Skip to content

M
mooc-rr-ressources
Commit 0893b72e authored by Laurence Farhi's avatar Laurence Farhi
Browse files
Options

modif du titre de la doc sur Jupiter + génération du .md

parent ee77013c
Hide whitespace changes
Inline Side-by-side
Showing with 433 additions and 143 deletions
module2/ressources/emacs_orgmode.md
View file @ 0893b72e
......@@ -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 <span class="tag" data-tag-name="TOC"><span class="smallcaps">TOC</span></span>
- [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. <span class="underline">You really want to make sure you do not
rely on org-mode 8</span>, 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/>](https://vigou3.gitlab.io/emacs-modified-macos/).
It ships with recent versions:
- Emacs 26.1
- Org-mode 9.1.13
- ESS 17.11
<https://vigou3.gitlab.io/emacs-modified-macos/>. 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/>](https://vigou3.gitlab.io/emacs-modified-windows/).
It ships with recent versions:
<https://vigou3.gitlab.io/emacs-modified-windows/>. 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))
(<https://gitlab.inria.fr/learninglab/mooc-rr/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
![](http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png)
and on
![](http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png).
- 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/>](http://company-mode.github.io/)
<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)
module2/ressources/jupyter.md 0 → 100644
View file @ 0893b72e
# 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: <https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>,
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 [mooc<sub>rr</sub> 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.
module2/ressources/jupyter.org
View file @ 0893b72e
# -*- 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
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment