From 5ce6b00b0147f0f6f6057aa9e9ae503c42d67769 Mon Sep 17 00:00:00 2001 From: Arnaud Legrand Date: Thu, 19 Jul 2018 16:09:56 +0200 Subject: [PATCH] Regenerate HTML filesxs --- .../ressources/introduction_to_markdown.html | 102 +++++----- module2/ressources/emacs_orgmode.html | 176 +++++++++--------- module2/ressources/jupyter.html | 98 +++++----- module2/ressources/rstudio.html | 80 ++++---- 4 files changed, 228 insertions(+), 228 deletions(-) diff --git a/module1/ressources/introduction_to_markdown.html b/module1/ressources/introduction_to_markdown.html index c9d4a86..ad6bfc2 100644 --- a/module1/ressources/introduction_to_markdown.html +++ b/module1/ressources/introduction_to_markdown.html @@ -4,26 +4,26 @@

Table of Contents

@@ -34,13 +34,13 @@ Voici un aperçu rapide de la syntaxe Markdown repris d'une présentation de Github ainsi que de celles d'Archer Reilly et de James H. Steiger.

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Syntaxe

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Syntaxe

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Headers

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Headers

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 # This is an <h1> tag
 ## This is an <h2> tag
@@ -49,9 +49,9 @@ H. Steiger.
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Emphasis

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Emphasis

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 *This text will be italic*
 _This will also be italic_
@@ -64,13 +64,13 @@ _You **can** combine them_
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Lists

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Lists

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Unordered

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Unordered

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 * Item 1
 * Item 2
@@ -79,9 +79,9 @@ _You **can** combine them_
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Ordered

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Ordered

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 1. Item 1
 1. Item 2
@@ -92,27 +92,27 @@ _You **can** combine them_
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Images

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Images

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 ![GitHub Logo](/images/logo.png)
 Format: ![Alt Text](url)
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Links

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Links

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 http://github.com - automatic!
 [GitHub](http://github.com)
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Blockquotes

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Blockquotes

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 As Kanye West said:
 
@@ -121,9 +121,9 @@ As Kanye West said:
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Inline code

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Inline code

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 I think you should use an
 `<addr>` element here instead.
@@ -131,9 +131,9 @@ I think you should use an
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Écrire des Maths

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Écrire des Maths

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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 @@ -177,9 +177,9 @@ This summation expression is in display form.

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Lettres grecques

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Lettres grecques

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@@ -223,8 +223,8 @@ This summation expression is in display form.
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Operators

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Operators

diff --git a/module2/ressources/emacs_orgmode.html b/module2/ressources/emacs_orgmode.html index c2bd1dc..a229ff2 100644 --- a/module2/ressources/emacs_orgmode.html +++ b/module2/ressources/emacs_orgmode.html @@ -4,64 +4,64 @@

Table of Contents

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Installing emacs, org-mode, ess, and auctex.

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Installing emacs, org-mode, ess, and auctex.

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OS-specific installation procedure

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OS-specific installation procedure

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Linux (Debian, Ubuntu)

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Linux (Debian, Ubuntu)

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We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -123,9 +123,9 @@ which is now deprecated.

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Mac OS X

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Mac OS X

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  • Option 1: Install the .dmg file from Vincent Goulet: @@ -158,9 +158,9 @@ brew install wget

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Windows

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Windows

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Install the .exe file from Vincent Goulet: https://vigou3.github.io/emacs-modified-windows/. It ships with recent @@ -174,9 +174,9 @@ versions:

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A simple "reproducible research" emacs configuration

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A simple "reproducible research" emacs configuration

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Emacs comes with very basic default configuration and it appears like everyone has its own taste. You will for example find here several @@ -189,9 +189,9 @@ adding a few org-mode specific configurations.

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Step 0: Backup and download our configuration

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Step 0: Backup and download our configuration

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The procedure we propose will wipe your already existing custom emacs configuration if you already have one. You should thus beforehand make @@ -212,9 +212,9 @@ rr_org/journal.org

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Step 1: Prepare your journal

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Step 1: Prepare your journal

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Create an org/ directory in the top of your home:

@@ -231,9 +231,9 @@ should give a try.

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Step 2: Set up Emacs configuration

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Step 2: Set up Emacs configuration

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Copy rr_org/init.el in your ~/.emacs.d/ directory.

@@ -245,9 +245,9 @@ configuration with the following command: emacs -q -l rr_org/init.el
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Step 3: Check whether the installation is working or not

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Step 3: Check whether the installation is working or not

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Open a new instance of Emacs and open a foo.org file. Copy the following lines in this file: @@ -278,9 +278,9 @@ is demonstrated in the first entr

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Step 4: Open and play with your journal:

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Step 4: Open and play with your journal:

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In step 1, you were told to create an journal in ~org/journal.org. First you probably want to make sure this file is @@ -292,22 +292,22 @@ forums.

