Skip to content

M
mooc-rr-ressources
Commit fd17629f authored by Arnaud Legrand's avatar Arnaud Legrand
Browse files
Options

Regenerate html files for the MOOC.

parent 76acc1b6
Show whitespace changes
Inline Side-by-side
Showing with 106 additions and 104 deletions
module2/ressources/emacs_orgmode.html
View file @ fd17629f
......@@ -4,47 +4,47 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0620a23">Installing emacs, org-mode, ess, and auctex.</a>
<li style="margin-bottom:0;"><a href="#org945f839">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3c63e2d">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orgd341044">macOS</a></li>
<li style="margin-bottom:0;"><a href="#org9f08150">Windows</a>
<li style="margin-bottom:0;"><a href="#orge325516">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org95706b9">macOS</a></li>
<li style="margin-bottom:0;"><a href="#orgb87390f">Windows</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org627e96b">Directory naming conventions</a></li>
<li style="margin-bottom:0;"><a href="#org023804e">Making R and Python available to the console</a></li>
<li style="margin-bottom:0;"><a href="#org89abfd4">Installing and configuring Matplotlib (graphic python library)</a></li>
<li style="margin-bottom:0;"><a href="#org69f7d5a">Directory naming conventions</a></li>
<li style="margin-bottom:0;"><a href="#orgfe267c7">Making R and Python available to the console</a></li>
<li style="margin-bottom:0;"><a href="#orgc458b5a">Installing and configuring Matplotlib (graphic python library)</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org88182bc">All platforms: pretty code in HTML export</a></li>
<li style="margin-bottom:0;"><a href="#org47ff448">All platforms: pretty code in HTML export</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org82a9da6">A simple "<i>reproducible research</i>" emacs configuration</a>
<li style="margin-bottom:0;"><a href="#org98a8b7e">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orge1f5003">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#orgd93d06a">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#orgc8799c3">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org3a69cf6">Step 3: Adapt the configuration to your specific needs if required</a></li>
<li style="margin-bottom:0;"><a href="#org6e757d6">Step 4: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org7b5b368">Step 5: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#orgd0815e9">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org9008837">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#orgd3b10f7">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org73ef313">Step 3: Adapt the configuration to your specific needs if required</a></li>
<li style="margin-bottom:0;"><a href="#orgc85363f">Step 4: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#orgadd0750">Step 5: Open and play with your journal:</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgc07c3d5">A stub of a replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org307cdb9">Emacs tips and tricks</a>
<li style="margin-bottom:0;"><a href="#org7b9442b">A stub of a replicable article</a></li>
<li style="margin-bottom:0;"><a href="#orgdde4be6">Emacs tips and tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgd5d3ba1">Cheat-sheets</a>
<li style="margin-bottom:0;"><a href="#org152ca8a">Cheat-sheets</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org9ae5f18">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org6571d83">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#org8a94d36">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org1765514">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgde8cbd9">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#orgcc0edda">Additional useful emacs packages</a>
<li style="margin-bottom:0;"><a href="#org4cc7124">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#orgd5c8443">Additional useful emacs packages</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3b26a95">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#org7fcac5c">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orgb58b5a8">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#orgc20d2e9">Magit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgc6ce93f">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#org9260c82">Other resources</a></li>
</ul>
</li>
</ul>
......@@ -65,13 +65,13 @@ the <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/
The next section provides information on how to install emacs.
</p>
<div id="outline-container-org0620a23" class="outline-2">
<h2 id="org0620a23">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org0620a23">
<div id="outline-container-org945f839" class="outline-2">
<h2 id="org945f839">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org945f839">
</div>
<div id="outline-container-org3c63e2d" class="outline-3">
<h3 id="org3c63e2d">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-org3c63e2d">
<div id="outline-container-orge325516" class="outline-3">
<h3 id="orge325516">Linux (Debian, Ubuntu)</h3>
<div class="outline-text-3" id="text-orge325516">
<p>
We provide here only instructions for Debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -133,9 +133,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-orgd341044" class="outline-3">
<h3 id="orgd341044">macOS</h3>
<div class="outline-text-3" id="text-orgd341044">
<div id="outline-container-org95706b9" class="outline-3">
<h3 id="org95706b9">macOS</h3>
<div class="outline-text-3" id="text-org95706b9">
<p>
<b>Note:</b> macOS comes with a prehistoric command-line-only version of Emacs located at <code>/usr/bin/emacs</code>. It's best to forget about it.
</p>
......@@ -190,9 +190,9 @@ in order to make Emacs accessible directly from <code>/Applications</code>.
