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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="#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;">
<li style="margin-bottom:0;"><a href="#org4a4ee20">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="#org048091d">Windows</a></li>
<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>
</ul>
</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;">
<li style="margin-bottom:0;"><a href="#org59fef98">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="#org3142fb4">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="#org26b639c">Step 4: Open and play with your journal:</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="#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>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgf2f9128">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="#org578a4a4">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#orgce9f641">Emacs Tips and tricks</a>
<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;">
<li style="margin-bottom:0;"><a href="#orgef979b2">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#orge1bce05">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#org0a30ece">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org0389dfc">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org151e7c0">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org29b5af4">Additional useful emacs packages</a>
<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>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgb61c58f">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org74978d6">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orge154c83">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org77f5398">Magit</a></li>
</ul>
</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>
</li>
</ul>
......@@ -45,24 +45,25 @@
<p>
<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
emacs/org-mode for 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/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3">three video tutorials of this sequence</a>, and</b> <b>which you
emacs/org-mode for this MOOC. These are very important sections in the
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
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>
The next section provides information on how to install emacs.
</p>
<div id="outline-container-org0fbdfa9" class="outline-2">
<h2 id="org0fbdfa9">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org0fbdfa9">
<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>
<div id="outline-container-org4a4ee20" class="outline-3">
<h3 id="org4a4ee20">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org4a4ee20">
<div id="outline-container-orgd0985c0" class="outline-3">
<h3 id="orgd0985c0">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-orgd0985c0">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -124,9 +125,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org101dae2" class="outline-3">
<h3 id="org101dae2">Mac OS X</h3>
<div class="outline-text-3" id="text-org101dae2">
<div id="outline-container-org802a903" class="outline-3">
<h3 id="org802a903">Mac OS X</h3>
<div class="outline-text-3" id="text-org802a903">
<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>:
......@@ -159,9 +160,9 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org048091d" class="outline-3">
<h3 id="org048091d">Windows</h3>
<div class="outline-text-3" id="text-org048091d">
<div id="outline-container-org947a24e" class="outline-3">
<h3 id="org947a24e">Windows</h3>
<div class="outline-text-3" id="text-org947a24e">
<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
......@@ -175,12 +176,13 @@ versions:
</div>
</div>
</div>
<div id="outline-container-orgccaf2ff" class="outline-2">
<h2 id="orgccaf2ff">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-orgccaf2ff">
<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">
<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
it before following the instructions given in this section may help.
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
instructions given in this section may help.
</p>
<p>
......@@ -195,9 +197,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-org59fef98" class="outline-3">
<h3 id="org59fef98">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org59fef98">
<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">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -218,9 +220,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-org19679a8" class="outline-3">
<h3 id="org19679a8">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-org19679a8">
<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">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -237,9 +239,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-org3142fb4" class="outline-3">
<h3 id="org3142fb4">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org3142fb4">
<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">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -251,9 +253,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org9657e1f" class="outline-3">
<h3 id="org9657e1f">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org9657e1f">
<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">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -284,9 +286,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p>
</div>
</div>
<div id="outline-container-org26b639c" class="outline-3">
<h3 id="org26b639c">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-org26b639c">
<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">
<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
......@@ -297,12 +299,13 @@ forums.
</div>
</div>
</div>
<div id="outline-container-orgf2f9128" class="outline-2">
<h2 id="orgf2f9128">A stub of replicable article</h2>
<div class="outline-text-2" id="text-orgf2f9128">
<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">
<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
it before following the instructions given in this section may help.
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
following the instructions given in this section may help.
</p>
<p>
......@@ -362,22 +365,22 @@ chunk of code when exporting.
