diff --git a/module2/ressources/emacs_orgmode.md b/module2/ressources/emacs_orgmode.md
index 3d0a695b9c83040181742c076ee3d65deac940ba..74b649e9dd7c3d1a81eddd88c85b8d932e7a7817 100644
--- a/module2/ressources/emacs_orgmode.md
+++ b/module2/ressources/emacs_orgmode.md
@@ -3,51 +3,49 @@ configuration* and *A stub of replicable article* explain how to set up
emacs/org-mode for this MOOC. These are very important sections in the
context of this MOOC. **These sections are illustrated in two out of the
[three video tutorials of this
-sequence](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4),
+sequence](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4),
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 ["emacs and git" video tutorial available at
the same
-place](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4).
+place](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4).
-The next section provides information on how to install emacs.
+The next section provides information on how to install
+emacs.
-Table of Contents
-=================
+# Table of Contents TOC
-- [Installing emacs, org-mode, ess, and
+ - [Installing emacs, org-mode, ess, and
auctex.](#installing-emacs-org-mode-ess-and-auctex)
- - [Linux (Debian, Ubuntu)](#linux-debian-ubuntu)
- - [macOS](#macos)
- - [Windows](#windows)
- - [All platforms: pretty code in HTML
+ - [Linux (Debian, Ubuntu)](#linux-debian-ubuntu)
+ - [macOS](#macos)
+ - [Windows](#windows)
+ - [All platforms: pretty code in HTML
export](#all-platforms-pretty-code-in-html-export)
-- [A simple "*reproducible research*" emacs configuration
+ - [A simple "*reproducible research*" emacs configuration
](#a-simple-reproducible-research-emacs-configuration-)
- - [Step 0: Backup and download our
+ - [Step 0: Backup and download our
configuration](#step-0-backup-and-download-our-configuration)
- - [Step 1: Prepare your journal](#step-1-prepare-your-journal)
- - [Step 2: Set up Emacs
+ - [Step 1: Prepare your journal](#step-1-prepare-your-journal)
+ - [Step 2: Set up Emacs
configuration](#step-2-set-up-emacs-configuration)
- - [Step 3: Adapt the configuration to your specific needs if
+ - [Step 3: Adapt the configuration to your specific needs if
required](#step-3-adapt-the-configuration-to-your-specific-needs-if-required)
- - [Step 4: Check whether the installation is working or
+ - [Step 4: Check whether the installation is working or
not](#step-4-check-whether-the-installation-is-working-or-not)
- - [Step 5: Open and play with your
+ - [Step 5: Open and play with your
journal:](#step-5-open-and-play-with-your-journal)
-- [A stub of a replicable article](#a-stub-of-a-replicable-article)
-- [Emacs tips and tricks](#emacs-tips-and-tricks)
- - [Cheat-sheets](#cheat-sheets)
- - [Video tutorials](#video-tutorials)
- - [Additional useful emacs
+ - [A stub of a replicable article](#a-stub-of-a-replicable-article)
+ - [Emacs tips and tricks](#emacs-tips-and-tricks)
+ - [Cheat-sheets](#cheat-sheets)
+ - [Video tutorials](#video-tutorials)
+ - [Additional useful emacs
packages](#additional-useful-emacs-packages)
- - [Other resources](#other-resources)
+ - [Other resources](#other-resources)
-Installing emacs, org-mode, ess, and auctex.
-============================================
+# Installing emacs, org-mode, ess, and auctex.
-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
@@ -56,63 +54,63 @@ for other distributions (e.g.n redhat, fedora).