</ul>
</div>
</div>
<div id="outline-container-org9f08150" class="outline-3">
<h3 id="org9f08150">Windows</h3>
<div class="outline-text-3" id="text-org9f08150">
<div id="outline-container-orgb87390f" class="outline-3">
<h3 id="orgb87390f">Windows</h3>
<div class="outline-text-3" id="text-orgb87390f">
<p>
Install the <code>.exe</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.gitlab.io/emacs-modified-windows/">https://vigou3.gitlab.io/emacs-modified-windows/</a>. It ships with recent
......@@ -205,9 +205,9 @@ versions:
</ul>
</div>
<div id="outline-container-org627e96b" class="outline-4">
<h4 id="org627e96b">Directory naming conventions</h4>
<div class="outline-text-4" id="text-org627e96b">
<div id="outline-container-org69f7d5a" class="outline-4">
<h4 id="org69f7d5a">Directory naming conventions</h4>
<div class="outline-text-4" id="text-org69f7d5a">
<p>
In the following instructions, we refer to your home
directory through the (UNIX) <code>~/</code> notation. On Windows, your home
......@@ -218,9 +218,9 @@ means we are referring to <code>C:\Users\yourname\org</code> (resp.
</p>
</div>
</div>
<div id="outline-container-org023804e" class="outline-4">
<h4 id="org023804e">Making R and Python available to the console</h4>
<div class="outline-text-4" id="text-org023804e">
<div id="outline-container-orgfe267c7" class="outline-4">
<h4 id="orgfe267c7">Making R and Python available to the console</h4>
<div class="outline-text-4" id="text-orgfe267c7">
<p>
When running a command, Windows will look for the command in the
directories indicated in the <code>PATH</code> environment variable. If none of
......@@ -237,9 +237,9 @@ explained <a href="http://sametmax.com/ajouter-un-chemin-a-la-variable-denvironn
</p>
</div>
</div>
<div id="outline-container-org89abfd4" class="outline-4">
<h4 id="org89abfd4">Installing and configuring Matplotlib (graphic python library)</h4>
<div class="outline-text-4" id="text-org89abfd4">
<div id="outline-container-orgc458b5a" class="outline-4">
<h4 id="orgc458b5a">Installing and configuring Matplotlib (graphic python library)</h4>
<div class="outline-text-4" id="text-orgc458b5a">
<p>
Open an DOS console and type the following command:
</p>
......@@ -275,9 +275,9 @@ starting with <code>backend</code>, which amounts to use the default <code>Agg</
</div>
</div>
<div id="outline-container-org88182bc" class="outline-3">
<h3 id="org88182bc">All platforms: pretty code in HTML export</h3>
<div class="outline-text-3" id="text-org88182bc">
<div id="outline-container-org47ff448" class="outline-3">
<h3 id="org47ff448">All platforms: pretty code in HTML export</h3>
<div class="outline-text-3" id="text-org47ff448">
<p>
To have code pretty printing when exporting to HTML, you should
install the <code>htmlize</code> package, which is done by opening emacs and
......@@ -290,9 +290,9 @@ M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key
</div>
</div>
<div id="outline-container-org82a9da6" class="outline-2">
<h2 id="org82a9da6">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-org82a9da6">
<div id="outline-container-org98a8b7e" class="outline-2">
<h2 id="org98a8b7e">A simple "<i>reproducible research</i>" emacs configuration</h2>
<div class="outline-text-2" id="text-org98a8b7e">
<p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Mise en place
Emacs/Orgmode"</i> in French). Watching it before following the
......@@ -311,14 +311,13 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-orge1f5003" class="outline-3">
<h3 id="orge1f5003">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-orge1f5003">
<div id="outline-container-orgd0815e9" class="outline-3">
<h3 id="orgd0815e9">Step 0: Backup and download our configuration</h3>
<div class="outline-text-3" id="text-orgd0815e9">
<p>
The procedure we propose will wipe your already existing custom Emacs
configuration if you have one. <b>You should thus beforehand make
a backup of <code>~/.emacs</code> and of <code>~/.emacs.d/init.el</code></b> (if these files
exist).
configuration if you have one. <b>You should thus beforehand make a
backup</b> of <code>~/.emacs</code> and of <code>~/.emacs.d/init.el</code> (if these files exist).
</p>
<p>
......@@ -331,12 +330,15 @@ rr_org/init.el
rr_org/journal.org
</pre>
<p>
Alternatively, <a href="rr_org/">the files you are looking for are available here</a>.
</p>
</div>
</div>
<div id="outline-container-orgd93d06a" class="outline-3">
<h3 id="orgd93d06a">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-orgd93d06a">
<div id="outline-container-org9008837" class="outline-3">
<h3 id="org9008837">Step 1: Prepare your journal</h3>
<div class="outline-text-3" id="text-org9008837">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -353,9 +355,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-orgc8799c3" class="outline-3">
<h3 id="orgc8799c3">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-orgc8799c3">
<div id="outline-container-orgd3b10f7" class="outline-3">
<h3 id="orgd3b10f7">Step 2: Set up Emacs configuration</h3>
<div class="outline-text-3" id="text-orgd3b10f7">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -367,9 +369,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org3a69cf6" class="outline-3">
<h3 id="org3a69cf6">Step 3: Adapt the configuration to your specific needs if required</h3>
<div class="outline-text-3" id="text-org3a69cf6">
<div id="outline-container-org73ef313" class="outline-3">
<h3 id="org73ef313">Step 3: Adapt the configuration to your specific needs if required</h3>
<div class="outline-text-3" id="text-org73ef313">
<p>
There are two situations in which it might be necessary to modify
<code>init.el</code>:
......@@ -398,9 +400,9 @@ beginning of the file for instructions.
