diff --git a/module2/ressources/emacs_orgmode.org b/module2/ressources/emacs_orgmode.org index 3def7685639299ae93efea20186839984214e9b5..26f8213dfbdc21cf47fca886d079aa4894752c5b 100644 --- a/module2/ressources/emacs_orgmode.org +++ b/module2/ressources/emacs_orgmode.org @@ -10,10 +10,10 @@ 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 [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][three video tutorials of this sequence]], and* *which you +out of the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][three video tutorials of this sequence]], 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 [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4]["emacs and git" video tutorial available at the same place]]. +the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4]["emacs and git" video tutorial available at the same place]]. The next section provides information on how to install emacs. @@ -164,7 +164,7 @@ M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key #+END_EXAMPLE * A simple "/reproducible research/" emacs configuration -This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] (/"Mise en place +This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] (/"Mise en place Emacs/Orgmode"/ in French). Watching it before following the instructions given in this section may help. @@ -189,7 +189,7 @@ tar zcf rr_org_archive.tgz $FILE_LIST #+RESULTS: -Then download [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/rr_org_archive.tgz][this archive]] and uncompress it. It contains the +Then download [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/rr_org_archive.tgz][this archive]] and uncompress it. It contains the following files and we will refer to them in the following: #+begin_src shell :results output :exports results @@ -257,7 +257,7 @@ 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 -This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] (/"Écrire un article +This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] (/"Écrire un article réplicable avec Emacs/Orgmode"/ in French). Watching it before following the instructions given in this section may help. @@ -274,11 +274,11 @@ make -C replicable_article/ all ../replicable_article.tgz #+RESULTS: -Download the following [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz][archive]], uncompress it and simply =make= to generate the +Download the following [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/replicable_article.tgz][archive]], uncompress it and simply =make= to generate the article. You should then be able to open the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf][resulting article]]. This is summarized in the following command: #+begin_src sh :results output :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 +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 #+end_src @@ -329,7 +329,7 @@ feel this is needed, you should follow the instructions from the official Web page: [[http://company-mode.github.io/][http://company-mode.github.io/]] *** Magit [[https://magit.vc/][Magit]] is an Emacs interface for Git. Its usage is briefly illustrated -in the context of this MOOC in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] +in the context of this MOOC in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] ("/Utilisation Emacs/git/" in French). It is very powerful and we use it on a daily basis but you should diff --git a/module2/ressources/gitlab.org b/module2/ressources/gitlab.org index 87bab681bc645df4d1c36c1fa074d80816ff61ee..a280924300903015de5f099b28cc7cee7a477329 100644 --- a/module2/ressources/gitlab.org +++ b/module2/ressources/gitlab.org @@ -24,7 +24,7 @@ GitLab. This document describes the software you need to have installed on your machine and how to handle authentication. The "Configuring Git" -section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85][video tutorial]] (in French). +section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][video tutorial]] (in French). Please read all these instructions carefully, in particular the one on "Configuring your password on GitLab". @@ -88,7 +88,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment (possibly several times). 1. Get your default password using the [[https://app-learninglab.inria.fr/jupyterhub/services/password][Gitlab credentials retrieval - tool]] as described on the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85][corresponding resource]]. + tool]] as described on the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][corresponding resource]]. #+BEGIN_CENTER [[file:gitlab_images/password_retrieval.png]] #+END_CENTER @@ -106,7 +106,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment #+BEGIN_CENTER [[file:gitlab_images/erreur405.png]] #+END_CENTER -2. Access [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/xblock/block-v1:inria+41016+session01bis+type@lti+block@05a0ce425f1741e5bee5049040f70529/handler/preview_handler][GitLab]]. +2. Access [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/5571950188c946e790f06d4bc90fb5f6][GitLab]] from the FUN plateform (click on "Accédez à Gitlab / Access to Gitlab" Button). /Note: Again, you have to access Gitlab from the FUN platform otherwise you may get a 405 error/ /when trying to direcly open diff --git a/module2/ressources/jupyter.org b/module2/ressources/jupyter.org index ab86238aeee4d8dd759026572364c5286cee9b71..8013f2ebeae0e65561cb691a2c206921422c866e 100644 --- a/module2/ressources/jupyter.org +++ b/module2/ressources/jupyter.org @@ -76,7 +76,7 @@ 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 [[https://sassoftware.github.io/sas_kernel/][Python SASKernel]] or the [[https://sassoftware.github.io/saspy/][Python SASPy]] package (step by step -explanations about this are given [[https://app-learninglab.inria.fr/gitlab/85bc36e0a8096c618fbd5993d1cca191/mooc-rr/blob/master/documents/tuto_jupyter_windows/tuto_jupyter_windows.md][here]]). +explanations about this are given [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/documents/tuto_jupyter_windows/tuto_jupyter_windows.md][here]]). 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 diff --git a/module2/ressources/rstudio.org b/module2/ressources/rstudio.org index 352e6959e74fc457b75d4a2da63a2966ee3955e3..25ea9cf6dd7bf0f19de4b34e237bb343fea39012 100644 --- a/module2/ressources/rstudio.org +++ b/module2/ressources/rstudio.org @@ -84,9 +84,9 @@ of these documents: * Using Git from RStudio If you have never used git with RStudio, *we strongly advise that you -follow [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/d132a854b0464ad29085cedaded23136][our tutorial on using git from RStudio]]* (/"RStudio et Gitlab"/ +follow [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/d132a854b0464ad29085cedaded23136][our tutorial on using git from RStudio]]* (/"RStudio et Gitlab"/ in French). Before proceeding, make sure you also have followed the -*[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85]["git/GitLab configuration" tutorial]]* (in French). +*[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["git/GitLab configuration" tutorial]]* (in French). Alternatively, you may want to watch [[https://www.youtube.com/embed/uHYcDQDbMY8][this video]] (in English). If you do not like videos, you should have a look at the [[https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html][step-by-step @@ -112,7 +112,7 @@ Open RStudio and do the following steps: [[file:rstudio_images/clone.png]] #+END_CENTER - If you're behind a proxy, git should be configured - accordingly. Check the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85]["Dealing with proxies" section]]. + accordingly. Check the [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["Dealing with proxies" section]]. - Git will then connect to Gitlab and fetch a whole copy of the repository. - RStudio should restart in a mode related to Git: diff --git a/module2/ressources/rstudio_fr.org b/module2/ressources/rstudio_fr.org index 6e4eb1d0631e52d81bb89f01f6277b2973861970..2237c92961afe5bda4bbb4efc1cf58774de8caad 100644 --- a/module2/ressources/rstudio_fr.org +++ b/module2/ressources/rstudio_fr.org @@ -86,11 +86,11 @@ ne sont pas toujours à jour : * Utiliser Git avec RStudio La première chose à faire est de configurer Git sur votre ordinateur. Pour ce faire, vous pouvez suivre la vidéo -[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/courseware/66bc811404b8481da5f794de54681c5e/2419fd0fb6a0484988ca9d65497dcaaf/1?activate_block_id=block-v1%3Ainria%2B41016%2Bsession01bis%2Btype%40vertical%2Bblock%407508aece244548349424dfd61ee3ba85][configurer Git pour Gitlab]] (en français) et le document -[[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/gitlab_fr.org][Git et Gitlab]] correspondant (en français). +[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][configurer Git pour Gitlab]] (en français) et le document +[[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/gitlab_fr.org][Git et Gitlab]] correspondant (en français). Vous pourrez alors utiliser Git avec RStudio. Pour ce faire, vous -pouvez suivre la vidéo [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/d132a854b0464ad29085cedaded23136][RStudio - Gitlab]] (en français) dont les étapes +pouvez suivre la vidéo [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/d132a854b0464ad29085cedaded23136][RStudio - Gitlab]] (en français) dont les étapes sont reprises ci-dessous. /(Nous vous signalons aussi cette/ [[https://www.youtube.com/embed/uHYcDQDbMY8][vidéo]] /(en anglais) ainsi que le/ [[https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html][tuto @@ -117,7 +117,7 @@ Ouvrir RStudio et procéder comme suit : [[file:rstudio_images/clone.png]] #+END_CENTER - Si vous êtes derrière un proxy, il faut le définir dans Git (voir le - paragraphe "Gérer les proxy" de la page sur [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session01bis/jump_to_id/7508aece244548349424dfd61ee3ba85][Git et Gitlab]]). + paragraphe "Gérer les proxy" de la page sur [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][Git et Gitlab]]). - Git se connecte à Gitlab et récupère une copie complète du dépôt. - RStudio redémarre dans un mode lié à Git : #+BEGIN_CENTER