Merge branch 'master' of gitlab.inria.fr:learninglab/mooc-rr/mooc-rr-ressources

module1/ressources/sequence1.org

@@ -279,3 +279,5 @@ The whole purpose of all these recording systems is to preserve values. They sho
 laboratory and should be adequate but not overelaborate. If too much is demanded of human nature, the system will break down.
 #+END_QUOTE 
 
+** Additional links
+A student of the course pointed to us a very interesting ressource on laboratory notebooks: [[https://colinpurrington.com/tips/lab-notebooks]].

module1/ressources/sequence4.org

@@ -13,8 +13,8 @@
 #+STARTUP: indent
 
 * Table of contents :TOC:
-- [[Version control with GitLab and Git]]
-- [[Version control with LibreOffice or DokuWiki]]
+- [[#version-control-with-gitlab-and-git-in-the-Reproducible-research-mooc][Version control with GitLab and Git]]
+- [[#version-control-with-libreoffice-or-dokuwiki][Version control with LibreOffice or DokuWiki]]
 
 * Version control with GitLab and Git in the "Reproducible research" MOOC
 We have created a GitLab server especially for this MOOC so that you can smoothly learn how to implement version control. 

module2/ressources/emacs_orgmode.org

@@ -158,7 +158,8 @@ instructions given in this section may help.
 Emacs comes with a very basic default configuration, so almost
 everyone wants to personalize it. Given the flexibility of Emacs, a
 configuration can become quite complex and in fact include what would
-otherwise be considered complete software packages. In the context of
+otherwise be considered complete software packages (see for example
+these Emacs Starter Kits [[https://kieranhealy.org/resources/emacs-starter-kit/][here]] or [[https://www.emacswiki.org/emacs/StarterKits][here]]). In the context of
 this MOOC, we propose a relatively minimalist configuration oriented
 towards "/reproducible research/" with Org-Mode. If you are new to
 Emacs, we strongly recommended that you use it with as little

module2/ressources/emacs_orgmode_fr.org

@@ -34,7 +34,7 @@ regarder la vidéo [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+sessi
   - [[#étape-6--ouvrez-et-commencez-à-utiliser--avec-votre-journal][Étape 6 : Ouvrez et commencez à utiliser  avec votre journal]]
 - [[#un-modèle-darticle-réplicable][Un modèle d'article réplicable]]
 - [[#emacs-trucs-et-astuces][Emacs trucs et astuces]]
-  - [[#pense-bête][Pense-bête]]
+  - [[#pense-bêtes][Pense-bêtes]]
   - [[#tutoriels-vidéo][Tutoriels vidéo]]
   - [[#paquets-emacs-utiles-supplémentaires][Paquets emacs utiles supplémentaires]]
   - [[#autres-ressources][Autres ressources]]
@@ -131,7 +131,7 @@ expliqué [[http://sametmax.com/ajouter-un-chemin-a-la-variable-denvironnement-p
 *** Installation et configuration de Matplotlib (bibliothèque graphique python)
 Ouvrez une console DOS et tapez la commande suivante :
 #+begin_src shell :results output :exports both
-python -m pip install install -U matplotlib
+python -m pip install -U matplotlib
 #+end_src
 [[file:emacs_orgmode_images/install_matplotlib.png]]
 
@@ -155,7 +155,8 @@ Cette section est illustrée dans une [[https://www.fun-mooc.fr/courses/course-v
 Emacs s'installe avec une configuration par défaut très basique que
 chacun va donc vouloir personnaliser. Compte tenu de la flexibilité
 d'Emacs, sa configuration peut vite devenir assez complexe et pourrait
-même faire l'objet d'un paquet à part entière. Dans le contexte de ce
+même faire l'objet d'un paquet à part entière (voir par exemple les
+différents Emacs Starter Kits [[https://kieranhealy.org/resources/emacs-starter-kit/][ici]] ou [[https://www.emacswiki.org/emacs/StarterKits][ici]]). Dans le contexte de ce
 MOOC, nous vous proposons une configuration relativement minimaliste
 orientée "/recherche reproductible/" avec Org-Mode. Si vous êtes peu
 familier d'Emacs, nous vous recommandons fortement de l'utiliser et de la modifier le moins possible. Il vous suffira de suivre

module2/ressources/jupyter.org

@@ -23,6 +23,7 @@ jupyter notebook
   - [[#making-sure-jupyter-allows-you-to-use-r][Making sure Jupyter allows you to use R]]
   - [[#latex-for-pdf-export][LaTeX for PDF export]]
   - [[#additional-tips][Additional tips]]
+  - [[#interacting-with-gitlab-and-git][Interacting with GitLab and Git]]
 