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Emacs Tips and tricks

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Emacs Tips and tricks

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Cheat-sheets

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Cheat-sheets

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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:

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Emacs

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Org-mode

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Org-mode

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Video tutorials

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Video tutorials

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For those of you who prefer video explanations, here is a Youtube channel with many step by step emacs tutorials.

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Additional useful emacs packages

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Additional useful emacs packages

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Company-mode

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Company-mode

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Company-mode is a text completion framework for Emacs. It allows to have smart completion in emacs for the most common languages. If you @@ -351,9 +351,9 @@ official webpage: http://company-mode.g

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Magit

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Magit

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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 @@ -364,9 +364,9 @@ you should follow the instructions from here:

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Other resources

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Other resources

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A replicable article

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A replicable article

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A stub of replicable article

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A stub of replicable article

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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 diff --git a/module2/ressources/jupyter.html b/module2/ressources/jupyter.html index 788db0f..4d7aa2e 100644 --- a/module2/ressources/jupyter.html +++ b/module2/ressources/jupyter.html @@ -4,31 +4,31 @@

Table of Contents

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Interacting with gitlab

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Interacting with gitlab

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This section needs some love. @@ -45,13 +45,13 @@ and to share your notebook with others.

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Additional Jupyter resources or tricks

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Additional Jupyter resources or tricks

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Tips and tricks

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Tips and tricks

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The following webpage lists several Jupyter tricks (in particular, it illustrates many Ipython magic commands) that should improve your @@ -61,9 +61,9 @@ now).

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Running R and Python in the same notebook

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Running R and Python in the same notebook

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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 @@ -105,9 +105,9 @@ plot((df)

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Exporting a notebook

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Exporting a notebook

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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 @@ -134,13 +134,13 @@ taste.

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Installing jupyter or jupyter hub on your own machine

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Installing jupyter or jupyter hub on your own machine

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Installing jupyter

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Installing jupyter

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Here is what you should install:

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Using R

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Using R

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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).

@@ -189,9 +189,9 @@ the same notebook section).
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Exporting your notebooks with latex

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Exporting your notebooks with latex

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Here is what I had to install to make sure the notebook export via latex works: @@ -203,9 +203,9 @@ sudo apt-get install texlive-xetex

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Interacting with gitlab

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Interacting with gitlab

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Here is our jupyter extension that allows to git push/pull from the notebooks: @@ -217,9 +217,9 @@ jupyter nbextension enable nb-git

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Interesting extensions to improve notebook readability

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Interesting extensions to improve notebook readability

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Here are two interesting extensions that can improve readability:

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Installing jupyterhub

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Installing jupyterhub

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Benoit may give a few hints on this. diff --git a/module2/ressources/rstudio.html b/module2/ressources/rstudio.html index dcf3535..a7dde5f 100644 --- a/module2/ressources/rstudio.html +++ b/module2/ressources/rstudio.html @@ -4,36 +4,36 @@

Table of Contents

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Installing Rstudio

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Installing Rstudio

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Linux (debian, ubuntu)

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Linux (debian, ubuntu)

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We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -55,9 +55,9 @@ for upgrading…

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Installing R

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Installing R

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Beforehand, you need to install the R language and convenient packages by running (as root): @@ -90,9 +90,9 @@ to run (as root):

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Installing rstudio

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Installing rstudio

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Rstudio is unfortunately not packaged within debian so the easiest is to download the corresponding debian package on the Rstudio webpage @@ -110,9 +110,9 @@ sudo apt-get update ; sudo apt-get -f install -

Mac OSX and Windows

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Mac OSX and Windows

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Some instructions on installing R and knitr must be missing. This @@ -136,13 +136,13 @@ install.packages("ggplot2")

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Installing Git

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Installing Git

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Linux (debian, ubuntu)

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Linux (debian, ubuntu)

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We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -158,9 +158,9 @@ Run (as root):

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Mac OSX and Windows

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Mac OSX and Windows

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  • Download and install Git from the Git website.
  • Optional Git clients (should not be needed if you work within @@ -180,9 +180,9 @@ Rstudio):
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Rstudio and git/github/gitlab

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Rstudio and git/github/gitlab

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We may want to redo a screencast in French for this @@ -203,9 +203,9 @@ Alternatively, we can point to:

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Cheat Sheets

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Cheat Sheets

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The Rstudio team has created a lot of good material and tutorials. You should definitively look at the Cheat sheets webpage. In particular -- 2.18.1