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<div id="content">
<h1 class="title">Emacs/org-mode</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgbd4e425">Installing emacs, org-mode, ess, and auctex.</a>
<ul>
<li><a href="#org324a7d6">OS-specific installation procedure</a>
<ul>
<li><a href="#orgd8c3f7e">Linux (Debian, Ubuntu)</a></li>
<li><a href="#org2bb1cef">Mac OS X</a></li>
<li><a href="#org4b4c660">Windows</a></li>
</ul>
</li>
<li><a href="#orgdc561eb">A simple "<i>reproducible research</i>" emacs configuration</a>
<ul>
<li><a href="#org8d266bd">Step 0: Backup and download our configuration</a></li>
<li><a href="#orgbe70ad9">Step 1: Prepare your journal</a></li>
<li><a href="#orgebee67f">Step 2: Set up Emacs configuration</a></li>
<li><a href="#orgdb9b220">Step 3: Check whether the installation is working or not</a></li>
<li><a href="#org3f1b5c3">Step 4: Open and play with your journal:</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgab544bb">Emacs Tips and tricks</a>
<ul>
<li><a href="#org7bb7d8c">Cheat-sheets</a>
<ul>
<li><a href="#org340d1fe">Emacs</a></li>
<li><a href="#org3f4a953">Org-mode</a></li>
</ul>
</li>
<li><a href="#orga548b84">Video tutorials</a></li>
<li><a href="#org5611504">Additional useful emacs packages</a>
<ul>
<li><a href="#org4a51dc5">Company-mode</a></li>
<li><a href="#orgba3524f">Magit</a></li>
</ul>
</li>
<li><a href="#org52918cd">Other resources</a></li>
</ul>
</li>
<li><a href="#orgd54946e">A replicable article</a>
<ul>
<li><a href="#org0b0e8a7">A stub of replicable article</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgbd4e425" class="outline-2">
<h2 id="orgbd4e425">Installing emacs, org-mode, ess, and auctex.</h2>
<div class="outline-text-2" id="text-orgbd4e425">
</div>
<div id="outline-container-org324a7d6" class="outline-3">
<h3 id="org324a7d6">OS-specific installation procedure</h3>
<div class="outline-text-3" id="text-org324a7d6">
</div>
<div id="outline-container-orgd8c3f7e" class="outline-4">
<h4 id="orgd8c3f7e">Linux (Debian, Ubuntu)</h4>
<div class="outline-text-4" id="text-orgd8c3f7e">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
</p>
<p>
Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
</p>
<ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/emacs25">emacs 25.1</a> and <a href="https://packages.debian.org/stretch/org-mode">org-mode 9.0.3</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/bionic/org-mode">org-mode 9.1.6</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/emacs25">emacs 25.2</a> and <a href="https://packages.ubuntu.com/artful/org-mode">org-mode 9.0.9</a></li>
</ul>
<p>
If your distribution is older than this, well, it may be a good time
for upgrading&#x2026;
</p>
<p>
Simply run (as root):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">apt-get update ; apt-get install emacs25 org-mode ess r-base auctex
</pre>
</div>
<p>
Then make sure you have a sufficiently recent version of emacs.
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">emacs --version 2&gt;&amp;1 | head -n 1
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
GNU Emacs 25.2.2
</pre>
<p>
Likewise, you'll want to check you have a recent version of org-mode:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">emacs -batch --funcall <span style="font-style: italic;">"org-version"</span> 2&gt;&amp;1 | grep version
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
Org mode version 9.1.11 (9.1.11-dist @ /usr/share/emacs/25.2/site-lisp/elpa/org-9.1.11/)
</pre>
<p>
The version numbers you get will depend on the distribution you are
running. <span class="underline">You really want to make sure you do not rely on org-mode 8</span>,
which is now deprecated.
