class="outline-4">
<h4 id="orgb61c58f">Company-mode</h4> <h4 id="orge154c83">Company-mode</h4>
<div class="outline-text-4" id="text-orgb61c58f"> <div class="outline-text-4" id="text-orge154c83">
<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
...@@ -421,12 +424,13 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode. ...@@ -421,12 +424,13 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org74978d6" class="outline-4"> <div id="outline-container-org77f5398" class="outline-4">
<h4 id="org74978d6">Magit</h4> <h4 id="org77f5398">Magit</h4>
<div class="outline-text-4" id="text-org74978d6"> <div class="outline-text-4" id="text-org77f5398">
<p> <p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. Its usage is briefly illustrated <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/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">video tutorial</a> (in French). 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
Emacs/git"</i> in French).
</p> </p>
<p> <p>
...@@ -440,9 +444,9 @@ invoke magit by using <code>C-x g</code>. ...@@ -440,9 +444,9 @@ invoke magit by using <code>C-x g</code>.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org425cf50" class="outline-3"> <div id="outline-container-orgb4f2246" class="outline-3">
<h3 id="org425cf50">Other resources</h3> <h3 id="orgb4f2246">Other resources</h3>
<div class="outline-text-3" id="text-org425cf50"> <div class="outline-text-3" id="text-orgb4f2246">
<ul class="org-ul"> <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://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> <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>
......
module2/ressources/gitlab.html
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...@@ -4,24 +4,24 @@ ...@@ -4,24 +4,24 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orge3f4bc8">Installing Git</a> <li style="margin-bottom:0;"><a href="#org3b51ceb">Installing Git</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgf47f6c9">Linux (debian, ubuntu)</a></li> <li style="margin-bottom:0;"><a href="#org00b8ed8">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org6c4b10f">Mac OSX and Windows</a></li> <li style="margin-bottom:0;"><a href="#org247f959">Mac OSX and Windows</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgca31098">Authenticating on GitLab</a> <li style="margin-bottom:0;"><a href="#org10e42dd">Authenticating on GitLab</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org69e4843">Option 1: HTTPS</a> <li style="margin-bottom:0;"><a href="#orgda58dab">Option 1: HTTPS</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org4c05db5">Configuring your GitLab password</a></li> <li style="margin-bottom:0;"><a href="#org7f96ff9">Configuring your GitLab password</a></li>
<li style="margin-bottom:0;"><a href="#orgcfbd789">Making sure git remembers your password</a></li> <li style="margin-bottom:0;"><a href="#org18555d7">Making sure git remembers your password</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#orgaa173db">Option 2: SSH</a> <li style="margin-bottom:0;"><a href="#org367edbb">Option 2: SSH</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org880f8ce">Installing SSH</a></li> <li style="margin-bottom:0;"><a href="#orge10264b">Installing SSH</a></li>
<li style="margin-bottom:0;"><a href="#org4481e63">Setting up SSH on GitLab</a></li> <li style="margin-bottom:0;"><a href="#orgac5801f">Setting up SSH on GitLab</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
...@@ -47,7 +47,7 @@ is very convenient but in most cases, you will want to have your own ...@@ -47,7 +47,7 @@ is very convenient but in most cases, you will want to have your own
local copy of the repository and you will have to synchronize your local copy of the repository and you will have to synchronize your
local copy with the remote GitLab one. To propagate your local copy with the remote GitLab one. To propagate your
modifications, you will obviously have to authenticate yourself on modifications, you will obviously have to authenticate yourself on
GitLab. How to do this is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/f6580ad8e997400faeffe9af4fd37063/2">video tutorial</a> (in French). GitLab. How to do this is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85">video tutorial</a> (in French).
</p> </p>
<p> <p>
...@@ -56,13 +56,13 @@ installed on your machine and how to handle authentication. Please ...@@ -56,13 +56,13 @@ installed on your machine and how to handle authentication. Please
read these instructions carefully. read these instructions carefully.
