Introduction à Markdown
Table of Contents
-
-
- Syntaxe +
- Syntaxe
-
-
- Headers -
- Emphasis -
- Lists +
- Headers +
- Emphasis +
- Lists -
- Images -
- Links -
- Blockquotes -
- Inline code +
- Images +
- Links +
- Blockquotes +
- Inline code
- - Écrire des Maths +
- Écrire des Maths
Syntaxe
-Syntaxe
+Headers
-Headers
+# This is an <h1> tag ## This is an <h2> tag @@ -301,9 +49,9 @@ H. Steiger.
Emphasis
-Emphasis
+*This text will be italic* _This will also be italic_ @@ -316,13 +64,13 @@ _You **can** combine them_
Lists
-Lists
+Unordered
-Unordered
+* Item 1 * Item 2 @@ -331,9 +79,9 @@ _You **can** combine them_
Ordered
-Ordered
+1. Item 1 1. Item 2 @@ -344,27 +92,27 @@ _You **can** combine them_
Images
-Images
+ Format: 
Links
-Links
+http://github.com - automatic! [GitHub](http://github.com)
Blockquotes
-Blockquotes
+As Kanye West said: @@ -373,9 +121,9 @@ As Kanye West said:
Inline code
-Inline code
+I think you should use an `<addr>` element here instead. @@ -383,9 +131,9 @@ I think you should use an
Écrire des Maths
-Écrire des Maths
+Equations can be formatted inline or as displayed formulas. In the latter case, they are centered and set off from the main text. In the @@ -429,9 +177,9 @@ This summation expression is in display form.
Lettres grecques
-Lettres grecques
+Operators
-Operators
Emacs/org-mode
Table of Contents
-
-
- Installing emacs, org-mode, ess, and auctex. +
- Installing emacs, org-mode, ess, and auctex.
-
-
- OS-specific installation procedure +
- OS-specific installation procedure -
- A simple "reproducible research" emacs configuration +
- A simple "reproducible research" emacs configuration
-
-
- Step 0: Backup and download our configuration -
- Step 1: Prepare your journal -
- Step 2: Set up Emacs configuration -
- Step 3: Check whether the installation is working or not -
- Step 4: Open and play with your journal: +
- Step 0: Backup and download our configuration +
- Step 1: Prepare your journal +
- Step 2: Set up Emacs configuration +
- Step 3: Check whether the installation is working or not +
- Step 4: Open and play with your journal:
- - Emacs Tips and tricks +
- Emacs Tips and tricks -
- A replicable article +
- A replicable article
Installing emacs, org-mode, ess, and auctex.
-Installing emacs, org-mode, ess, and auctex.
+OS-specific installation procedure
-OS-specific installation procedure
+Linux (Debian, Ubuntu)
-Linux (Debian, Ubuntu)
+We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -353,9 +123,9 @@ which is now deprecated.
Mac OS X
-Mac OS X
+Option 1: Install the
.dmgfile from Vincent Goulet: @@ -388,9 +158,9 @@ brew install wget
Windows
-Windows
+
Install the .exe file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-windows/. It ships with recent
@@ -404,9 +174,9 @@ versions:
A simple "reproducible research" emacs configuration
-A simple "reproducible research" emacs configuration
+Emacs comes with very basic default configuration and it appears like everyone has its own taste. You will for example find here several @@ -419,9 +189,9 @@ adding a few org-mode specific configurations.
Step 0: Backup and download our configuration
-Step 0: Backup and download our configuration
+The procedure we propose will wipe your already existing custom emacs configuration if you already have one. You should thus beforehand make @@ -442,9 +212,9 @@ rr_org/journal.org
Step 1: Prepare your journal
-Step 1: Prepare your journal
+
Create an org/ directory in the top of your home:
Step 2: Set up Emacs configuration
-Step 2: Set up Emacs configuration
+
Copy rr_org/init.el in your ~/.emacs.d/ directory.
emacs -q -l rr_org/init.el
Step 3: Check whether the installation is working or not
-Step 3: Check whether the installation is working or not
+
Open a new instance of Emacs and open a foo.org file. Copy the
following lines in this file:
@@ -508,9 +278,9 @@ is demonstrated in the first entr
Step 4: Open and play with your journal:
-Step 4: Open and play with your journal:
+
In step 1, you were told to create an journal in
~org/journal.org. First you probably want to make sure this file is
@@ -522,22 +292,22 @@ forums.
Emacs Tips and tricks
-Emacs Tips and tricks
+Cheat-sheets
-Cheat-sheets
+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:
Emacs
-Emacs
+- Common and step-by-step emacs shortcuts for our reproducible research configuration
- The official GNU emacs refcard @@ -546,9 +316,9 @@ cheat-sheats. Here is a selection in case it helps:
Org-mode
-Org-mode
+- Common and step-by-step org-mode shortcuts for our reproducible research configuration
- The official org-mode refcard @@ -557,22 +327,22 @@ cheat-sheats. Here is a selection in case it helps:
Video tutorials
-Video tutorials
+For those of you who prefer video explanations, here is a Youtube channel with many step by step emacs tutorials.