</p>
</div>
</div>
<div id="outline-container-org2bb1cef" class="outline-4">
<h4 id="org2bb1cef">Mac OS X</h4>
<div class="outline-text-4" id="text-org2bb1cef">
<ul class="org-ul">
<li><p>
<b>Option 1</b>: Install the <code>.dmg</code> file from <a href="http://vgoulet.act.ulaval.ca/">Vincent Goulet</a>:
<a href="https://vigou3.github.io/emacs-modified-macos/">https://vigou3.github.io/emacs-modified-macos/</a>. It ships with recent
versions:
</p>
<ul class="org-ul">
<li>Emacs 26.1</li>
<li>Org-mode 9.1.13</li>
<li>ESS 17.11</li>
</ul>
<p>
In that case you may have several versions of emacs installed on
your machine and launching emacs from a terminal may not run the one
you just installed. If anyone know how to get rid of this&#x2026;
</p></li>
<li><p>
<b>Option 2</b>: If you already use <code>brew</code>, simply do the following
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">brew update
brew install emacs [--with-cocoa]
brew linkapps emacs
brew tap homebrew/science
brew install ess
brew install auctex <span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">The name may be slightly more complicated here</span>
brew install wget
</pre>
</div></li>
</ul>
</div>
</div>
<div id="outline-container-org4b4c660" class="outline-4">
<h4 id="org4b4c660">Windows</h4>
<div class="outline-text-4" id="text-org4b4c660">
<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
versions:
</p>
<ul class="org-ul">
<li>Emacs 26.1</li>
<li>Org-mode 9.1.13</li>
<li>ESS 17.11</li>
</ul>
</div>
</div>
</div>
<div id="outline-container-orgdc561eb" class="outline-3">
<h3 id="orgdc561eb">A simple "<i>reproducible research</i>" emacs configuration</h3>
<div class="outline-text-3" id="text-orgdc561eb">
<p>
Emacs comes with very basic default configuration and it appears like
everyone has its own taste. You will for example find <a href="https://www.emacswiki.org/emacs/StarterKits">here</a> several
default Emacs configurations that reflect the preferences of their
creators. Likewise the configuration of Org-Mode is incredibly
flexible (see for example <a href="https://orgmode.org/worg/org-configs/index.html">the org-mode website</a> for more
references). In the context of this MOOC, we propose you a relatively
minimalistic one that is rather "<i>reproducible research</i>" oriented by
adding a few org-mode specific configurations.
</p>
</div>
<div id="outline-container-org8d266bd" class="outline-4">
<h4 id="org8d266bd">Step 0: Backup and download our configuration</h4>
<div class="outline-text-4" id="text-org8d266bd">
<p>
The procedure we propose will wipe your already existing custom emacs
configuration if you already 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 file
exists).
</p>
<p>
Then download <a href="rr_org_archive.tgz">this archive</a> and uncompress it. It contains the
following files and we will refer to them in the following:
</p>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
rr_org/init.el
rr_org/journal.org
</pre>
</div>
</div>
<div id="outline-container-orgbe70ad9" class="outline-4">
<h4 id="orgbe70ad9">Step 1: Prepare your journal</h4>
<div class="outline-text-4" id="text-orgbe70ad9">
<p>
Create an <code>org/</code> directory in the top of your home:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">mkdir -p ~/org/
</pre>
</div>
<p>
Then copy <code>rr_org/journal.org</code> file in your <code>~/org/</code> directory. This
file will be your laboratory notebook and all the notes you will
capture with <code>C-c c</code> will go automatically go in this file. The first
entry of this notebook is populated with <a href="rr_org/journal.html#MissingReference">many emacs shortcuts</a> that you
should give a try.
</p>
</div>
</div>
<div id="outline-container-orgebee67f" class="outline-4">
<h4 id="orgebee67f">Step 2: Set up Emacs configuration</h4>
<div class="outline-text-4" id="text-orgebee67f">
<p>
Copy <code>rr_org/init.el</code> in your <code>~/.emacs.d/</code> directory.
</p>
<p>
Alternatively, if you do not want to mess with your already existing
emacs configuration, you may launch emacs with this specific
configuration with the following command: <code>emacs -q -l rr_org/init.el</code>.
</p>
</div>
</div>
<div id="outline-container-orgdb9b220" class="outline-4">
<h4 id="orgdb9b220">Step 3: Check whether the installation is working or not</h4>
<div class="outline-text-4" id="text-orgdb9b220">
<p>
Open a new instance of Emacs and open a <code>foo.org</code> file. Copy the
following lines in this file:
</p>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
#+begin_src shell :session foo :results output :exports both
ls -la
#+end_src
</pre>
<p>
Put your cursor inside this code block and execute it with the
following command: <code>C-c C-c</code> (If you are not familiar with Emacs
commands, this one means '<code>Ctrl + C</code>' twice)
</p>
<p>
A <code>#+RESULTS:</code> block with the result of the command should appear if it
worked.
</p>
<p>
In the video, we already have demonstrated the main features and
shortcuts of emacs/org-mode that will help you maintain a document and
benefit from literate programming. The list of features and shortcuts
is demonstrated in the <a href="rr_org/journal.html#MissingReference">first entry of your labbook</a>.
</p>
</div>
</div>
<div id="outline-container-org3f1b5c3" class="outline-4">
<h4 id="org3f1b5c3">Step 4: Open and play with your journal:</h4>
<div class="outline-text-4" id="text-org3f1b5c3">
<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
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.
</p>
</div>
</div>
</div>
</div>
<div id="outline-container-orgab544bb" class="outline-2">
<h2 id="orgab544bb">Emacs Tips and tricks</h2>
<div class="outline-text-2" id="text-orgab544bb">
</div>
<div id="outline-container-org7bb7d8c" class="outline-3">
<h3 id="org7bb7d8c">Cheat-sheets</h3>
<div class="outline-text-3" id="text-org7bb7d8c">
<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-org340d1fe" class="outline-4">
<h4 id="org340d1fe">Emacs</h4>
<div class="outline-text-4" id="text-org340d1fe">
<ul class="org-ul">
<li><a href="org/journal.html#MissingReference">Common and step-by-step emacs shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf">The official GNU emacs refcard</a></li>
<li>Two graphical cheat-sheats by Sacha Hua on <a href="http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png">how to learn emacs</a> and on
<a href="http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png">how to learn emacs shortcuts</a>.</li>
</ul>
</div>
</div>
<div id="outline-container-org3f4a953" class="outline-4">
<h4 id="org3f4a953">Org-mode</h4>
<div class="outline-text-4" id="text-org3f4a953">
<ul class="org-ul">
<li><a href="org/journal.html#MissingReference">Common and step-by-step org-mode shortcuts for our <i>reproducible research</i> configuration</a></li>
<li><a href="https://orgmode.org/worg/orgcard.html">The official org-mode refcard</a></li>
<li><a href="https://orgmode.org/worg/dev/org-syntax.html">The official description of the org-mode syntax</a> and a <a href="https://gist.github.com/hoeltgman/3825415">relatively concise description of the org-mode syntax</a>.</li>
</ul>
</div>
</div>
</div>
<div id="outline-container-orga548b84" class="outline-3">
<h3 id="orga548b84">Video tutorials</h3>
<div class="outline-text-3" id="text-orga548b84">
<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-org5611504" class="outline-3">
<h3 id="org5611504">Additional useful emacs packages</h3>
<div class="outline-text-3" id="text-org5611504">
</div>
<div id="outline-container-org4a51dc5" class="outline-4">
<h4 id="org4a51dc5">Company-mode</h4>
<div class="outline-text-4" id="text-org4a51dc5">
<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
feel this is needed, you should follow the instructions from the
official webpage: <a href="http://company-mode.github.io/">http://company-mode.github.io/</a>
</p>
</div>
</div>
<div id="outline-container-orgba3524f" class="outline-4">
<h4 id="orgba3524f">Magit</h4>
<div class="outline-text-4" id="text-orgba3524f">
<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>
</p>
</div>
</div>
</div>
<div id="outline-container-org52918cd" class="outline-3">
<h3 id="org52918cd">Other resources</h3>
<div class="outline-text-3" id="text-org52918cd">
<ul class="org-ul">
<li><a href="https://orgmode.org/orgguide.pdf">The compact Org-mode Guide</a></li>
<li><a href="https://github.com/dfeich/org-babel-examples">Many examples illustrating the use of different languages in org-mode</a></li>
</ul>
</div>
</div>
</div>
<div id="outline-container-orgd54946e" class="outline-2">
<h2 id="orgd54946e">A replicable article</h2>
<div class="outline-text-2" id="text-orgd54946e">
</div>
<div id="outline-container-org0b0e8a7" class="outline-3">
<h3 id="org0b0e8a7">A stub of replicable article</h3>
<div class="outline-text-3" id="text-org0b0e8a7">
<p>
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands <code>R</code> and <code>pdflatex</code>, you will not be
able to generate this document. The article downloads the
corresponding LaTeX packages so you also need to have a working <code>wget</code>
command (alternatively, you can use <code>curl</code>). You may still read the
source (<a href="replicable_article/article.html">article.org</a>) and understand how it works though.
