-
-
- Installing emacs, org-mode, ess, and auctex. +
- Installing emacs, org-mode, ess, and auctex. -
- 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: Adapt the configuration to your specific needs if required -
- Step 4: Check whether the installation is working or not -
- Step 5: 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: Adapt the configuration to your specific needs if required +
- Step 4: Check whether the installation is working or not +
- Step 5: Open and play with your journal:
- - A stub of replicable article -
- Emacs Tips and tricks +
- A stub of replicable article +
- Emacs Tips and tricks
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 @@ -132,11 +132,11 @@ 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.
+Note: macOS comes with a prehistoric command-line-only version of Emacs located at /usr/bin/emacs. It's best to forget about it.
-
@@ -189,9 +189,9 @@ in order to make Emacs accessible directly from
/Applications.
Windows
-Windows
+
Install the .exe file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-windows/. It ships with recent
@@ -202,10 +202,19 @@ versions:
+To have code pretty printing when exporting to html, it appears like
+you should install the htmlize package, which is done by opening emacs
+and typing the following command:
+
+M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" key +
Directory naming conventions
-Directory naming conventions
+
In all the following instructions, it is common to refer to your home
directory through the (UNIX) ~/ notation. On Windows, your home
@@ -216,9 +225,9 @@ means we are referring to C:\Users\yourname\org (resp.
Making R and Python available to the console
-Making R and Python available to the console
+
When running a command, windows will look for the command in the
directories indicated in the
Open an DOS console and type the following command:
This section is illustrated in a video tutorial ("Mise en place
Emacs/Orgmode" in French). Watching it before following the
@@ -296,9 +305,9 @@ adding a few org-mode specific configurations.
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. You should thus beforehand make
@@ -319,9 +328,9 @@ rr_org/journal.org
Create an
Copy
There are two situations in which it might be necessary to modify
Open a new instance of Emacs and open a
In step 1, you were told to create an journal in
This section is illustrated in a video tutorial ("Écrire un article
réplicable avec Emacs/Orgmode" in French). Watching it before
@@ -495,22 +504,22 @@ chunk of code when exporting.
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:
For those of you who prefer video explanations, here is a Youtube
channel with many step by step emacs tutorials.
Company-mode is a text completion framework for Emacs. It allows to
have smart completion in emacs for the most common languages. If you
@@ -554,9 +563,9 @@ official Web page: http://company-mode.
Magit is an emacs interface for Git. Its usage is briefly illustrated
in the context of this MOOC in a video tutorial ("Utilisation
@@ -574,9 +583,9 @@ invoke magit by using
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
@@ -83,9 +83,9 @@ Run (as root):
@@ -140,9 +140,9 @@ email@example.com
You may be behind a proxy, in which case you may have trouble cloning
or fetching from a remote repository or you may get an error like
@@ -164,9 +164,9 @@ will be prompted for it every time it is needed.
Warning (Jupyter users) : changing your default Gitlab password will prevent you from committing in Jupyter. You will have to do the extra step of changing your Jupyter
-If you wish to modify your password, you shoul go to
If you clone your repository by simply pasting the GitLab URL, you will be
prompted for your login and your password every time you want to
@@ -278,9 +278,9 @@ Use it at your own risk.
There are two ways of authenticating and synchronizing your local
repository with GitLab: through HTTPS or through SSH. The first one is
@@ -293,13 +293,13 @@ your SSH public key on GitLab. This section provides with information
on how to do this.
You do not have anything to do as it is installed by default.
You should install the Putty client. Once it is installed, look for
the section on generating an SSH key.
@@ -332,9 +332,9 @@ the section on generati
Here are all the official explanations on how to set up your SSH key
on GitLab. Alternatively, you may also want to have a look at this
@@ -345,9 +345,9 @@ video:
This section describes a generic (through the command line) way to
synchronize your local files with Gitlab. You will not need this if
diff --git a/module2/ressources/jupyter.html b/module2/ressources/jupyter.html
index e6040b4ae88653e958e97a055cbbd0ad41c59cfc..7c2741c591555842e399ae9336c2b4ec9bce7844 100644
--- a/module2/ressources/jupyter.html
+++ b/module2/ressources/jupyter.html
@@ -4,22 +4,28 @@
The following webpage lists several Jupyter tricks (in particular, it
illustrates many
-The best solution to this is to install rpy2. On my machine, I have
-installed the
-An other (not really recommended if the first one is available)
-alternative consists in going through the python package manager with
-
-Then you'll be able to use both languages in the same notebook by:
+
@@ -93,51 +78,57 @@ plot(df)
-Note that this
-Obviously, you can convert to html or pdf using the using the
+None of these other languages have been deployed in the context of our
+MOOC but you may want to read the next sections to know more about how
+to set up your own Jupyter notebooks on your computer and benefit from these
+extensions.
+
-If you want to use a specific style, then the
-Instead of going directly through LaTeX and playing too much with the
-
Follow these instructions if you wish to have a Jupyter environment on
-your own machine similar to the one we set up for this MOOC.
