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Final (?) reorganization and link to FUN video tutorials

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module2/ressources/emacs_orgmode.html
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......@@ -4,39 +4,39 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8e60217">Installing emacs, org-mode, ess, and auctex.</a>
<li style="margin-bottom:0;"><a href="#org6cfce99">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org90ba83d">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orgc1dd1e3">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org62cb87b">Windows</a></li>
<li style="margin-bottom:0;"><a href="#org8d53875">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org944c375">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org64b96e7">Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org71d5afd">A simple "<i>reproducible research</i>" emacs configuration</a>
<li style="margin-bottom:0;"><a href="#orgf731fcb">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org8c38e5f">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org5d0c52b">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org04abd1a">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org2ac8291">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#orgc0e8300">Step 4: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#org1212448">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#orga58da00">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org5f660e7">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#orgcfcc2ff">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#orged2e102">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgec2f0d0">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#orge37f27c">Emacs Tips and tricks</a>
<li style="margin-bottom:0;"><a href="#org2c8a2b3">A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org6025dd0">Emacs Tips and tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3c808db">Cheat-sheets</a>
<li style="margin-bottom:0;"><a href="#org9df9d92">Cheat-sheets</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgbbb0dee">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org35b96e8">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#org76a8ca9">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#orgc325c7b">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgebb57d1">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org538c45f">Additional useful emacs packages</a>
<li style="margin-bottom:0;"><a href="#org70f6690">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org365abd5">Additional useful emacs packages</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orga430a9e">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#orga2a61a4">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orgd4c07e0">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org49509c0">Magit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org7097ad4">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#orgd1052e7">Other resources</a></li>
</ul>
</li>
</ul>
......@@ -45,25 +45,24 @@
<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
org-mode for this MOOC. <b>I have prepared two video tutorials (here and
here) for each, 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 "emacs and git" video tutorial.
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 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>.
</p>
<p>
The next sections provide information on how to install emacs. Before
proceeding, make sure you have read the "Git and GitLab" instructions
(tutorial and resources from the 4th sequence of the 2nd module).
The next section provides information on how to install emacs.
</p>
<div id="outline-container-org8e60217" class="outline-2">
<h2 id="org8e60217">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org8e60217">
<div id="outline-container-org6cfce99" class="outline-2">
<h2 id="org6cfce99">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org6cfce99">
</div>
<div id="outline-container-org90ba83d" class="outline-3">
<h3 id="org90ba83d">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org90ba83d">
<div id="outline-container-org8d53875" class="outline-3">
<h3 id="org8d53875">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org8d53875">
<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 +124,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-orgc1dd1e3" class="outline-3">
<h3 id="orgc1dd1e3">Mac OS X</h3>
<div class="outline-text-3" id="text-orgc1dd1e3">
<div id="outline-container-org944c375" class="outline-3">
<h3 id="org944c375">Mac OS X</h3>
<div class="outline-text-3" id="text-org944c375">
<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 +159,9 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org62cb87b" class="outline-3">
<h3 id="org62cb87b">Windows</h3>
<div class="outline-text-3" id="text-org62cb87b">
<div id="outline-container-org64b96e7" class="outline-3">
<h3 id="org64b96e7">Windows</h3>
<div class="outline-text-3" id="text-org64b96e7">
<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
......@@ -176,11 +175,11 @@ versions:
</div>
</div>
</div>
<div id="outline-container-org71d5afd" class="outline-2">
<h2 id="org71d5afd">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-org71d5afd">
<div id="outline-container-orgf731fcb" class="outline-2">
<h2 id="orgf731fcb">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-orgf731fcb">
<p>
This section is illustrated in a video tutorial (in French). Watching
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.