 * Jupyter tips and tricks
 The following [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][webpage]] lists several Jupyter tricks (in particular, it
@@ -344,14 +345,17 @@ Here are a few extensions that can ease your life:
   #+END_CENTER
   NB: In the first edition of the MOOC some people had issues making
   it work under Windows.
-*** • Interacting with GitLab and GitHub
+** • Interacting with GitLab and git
 To ease your experience, we added pull/push buttons that allow
 you to commit and sync with GitLab. This development was specific to
 the MOOC but inspired from a previous [[https://github.com/Lab41/sunny-side-up][proof of concept]]. We have
 recently discovered that someone else developed about at the same time
 a [[https://github.com/sat28/githubcommit][rather generic version of this Jupyter plugin]]. Otherwise, remember
 that it is very easy to insert a shell cell in Jupyter in which you
-can easily issue git commands. This is how we work most of the time.
+can easily issue git commands. This is how we work most of the time. If you choose this solution, you will have to configure Git on your
+computer. To do this, you can follow the video 
+[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][Configure git for Gitlab]] and read the document
+[[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/gitlab.org][Git and GitLab]].
 
 This being said, you may have noticed that Jupyter keeps a perfect
 track of the sequence in which cells have been run by updating the

module2/ressources/jupyter_fr.org

@@ -16,6 +16,7 @@
   - [[#sassurer-que-jupyter-vous-permet-dutiliser-r][S'assurer que Jupyter vous permet d'utiliser R]]
   - [[#latex-pour-la-génération-de-pdf][LaTeX pour la génération de PDF]]
   - [[#conseils-additionnels][Conseils additionnels]]
+  - [[#interaction-avec-gitlab-et-git][Interaction avec GitLab et git]]
 
 * Jupyter : Trucs et astuces
 Cette [[https://www.dataquest.io/blog/jupyter-notebook-tips-tricks-shortcuts/][page web]] (en anglais) recense un certain nombre d'astuces
@@ -381,7 +382,7 @@ vie :
   N.B. : Dans la première édition de ce MOOC, certains participants nous
   ont rapporté avoir eu des difficultés à faire fonctionner cette
   extension sous Windows.
-*** • Interaction avec GitLab et GitHub
+** • Interaction avec GitLab et git
 Pour rendre vous simplifier la vie, nous avons rajouté des boutons
 =pull/push= dans Jupyter qui vous permettent de synchroniser vos
 modifications avec GitLab. Ce développement spécifique pour ce MOOC
@@ -393,7 +394,10 @@ intéresse, c'est donc une piste intéressante à explorer. Sinon,
 souvenez-vous qu'il est très simple d'insérer une cellule shell dans
 Jupyter et vous pouvez facilement y insérer des commandes
 Git. C'est la façon dont nous travaillons en pratique la majorité du
-temps.
+temps. Si vous optez pour cette solution, il vous faudra configurer Git sur votre
+ordinateur. Pour ce faire, vous pouvez suivre la vidéo
+[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][configurer Git pour Gitlab]] et le document
+[[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/gitlab_fr.org][Git et Gitlab]] correspondant.
 