+your own computer similar to the one we set up for this MOOC.
@@ -161,46 +152,161 @@ activate mooc_rr
# Linux and MacOS activate the environment
source activate mooc_rr
+# Linux, MacOS and Windows: launch the notebook
jupyter notebook
-Note that Jupyter notebooks are only a small part of the picture and
-that Jupyter is now part of a bigger project: JupyterLab, 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 but
-this is probably the best option now if you want to benefit from
-cutting-edge Jupyter notebooks.
+The previous environment should ship with R but if you proceeded
+otherwise and only have python available in Jupyter, you may want to
+read the following section.
+
+Do the following in R console:
+
+Install the
+Define a proxy if needed:
+
+Install the
+On Linux, the rpy2 package is available in standard distributions
+An other (not really recommended if the first one is available)
+alternative consists in going through the python package manager with
+
-Here is what we had to install on our recent debian machine to make sure
-the notebook export via latex works:
+Windows
+
+Download
+Open a DOS console and type the following command:
+
+Install also
+Here is what we had to install on our recent debian computer to make sure
+the notebook export via LaTeX works:
+Obviously, you can convert to html or pdf using the using the
+If you want to use a specific style, then the
+Instead of going directly through LaTeX and playing too much with the
+
+Windows
+
+Download and install MiKTeX from the MiKTeX webpage
+by choosing the right operating system. You will be prompted to install some specific
+packages when exporting to pdf.
+
Here are a few extensions that can ease your life:
To ease your experience, we added some pull/push buttons that allow
you to commit and sync with GitLab. This development was specific to
@@ -259,6 +366,33 @@ developed to offer a nice version control experience.
+For any reason, you may be unsatisfied with the use of R or of
+Python. Many other languages are available:
+https://github.com/jupyter/jupyter/wiki/Jupyter-kernels, including
+non-free languages like SAS, Mathematica, Matlab…
+
+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 or the Python SASPy package (step by step
+explanations about this are given here).
+
+Since such software cannot easily be opened for inspection not widely
+used, we discourage this approach 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.
+
We provide here only instructions for debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
@@ -94,9 +94,9 @@ for upgrading…
Beforehand, you need to install the R language and convenient packages
by running (as root):
@@ -129,9 +129,9 @@ to run (as root):
Rstudio is unfortunately not packaged within debian so the easiest is
to download the corresponding debian package on the Rstudio webpage
@@ -149,46 +149,42 @@ sudo apt-get update ; sudo apt-get -f install
-
Some instructions on installing R and knitr must be missing. This
should be tested and improved.
-Download and install rstudio from the Rstudio webpage by choosing the
-right operating system.
-
-Then open Rstudio and type the following commands in the console to
-install knitr and ggplot2:
-
Open RStudio and do the following steps:
-Create a new version controled project:
@@ -207,7 +203,7 @@ Get the url from your gitlab repository:
@@ -218,7 +214,7 @@ repeatedly giving it later on).
PATH environment variable. If none of
@@ -236,9 +245,9 @@ explained
-Installing and configuring Matplotlib (graphic python library)
-Installing and configuring Matplotlib (graphic python library)
+backend, which amounts to use the default Agg
A simple "reproducible research" emacs configuration
-A simple "reproducible research" emacs configuration
+Step 0: Backup and download our configuration
-Step 0: Backup and download our configuration
+Step 1: Prepare your journal
-Step 1: Prepare your journal
+org/ directory in the top of your home:
Step 2: Set up Emacs configuration
-Step 2: Set up Emacs configuration
+rr_org/init.el in your ~/.emacs.d/ directory.
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
+init.el:
@@ -383,9 +392,9 @@ 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
+foo.org file. Copy the
following lines in this file:
@@ -416,9 +425,9 @@ is demonstrated in the
-Step 5: Open and play with your journal:
-Step 5: Open and play with your journal:
+~org/journal.org. First you probably want to make sure this file is
@@ -429,9 +438,9 @@ FUN forums.
A stub of replicable article
-A stub of replicable article
+Emacs Tips and tricks
-Emacs Tips and tricks
+Cheat-sheets
-Cheat-sheets
+Emacs
-Emacs
+
Org-mode
-Org-mode
+
Video tutorials
-Video tutorials
+Additional useful emacs packages
-Additional useful emacs packages
+Company-mode
-Company-mode
+Magit
-Magit
+C-x g.
Other resources
-Other resources
+
Table of Contents
-
-
Installing Git
-Installing Git
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+Mac OSX and Windows
-Mac OSX and Windows
+
Configuring Git
-Configuring Git
+Telling Git who you are: Name and Email
-Telling Git who you are: Name and Email
+
Dealing with proxies
-Dealing with proxies
+Getting your default password on GitLab (and possibly changing it)
-Getting your default password on GitLab (and possibly changing it)
+~/.git-credentials
Account >
- Settings > Password and define your password using the default
+If you wish to modify your password, you shoul go to Account > Settings > Password
+and define your password using the default
password you just retrieved. Again, if you use the Jupyter
notebooks we have deployed for the MOOC, remember that changing
your default Gitlab password will prevent you from committing in
@@ -242,9 +242,9 @@ section).
