diff --git a/module2/ressources/emacs_orgmode.org b/module2/ressources/emacs_orgmode.org index 3feae860bfed0b67d7c8c7ea55c7a681b4aa3503..7c231f246c7474249be59451c0de61a601376d8f 100644 --- a/module2/ressources/emacs_orgmode.org +++ b/module2/ressources/emacs_orgmode.org @@ -11,6 +11,9 @@ emacs configuration_ and _A stub of replicable article_ explain how to set up org-mode for this MOOC. *You really should follow them carefully or you may have trouble doing the exercices later on*. +The next sections provide information on how to install emacs. Before +proceeding, make sure you have read the "Git and GitLab" instructions. + * Installing emacs, org-mode, ess, and auctex. ** OS-specific installation procedure *** Linux (Debian, Ubuntu) diff --git a/module2/ressources/gitlab.org b/module2/ressources/gitlab.org new file mode 100644 index 0000000000000000000000000000000000000000..da17909afe751a059992e8081505e7913e347dda --- /dev/null +++ b/module2/ressources/gitlab.org @@ -0,0 +1,111 @@ +# -*- mode: org -*- +#+TITLE: Git and GitLab +#+AUTHOR: Arnaud Legrand +#+DATE: June, 2018 +#+STARTUP: overview indent +#+OPTIONS: num:nil toc:t +#+PROPERTY: header-args :eval never-export + +So far, you only used git via the web interface from the GitLab we +deployed for the MOOC. + +#+BEGIN_CENTER +https://app-learninglab.inria.fr/gitlab/ +#+END_CENTER + +If you access this link from the FUN platform, you do not have to +authenticate and you can readily read and modify all your files. This +is very convenient but in most cases, you will want to have your own +local copy of the repository and you will have to synchronize your +local copy with the remote GitLab one. To propagate your +modifications, you will obviously have to authenticate yourself on +GitLab. This document describes the software you need to have +installed on your machine and how to handle authentification. Please +read these instructions carefully. + +* Installing Git +** 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 +for other distributions (e.g., redhat, fedora). + +Run (as root): +#+begin_src sh :results output :exports both +apt-get update ; apt-get install git +#+end_src +** Mac OSX and Windows +- Download and install Git from the [[https://git-scm.com/downloads][Git website]]. +- Optional Git clients (should not be needed if you work within + Rstudio): + - [[https://www.sourcetreeapp.com/][SourceTree]] + - [[https://desktop.github.com/][GitHub Desktop]] + #+BEGIN_QUOTE + [[https://github.com/desktop/desktop/issues/852][Apparently]], this works with GitLab and https. + #+END_QUOTE +* Authenticating on GitLab +There are two ways of authenticating and synchronizing your local +repository with GitLab: through HTTPS or through SSH. The first one +does not require any particular software installation on your machine +so this is what I recommend for this MOOC. Yet, I also describe the +second one as it is the one I prefer (once it is well configured, it +never asks me for any password anymore and I don't have to remember +anything). +** Option 1: HTTPS +*** Configuring your GitLab password +In this video, I explain how to change your password on our GitLab. +#+BEGIN_CENTER +Youtube Video +#+END_CENTER +*** Making sure git remembers your password +My GitLab id is =3211ac4f2fb71deaeff9252764c368e7=. Say I've configured +my password to be =tototutu= (what a weak password...) and I want to +clone my =mooc-rr= repository. If you clone your repos by simply pasting +the GitLab url (e.g., with the following command line) you will be +prompted for your login and your password every time you want to +propagate your local modifications. +#+begin_src shell :results output :exports both +git clone https://app-learninglab.inria.fr/gitlab/3211ac4f2fb71deaeff9252764c368e7/mooc-rr +#+end_src +This can be quite painful, which is why you can also provide them once +and for all when cloning, as follows: +#+begin_src shell :results output :exports both +git clone https://3211ac4f2fb71deaeff9252764c368e7:tototutu@app-learninglab.inria.fr/gitlab/3211ac4f2fb71deaeff9252764c368e7/mooc-rr +#+end_src +This is very convenient but there is one drawback to understand. This +means your password is stored, unencrypted on your hard drive. If +anyone ever gets an access to your machine, he will gain access rights +to all your repos, which can be problematic. This is why the really +good way to do this is to follow [[https://stackoverflow.com/questions/5343068/is-there-a-way-to-skip-password-typing-when-using-https-on-github][these instructions]]: +#+begin_src shell :results output :exports both +git config --global credential.helper cache # remember my password +git