</p>
......@@ -196,9 +195,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-org8c38e5f" class="outline-3">
<h3 id="org8c38e5f">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org8c38e5f">
<div id="outline-container-org1212448" class="outline-3">
<h3 id="org1212448">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-org1212448">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -219,9 +218,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-org5d0c52b" class="outline-3">
<h3 id="org5d0c52b">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-org5d0c52b">
<div id="outline-container-orga58da00" class="outline-3">
<h3 id="orga58da00">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-orga58da00">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -238,9 +237,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-org04abd1a" class="outline-3">
<h3 id="org04abd1a">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org04abd1a">
<div id="outline-container-org5f660e7" class="outline-3">
<h3 id="org5f660e7">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-org5f660e7">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -252,9 +251,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org2ac8291" class="outline-3">
<h3 id="org2ac8291">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org2ac8291">
<div id="outline-container-orgcfcc2ff" class="outline-3">
<h3 id="orgcfcc2ff">Step 3: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-orgcfcc2ff">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -285,9 +284,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p>
</div>
</div>
<div id="outline-container-orgc0e8300" class="outline-3">
<h3 id="orgc0e8300">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-orgc0e8300">
<div id="outline-container-orged2e102" class="outline-3">
<h3 id="orged2e102">Step 4: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-orged2e102">
<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
......@@ -298,11 +297,11 @@ forums.
</div>
</div>
</div>
<div id="outline-container-orgec2f0d0" class="outline-2">
<h2 id="orgec2f0d0">A stub of replicable article</h2>
<div class="outline-text-2" id="text-orgec2f0d0">
<div id="outline-container-org2c8a2b3" class="outline-2">
<h2 id="org2c8a2b3">A stub of replicable article</h2>
<div class="outline-text-2" id="text-org2c8a2b3">
<p>
This section is illustrated in a video tutorial (in French). Watching
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.
</p>
......@@ -363,22 +362,22 @@ chunk of code when exporting.
</div>
</div>
<div id="outline-container-orge37f27c" class="outline-2">
<h2 id="orge37f27c">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orge37f27c">
<div id="outline-container-org6025dd0" class="outline-2">
<h2 id="org6025dd0">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org6025dd0">
</div>
<div id="outline-container-org3c808db" class="outline-3">
<h3 id="org3c808db">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org3c808db">
<div id="outline-container-org9df9d92" class="outline-3">
<h3 id="org9df9d92">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org9df9d92">
<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-orgbbb0dee" class="outline-4">
<h4 id="orgbbb0dee">Emacs</h4>
<div class="outline-text-4" id="text-orgbbb0dee">
<div id="outline-container-org76a8ca9" class="outline-4">
<h4 id="org76a8ca9">Emacs</h4>
<div class="outline-text-4" id="text-org76a8ca9">
<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>
......@@ -387,9 +386,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-org35b96e8" class="outline-4">
<h4 id="org35b96e8">Org-mode</h4>
<div class="outline-text-4" id="text-org35b96e8">
<div id="outline-container-orgc325c7b" class="outline-4">
<h4 id="orgc325c7b">Org-mode</h4>
<div class="outline-text-4" id="text-orgc325c7b">
<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>
......@@ -398,22 +397,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-orgebb57d1" class="outline-3">
<h3 id="orgebb57d1">Video tutorials</h3>
<div class="outline-text-3" id="text-orgebb57d1">
<div id="outline-container-org70f6690" class="outline-3">
<h3 id="org70f6690">Video tutorials</h3>
<div class="outline-text-3" id="text-org70f6690">
<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-org538c45f" class="outline-3">
<h3 id="org538c45f">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org538c45f">
<div id="outline-container-org365abd5" class="outline-3">
<h3 id="org365abd5">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org365abd5">
</div>
<div id="outline-container-orga430a9e" class="outline-4">
<h4 id="orga430a9e">Company-mode</h4>
<div class="outline-text-4" id="text-orga430a9e">
<div id="outline-container-orgd4c07e0" class="outline-4">
<h4 id="orgd4c07e0">Company-mode</h4>
<div class="outline-text-4" id="text-orgd4c07e0">
<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
......@@ -422,29 +421,28 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode.
</p>
</div>
</div>
<div id="outline-container-orga2a61a4" class="outline-4">
<h4 id="orga2a61a4">Magit</h4>
<div class="outline-text-4" id="text-orga2a61a4">
<div id="outline-container-org49509c0" class="outline-4">
<h4 id="org49509c0">Magit</h4>
<div class="outline-text-4" id="text-org49509c0">
<p>
Magit]] is an emacs interface for Git. It is briefly illustrated in a
video tutorial.
<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).