</p>
</div>
</div>
<div id="outline-container-org6e757d6" class="outline-3">
<h3 id="org6e757d6">Step 4: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-org6e757d6">
<div id="outline-container-orgc85363f" class="outline-3">
<h3 id="orgc85363f">Step 4: Check whether the installation is working or not</h3>
<div class="outline-text-3" id="text-orgc85363f">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -431,9 +433,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p>
</div>
</div>
<div id="outline-container-org7b5b368" class="outline-3">
<h3 id="org7b5b368">Step 5: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-org7b5b368">
<div id="outline-container-orgadd0750" class="outline-3">
<h3 id="orgadd0750">Step 5: Open and play with your journal:</h3>
<div class="outline-text-3" id="text-orgadd0750">
<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
......@@ -444,9 +446,9 @@ FUN forums.
</div>
</div>
</div>
<div id="outline-container-orgc07c3d5" class="outline-2">
<h2 id="orgc07c3d5">A stub of a replicable article</h2>
<div class="outline-text-2" id="text-orgc07c3d5">
<div id="outline-container-org7b9442b" class="outline-2">
<h2 id="org7b9442b">A stub of a replicable article</h2>
<div class="outline-text-2" id="text-org7b9442b">
<p>
This section is illustrated in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Écrire un article
réplicable avec Emacs/Orgmode"</i> in French). Watching it before
......@@ -510,22 +512,22 @@ chunk of code when exporting.
</div>
</div>
<div id="outline-container-org307cdb9" class="outline-2">
<h2 id="org307cdb9">Emacs tips and tricks</h2>
<div class="outline-text-2" id="text-org307cdb9">
<div id="outline-container-orgdde4be6" class="outline-2">
<h2 id="orgdde4be6">Emacs tips and tricks</h2>
<div class="outline-text-2" id="text-orgdde4be6">
</div>
<div id="outline-container-orgd5d3ba1" class="outline-3">
<h3 id="orgd5d3ba1">Cheat-sheets</h3>
<div class="outline-text-3" id="text-orgd5d3ba1">
<div id="outline-container-org152ca8a" class="outline-3">
<h3 id="org152ca8a">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org152ca8a">
<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-org9ae5f18" class="outline-4">
<h4 id="org9ae5f18">Emacs</h4>
<div class="outline-text-4" id="text-org9ae5f18">
<div id="outline-container-org8a94d36" class="outline-4">
<h4 id="org8a94d36">Emacs</h4>
<div class="outline-text-4" id="text-org8a94d36">
<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>
......@@ -534,9 +536,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-org6571d83" class="outline-4">
<h4 id="org6571d83">Org-mode</h4>
<div class="outline-text-4" id="text-org6571d83">
<div id="outline-container-org1765514" class="outline-4">
<h4 id="org1765514">Org-mode</h4>
<div class="outline-text-4" id="text-org1765514">
<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>
......@@ -545,22 +547,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-orgde8cbd9" class="outline-3">
<h3 id="orgde8cbd9">Video tutorials</h3>
<div class="outline-text-3" id="text-orgde8cbd9">
<div id="outline-container-org4cc7124" class="outline-3">
<h3 id="org4cc7124">Video tutorials</h3>
<div class="outline-text-3" id="text-org4cc7124">
<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-orgcc0edda" class="outline-3">
<h3 id="orgcc0edda">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-orgcc0edda">
<div id="outline-container-orgd5c8443" class="outline-3">
<h3 id="orgd5c8443">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-orgd5c8443">
</div>
<div id="outline-container-org3b26a95" class="outline-4">
<h4 id="org3b26a95">Company-mode</h4>
<div class="outline-text-4" id="text-org3b26a95">
<div id="outline-container-orgb58b5a8" class="outline-4">
<h4 id="orgb58b5a8">Company-mode</h4>
<div class="outline-text-4" id="text-orgb58b5a8">
<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
......@@ -569,9 +571,9 @@ official Web page: <a href="http://company-mode.github.io/">http://company-mode.
</p>
</div>
</div>
<div id="outline-container-org7fcac5c" class="outline-4">
<h4 id="org7fcac5c">Magit</h4>
<div class="outline-text-4" id="text-org7fcac5c">
<div id="outline-container-orgc20d2e9" class="outline-4">
<h4 id="orgc20d2e9">Magit</h4>
<div class="outline-text-4" id="text-orgc20d2e9">
<p>
<a href="https://magit.vc/">Magit</a> is an Emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a <a href="https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4">video tutorial</a> (<i>"Utilisation
......@@ -589,9 +591,9 @@ invoke magit by using <code>C-x g</code>.
</div>
</div>
</div>
<div id="outline-container-orgc6ce93f" class="outline-3">
<h3 id="orgc6ce93f">Other resources</h3>
<div class="outline-text-3" id="text-orgc6ce93f">
<div id="outline-container-org9260c82" class="outline-3">
<h3 id="org9260c82">Other resources</h3>
<div class="outline-text-3" id="text-org9260c82">
<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>
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment