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mooc-rr-ressources
Commit 04f42b47 authored by Laurence Farhi's avatar Laurence Farhi
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remplacement des liens app-learninglab.inria.fr/gitlab par gitlab.inria.fr si... 

remplacement des liens app-learninglab.inria.fr/gitlab par gitlab.inria.fr si possible + remplacement sessions01bis par session02
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module2/ressources/emacs_orgmode.org
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...@@ -10,10 +10,10 @@ ...@@ -10,10 +10,10 @@
and /A stub of replicable article/ explain how to set up and /A stub of replicable article/ explain how to set up
emacs/org-mode for this MOOC. These are very important sections in the emacs/org-mode for this MOOC. These are very important sections in the
context of this MOOC. *These sections are illustrated in two 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 really should follow carefully*. *Otherwise, you may have trouble doing
the exercises later on*. Likewise, I strongly encourage you to watch 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. 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 ...@@ -164,7 +164,7 @@ M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key
#+END_EXAMPLE #+END_EXAMPLE
* A simple "/reproducible research/" emacs configuration * 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 Emacs/Orgmode"/ in French). Watching it before following the
instructions given in this section may help. instructions given in this section may help.
...@@ -189,7 +189,7 @@ tar zcf rr_org_archive.tgz $FILE_LIST ...@@ -189,7 +189,7 @@ tar zcf rr_org_archive.tgz $FILE_LIST
#+RESULTS: #+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: following files and we will refer to them in the following:
#+begin_src shell :results output :exports results #+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 ...@@ -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 to set this up but if you have any trouble, feel free to ask on the
FUN forums. FUN forums.
* A stub of a replicable article * 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 réplicable avec Emacs/Orgmode"/ in French). Watching it before
following the instructions given in this section may help. following the instructions given in this section may help.
...@@ -274,11 +274,11 @@ make -C replicable_article/ all ../replicable_article.tgz ...@@ -274,11 +274,11 @@ make -C replicable_article/ all ../replicable_article.tgz
#+RESULTS: #+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 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: is summarized in the following command:
#+begin_src sh :results output :exports both #+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 tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
#+end_src #+end_src
...@@ -329,7 +329,7 @@ feel this is needed, you should follow the instructions from the ...@@ -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/]] official Web page: [[http://company-mode.github.io/][http://company-mode.github.io/]]
*** Magit *** Magit
[[https://magit.vc/][Magit]] is an Emacs interface for Git. Its usage is briefly illustrated [[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). ("/Utilisation Emacs/git/" in French).
It is very powerful and we use it on a daily basis but you should It is very powerful and we use it on a daily basis but you should
......
module2/ressources/gitlab.org
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...@@ -24,7 +24,7 @@ GitLab. ...@@ -24,7 +24,7 @@ GitLab.
This document describes the software you need to have installed on This document describes the software you need to have installed on
your machine and how to handle authentication. The "Configuring Git" 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 Please read all these instructions carefully, in particular the one on
"Configuring your password on GitLab". "Configuring your password on GitLab".
...@@ -88,7 +88,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment ...@@ -88,7 +88,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment
(possibly several times). (possibly several times).
1. Get your default password using the [[https://app-learninglab.inria.fr/jupyterhub/services/password][Gitlab credentials retrieval 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 #+BEGIN_CENTER
[[file:gitlab_images/password_retrieval.png]] [[file:gitlab_images/password_retrieval.png]]
#+END_CENTER #+END_CENTER
...@@ -106,7 +106,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment ...@@ -106,7 +106,7 @@ step of changing your =~/.git-credentials= in the Jupyter environment
#+BEGIN_CENTER #+BEGIN_CENTER
[[file:gitlab_images/erreur405.png]] [[file:gitlab_images/erreur405.png]]
#+END_CENTER #+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 /Note: Again, you have to access Gitlab from the FUN platform
otherwise you may get a 405 error/ /when trying to direcly open otherwise you may get a 405 error/ /when trying to direcly open
......
module2/ressources/jupyter.org
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...@@ -76,7 +76,7 @@ to set up your own Jupyter on your computer and benefit from these extensions. ...@@ -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 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 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 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 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 essence. But perfection does not exist anyway and using Jupyter
......
module2/ressources/rstudio.org
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...@@ -84,9 +84,9 @@ of these documents: ...@@ -84,9 +84,9 @@ of these documents:
* Using Git from RStudio * Using Git from RStudio
If you have never used git with RStudio, *we strongly advise that you 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 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 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 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: ...@@ -112,7 +112,7 @@ Open RStudio and do the following steps:
[[file:rstudio_images/clone.png]] [[file:rstudio_images/clone.png]]
#+END_CENTER #+END_CENTER
- If you're behind a proxy, git should be configured - 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 - Git will then connect to Gitlab and fetch a whole copy of the
repository. repository.
- RStudio should restart in a mode related to Git: - RStudio should restart in a mode related to Git:
......
module2/ressources/rstudio_fr.org
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...@@ -86,11 +86,11 @@ ne sont pas toujours à jour : ...@@ -86,11 +86,11 @@ ne sont pas toujours à jour :
* Utiliser Git avec RStudio * Utiliser Git avec RStudio
La première chose à faire est de configurer Git sur votre La première chose à faire est de configurer Git sur votre
ordinateur. Pour ce faire, vous pouvez suivre la vidéo 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://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][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://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 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. 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 /(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 : ...@@ -117,7 +117,7 @@ Ouvrir RStudio et procéder comme suit :
[[file:rstudio_images/clone.png]] [[file:rstudio_images/clone.png]]
#+END_CENTER #+END_CENTER
- Si vous êtes derrière un proxy, il faut le définir dans Git (voir le - 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. - Git se connecte à Gitlab et récupère une copie complète du dépôt.
- RStudio redémarre dans un mode lié à Git : - RStudio redémarre dans un mode lié à Git :
#+BEGIN_CENTER #+BEGIN_CENTER
......
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