</div>
</div>
<div id="outline-container-orge35ff2f" class="outline-2">
<h2 id="orge35ff2f">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orge35ff2f">
<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>
<div id="outline-container-orgd3ea437" class="outline-3">
<h3 id="orgd3ea437">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgd3ea437">
<div id="outline-container-orge3bb1b2" class="outline-3">
<h3 id="orge3bb1b2">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orge3bb1b2">
<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-orgef979b2" class="outline-4">
<h4 id="orgef979b2">Emacs</h4>
<div class="outline-text-4" id="text-orgef979b2">
<div id="outline-container-org0a30ece" class="outline-4">
<h4 id="org0a30ece">Emacs</h4>
<div class="outline-text-4" id="text-org0a30ece">
<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>
......@@ -386,9 +389,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-orge1bce05" class="outline-4">
<h4 id="orge1bce05">Org-mode</h4>
<div class="outline-text-4" id="text-orge1bce05">
<div id="outline-container-org0389dfc" class="outline-4">
<h4 id="org0389dfc">Org-mode</h4>
<div class="outline-text-4" id="text-org0389dfc">
<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>
......@@ -397,22 +400,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-org151e7c0" class="outline-3">
<h3 id="org151e7c0">Video tutorials</h3>
<div class="outline-text-3" id="text-org151e7c0">
<div id="outline-container-orgc9149b2" class="outline-3">
<h3 id="orgc9149b2">Video tutorials</h3>
<div class="outline-text-3" id="text-orgc9149b2">
<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-org29b5af4" class="outline-3">
<h3 id="org29b5af4">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org29b5af4">
<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>
<div id="outline-container-orgb61c58f" class="outline-4">
<h4 id="orgb61c58f">Company-mode</h4>
<div class="outline-text-4" id="text-orgb61c58f">
<div id="outline-container-orge154c83" class="outline-4">
<h4 id="orge154c83">Company-mode</h4>
<div class="outline-text-4" id="text-orge154c83">
<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
......@@ -421,12 +424,13 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode.
</p>
</div>
</div>
<div id="outline-container-org74978d6" class="outline-4">
<h4 id="org74978d6">Magit</h4>
<div class="outline-text-4" id="text-org74978d6">
<div id="outline-container-org77f5398" class="outline-4">
<h4 id="org77f5398">Magit</h4>
<div class="outline-text-4" id="text-org77f5398">
<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/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>
......@@ -440,9 +444,9 @@ invoke magit by using <code>C-x g</code>.
</div>
</div>
</div>
<div id="outline-container-org425cf50" class="outline-3">
<h3 id="org425cf50">Other resources</h3>
<div class="outline-text-3" id="text-org425cf50">
<div id="outline-container-orgb4f2246" class="outline-3">
<h3 id="orgb4f2246">Other resources</h3>
<div class="outline-text-3" id="text-orgb4f2246">
<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>
......
module2/ressources/gitlab.html
View file @ 6399576d
......@@ -4,24 +4,24 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<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;">
<li style="margin-bottom:0;"><a href="#orgf47f6c9">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="#org00b8ed8">Linux (debian, ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org247f959">Mac OSX and Windows</a></li>
</ul>
</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;">
<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;">
<li style="margin-bottom:0;"><a href="#org4c05db5">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="#org7f96ff9">Configuring your GitLab password</a></li>
<li style="margin-bottom:0;"><a href="#org18555d7">Making sure git remembers your password</a></li>
</ul>
</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;">
<li style="margin-bottom:0;"><a href="#org880f8ce">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="#orge10264b">Installing SSH</a></li>
<li style="margin-bottom:0;"><a href="#orgac5801f">Setting up SSH on GitLab</a></li>
</ul>
</li>
</ul>
......@@ -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 with the remote GitLab one. To propagate your
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>
......@@ -56,13 +56,13 @@ installed on your machine and how to handle authentication. Please
read these instructions carefully.