Today, the stable versions of the most common distributions provide
recent enough versions of emacs and org-mode:
-- Debian (stretch) ships with [emacs
- 25.1](https://packages.debian.org/stretch/emacs25) and [org-mode
- 9.0.3](https://packages.debian.org/stretch/org-mode)
-- Ubuntu (bionic 18.04) ships with [emacs
- 25.2](https://packages.ubuntu.com/bionic/emacs25) and [org-mode
- 9.1.6](https://packages.ubuntu.com/bionic/org-mode)
-- Ubuntu (artful 17.04) ships with [emacs
- 25.2](https://packages.ubuntu.com/artful/emacs25) and [org-mode
- 9.0.9](https://packages.ubuntu.com/artful/org-mode)
+ - Debian (stretch) ships with
+ [emacs 25.1](https://packages.debian.org/stretch/emacs25) and
+ [org-mode 9.0.3](https://packages.debian.org/stretch/org-mode)
+ - Ubuntu (bionic 18.04) ships with
+ [emacs 25.2](https://packages.ubuntu.com/bionic/emacs25) and
+ [org-mode 9.1.6](https://packages.ubuntu.com/bionic/org-mode)
+ - Ubuntu (artful 17.04) ships with
+ [emacs 25.2](https://packages.ubuntu.com/artful/emacs25) and
+ [org-mode 9.0.9](https://packages.ubuntu.com/artful/org-mode)
If your distribution is older than this, well, it may be a good time for
-upgrading...
+upgrading…
Simply run (as root):
-``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+``` bash
apt-get update ; apt-get install emacs25 org-mode ess r-base auctex
```
Then make sure you have a sufficiently recent version of emacs.
-``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+``` bash
emacs --version 2>&1 | head -n 1
```
-``` {.example}
+``` example
GNU Emacs 25.2.2
```
Likewise, you'll want to check you have a recent version of org-mode:
-``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+``` bash
emacs -batch --funcall "org-version" 2>&1 | grep version
```
-``` {.example}
+``` example
Org mode version 9.1.11 (9.1.11-dist @ /usr/share/emacs/25.2/site-lisp/elpa/org-9.1.11/)
```
The version numbers you get will depend on the distribution you are
-running. **You really want to make sure you do not rely on org-mode 8**,
-which is now deprecated.
+running. You really want to make sure you do not
+rely on org-mode 8, which is now deprecated.
-macOS
------
+## macOS
**Note:** macOS comes with a prehistoric command-line-only version of
Emacs located at `/usr/bin/emacs`. It's best to forget about it.
-- **Option 1**: Install the `.dmg` file from [Vincent
+ - **Option 1**: Install the `.dmg` file from [Vincent
Goulet](http://vgoulet.act.ulaval.ca/):
- [](https://vigou3.gitlab.io/emacs-modified-macos/).
- It ships with recent versions:
- - Emacs 26.1
- - Org-mode 9.1.13
- - ESS 17.11
-
+ . It ships with
+ recent versions:
+
+ - Emacs 26.1
+ - Org-mode 9.1.13
+ - ESS 17.11
+
If you install this version of Emacs, or in fact any other version
of Emacs distributed as a clickable application in a `.dmg` file,
you must type the full path to the executable if you want to run
@@ -120,10 +118,10 @@ Emacs located at `/usr/bin/emacs`. It's best to forget about it.
at `/Applications/Emacs.app`, then the executable is at
`/Applications/Emacs.app/Contents/MacOS/Emacs`
-- **Option 2**: If you use [Homebrew](https://docs.brew.sh/), do the
+ - **Option 2**: If you use [Homebrew](https://docs.brew.sh/), do the
following:
-
- ``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+
+ ``` bash
brew update
brew install emacs --with-cocoa
brew linkapps emacs
@@ -133,31 +131,30 @@ Emacs located at `/usr/bin/emacs`. It's best to forget about it.
brew tap brewsci/science
brew install ess
```
-
+
This provides an `emacs` command for use from the command line, plus
a clickable application at `Cellar/emacs/26.1_1/Emacs.app` inside
your Homebrew directory. If you installed Homebrew at the default
location `/usr/local`, then this is
`/usr/local/Cellar/emacs/26.1_1/Emacs.app`. If you installed
Homebrew on an account with administrator privileges, you can add
-
- ``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+
+ ``` bash
brew linkapps emacs
```
-
+
in order to make Emacs accessible directly from `/Applications`.