</p> </p>
<div id="outline-container-orge3f4bc8" class="outline-2"> <div id="outline-container-org3b51ceb" class="outline-2">
<h2 id="orge3f4bc8">Installing Git</h2> <h2 id="org3b51ceb">Installing Git</h2>
<div class="outline-text-2" id="text-orge3f4bc8"> <div class="outline-text-2" id="text-org3b51ceb">
</div> </div>
<div id="outline-container-orgf47f6c9" class="outline-3"> <div id="outline-container-org00b8ed8" class="outline-3">
<h3 id="orgf47f6c9">Linux (debian, ubuntu)</h3> <h3 id="org00b8ed8">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-orgf47f6c9"> <div class="outline-text-3" id="text-org00b8ed8">
<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
...@@ -78,9 +78,9 @@ Run (as root): ...@@ -78,9 +78,9 @@ Run (as root):
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org6c4b10f" class="outline-3"> <div id="outline-container-org247f959" class="outline-3">
<h3 id="org6c4b10f">Mac OSX and Windows</h3> <h3 id="org247f959">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org6c4b10f"> <div class="outline-text-3" id="text-org247f959">
<ul class="org-ul"> <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;">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 <li style="margin-bottom:0;">Optional Git clients (should not be needed if you work within
...@@ -100,9 +100,9 @@ Rstudio): ...@@ -100,9 +100,9 @@ Rstudio):
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgca31098" class="outline-2"> <div id="outline-container-org10e42dd" class="outline-2">
<h2 id="orgca31098">Authenticating on GitLab</h2> <h2 id="org10e42dd">Authenticating on GitLab</h2>
<div class="outline-text-2" id="text-orgca31098"> <div class="outline-text-2" id="text-org10e42dd">
<p> <p>
There are two ways of authenticating and synchronizing your local There are two ways of authenticating and synchronizing your local
repository with GitLab: through HTTPS or through SSH. The first one repository with GitLab: through HTTPS or through SSH. The first one
...@@ -113,22 +113,22 @@ never asks me for any password anymore and I don't have to remember ...@@ -113,22 +113,22 @@ never asks me for any password anymore and I don't have to remember
anything). anything).
</p> </p>
</div> </div>
<div id="outline-container-org69e4843" class="outline-3"> <div id="outline-container-orgda58dab" class="outline-3">
<h3 id="org69e4843">Option 1: HTTPS</h3> <h3 id="orgda58dab">Option 1: HTTPS</h3>
<div class="outline-text-3" id="text-org69e4843"> <div class="outline-text-3" id="text-orgda58dab">
</div> </div>
<div id="outline-container-org4c05db5" class="outline-4"> <div id="outline-container-org7f96ff9" class="outline-4">
<h4 id="org4c05db5">Configuring your GitLab password</h4> <h4 id="org7f96ff9">Configuring your GitLab password</h4>
<div class="outline-text-4" id="text-org4c05db5"> <div class="outline-text-4" id="text-org7f96ff9">
<p> <p>
In this <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/f6580ad8e997400faeffe9af4fd37063/2">video tutorial</a> (in French), I explain how to change your In this <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85">video tutorial</a> (in French), I explain how to change your
password on our GitLab. password on our GitLab.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgcfbd789" class="outline-4"> <div id="outline-container-org18555d7" class="outline-4">
<h4 id="orgcfbd789">Making sure git remembers your password</h4> <h4 id="org18555d7">Making sure git remembers your password</h4>
<div class="outline-text-4" id="text-orgcfbd789"> <div class="outline-text-4" id="text-org18555d7">
<p> <p>
My GitLab id is <code>3211ac4f2fb71deaeff9252764c368e7</code>. Say I've configured My GitLab id is <code>3211ac4f2fb71deaeff9252764c368e7</code>. Say I've configured
my password to be <code>tototutu</code> (what a weak password&#x2026;) and I want to my password to be <code>tototutu</code> (what a weak password&#x2026;) and I want to
...@@ -168,9 +168,9 @@ cached in memory and they will not be asked again before an hour. ...@@ -168,9 +168,9 @@ cached in memory and they will not be asked again before an hour.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgaa173db" class="outline-3"> <div id="outline-container-org367edbb" class="outline-3">
<h3 id="orgaa173db">Option 2: SSH</h3> <h3 id="org367edbb">Option 2: SSH</h3>
<div class="outline-text-3" id="text-orgaa173db"> <div class="outline-text-3" id="text-org367edbb">
<p> <p>
My preferred (although more technical) solution is to install SSH, to My preferred (although more technical) solution is to install SSH, to
create a pair or private/public keys, and to upload your SSH public create a pair or private/public keys, and to upload your SSH public
...@@ -178,13 +178,13 @@ key on GitLab. This section provides with information on how to do ...@@ -178,13 +178,13 @@ key on GitLab. This section provides with information on how to do
this. this.