Additional useful emacs packages
-Additional useful emacs packages
+Company-mode
-Company-mode
+Company-mode is a text completion framework for Emacs. It allows to have smart completion in emacs for the most common languages. If you @@ -581,9 +351,9 @@ official webpage: http://company-mode.g
Magit
-Magit
+Magit 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 @@ -594,9 +364,9 @@ you should follow the instructions from here:
Other resources
-Other resources
+- The compact Org-mode Guide
- Many examples illustrating the use of different languages in org-mode @@ -604,13 +374,13 @@ you should follow the instructions from here:
A replicable article
-A replicable article
+A stub of replicable article
-A stub of replicable article
+
Remember, you need a working LaTeX and R environment. If you can't
open a terminal and run the commands R and pdflatex, you will not be
@@ -667,11 +437,3 @@ chunk of code when exporting.
Rstudio
+Jupyter
Table of Contents
-
-
- Interacting with gitlab -
- Additional Jupyter resources or tricks +
- Interacting with gitlab +
- Additional Jupyter resources or tricks -
- Installing jupyter or jupyter hub on your own machine +
- Installing jupyter or jupyter hub on your own machine
-
-
- Installing jupyter -
- Using R -
- Exporting your notebooks with latex -
- Interacting with gitlab -
- Interesting extensions to improve notebook readability -
- Installing jupyterhub +
- Installing jupyter +
- Using R +
- Exporting your notebooks with latex +
- Interacting with gitlab +
- Interesting extensions to improve notebook readability +
- Installing jupyterhub
Interacting with gitlab
-Interacting with gitlab
+This section needs some love. @@ -275,13 +45,13 @@ and to share your notebook with others.
Additional Jupyter resources or tricks
-Additional Jupyter resources or tricks
+Tips and tricks
-Tips and tricks
+
The following webpage lists several Jupyter tricks (in particular, it
illustrates many Ipython magic commands) that should improve your
@@ -291,9 +61,9 @@ now).
Running R and Python in the same notebook
-Running R and Python in the same notebook
+
The best solution to this is to install rpy2. On my machine, I have
installed the python3-rpy2 debian package with apt-get install. An
@@ -335,9 +105,9 @@ plot((df)
Exporting a notebook
-Exporting a notebook
+
Obviously, you can convert to html or pdf using the using the File >
Download as > HTML (or PDF) menu option. This can also be done from
@@ -364,13 +134,13 @@ taste.
Installing jupyter or jupyter hub on your own machine
-Installing jupyter or jupyter hub on your own machine
+Installing jupyter
-Installing jupyter
+Here is what you should install:
@@ -401,16 +171,16 @@ The ipython notebook can then be run with the following command:Using R
-Using R
+If you also want to have the R kernel in jupyter, follow these instructions.
-Alternatively, you can install rpy2 (see the Running R and Python in
+Alternatively, you can install rpy2 (see the Running R and Python in
the same notebook section).
Exporting your notebooks with latex
-Exporting your notebooks with latex
+Here is what I had to install to make sure the notebook export via latex works: @@ -433,9 +203,9 @@ sudo apt-get install texlive-xetex
Interacting with gitlab
-Interacting with gitlab
+Here is our jupyter extension that allows to git push/pull from the notebooks: @@ -447,9 +217,9 @@ jupyter nbextension enable nb-git
Interesting extensions to improve notebook readability
-Interesting extensions to improve notebook readability
+Here are two interesting extensions that can improve readability:
@@ -475,9 +245,9 @@ jupyter-serverextension enable --py hide_codeInstalling jupyterhub
-Installing jupyterhub
+Benoit may give a few hints on this. @@ -487,11 +257,3 @@ Benoit may give a few hints on this.
Rstudio
Table of Contents
Installing Rstudio
-Installing Rstudio
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -285,9 +55,9 @@ for upgrading…
Installing R
-Installing R
+Beforehand, you need to install the R language and convenient packages by running (as root): @@ -320,9 +90,9 @@ to run (as root):
Installing rstudio
-Installing rstudio
+
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the Rstudio webpage
@@ -340,9 +110,9 @@ sudo apt-get update ; sudo apt-get -f install
-
Some instructions on installing R and knitr must be missing. This
@@ -366,13 +136,13 @@ install.packages("ggplot2")
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
@@ -388,9 +158,9 @@ Run (as root):
We may want to redo a screencast in French for this
@@ -433,9 +203,9 @@ Alternatively, we can point to:
The Rstudio team has created a lot of good material and tutorials. You
should definitively look at the Cheat sheets webpage. In particular
@@ -462,11 +232,3 @@ of these documents:
Mac OSX and Windows
-Mac OSX and Windows
+
Installing Git
-Installing Git
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+Mac OSX and Windows
-Mac OSX and Windows
+
Rstudio and git/github/gitlab
-Rstudio and git/github/gitlab
+
Cheat Sheets
-Cheat Sheets
+