</p>
<p>
Download the <a href="replicable_article/replicable_article.tgz">archive</a>, untar it and simply make to generate the
article. You should then be able to open the <a href="replicable_article/article.pdf">resulting article</a>. This
is summarized in the following command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">wget --no-check-certificate -O replicable.tgz https://github.com/alegrand/RR_webinars/raw/master/1_replicable_article_laboratory_notebook/replicable/replicable.tgz <span style="font-weight: bold; font-style: italic;">### </span><span style="font-weight: bold; font-style: italic;">Fix the broken URL</span>
tar zxf replicable.tgz; <span style="font-weight: bold;">cd</span> replicable; make ; evince article.pdf
</pre>
</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:
</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
</pre>
</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
system-wide. In that case, try to remove the <code>-q</code> in the previous
command line to load your personal emacs configuration.
</p>
<p>
Finally, when you'll be tired of always reexecuting all the source
code when exporting, just look for the following line in <a href="replicable_article/article.html">article.org</a>:
</p>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
# #+PROPERTY: header-args :eval never-export
</pre>
<p>
If you remove the <code># </code> in the beginning of the line, it will not be a
comment anymore and will indicate org-mode to stop evaluating every
chunk of code when exporting.
</p>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: June, 2018</p>
<p class="author">Author: Arnaud Legrand</p>
<p class="date">Created: 2018-07-19 jeu. 14:26</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>
module2/ressources/jupyter.html 0 → 100644
View file @ 6954e259
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<body>
<div id="content">
<h1 class="title">Rstudio</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org320e086">Interacting with gitlab</a></li>
<li><a href="#org5fa8060">Additional Jupyter resources or tricks</a>
<ul>
<li><a href="#org602d8a4">Tips and tricks</a></li>
<li><a href="#orgf07bc97">Running R and Python in the same notebook</a></li>
<li><a href="#org6fe9a0a">Exporting a notebook</a></li>
</ul>
</li>
<li><a href="#org27a7607">Installing jupyter or jupyter hub on your own machine</a>
<ul>
<li><a href="#org3da1dd0">Installing jupyter</a></li>
<li><a href="#orge6d06de">Using R</a></li>
<li><a href="#org5d221f3">Exporting your notebooks with latex</a></li>
<li><a href="#orgcd67c04">Interacting with gitlab</a></li>
<li><a href="#orgd5ecec1">Interesting extensions</a></li>
<li><a href="#org44b207c">Installing jupyterhub</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org320e086" class="outline-2">
<h2 id="org320e086">Interacting with gitlab</h2>
<div class="outline-text-2" id="text-org320e086">
<blockquote>
<p>
This section needs some love.
</p>
</blockquote>
<p>
As you may have seen from the videos, we provide two buttons to sync
with gitlab. Indeed, even if you recover your files when you log back
into fun, the jupyter runs on a different machine than the gitlab
server and you need to commit your notebook every time you have made a
significant step. This is also the only way to really make it public
and to share your notebook with others.
</p>
</div>
</div>
<div id="outline-container-org5fa8060" class="outline-2">
<h2 id="org5fa8060">Additional Jupyter resources or tricks</h2>
<div class="outline-text-2" id="text-org5fa8060">
</div>
<div id="outline-container-org602d8a4" class="outline-3">
<h3 id="org602d8a4">Tips and tricks</h3>
<div class="outline-text-3" id="text-org602d8a4">
<p>
The following <a href="https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/">webpage</a> lists several Jupyter tricks (in particular, it
illustrates many <code>Ipython magic</code> commands) that should improve your
efficiency (note that this blog post is about two years old so some of
the tricks may have been integrated in the default behavior of jupyter
now).