</p> </p>
</div> </div>
<div id="outline-container-org880f8ce" class="outline-4"> <div id="outline-container-orge10264b" class="outline-4">
<h4 id="org880f8ce">Installing SSH</h4> <h4 id="orge10264b">Installing SSH</h4>
<div class="outline-text-4" id="text-org880f8ce"> <div class="outline-text-4" id="text-orge10264b">
</div> </div>
<ul class="org-ul"> <ul class="org-ul">
<li style="margin-bottom:0;"><a id="orga22af4e"></a>Linux (debian, ubuntu)<br /> <li style="margin-bottom:0;"><a id="orgabfaf26"></a>Linux (debian, ubuntu)<br />
<div class="outline-text-5" id="text-orga22af4e"> <div class="outline-text-5" id="text-orgabfaf26">
<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
...@@ -200,15 +200,15 @@ Run (as root): ...@@ -200,15 +200,15 @@ Run (as root):
</div> </div>
</div> </div>
</li> </li>
<li style="margin-bottom:0;"><a id="orgdea2c28"></a>Mac OSX<br /> <li style="margin-bottom:0;"><a id="org89976c7"></a>Mac OSX<br />
<div class="outline-text-5" id="text-orgdea2c28"> <div class="outline-text-5" id="text-org89976c7">
<p> <p>
You do not have anything to do as it is installed by default. You do not have anything to do as it is installed by default.
</p> </p>
</div> </div>
</li> </li>
<li style="margin-bottom:0;"><a id="org991d2af"></a>Windows<br /> <li style="margin-bottom:0;"><a id="orgb8fc08c"></a>Windows<br />
<div class="outline-text-5" id="text-org991d2af"> <div class="outline-text-5" id="text-orgb8fc08c">
<p> <p>
You should install the <a href="https://www.ssh.com/ssh/putty/windows/">Putty</a> client. Once it is installed, look for You should install the <a href="https://www.ssh.com/ssh/putty/windows/">Putty</a> client. Once it is installed, look for
the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generating an SSH key</a>. the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generating an SSH key</a>.
...@@ -217,9 +217,9 @@ the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generati ...@@ -217,9 +217,9 @@ the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generati
</li> </li>
</ul> </ul>
</div> </div>
<div id="outline-container-org4481e63" class="outline-4"> <div id="outline-container-orgac5801f" class="outline-4">
<h4 id="org4481e63">Setting up SSH on GitLab</h4> <h4 id="orgac5801f">Setting up SSH on GitLab</h4>
<div class="outline-text-4" id="text-org4481e63"> <div class="outline-text-4" id="text-orgac5801f">
<p> <p>
Here are <a href="https://docs.gitlab.com/ee/ssh/">all the official explanations on how to set up your SSH key Here are <a href="https://docs.gitlab.com/ee/ssh/">all the official explanations on how to set up your SSH key
on GitLab</a>. Alternatively, you may also want to have a look at this on GitLab</a>. Alternatively, you may also want to have a look at this
......