-Windows
--------
+## Windows
Install the `.exe` file from [Vincent
Goulet](http://vgoulet.act.ulaval.ca/):
-[](https://vigou3.gitlab.io/emacs-modified-windows/).
-It ships with recent versions:
+. It ships with recent
+versions:
-- Emacs 26.1
-- Org-mode 9.1.13
-- ESS 17.11
+ - Emacs 26.1
+ - Org-mode 9.1.13
+ - ESS 17.11
### Directory naming conventions
@@ -185,7 +182,7 @@ explained
Open an DOS console and type the following command:
-``` {.shell .rundoc-block rundoc-language="shell" rundoc-results="output" rundoc-exports="both"}
+``` shell
python -m pip install -U matplotlib
```
@@ -195,7 +192,7 @@ Then you will want to deactivate interactive plots in matplotlib. To
this end, you first need to know where the matplotlib configuration is
located. Open a python console the type the following code:
-``` {.python .rundoc-block rundoc-language="python" rundoc-results="output" rundoc-exports="both"}
+``` python
import matplotlib
matplotlib.matplotlib_fname()
```
@@ -205,23 +202,22 @@ matplotlib.matplotlib_fname()
Open the `matplotlibrc` file and modify the line starting with `backend`
to make it `backend : Agg`.
-All platforms: pretty code in HTML export
------------------------------------------
+## All platforms: pretty code in HTML export
To have code pretty printing when exporting to HTML, you should install
the `htmlize` package, which is done by opening emacs and typing the
-following command:
+following
+command:
-``` {.example}
+``` example
M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" key
```
-A simple "*reproducible research*" emacs configuration
-======================================================
+# A simple "*reproducible research*" emacs configuration
This section is illustrated in a [video
-tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
-(/"Mise en place Emacs/Orgmode"/ in French). Watching it before
+tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
+(*"Mise en place Emacs/Orgmode"* 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
@@ -235,8 +231,7 @@ references). In the context of this MOOC, we propose you a relatively
minimalist one that is rather "*reproducible research*" oriented by
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 have one. **You should thus beforehand make a
@@ -244,11 +239,11 @@ backup** of `~/.emacs` and of `~/.emacs.d/init.el` (if these files
exist).
Then download [this
-archive](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/rr_org_archive.tgz)
+archive](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/rr_org_archive.tgz)
and uncompress it. It contains the following files and we will refer to
them in the following:
-``` {.example}
+``` example
rr_org/init.el
rr_org/journal.org
```
@@ -256,12 +251,11 @@ rr_org/journal.org
Alternatively, [the files you are looking for are available
here](rr_org/).
-Step 1: Prepare your journal
-----------------------------
+## Step 1: Prepare your journal
Create an `org/` directory in the top of your home:
-``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+``` bash
mkdir -p ~/org/
```
@@ -269,11 +263,10 @@ Then copy `rr_org/journal.org` file in your `~/org/` directory. This
file will be your laboratory notebook and all the notes you will capture
with `C-c c` will go automatically go in this file. The first entry of
this notebook is populated with [many Emacs
-shortcuts](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
+shortcuts](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
that you should give a try.
-Step 2: Set up Emacs configuration
-----------------------------------
+## Step 2: Set up Emacs configuration
Copy `rr_org/init.el` in your `~/.emacs.d/` directory.
@@ -281,8 +274,7 @@ 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: `emacs -q -l rr_org/init.el`.
-Step 3: Adapt the configuration to your specific needs if required
-------------------------------------------------------------------
+## Step 3: Adapt the configuration to your specific needs if required
There are two situations in which it might be necessary to modify
`init.el`:
@@ -291,22 +283,20 @@ There are two situations in which it might be necessary to modify
sites (HTTP(S) protocol).
2. You have multiple installations of Python or R on your computer, or
they are in unusual places and not fully configured. If you can run
- - "python3" and "R" under Linux and macOS
- - "Python" and "R" under Windows
-
+ - "python3" and "R" under Linux and macOS
+ - "Python" and "R" under Windows
in a terminal without getting an error message, then you should not
have to do anything.
If you do have to modify `init.el`, check the comments at the beginning
of the file for instructions.
-Step 4: Check whether the installation is working or not
---------------------------------------------------------
+## Step 4: 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:
-``` {.example}
+``` example
#+begin_src shell :session foo :results output :exports both
ls -la # or dir under windows
#+end_src
@@ -323,22 +313,20 @@ 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 [first entry of your
-labbook](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org).
+labbook](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org).
-Step 5: Open and play with your journal:
-----------------------------------------
+## Step 5: 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 stored in a version
control system like git. We leave it up to you to set this up but if you
have any trouble, feel free to ask on the FUN forums.
-A stub of a replicable article
-==============================
+# A stub of a replicable article
This section is illustrated in a [video
-tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
-(/"Écrire un article réplicable avec Emacs/Orgmode"/ in French).
+tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
+(*"Écrire un article réplicable avec Emacs/Orgmode"* in French).
Watching it before following the instructions given in this section may
help.
@@ -348,42 +336,45 @@ not be able to generate this document. When being compiled, the article
downloads the corresponding LaTeX packages so you also need to have a
working `wget` command (alternatively, it uses `curl`). Once downloaded,
you may still read the source
-([article.org](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org))
+()
and understand how it works though.
Download the following
-[archive](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz),
+[archive](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/replicable_article.tgz),
uncompress it and simply `make` to generate the article. You should then
be able to open the [resulting
-article](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf).
-This is summarized in the following command:
+article](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf).
+This is summarized in the following
+command:
-``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
-wget --no-check-certificate -O replicable_article.tgz https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz
+``` bash
+wget --no-check-certificate -O replicable_article.tgz https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/replicable_article.tgz
tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
```
**Possible issues**:
-- If the `make` command fails (especially on Mac), it may be because
+ - 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:
-
- ``` {.bash .rundoc-block rundoc-language="sh" rundoc-results="output" rundoc-exports="both"}
+ open the article directly with the following
+ command:
+
+ ``` bash
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org
```
-
+
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,
+
+ - 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 re-executing all the source code
when exporting, just look for the following line in
-[article.org](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org):
+[article.org](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org):
-``` {.example}
+``` example
# #+PROPERTY: header-args :eval never-export
```
@@ -391,11 +382,9 @@ If you remove the `# ` 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.
-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.
@@ -403,37 +392,35 @@ Here is a selection in case it helps:
### Emacs
-- [Common and step-by-step Emacs shortcuts for our *reproducible
+ - [Common and step-by-step Emacs shortcuts for our *reproducible
research*
- configuration](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
-- [The official GNU emacs
+ configuration](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
+ - [The official GNU emacs
refcard](https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf)
-- Two graphical cheat-sheats by Sacha Chua on
- 
- and on
- .
+ - Two graphical cheat-sheats by Sacha Chua on [how to learn
+ Emacs](http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png)
+ and on [how to learn Emacs
+ shortcuts](http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png).
### Org-mode
-- [Common and step-by-step org-mode shortcuts for our *reproducible
+ - [Common and step-by-step org-mode shortcuts for our *reproducible
research*
- configuration](https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
-- [The official org-mode
+ configuration](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org)
+ - [The official org-mode
refcard](https://orgmode.org/worg/orgcard.html)
-- [The official description of the org-mode
+ - [The official description of the org-mode
syntax](https://orgmode.org/worg/dev/org-syntax.html) and a
[relatively concise description of the org-mode
syntax](https://gist.github.com/hoeltgman/3825415).
-Video tutorials
----------------
+## Video tutorials
For those of you who prefer video explanations, here is a [Youtube
channel with many step by step emacs
tutorials](https://www.youtube.com/playlist?list=PL9KxKa8NpFxIcNQa9js7dQQIHc81b0-Xg).
-Additional useful emacs packages
---------------------------------
+## Additional useful emacs packages
### Company-mode
@@ -441,13 +428,13 @@ Additional useful emacs packages
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 Web page:
-[](http://company-mode.github.io/)
+
### Magit
[Magit](https://magit.vc/) is an Emacs interface for Git. Its usage is
briefly illustrated in the context of this MOOC in a [video
-tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
+tutorial](https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4)
("*Utilisation Emacs/git*" in French).
It is very powerful and we use it on a daily basis but you should
@@ -458,10 +445,8 @@ walk-through](https://magit.vc/screenshots/) or [this really short
the previous "*reproducible research*" emacs configuration, you can
easily invoke magit by using `C-x g`.
-Other resources
----------------
+## Other resources
-- [The compact Org-mode Guide](https://orgmode.org/orgguide.pdf)
-- [Many examples illustrating the use of different languages in
+ - [The compact Org-mode Guide](https://orgmode.org/orgguide.pdf)
+ - [Many examples illustrating the use of different languages in
org-mode](https://github.com/dfeich/org-babel-examples)
-
diff --git a/module2/ressources/jupyter.md b/module2/ressources/jupyter.md
new file mode 100644
index 0000000000000000000000000000000000000000..7c6dcd6fedf3b61747b92c9c752269450a07320f
--- /dev/null
+++ b/module2/ressources/jupyter.md
@@ -0,0 +1,305 @@
+# 1\. Jupyter tips and tricks
+
+The following
+[webpage](https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/)
+lists several Jupyter tricks (in particular, it illustrates many
+`IPython magic` 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).
+
+## Creating or importing a notebook
+
+Using the Jupyter environment we deployed for this MOOC will allow to
+easily access any file from your default GitLab project. There are
+situations however where you may want to play with other notebooks.
+
+ - Adding a brand new notebook in a given directory
+ Simply follow the following steps:
+
+ 1. From the menu: `File -> Open`. You're now in the Jupyter file
+ manager.
+
+ 2. Navigate to the directory where you want your notebook to be
+ created.
+
+ 3. Then from the top right button: `New -> Notebook: Python 3`.
+
+ 4. Give your notebook a name from the menu: `File -> Rename`.
+
+ N.B.: If you create a file by doing `File -> New Notebook ->
+ Python 3`, the new notebook will be created in the current
+ directory. Moving it afterward is possible but a bit cumbersome
+ (you'll have to go through the Jupyter file manager by following
+ the menu `File -> Open`, then select it, `Shut` it `down`, and
+ `Move` and/or `Rename`).
+
+ - Importing an already existing notebook
+ If your notebook is already in your GitLab project, then simply
+ synchronize by using the `Git pull` button and use the `File ->
+ Open` menu. Otherwise, imagine, you want to import the [following
+ notebook](https://app-learninglab.inria.fr/gitlab/moocrr-session1/moocrr-reproducibility-study/blob/master/src/Python3/challenger.ipynb)
+ from someone else's repository to re-execute it.
+
+ 1. Download the file on your computer. E.g., for this [GitLab
+ hosted
+ notebook](https://app-learninglab.inria.fr/gitlab/moocrr-session1/moocrr-reproducibility-study/blob/master/src/Python3/challenger.ipynb),
+ click on `Open raw` (a small `` within a document icon) and
+ save (`Ctrl-S` on most browsers) the content (a long Json text
+ file).
+ 2. Open the Jupyter file manager from the menu `File -> Open` and
+ navigate to the directory where you want to upload your
+ notebook.
+ 3. Then from the top right button, `Upload` the previously
+ downloaded notebook and confirm the upload.
+ 4. Open the freshly uploaded notebook through the Jupyter file
+ manager.
+
+## Running R and Python in the same notebook
+
+`rpy2` package allows to use both languages in the same notebook by:
+
+1. Loading `rpy2`:
+
+ ``` python
+ %load_ext rpy2.ipython
+ ```
+
+2. Using the `%R` Ipython magic:
+
+ ``` python
+ %%R
+ summary(cars)
+ ```
+
+ Python objects can then even be passed to R as follows (assuming
+ `df` is a pandas dataframe):
+
+ ``` python
+ %%R -i df
+ plot(df)
+ ```
+
+Note that this `%%R` notation indicates that R should be used for the
+whole cell but an other possibility is to use `%R` to have a single line
+of R within a python cell.
+
+## Other languages
+
+Jupyter is not limited to Pytyhon and R. Many other languages are
+available: ,
+including non-free languages like SAS, Mathematica, Matlab… Note that
+the maturity of these kernels differs widely.
+
+None of these other languages have been deployed in the context of our
+MOOC but you may want to read the next sections to learn how to set up
+your own Jupyter on your computer and benefit from these extensions.
+
+Since the question was asked several times, if you really need to stay
+with SAS, you should know that SAS can be used within Jupyter using
+either the [Python SASKernel](https://sassoftware.github.io/sas_kernel/)
+or the [Python SASPy](https://sassoftware.github.io/saspy/) package
+(step by step explanations about this are given
+[here](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/documents/tuto_jupyter_windows/tuto_jupyter_windows.md)).
+
+Since proprietary software such as SAS cannot easily be inspected, we
+discourage its use as it hinders reproducibility by essence. But
+perfection does not exist anyway and using Jupyter literate programming
+approach allied with systematic control version and environment control
+will certainly help anyway.
+
+# 2\. Installing and configuring Jupyter on your computer
+
+In this section, we explain how to set up a Jupyter environment on your
+own computer similar to the one deployed for this MOOC.
+
+Note that Jupyter notebooks are only a small part of the picture and
+that Jupyter is now part of a bigger project:
+[JupyterLab](https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906),
+which allows you to mix various components (including notebooks) in your
+browser. In the context of this MOOC, our time frame was too short to
+benefit from JupyterLab which was still under active development. You
+may, however, prefer JupyterLab when doing an installation on your own
+computer.
+
+## 2.1 Installing Jupyter
+
+Follow these instructions if you wish to have a Jupyter environment on
+your own computer similar to the one we set up for this MOOC.
+
+First, download and install the [latest version of
+Miniconda](https://conda.io/miniconda.html). We use Miniconda version
+`4.5.4` and Python version `3.6` on our server.
+
+Miniconda is a light version of Anaconda, which includes Python, the
+Jupyter Notebook, and other commonly used packages for scientific
+computing and data science.
+
+Then download the [moocrr environment
+file](https://gist.github.com/brospars/4671d9013f0d99e1c961482dab533c57)
+and create the environment using conda:
+
+``` shell
+conda env create -f environment.yml
+
+# Windows activate the environment
+activate mooc_rr
+
+# Linux and MacOS activate the environment
+source activate mooc_rr
+
+# Linux, MacOS and Windows: launch the notebook
+jupyter notebook
+```
+
+## 2.2 Making sure Jupyter allows you to use R
+
+The environment described in the last section should include R, but if
+you proceeded otherwise and only have Python available in Jupyter, you
+may want to read the following
+section.
+
+### • Installing [IRKernel](https://github.com/IRkernel/IRkernel) (R package)
+
+Do the following in R console:
+
+Install the `devtools` package:
+
+``` r
+install.packages('devtools',dep=TRUE)
+```
+
+Define a proxy if needed:
+
+``` r
+library(httr)
+set_config(use_proxy(url="proxy", port=80, username="username", password="password"))
+```
+
+Install the `IRkernel` package:
+
+``` r
+devtools::install_github('IRkernel/IRkernel')
+IRkernel::installspec() # to register the kernel in the current R installation
+```
+
+### • Installing rpy2 (Python package)
+
+On Linux, the rpy2 package is available in standard distributions
+
+``` shell
+sudo apt-get install python3-rpy2 python3-tzlocal
+```
+
+An alternative (not really recommended if the first one is available)
+consists in going through the python package manager with
+
+``` python
+pip3 install rpy2
+```
+
+**Windows**
+
+Download the `rpy2` [binary
+file](https://www.lfd.uci.edu/~gohlke/pythonlibs/#rpy2) by choosing the
+right operating system.