</p>
</div>
</div>
<div id="outline-container-orgf07bc97" class="outline-3">
<h3 id="orgf07bc97">Running R and Python in the same notebook</h3>
<div class="outline-text-3" id="text-orgf07bc97">
<p>
The best solution to this is to install rpy2. On my machine, I have
installed the <code>python3-rpy2</code> debian package with <code>apt-get install</code>. An
other alternative consists in going through the python package manager
with
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">pip install rpy2
</pre>
</div>
<p>
Then you'll be able to use both languages in the same notebook by:
</p>
<ol class="org-ol">
<li><p>
Loading <code>rpy2</code>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%load_ext rpy2.ipython
</pre>
</div></li>
<li><p>
Using the <code>%R</code> Ipython magic:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%R
summary(cars)
</pre>
</div>
<p>
Python objects can then even be passed to R as follows (assuming df
is a pandas dataframe:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%%R -i df
plot((df)
</pre>
</div></li>
</ol>
</div>
</div>
<div id="outline-container-org6fe9a0a" class="outline-3">
<h3 id="org6fe9a0a">Exporting a notebook</h3>
<div class="outline-text-3" id="text-org6fe9a0a">
<p>
Obviously, you can convert to html or pdf using the using the <code>File &gt;
Download as &gt; HTML</code> (or <code>PDF</code>) menu option. This can also be done from
the command line with the following command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">ipython3 nbconvert --to pdf Untitled.ipynb
</pre>
</div>
<p>
If you want to use a specific style, then the nbconvert exporter
should be customised. This is discussed and demoed <a href="http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html">here</a>. We encourage
you to simply read the <a href="https://nbconvert.readthedocs.io/en/latest/">doc of nbconvert</a>.
</p>
<p>
Instead of going directly through LaTeX and playing too much with the
nbconvert exporter, an other option consists in exporting to Markdown
and playing with <a href="https://pandoc.org/">pandoc</a>. Both approaches work, it's rather a matter of
taste.
</p>
</div>
</div>
</div>
<div id="outline-container-org27a7607" class="outline-2">
<h2 id="org27a7607">Installing jupyter or jupyter hub on your own machine</h2>
<div class="outline-text-2" id="text-org27a7607">
</div>
<div id="outline-container-org3da1dd0" class="outline-3">
<h3 id="org3da1dd0">Installing jupyter</h3>
<div class="outline-text-3" id="text-org3da1dd0">
<p>
Here is what you should install:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get install jupyter-notebook python3-pip python3-matplotlib python3-numpy
</pre>
</div>
<p>
On my machine, I got the version 5.4.1:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter-notebook --version
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="example">
5.4.1
</pre>
<p>
The ipython notebook can then be run with the following command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter-notebook
</pre>
</div>
</div>
</div>
<div id="outline-container-orge6d06de" class="outline-3">
<h3 id="orge6d06de">Using R</h3>
<div class="outline-text-3" id="text-orge6d06de">
<p>
If you also want to have the R kernel in jupyter, follow <a href="https://github.com/IRkernel/IRkernel#installation">these
instructions</a>.
</p>
<p>
Alternatively, you can install <code>rpy2</code> (see the <a href="#orgf07bc97">Running R and Python in
the same notebook</a> section).
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get python3-rpy2
</pre>
</div>
</div>
</div>
<div id="outline-container-org5d221f3" class="outline-3">
<h3 id="org5d221f3">Exporting your notebooks with latex</h3>
<div class="outline-text-3" id="text-org5d221f3">
<p>
Here is what I had to install to make sure the notebook export via
latex works:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">sudo apt-get install wkhtmltopdf
sudo apt-get install texlive-xetex
</pre>
</div>
</div>
</div>
<div id="outline-container-orgcd67c04" class="outline-3">
<h3 id="orgcd67c04">Interacting with gitlab</h3>
<div class="outline-text-3" id="text-orgcd67c04">
<p>
Here is our <a href="https://github.com/brospars/nb-git">jupyter extension that allows to git push/pull from the
notebooks</a>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">jupyter nbextension install https://raw.githubusercontent.com/brospars/nb-git/master/nb-git.js
jupyter nbextension enable nb-git
</pre>
</div>
</div>
</div>
<div id="outline-container-orgd5ecec1" class="outline-3">
<h3 id="orgd5ecec1">Interesting extensions</h3>
<div class="outline-text-3" id="text-orgd5ecec1">
<ul class="org-ul">
<li><p>
<a href="https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook">Code folding</a>
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 install jupyter_contrib_nbextensions
<span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">jupyter contrib nbextension install --user # not done yet</span>
</pre>
</div></li>
<li><p>
<a href="https://github.com/kirbs-/hide_code">Hiding code</a>
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">sudo pip3 install hide_code
sudo jupyter-nbextension install --py hide_code
jupyter-nbextension enable --py hide_code
jupyter-serverextension enable --py hide_code
</pre>
</div></li>
</ul>
</div>
</div>
<div id="outline-container-org44b207c" class="outline-3">
<h3 id="org44b207c">Installing jupyterhub</h3>
<div class="outline-text-3" id="text-org44b207c">
<blockquote>
<p>
Benoit may give a few hints on this.