module2/ressources/rstudio.html
View file @ 6399576d
...@@ -4,15 +4,15 @@ ...@@ -4,15 +4,15 @@
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgc8caf11">Installing Rstudio</a> <li style="margin-bottom:0;"><a href="#org8d005af">Installing Rstudio</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8c06a11">Linux (debian, ubuntu)</a> <li style="margin-bottom:0;"><a href="#orgc6785d0">Linux (debian, ubuntu)</a>
<ul style="margin:0 0;"> <ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org7e55379">Installing R</a></li> <li style="margin-bottom:0;"><a href="#org023d7d1">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgcce3554">Installing rstudio</a></li> <li style="margin-bottom:0;"><a href="#org8b528c6">Installing rstudio</a></li>
</ul> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org83ecc09">Mac OSX and Windows</a></li> <li style="margin-bottom:0;"><a href="#org88ad478">Mac OSX and Windows</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
...@@ -24,8 +24,8 @@ This document provides information on how to install Rstudio. ...@@ -24,8 +24,8 @@ This document provides information on how to install Rstudio.
<p> <p>
If you have never used git with Rstudio, <b>we strongly advise that you If you have never used git with Rstudio, <b>we strongly advise that you
follow <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/d6b5dbe8add046e4bde324ed3fc936fa/3">our tutorial on using git from Rstudio</a></b> (in French). Before follow <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/d132a854b0464ad29085cedaded23136">our tutorial on using git from Rstudio</a></b> (<i>"Rstudio et Gitlab"</i> in French). Before
proceeding, make sure you also have followed the <b><a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/f6580ad8e997400faeffe9af4fd37063/2">"git/GitLab proceeding, make sure you also have followed the <b><a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85">"git/GitLab
configuration" tutorial</a></b> (in French). configuration" tutorial</a></b> (in French).
</p> </p>
...@@ -60,13 +60,13 @@ of these documents: ...@@ -60,13 +60,13 @@ of these documents:
<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> <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 id="outline-container-orgc8caf11" class="outline-2"> <div id="outline-container-org8d005af" class="outline-2">
<h2 id="orgc8caf11">Installing Rstudio</h2> <h2 id="org8d005af">Installing Rstudio</h2>
<div class="outline-text-2" id="text-orgc8caf11"> <div class="outline-text-2" id="text-org8d005af">
</div> </div>
<div id="outline-container-org8c06a11" class="outline-3"> <div id="outline-container-orgc6785d0" class="outline-3">
<h3 id="org8c06a11">Linux (debian, ubuntu)</h3> <h3 id="orgc6785d0">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8c06a11"> <div class="outline-text-3" id="text-orgc6785d0">
<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
...@@ -88,9 +88,9 @@ for upgrading&#x2026; ...@@ -88,9 +88,9 @@ for upgrading&#x2026;
</p> </p>
</div> </div>
<div id="outline-container-org7e55379" class="outline-4"> <div id="outline-container-org023d7d1" class="outline-4">
<h4 id="org7e55379">Installing R</h4> <h4 id="org023d7d1">Installing R</h4>
<div class="outline-text-4" id="text-org7e55379"> <div class="outline-text-4" id="text-org023d7d1">
<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):
...@@ -123,9 +123,9 @@ to run (as root): ...@@ -123,9 +123,9 @@ to run (as root):
</div> </div>
</div> </div>
<div id="outline-container-orgcce3554" class="outline-4"> <div id="outline-container-org8b528c6" class="outline-4">
<h4 id="orgcce3554">Installing rstudio</h4> <h4 id="org8b528c6">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgcce3554"> <div class="outline-text-4" id="text-org8b528c6">
<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>
...@@ -143,9 +143,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo ...@@ -143,9 +143,9 @@ 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-org83ecc09" class="outline-3"> <div id="outline-container-org88ad478" class="outline-3">
<h3 id="org83ecc09">Mac OSX and Windows</h3> <h3 id="org88ad478">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org83ecc09"> <div class="outline-text-3" id="text-org88ad478">
<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
......
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