</p>
<p>
It is very powerful and we use
it on a daily basis but you should definitely understand what git does
behind the scene beforehand. If you feel this would be useful for you,
you should follow the instructions from here:
<a href="https://www.emacswiki.org/emacs/Magit">https://www.emacswiki.org/emacs/Magit</a>. If you installed the previous
"<i>reproducible research</i>" emacs configuration, you can easily invoke
magit by using <code>C-x g</code>.
It is very powerful and we use it on a daily basis but you should
definitely understand what git does behind the scene beforehand. If
you feel this would be useful for you, you should follow <a href="https://magit.vc/screenshots/">this visual
walk-through</a> or <a href="https://www.emacswiki.org/emacs/Magit">this really short "crash course"</a>. If you installed the
previous "<i>reproducible research</i>" emacs configuration, you can easily
invoke magit by using <code>C-x g</code>.
</p>
</div>
</div>
</div>
<div id="outline-container-org7097ad4" class="outline-3">
<h3 id="org7097ad4">Other resources</h3>
<div class="outline-text-3" id="text-org7097ad4">
<div id="outline-container-orgd1052e7" class="outline-3">
<h3 id="orgd1052e7">Other resources</h3>
<div class="outline-text-3" id="text-orgd1052e7">
<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/emacs_orgmode.org
View file @ bfbf4f51
......@@ -8,14 +8,13 @@
*Disclaimer:* The two sections _A simple "/reproducible research/" emacs
configuration_ and _A stub of replicable article_ explain how to set up
org-mode for this MOOC. *I have prepared two video tutorials (here and
here) for each, which you really should follow carefully*. *Otherwise,
you may have trouble doing the exercises later on*. Likewise, I
strongly encourage you to watch the "emacs and git" video tutorial.
org-mode for this MOOC. *These sections are illustrated in two out of
the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3][three video tutorials of this sequence]], and* *which you really
should follow carefully*. *Otherwise, you may have trouble doing the
exercises later on*. Likewise, I strongly encourage you to watch the
[[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]].
The next sections provide information on how to install emacs. Before
proceeding, make sure you have read the "Git and GitLab" instructions
(tutorial and resources from the 4th sequence of the 2nd module).
The next section provides information on how to install emacs.
* Installing emacs, org-mode, ess, and auctex.
** Linux (Debian, Ubuntu)
......@@ -83,7 +82,7 @@ versions:
- Org-mode 9.1.13
- ESS 17.11
* A simple "/reproducible research/" emacs configuration
This section is illustrated in a video tutorial (in French). Watching
This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3][video tutorial]] (in French). Watching
it before following the instructions given in this section may help.
Emacs comes with very basic default configuration and it appears like
......@@ -159,7 +158,7 @@ backed up in a revision control system like git. We leave it up to set
this up but if you have any trouble, feel free to ask on the FUN
forums.
* A stub of replicable article
This section is illustrated in a video tutorial (in French). Watching
This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3][video tutorial]] (in French). Watching
it before following the instructions given in this section may help.
Remember, you need a working LaTeX and R environment. If you can't
......@@ -229,16 +228,15 @@ have smart completion in emacs for the most common languages. If you
feel this is needed, you should follow the instructions from the
official Web page: http://company-mode.github.io/
*** Magit
Magit]] is an emacs interface for Git. It is briefly illustrated in a
video tutorial.
It is very powerful and we use
it on a daily basis but you should definitely understand what git does
behind the scene beforehand. If you feel this would be useful for you,
you should follow the instructions from here:
https://www.emacswiki.org/emacs/Magit. If you installed the previous
"/reproducible research/" emacs configuration, you can easily invoke
magit by using ~C-x g~.
[[https://magit.vc/][Magit]] is an emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/aefd774dcd2342c6aa769c87e2d0993a/3][video tutorial]] (in French).
It is very powerful and we use it on a daily basis but you should
definitely understand what git does behind the scene beforehand. If
you feel this would be useful for you, you should follow [[https://magit.vc/screenshots/][this visual
walk-through]] or [[https://www.emacswiki.org/emacs/Magit][this really short "crash course"]]. If you installed the
previous "/reproducible research/" emacs configuration, you can easily
invoke magit by using ~C-x g~.
** Other resources
- [[https://orgmode.org/orgguide.pdf][The compact Org-mode Guide]]
- [[https://github.com/dfeich/org-babel-examples][Many examples illustrating the use of different languages in org-mode]]
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