</p>
</blockquote>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: June, 2018</p>
<p class="author">Author: Arnaud Legrand</p>
<p class="date">Created: 2018-07-19 jeu. 14:26</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>
module2/ressources/rstudio.html 0 → 100644
View file @ 6954e259
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<div id="content">
<h1 class="title">Rstudio</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd1dde5d">Installing Rstudio</a>
<ul>
<li><a href="#org6c44981">Linux (debian, ubuntu)</a>
<ul>
<li><a href="#orgf09ee89">Installing R</a></li>
<li><a href="#org4d45ca1">Installing rstudio</a></li>
</ul>
</li>
<li><a href="#org9a28181">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#org457ec7b">Installing Git</a>
<ul>
<li><a href="#org7c87525">Linux (debian, ubuntu)</a></li>
<li><a href="#org6214e86">Mac OSX and Windows</a></li>
</ul>
</li>
<li><a href="#org3a9a358">Rstudio and git/github/gitlab</a></li>
<li><a href="#orgf5abee5">Cheat Sheets</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgd1dde5d" class="outline-2">
<h2 id="orgd1dde5d">Installing Rstudio</h2>
<div class="outline-text-2" id="text-orgd1dde5d">
</div>
<div id="outline-container-org6c44981" class="outline-3">
<h3 id="org6c44981">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org6c44981">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
</p>
<p>
Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
</p>
<ul class="org-ul">
<li>Debian (stretch) ships with <a href="https://packages.debian.org/stretch/r-base">R 3.3.3-1</a>, <a href="https://packages.debian.org/stretch/r-cran-knitr">knitr 1.15.1</a>, and <a href="https://packages.debian.org/stretch/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (bionic 18.04) ships with <a href="https://packages.ubuntu.com/bionic/r-base">R 3.4.4</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-knitr">knitr 1.17</a>, and <a href="https://packages.ubuntu.com/bionic/r-cran-ggplot2">ggplot 2.2.1</a></li>
<li>Ubuntu (artful 17.04) ships with <a href="https://packages.ubuntu.com/artful/r-base">R 3.4.2</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-knitr">knitr 1.15</a>, and <a href="https://packages.ubuntu.com/artful/r-cran-ggplot2">ggplot 2.2.1</a></li>
</ul>
<p>
If your distribution is older than this, well, it may be a good time
for upgrading&#x2026;
</p>
</div>
<div id="outline-container-orgf09ee89" class="outline-4">
<h4 id="orgf09ee89">Installing R</h4>
<div class="outline-text-4" id="text-orgf09ee89">
<p>
Beforehand, you need to install the R language and convenient packages
by running (as root):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">apt-get update ; sudo apt-get install r-base r-cran-knitr r-cran-ggplot2
</pre>
</div>
<p>
Alternatively, if the installation of <code>r-cran-gplot2</code> or <code>r-cran-knitr</code>
fails, you may want to install them locally (through the R packaging
system) and manually by running the following commands in R (or
Rstudio):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-R">install.packages(<span style="font-style: italic;">"knitr"</span>)
install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</pre>
</div>
<p>
If you plan to export pdf documents with LaTeX, you probably also want
to run (as root):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">apt-get update ; apt-get install texlive-base
</pre>
</div>
</div>
</div>
<div id="outline-container-org4d45ca1" class="outline-4">
<h4 id="org4d45ca1">Installing rstudio</h4>
<div class="outline-text-4" id="text-org4d45ca1">
<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>
and then to install it manually (depending on when you do this, you
can obviously change the version number). Here is how to install it:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell"><span style="font-weight: bold;">cd</span> /tmp/
wget https://download1.rstudio.org/rstudio-xenial-1.1.453-amd64.deb
sudo dpkg -i rstudio-xenial-1.1.453-amd64.deb
sudo apt-get update ; sudo apt-get -f install <span style="font-weight: bold; font-style: italic;"># </span><span style="font-weight: bold; font-style: italic;">to fix possibly missing dependencies</span>
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org9a28181" class="outline-3">
<h3 id="org9a28181">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org9a28181">
<blockquote>
<p>
Some instructions on installing R and knitr must be missing. This
should be tested and improved.