config --global credential.helper "cache --timeout=3600" # for one hour at most +#+end_src +With this setup, you will be prompted for your password but it will be +cached in memory and they will not be asked again before an hour. +** Option 2: SSH +My prefered (although more technical) solution is to install SSH, to +create a pair or private/public keys, and to upload your SSH public +key on GitLab. This section provides with information on how to do +this. +*** Installing SSH +**** 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 +for other distributions (e.g., redhat, fedora). + +Run (as root): +#+begin_src sh :results output :exports both +apt-get update ; apt-get install openssh-client +#+end_src +**** Mac OSX +You do not have anything to do as it is installed by default. +**** Windows +You should install the [[https://www.ssh.com/ssh/putty/windows/][Putty]] client. Once it is installed, look for +the section on [[https://www.ssh.com/ssh/putty/windows/puttygen][generating an SSH key]]. +*** Setting up SSH on Framagit +Here are [[https://docs.gitlab.com/ee/ssh/][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 +video: +#+BEGIN_EXPORT html + +#+END_EXPORT diff --git a/module2/ressources/rstudio.org b/module2/ressources/rstudio.org index e9587e9efdf35257cbb527bf69bb6b5cb5686d8e..7eac1320003ad7a2b47e530c4156d469ea654c46 100644 --- a/module2/ressources/rstudio.org +++ b/module2/ressources/rstudio.org @@ -14,16 +14,15 @@ may want to watch this video: #+END_EXPORT -The next sections provide information on how to install Rstudio, Git -(to interact with GitLab), and SSH (to avoid typing your password -every time you synchronize with GitLab). +The next sections provide information on how to install Rstudio. Before +proceeding, make sure you have read the "Git and GitLab" instructions. Finally, you need to know that the Rstudio team has created a lot of very good material and tutorials. You should definitively look at the [[https://www.rstudio.com/resources/cheatsheets/][Cheat sheets webpage]]. In particular you want to have look at the ones on: - [[https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf][The Rstudio IDE]], -- [[https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf][R Markdown]], +- [[https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf][R Markdown]] (here is also a [[https://rmarkdown.rstudio.com/][nice step-by-step presentation of Rmarkdown]]), - The [[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf][R Markdown Reference guide]], - [[https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf][Data visualization with ggplot2]], - [[https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf][Data transformation with dplyr]] @@ -97,52 +96,3 @@ install knitr and ggplot2: install.packages("knitr") install.packages("ggplot2") #+END_SRC -* Installing Git -** 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 -for other distributions (e.g., redhat, fedora). - -Run (as root): -#+begin_src sh :results output :exports both -apt-get update ; apt-get install git -#+end_src -** Mac OSX and Windows -- Download and install Git from the [[https://git-scm.com/downloads][Git website]]. -- Optional Git clients (should not be needed if you work within - Rstudio): - - [[https://www.sourcetreeapp.com/][SourceTree]] - - [[https://desktop.github.com/][GitHub Desktop]] - #+BEGIN_QUOTE - [[https://github.com/desktop/desktop/issues/852][Apparently]], this works with GitLab and https. - #+END_QUOTE -* Setting up SSH -There are two ways of synchronizing your local repository with GitLab: -through HTTPS or through SSH. The first one does not require any -particular configuration but you will be regularly prompted for your -GitLab password, which can be quite tedious. To avoid this, the best -solution is to set install SSH, to create a pair or private/public -keys, and to upload your SSH public key on GitLab. This section -provides with information on how to do this. -** Installation -*** 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 -for other distributions (e.g., redhat, fedora). - -Run (as root): -#+begin_src sh :results output :exports both -apt-get update ; apt-get install openssh-client -#+end_src -*** Mac OSX -You do not have anything to do as it is installed by default. -*** Windows -You should install the [[https://www.ssh.com/ssh/putty/windows/][Putty]] client. Once it is installed, look for -the section on [[https://www.ssh.com/ssh/putty/windows/puttygen][generating an SSH key]]. -** Setting up SSH on Framagit -Here are [[https://docs.gitlab.com/ee/ssh/][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 -video: -#+BEGIN_EXPORT html - -#+END_EXPORT