+
+Open a DOS console and type the following
+command:
+
+``` shell
+python -m pip install rpy2‑2.9.4‑cp37‑cp37m‑win_amd64.whl # adapt filename
+```
+
+Install also `tzlocal`:
+
+``` shell
+python -m pip install tzlocal
+```
+
+## 2.3 Additional tips
+
+### • Exporting a notebook
+
+Here is what we had to install on a recent Debian computer to make sure
+the notebook export via LaTeX works:
+
+``` shell
+sudo apt-get install texlive-xetex wkhtmltopdf
+```
+
+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
+the command line with the following command:
+
+``` bash
+ipython3 nbconvert --to pdf Untitled.ipynb
+```
+
+If you want to use a specific style, then the `nbconvert` exporter
+should be customized. This is discussed and demoed
+[here](http://markus-beuckelmann.de/blog/customizing-nbconvert-pdf.html).
+We encourage you to simply read the [doc of
+nbconvert](https://nbconvert.readthedocs.io/en/latest/).
+
+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 [pandoc](https://pandoc.org/). Both approaches work,
+it's rather a matter of taste.
+
+**Windows**
+
+Download and install MiKTeX from the [MiKTeX
+webpage](https://miktex.org/download) by choosing the right operating
+system. You will be prompted to install some specific packages when
+exporting to pdf.
+
+### • Improving notebook readability
+
+Here are a few extensions that can ease your life:
+
+ - [Code
+ folding](https://stackoverflow.com/questions/33159518/collapse-cell-in-jupyter-notebook)
+ to improve readability when browsing the notebook.
+
+ ``` shell
+ pip3 install jupyter_contrib_nbextensions
+ # jupyter contrib nbextension install --user # not done yet
+ ```
+
+ - [Hiding code](https://github.com/kirbs-/hide_code) to improve
+ readability when exporting.
+
+ ``` bash
+ sudo pip3 install hide_code
+ sudo jupyter-nbextension install --py hide_code
+ jupyter-nbextension enable --py hide_code
+ jupyter-serverextension enable --py hide_code
+ ```
+
+### • Interacting with GitLab and GitHub
+
+To ease your experience, we added pull/push buttons that allow you to
+commit and sync with GitLab. This development was specific to the MOOC
+but inspired from a previous [proof of
+concept](https://github.com/Lab41/sunny-side-up). We have recently
+discovered that someone else developed about at the same time a [rather
+generic version of this Jupyter
+plugin](https://github.com/sat28/githubcommit). Otherwise, remember that
+it is very easy to insert a shell cell in Jupyter in which you can
+easily issue git commands. This is how we work most of the time.
+
+This being said, you may have noticed that Jupyter keeps a perfect track
+of the sequence in which cells have been run by updating the "output
+index". This is a very good property from the reproducibility point of
+view but depending on your usage, you may find it a bit painful when
+committing. Some people have thus developed [specific git
+hooks](https://gist.github.com/pbugnion/ea2797393033b54674af) to ignore
+these numbers when committing Jupyter notebooks. There is a long an
+interesting discussion about various options on
+[StackOverflow](https://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control).
+
+For those who use
+[JupyterLab](https://blog.jupyter.org/jupyterlab-is-ready-for-users-5a6f039b8906)
+rather than the plain Jupyter, a specific [JupyterLab git
+plugin](https://github.com/jupyterlab/jupyterlab-git) has been developed
+to offer a nice version control experience.
diff --git a/module2/ressources/jupyter.org b/module2/ressources/jupyter.org
index 8013f2ebeae0e65561cb691a2c206921422c866e..1d1d53791ccd39dc8b4795e3b2475c52cf4e519f 100644
--- a/module2/ressources/jupyter.org
+++ b/module2/ressources/jupyter.org
@@ -1,5 +1,5 @@
# -*- mode: org -*-
-#+TITLE: Jupyter
+#+TITLE: Jupyter : tips and tricks, Installing and configuring
#+AUTHOR: Arnaud Legrand, Benoit Rospars, Konrad Hinsen
#+DATE: June, 2018
#+STARTUP: overview indent