</p>
<div id="outline-container-orge3f4bc8" class="outline-2">
<h2 id="orge3f4bc8">Installing Git</h2>
<div class="outline-text-2" id="text-orge3f4bc8">
<div id="outline-container-org3b51ceb" class="outline-2">
<h2 id="org3b51ceb">Installing Git</h2>
<div class="outline-text-2" id="text-org3b51ceb">
</div>
<div id="outline-container-orgf47f6c9" class="outline-3">
<h3 id="orgf47f6c9">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-orgf47f6c9">
<div id="outline-container-org00b8ed8" class="outline-3">
<h3 id="org00b8ed8">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org00b8ed8">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -78,9 +78,9 @@ Run (as root):
</div>
</div>
</div>
<div id="outline-container-org6c4b10f" class="outline-3">
<h3 id="org6c4b10f">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org6c4b10f">
<div id="outline-container-org247f959" class="outline-3">
<h3 id="org247f959">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org247f959">
<ul class="org-ul">
<li style="margin-bottom:0;">Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li style="margin-bottom:0;">Optional Git clients (should not be needed if you work within
......@@ -100,9 +100,9 @@ Rstudio):
</div>
</div>
</div>
<div id="outline-container-orgca31098" class="outline-2">
<h2 id="orgca31098">Authenticating on GitLab</h2>
<div class="outline-text-2" id="text-orgca31098">
<div id="outline-container-org10e42dd" class="outline-2">
<h2 id="org10e42dd">Authenticating on GitLab</h2>
<div class="outline-text-2" id="text-org10e42dd">
<p>
There are two ways of authenticating and synchronizing your local
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
anything).
</p>
</div>
<div id="outline-container-org69e4843" class="outline-3">
<h3 id="org69e4843">Option 1: HTTPS</h3>
<div class="outline-text-3" id="text-org69e4843">
<div id="outline-container-orgda58dab" class="outline-3">
<h3 id="orgda58dab">Option 1: HTTPS</h3>
<div class="outline-text-3" id="text-orgda58dab">
</div>
<div id="outline-container-org4c05db5" class="outline-4">
<h4 id="org4c05db5">Configuring your GitLab password</h4>
<div class="outline-text-4" id="text-org4c05db5">
<div id="outline-container-org7f96ff9" class="outline-4">
<h4 id="org7f96ff9">Configuring your GitLab password</h4>
<div class="outline-text-4" id="text-org7f96ff9">
<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.
</p>
</div>
</div>
<div id="outline-container-orgcfbd789" class="outline-4">
<h4 id="orgcfbd789">Making sure git remembers your password</h4>
<div class="outline-text-4" id="text-orgcfbd789">
<div id="outline-container-org18555d7" class="outline-4">
<h4 id="org18555d7">Making sure git remembers your password</h4>
<div class="outline-text-4" id="text-org18555d7">
<p>
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
......@@ -168,9 +168,9 @@ cached in memory and they will not be asked again before an hour.
</div>
</div>
</div>
<div id="outline-container-orgaa173db" class="outline-3">
<h3 id="orgaa173db">Option 2: SSH</h3>
<div class="outline-text-3" id="text-orgaa173db">
<div id="outline-container-org367edbb" class="outline-3">
<h3 id="org367edbb">Option 2: SSH</h3>
<div class="outline-text-3" id="text-org367edbb">
<p>
My preferred (although more technical) solution is to install SSH, to
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
this.
</p>
</div>
<div id="outline-container-org880f8ce" class="outline-4">
<h4 id="org880f8ce">Installing SSH</h4>
<div class="outline-text-4" id="text-org880f8ce">
<div id="outline-container-orge10264b" class="outline-4">
<h4 id="orge10264b">Installing SSH</h4>
<div class="outline-text-4" id="text-orge10264b">
</div>
<ul class="org-ul">
<li style="margin-bottom:0;"><a id="orga22af4e"></a>Linux (debian, ubuntu)<br />
<div class="outline-text-5" id="text-orga22af4e">
<li style="margin-bottom:0;"><a id="orgabfaf26"></a>Linux (debian, ubuntu)<br />
<div class="outline-text-5" id="text-orgabfaf26">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -200,15 +200,15 @@ Run (as root):
</div>
</div>
</li>
<li style="margin-bottom:0;"><a id="orgdea2c28"></a>Mac OSX<br />
<div class="outline-text-5" id="text-orgdea2c28">
<li style="margin-bottom:0;"><a id="org89976c7"></a>Mac OSX<br />
<div class="outline-text-5" id="text-org89976c7">
<p>
You do not have anything to do as it is installed by default.