</p>
</blockquote>
<p>
Download and install rstudio from the <a href="https://www.rstudio.com/products/rstudio/download/#download">Rstudio webpage</a> by choosing the
right operating system.
</p>
<p>
Then open Rstudio and type the following commands in the console to
install knitr and ggplot2:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-R">install.packages(<span style="font-style: italic;">"knitr"</span>)
install.packages(<span style="font-style: italic;">"ggplot2"</span>)
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org457ec7b" class="outline-2">
<h2 id="org457ec7b">Installing Git</h2>
<div class="outline-text-2" id="text-org457ec7b">
</div>
<div id="outline-container-org7c87525" class="outline-3">
<h3 id="org7c87525">Linux (debian, ubuntu)</h3>
<div class="outline-text-3" id="text-org7c87525">
<p>
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
</p>
<p>
Run (as root):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-sh">apt-get update ; apt-get install git
</pre>
</div>
</div>
</div>
<div id="outline-container-org6214e86" class="outline-3">
<h3 id="org6214e86">Mac OSX and Windows</h3>
<div class="outline-text-3" id="text-org6214e86">
<ul class="org-ul">
<li>Download and install Git from the <a href="https://git-scm.com/downloads">Git website</a>.</li>
<li>Optional Git clients (should not be needed if you work within
Rstudio):
<ul class="org-ul">
<li><a href="https://www.sourcetreeapp.com/">SourceTree</a></li>
<li><p>
<a href="https://desktop.github.com/">GitHub Desktop</a>
</p>
<blockquote>
<p>
<a href="https://github.com/desktop/desktop/issues/852">Apparently</a>, this works with gitlab and https.
</p>
</blockquote></li>
</ul></li>
</ul>
</div>
</div>
</div>
<div id="outline-container-org3a9a358" class="outline-2">
<h2 id="org3a9a358">Rstudio and git/github/gitlab</h2>
<div class="outline-text-2" id="text-org3a9a358">
<blockquote>
<p>
We may want to redo a screencast in French for this
</p>
</blockquote>
<ul class="org-ul">
<li><a href="https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/">This video on using git/githugb/gitlab from Rstudio</a> (starting at time 9:09)</li>
</ul>
<p>
Alternatively, we can point to:
<a href="http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/">http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/</a>
</p>
<ul class="org-ul">
<li>Part 1/item 2: Setup Git in RStudio</li>
<li>Part 2 (to adapt to gitlab)</li>
<li>Part 3</li>
</ul>
</div>
</div>
<div id="outline-container-orgf5abee5" class="outline-2">
<h2 id="orgf5abee5">Cheat Sheets</h2>
<div class="outline-text-2" id="text-orgf5abee5">
<p>
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the <a href="https://www.rstudio.com/resources/cheatsheets/">Cheat sheets webpage</a>. In particular
you want to have look at the ones on:
</p>
<ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf">the Rstudio IDE</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf">R Markdown</a>,</li>
<li>the <a href="https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf">R Markdown Reference guide</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf">data visualization with ggplot2</a>,</li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf">data transformation with dplyr</a></li>
</ul>
<p>
In case it helps, here are some (sometimes outdated) French versions
of these documents:
</p>
<ul class="org-ul">
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf">L'IDE Rstudio</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf">Visualisation de données avec ggplot2</a></li>
<li><a href="https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf">Transformation de données avec dplyr</a></li>
<li><a href="https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf">Un court document sur R Markdown</a></li>
</ul>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: June, 2018</p>
<p class="author">Author: Arnaud Legrand</p>
<p class="date">Created: 2018-07-19 jeu. 14:26</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
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