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module2/ressources/emacs_orgmode.html
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......@@ -4,43 +4,43 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orge2682fe">Installing emacs, org-mode, ess, and auctex.</a>
<li style="margin-bottom:0;"><a href="#org409eed0">Installing emacs, org-mode, ess, and auctex.</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#orgfb87b58">OS-specific installation procedure</a>
<li style="margin-bottom:0;"><a href="#orgc77d6b9">OS-specific installation procedure</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org5a37149">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#org8b6fe53">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org54a19e2">Windows</a></li>
<li style="margin-bottom:0;"><a href="#orgc1fd040">Linux (Debian, Ubuntu)</a></li>
<li style="margin-bottom:0;"><a href="#orgb09ebaf">Mac OS X</a></li>
<li style="margin-bottom:0;"><a href="#org988b23d">Windows</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org6ff953e"><span class="todo TODO">TODO</span> A simple "<i>reproducible research</i>" emacs configuration</a>
<li style="margin-bottom:0;"><a href="#orgd2fefe4"><span class="todo TODO">TODO</span> A simple "<i>reproducible research</i>" emacs configuration</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3defa4c">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#orgbfcfdb3">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#org649b08d">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org852428c">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#orgc4da1bc">Step 4: Open and play with your journal:</a></li>
<li style="margin-bottom:0;"><a href="#orgd0d6712">Step 0: Backup and download our configuration</a></li>
<li style="margin-bottom:0;"><a href="#org96068ca">Step 1: Prepare your journal</a></li>
<li style="margin-bottom:0;"><a href="#orgdb3ee66">Step 2: Set up Emacs configuration</a></li>
<li style="margin-bottom:0;"><a href="#org5873b8e">Step 3: Check whether the installation is working or not</a></li>
<li style="margin-bottom:0;"><a href="#org3914954">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orgfbade65"><span class="todo TODO">TODO</span> A stub of replicable article</a></li>
<li style="margin-bottom:0;"><a href="#org25d2b3b"><span class="todo TODO">TODO</span> A stub of replicable article</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org75bf9e8">Emacs Tips and tricks</a>
<li style="margin-bottom:0;"><a href="#org18244de">Emacs Tips and tricks</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3d37ba5">Cheat-sheets</a>
<li style="margin-bottom:0;"><a href="#org42e3c12">Cheat-sheets</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org6f00716">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org3e5fd61">Org-mode</a></li>
<li style="margin-bottom:0;"><a href="#org4c20ffc">Emacs</a></li>
<li style="margin-bottom:0;"><a href="#org1f247fa">Org-mode</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org055d2c1">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org3801d38">Additional useful emacs packages</a>
<li style="margin-bottom:0;"><a href="#orga987581">Video tutorials</a></li>
<li style="margin-bottom:0;"><a href="#org88591d9">Additional useful emacs packages</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org63a1f09">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#orgda86607">Magit</a></li>
<li style="margin-bottom:0;"><a href="#orgdbba0c2">Company-mode</a></li>
<li style="margin-bottom:0;"><a href="#orgdfa2dbe">Magit</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org60f26c4">Other resources</a></li>
<li style="margin-bottom:0;"><a href="#org1917d59">Other resources</a></li>
</ul>
</li>
</ul>
......@@ -58,17 +58,17 @@ The next sections provide information on how to install emacs. Before
proceeding, make sure you have read the "Git and GitLab" instructions.
</p>
<div id="outline-container-orge2682fe" class="outline-2">
<h2 id="orge2682fe">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orge2682fe">
<div id="outline-container-org409eed0" class="outline-2">
<h2 id="org409eed0">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-org409eed0">
</div>
<div id="outline-container-orgfb87b58" class="outline-3">
<h3 id="orgfb87b58">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-orgfb87b58">
<div id="outline-container-orgc77d6b9" class="outline-3">
<h3 id="orgc77d6b9">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-orgc77d6b9">
</div>
<div id="outline-container-org5a37149" class="outline-4">
<h4 id="org5a37149">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-org5a37149">
<div id="outline-container-orgc1fd040" class="outline-4">
<h4 id="orgc1fd040">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-orgc1fd040">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
......@@ -130,9 +130,9 @@ which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org8b6fe53" class="outline-4">
<h4 id="org8b6fe53">Mac OS X</h4>
<div class="outline-text-4" id="text-org8b6fe53">
<div id="outline-container-orgb09ebaf" class="outline-4">
<h4 id="orgb09ebaf">Mac OS X</h4>
<div class="outline-text-4" id="text-orgb09ebaf">
<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>:
......@@ -165,9 +165,9 @@ brew install wget
</ul>
</div>
</div>
<div id="outline-container-org54a19e2" class="outline-4">
<h4 id="org54a19e2">Windows</h4>
<div class="outline-text-4" id="text-org54a19e2">
<div id="outline-container-org988b23d" class="outline-4">
<h4 id="org988b23d">Windows</h4>
<div class="outline-text-4" id="text-org988b23d">
<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
......@@ -181,9 +181,9 @@ versions:
</div>
</div>
</div>
<div id="outline-container-org6ff953e" class="outline-3">
<h3 id="org6ff953e"><span class="todo TODO">TODO</span> A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-org6ff953e">
<div id="outline-container-orgd2fefe4" class="outline-3">
<h3 id="orgd2fefe4"><span class="todo TODO">TODO</span> A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-orgd2fefe4">
<blockquote>
<p>
There will be a mini video illustrating these steps at some point
......@@ -202,9 +202,9 @@ adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-org3defa4c" class="outline-4">
<h4 id="org3defa4c">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-org3defa4c">
<div id="outline-container-orgd0d6712" class="outline-4">
<h4 id="orgd0d6712">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-orgd0d6712">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. <b>You should thus beforehand make
......@@ -225,9 +225,9 @@ rr_org/journal.org
</div>
</div>
<div id="outline-container-orgbfcfdb3" class="outline-4">
<h4 id="orgbfcfdb3">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-orgbfcfdb3">
<div id="outline-container-org96068ca" class="outline-4">
<h4 id="org96068ca">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-org96068ca">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
......@@ -244,9 +244,9 @@ should give a try.