</p>
</div>
</li>
<li style="margin-bottom:0;"><a id="org991d2af"></a>Windows<br />
<div class="outline-text-5" id="text-org991d2af">
<li style="margin-bottom:0;"><a id="orgb8fc08c"></a>Windows<br />
<div class="outline-text-5" id="text-orgb8fc08c">
<p>
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>.
......@@ -217,9 +217,9 @@ the section on <a href="https://www.ssh.com/ssh/putty/windows/puttygen">generati
</li>
</ul>
</div>
<div id="outline-container-org4481e63" class="outline-4">
<h4 id="org4481e63">Setting up SSH on GitLab</h4>
<div class="outline-text-4" id="text-org4481e63">
<div id="outline-container-orgac5801f" class="outline-4">
<h4 id="orgac5801f">Setting up SSH on GitLab</h4>
<div class="outline-text-4" id="text-orgac5801f">
<p>
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
......
module2/ressources/rstudio.html
View file @ 6399576d
......@@ -4,15 +4,15 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<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;">
<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;">
<li style="margin-bottom:0;"><a href="#org7e55379">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#orgcce3554">Installing rstudio</a></li>
<li style="margin-bottom:0;"><a href="#org023d7d1">Installing R</a></li>
<li style="margin-bottom:0;"><a href="#org8b528c6">Installing rstudio</a></li>
</ul>
</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>
</li>
</ul>
......@@ -24,8 +24,8 @@ This document provides information on how to install Rstudio.
<p>
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
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
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/jump_to_id/7508aece244548349424dfd61ee3ba85">"git/GitLab
configuration" tutorial</a></b> (in French).
</p>
......@@ -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>
</ul>
<div id="outline-container-orgc8caf11" class="outline-2">
<h2 id="orgc8caf11">Installing Rstudio</h2>
<div class="outline-text-2" id="text-orgc8caf11">
<div id="outline-container-org8d005af" class="outline-2">
<h2 id="org8d005af">Installing Rstudio</h2>
<div class="outline-text-2" id="text-org8d005af">
</div>
<div id="outline-container-org8c06a11" class="outline-3">
<h3 id="org8c06a11">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org8c06a11">
<div id="outline-container-orgc6785d0" class="outline-3">
<h3 id="orgc6785d0">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-orgc6785d0">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -88,9 +88,9 @@ for upgrading&#x2026;
</p>
</div>
<div id="outline-container-org7e55379" class="outline-4">
<h4 id="org7e55379">Installing R</h4>
<div class="outline-text-4" id="text-org7e55379">
<div id="outline-container-org023d7d1" class="outline-4">
<h4 id="org023d7d1">Installing R</h4>
<div class="outline-text-4" id="text-org023d7d1">
<p>
Beforehand, you need to install the R language and convenient packages
by running (as root):
......@@ -123,9 +123,9 @@ to run (as root):
</div>
</div>
<div id="outline-container-orgcce3554" class="outline-4">
<h4 id="orgcce3554">Installing rstudio</h4>
<div class="outline-text-4" id="text-orgcce3554">
<div id="outline-container-org8b528c6" class="outline-4">
<h4 id="org8b528c6">Installing rstudio</h4>
<div class="outline-text-4" id="text-org8b528c6">
<p>
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the <a href="https://www.rstudio.com/products/rstudio/download/#download">Rstudio webpage</a>
......@@ -143,9 +143,9 @@ sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; fo
</div>
</div>
</div>
<div id="outline-container-org83ecc09" class="outline-3">
<h3 id="org83ecc09">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org83ecc09">
<div id="outline-container-org88ad478" class="outline-3">
<h3 id="org88ad478">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org88ad478">
<blockquote>
<p>
Some instructions on installing R and knitr must be missing. This
......
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