Remembering your password locally
-Remembering your password locally
+Optional: authenticating through SSH
-Optional: authenticating through SSH
+Installing SSH
-Installing SSH
+
-
-
-
+
-
+Setting up SSH on GitLab
-Setting up SSH on GitLab
+Using Git through the command line to synchronize your local files with Gitlab
-Using Git through the command line to synchronize your local files with Gitlab
+Table of Contents
-
Additional Jupyter resources or tricks
-Tips and tricks
-1. Jupyter Tips and tricks
+Ipython magic commands) that should improve your
@@ -43,28 +45,11 @@ the tricks may have been integrated in the default behavior of Jupyter
now).
Running R and Python in the same notebook
-python3-rpy2 debian package with apt-get install. E.g.,
-sudo apt-get install python3-rpy2 python3-tzlocal
-
-pip3 install rpy2
-
-Running R and Python in the same notebook
+rpy2 package allows to use both languages in the same notebook by:
%%R notation allows you to use R for the whole cell but
+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.
Exporting a notebook
-Other languages
+File >
-Download as > HTML (or PDF) menu option. This can also be done from
-the command line with the following command:
+For any reason, you may be unsatisfied with the use of R or of
+Python. Many other languages are available:
+https://github.com/jupyter/jupyter/wiki/Jupyter-kernels, including
+non-free languages like SAS, Mathematica, Matlab…
ipython3 nbconvert --to pdf Untitled.ipynb
-
+2. Installing and configuring Jupyter on your computer
+nbconvert exporter
-should be customized. This is discussed and demoed here. We encourage
-you to simply read the doc of nbconvert.
+In this Section, we provide information on how to set up on your own
+computer a Jupyter environment similar to the one deployed for this
+MOOC.
nbconvert exporter, an other option consists in exporting to Markdown
-and playing with pandoc. Both approaches work, it's rather a matter of
-taste.
+Note that Jupyter notebooks are only a small part of the picture and
+that Jupyter is now part of a bigger project: JupyterLab, 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 but
+this is probably the best option now if you want to benefit from
+cutting-edge Jupyter notebooks.
Installing Jupyter on your own machine
-Installing Jupyter
-2.1 Installing Jupyter
+Side note about Jupyter, JupyterLab, JupyterHub, …
-2.2 Making sure Jupyter allows you to use R
+• Installing IRKernel (R package)
+devtools package:
+install.packages('devtools',dep=TRUE)
+
+library(httr)
+set_config(use_proxy(url="proxy", port=80, username="username", password="password"))
+
+IRkernel package:
+devtools::install_github('IRkernel/IRkernel')
+IRkernel::installspec() # to register the kernel in the current R installation
+
+• Installing rpy2 (Python package)
+sudo apt-get install python3-rpy2 python3-tzlocal
+
pip3 install rpy2
+
Exporting your notebooks with latex
-rpy2 binary file by choosing the right operating system.
+python -m pip install rpy2‑2.9.4‑cp37‑cp37m‑win_amd64.whl # adapt filename
+
+tzlocal:
+python -m pip install tzlocal
+
+2.3 Additional tips
+• Exporting a notebook
+sudo apt-get install texlive-xetex wkhtmltopdf
File > Download as > HTML (or PDF) menu option. This can also be done from
+the command line with the following command:
+ipython3 nbconvert --to pdf Untitled.ipynb
+
+nbconvert exporter
+should be customized. This is discussed and demoed here. We encourage
+you to simply read the doc of nbconvert.
+nbconvert exporter, an other option consists in exporting to Markdown
+and playing with pandoc. Both approaches work, it's rather a matter of
+taste.
+Jupyter extensions/plugins
-• Side note about Jupyter, JupyterLab, JupyterHub…
Improving notebook readability
-• Improving notebook readability
+Interacting with GitLab and GitHub
-• Interacting with GitLab and GitHub
+• Using other languages (e.g., SAS, Matlab, Mathematica, etc.)
+Table of Contents
Installing Rstudio
-Installing Rstudio
+Linux (debian, ubuntu)
-Linux (debian, ubuntu)
+Installing R
-Installing R
+Installing rstudio
-Installing rstudio
+Mac OSX and Windows
-Mac OSX and Windows
+
-
+
knitr and ggplot2:install.packages("knitr")
-install.packages("ggplot2")
+
install.packages("knitr", dep=TRUE)
+install.packages("ggplot2", dep=TRUE)
Using Git from Rstudio
-Using Git from Rstudio
+Cloning a repository
-Cloning a repository
+
File / New Project / Version
- Control
+Create a new version controled project: File / New Project / Version Control
File / New Project / Version
Modifying a file
-Modifying a file
+
Module2/exo1/toy_document.Rmd and perform a simple
modification.commit