</p>
</div>
</div>
<div id="outline-container-org649b08d" class="outline-4">
<h4 id="org649b08d">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-org649b08d">
<div id="outline-container-orgdb3ee66" class="outline-4">
<h4 id="orgdb3ee66">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-orgdb3ee66">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
......@@ -258,9 +258,9 @@ configuration with the following command: <code>emacs -q -l rr_org/init.el</code
</p>
</div>
</div>
<div id="outline-container-org852428c" class="outline-4">
<h4 id="org852428c">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org852428c">
<div id="outline-container-org5873b8e" class="outline-4">
<h4 id="org5873b8e">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-org5873b8e">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
......@@ -291,9 +291,9 @@ is demonstrated in the <a href="https://app-learninglab.inria.fr/gitlab/learning
</p>
</div>
</div>
<div id="outline-container-orgc4da1bc" class="outline-4">
<h4 id="orgc4da1bc">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-orgc4da1bc">
<div id="outline-container-org3914954" class="outline-4">
<h4 id="org3914954">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org3914954">
<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
......@@ -304,9 +304,9 @@ forums.
</div>
</div>
</div>
<div id="outline-container-orgfbade65" class="outline-3">
<h3 id="orgfbade65"><span class="todo TODO">TODO</span> A stub of replicable article</h3>
<div class="outline-text-3" id="text-orgfbade65">
<div id="outline-container-org25d2b3b" class="outline-3">
<h3 id="org25d2b3b"><span class="todo TODO">TODO</span> A stub of replicable article</h3>
<div class="outline-text-3" id="text-org25d2b3b">
<blockquote>
<p>
There will be a mini video illustrating these steps at some point
......@@ -323,11 +323,7 @@ source (<a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-re
</p>
<p>
Download the following <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz">archive</a> and untar it.
</p>
<p>
and simply <code>make</code> to generate the
Download the following <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz">archive</a>, untar it and simply <code>make</code> to generate the
article. You should then be able to open the <a href="https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf">resulting article</a>. This
is summarized in the following command:
</p>
......@@ -338,9 +334,13 @@ tar zxf replicable.tgz; <span style="font-weight: bold;">cd</span> replicable; m
</div>
<p>
If the <code>make</code> command fails (especially on Mac), it may be because emacs
or something else is not correctly installed. In that case, open the
article directly with the following command:
<b>Possible issues</b>:
</p>
<ul class="org-ul">
<li style="margin-bottom:0;"><p>
If the <code>make</code> command fails (especially on Mac), it may be because
emacs or something else is not correctly installed. In that case,
open the article directly with the following command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">emacs -q --eval <span style="font-style: italic;">"(setq enable-local-eval t)"</span> --eval <span style="font-style: italic;">"(setq enable-local-variables t)"</span> article.org
......@@ -348,14 +348,12 @@ article directly with the following command:
</div>
<p>
and export it to pdf with the following shortcut: <code>C-c C-e l o</code>
</p>
<p>
If it still doesn't work and emacs complains about not finding ESS, it
may be because you installed ESS in your home instead of
</p></li>
<li style="margin-bottom:0;">If it still doesn't work and emacs complains about not finding ESS,
it may be because you installed ESS in your home instead of
system-wide. In that case, try to remove the <code>-q</code> in the previous
command line to load your personal emacs configuration.
</p>
command line to load your personal emacs configuration.</li>
</ul>
<p>
Finally, when you'll be tired of always reexecuting all the source
......@@ -373,22 +371,22 @@ chunk of code when exporting.
</div>
</div>
<div id="outline-container-org75bf9e8" class="outline-2">
<h2 id="org75bf9e8">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org75bf9e8">
<div id="outline-container-org18244de" class="outline-2">
<h2 id="org18244de">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-org18244de">
</div>
<div id="outline-container-org3d37ba5" class="outline-3">
<h3 id="org3d37ba5">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org3d37ba5">
<div id="outline-container-org42e3c12" class="outline-3">
<h3 id="org42e3c12">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org42e3c12">
<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-org6f00716" class="outline-4">
<h4 id="org6f00716">Emacs</h4>
<div class="outline-text-4" id="text-org6f00716">
<div id="outline-container-org4c20ffc" class="outline-4">
<h4 id="org4c20ffc">Emacs</h4>
<div class="outline-text-4" id="text-org4c20ffc">
<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>
......@@ -397,9 +395,9 @@ cheat-sheats. Here is a selection in case it helps:
</ul>
</div>
</div>
<div id="outline-container-org3e5fd61" class="outline-4">
<h4 id="org3e5fd61">Org-mode</h4>
<div class="outline-text-4" id="text-org3e5fd61">
<div id="outline-container-org1f247fa" class="outline-4">
<h4 id="org1f247fa">Org-mode</h4>
<div class="outline-text-4" id="text-org1f247fa">
<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>
......@@ -408,22 +406,22 @@ cheat-sheats. Here is a selection in case it helps:
</div>
</div>
</div>
<div id="outline-container-org055d2c1" class="outline-3">
<h3 id="org055d2c1">Video tutorials</h3>
<div class="outline-text-3" id="text-org055d2c1">
<div id="outline-container-orga987581" class="outline-3">
<h3 id="orga987581">Video tutorials</h3>
<div class="outline-text-3" id="text-orga987581">
<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-org3801d38" class="outline-3">
<h3 id="org3801d38">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org3801d38">
<div id="outline-container-org88591d9" class="outline-3">
<h3 id="org88591d9">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org88591d9">
</div>
<div id="outline-container-org63a1f09" class="outline-4">
<h4 id="org63a1f09">Company-mode</h4>
<div class="outline-text-4" id="text-org63a1f09">
<div id="outline-container-orgdbba0c2" class="outline-4">
<h4 id="orgdbba0c2">Company-mode</h4>
<div class="outline-text-4" id="text-orgdbba0c2">
<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
......@@ -432,22 +430,24 @@ official webpage: <a href="http://company-mode.github.io/">http://company-mode.g
</p>
</div>
</div>
<div id="outline-container-orgda86607" class="outline-4">
<h4 id="orgda86607">Magit</h4>
<div class="outline-text-4" id="text-orgda86607">
<div id="outline-container-orgdfa2dbe" class="outline-4">
<h4 id="orgdfa2dbe">Magit</h4>
<div class="outline-text-4" id="text-orgdfa2dbe">
<p>
<a href="https://magit.vc/">Magit</a> is an emacs interface for Git. It is very powerfull 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>
<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>.
</p>
</div>
</div>
</div>
<div id="outline-container-org60f26c4" class="outline-3">
<h3 id="org60f26c4">Other resources</h3>
<div class="outline-text-3" id="text-org60f26c4">
<div id="outline-container-org1917d59" class="outline-3">
<h3 id="org1917d59">Other resources</h3>
<div class="outline-text-3" id="text-org1917d59">
<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 @ cea02efd
......@@ -174,9 +174,8 @@ make -C replicable_article/ all replicable_article.tgz
#+end_src
#+RESULTS:
Download the following [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz][archive]] and untar it.
and simply =make= to generate the
Download the following [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article/replicable_article.tgz][archive]], untar it and simply =make= to generate the
article. You should then be able to open the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf][resulting article]]. This
is summarized in the following command:
#+begin_src sh :results output :exports both
......@@ -184,18 +183,18 @@ wget --no-check-certificate -O replicable.tgz https://github.com/alegrand/RR_web
tar zxf replicable.tgz; cd replicable; make ; evince article.pdf
#+end_src
If the =make= command fails (especially on Mac), it may be because emacs
or something else is not correctly installed. In that case, open the
article directly with the following command:
#+begin_src sh :results output :exports both
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org
#+end_src
and export it to pdf with the following shortcut: =C-c C-e l o=
If it still doesn't work and emacs complains about not finding ESS, it
may be because you installed ESS in your home instead of
system-wide. In that case, try to remove the =-q= in the previous
command line to load your personal emacs configuration.
*Possible issues*:
- If the =make= command fails (especially on Mac), it may be because
emacs or something else is not correctly installed. In that case,
open the article directly with the following command:
#+begin_src sh :results output :exports both
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org
#+end_src
and export it to pdf with the following shortcut: =C-c C-e l o=
- If it still doesn't work and emacs complains about not finding ESS,
it may be because you installed ESS in your home instead of
system-wide. In that case, try to remove the =-q= in the previous
command line to load your personal emacs configuration.
Finally, when you'll be tired of always reexecuting all the source
code when exporting, just look for the following line in [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]:
......
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