 Ceci étant dit, vous avez certainement remarqué que Jupyter conserve
 une trace parfaite de l'ordre dans lequel les cellules ont été

module2/ressources/rr_org/init.el

@@ -227,51 +227,64 @@ Entered on %U
      ))
   (setq org-src-preserve-indentation t)
 
-(require 'org-tempo nil t)
+(setq rrmooc/new-org-templates (version<= "9.2" (org-version)))
+(when  rrmooc/new-org-templates
+  (require 'org-tempo))
 
-(add-to-list 'org-structure-template-alist
-        '("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>"))
+(require 'subr-x)
+(defun rrmooc/add-org-template (old-style-template)
+  (add-to-list 'org-structure-template-alist
+	       (if rrmooc/new-org-templates
+		   (cons
+		    (first old-style-template)
+		    (string-trim-right (substring (second old-style-template) 8 -9)))
+		 old-style-template)))
+
+(unless rrmooc/new-org-templates
+  ;; this template is predefined in the new templating system
+  (rrmooc/add-org-template
+   '("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>")))
 
-(add-to-list 'org-structure-template-alist
-        '("m" "#+begin_src emacs-lisp :tangle init.el\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
+(rrmooc/add-org-template
+ '("m" "#+begin_src emacs-lisp\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("r" "#+begin_src R :results output :session *R* :exports both\n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("R" "#+begin_src R :results output graphics :file (org-babel-temp-file \"figure\" \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("RR" "#+begin_src R :results output graphics :file  (org-babel-temp-file (concat (file-name-directory (or load-file-name buffer-file-name)) \"figure-\") \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("p" "#+begin_src python :results output :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("P" "#+begin_src python :results output :session :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("PP" "#+begin_src python :results file :session :var matplot_lib_filename=(org-babel-temp-file \"figure\" \".png\") :exports both\nimport matplotlib.pyplot as plt\n\nimport numpy\nx=numpy.linspace(-15,15)\nplt.figure(figsize=(10,5))\nplt.plot(x,numpy.cos(x)/x)\nplt.tight_layout()\n\nplt.savefig(matplot_lib_filename)\nmatplot_lib_filename\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 
 (if (memq system-type '(windows-nt ms-dos))
     ;; Non-session shell execution does not seem to work under Windows, so we use
     ;; a named session just like for B.
-    (add-to-list 'org-structure-template-alist
+    (rrmooc/add-org-template
      '("b" "#+begin_src shell :session session :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
-  (add-to-list 'org-structure-template-alist
+  (rrmooc/add-org-template
    '("b" "#+begin_src shell :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>")))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("B" "#+begin_src shell :session *shell* :results output :exports both \n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
 
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("g" "#+begin_src dot :results output graphics :file \"/tmp/graph.pdf\" :exports both
-   digraph G {
-      node [color=black,fillcolor=white,shape=rectangle,style=filled,fontname=\"Helvetica\"];
-      A[label=\"A\"]
-      B[label=\"B\"]
-      A->B
-   }\n#+end_src" "<src lang=\"dot\">\n\n</src>"))
+digraph G {
+node [color=black,fillcolor=white,shape=rectangle,style=filled,fontname=\"Helvetica\"];
+A[label=\"A\"]
+B[label=\"B\"]
+A->B
+}\n#+end_src" "<src lang=\"dot\">\n\n</src>"))
 
 (global-set-key (kbd "C-c S-t") 'org-babel-execute-subtree)
 

module2/ressources/rr_org/init.org

@@ -83,7 +83,7 @@ document, simply =M-x org-babel-tangle=.
                                    ("melpa-stable" . 10)))
 #+END_SRC
 * Install missing packages
-#+begin_src emacs-lisp
+#+begin_src emacs-lisp :tangle init.el
 (dolist (pkg '(ess
                auctex
                htmlize
@@ -92,7 +92,7 @@ document, simply =M-x org-babel-tangle=.
     (package-install pkg)))
 #+end_src
 * Import environment variables
-#+begin_src emacs-lisp
+#+begin_src emacs-lisp :tangle init.el
 (exec-path-from-shell-initialize)
 (exec-path-from-shell-copy-env "PYTHONPATH")
 #+end_src
@@ -366,32 +366,47 @@ Additional shortcuts for navigating through org-mode documents:
 ** Adding source code blocks: 					       :LUKA:
 *** Enable the old template system with Orgmode 9.2 and later
 #+begin_src emacs-lisp :tangle init.el
-(require 'org-tempo nil t)
+(setq rrmooc/new-org-templates (version<= "9.2" (org-version)))
+(when  rrmooc/new-org-templates
+  (require 'org-tempo))
+#+end_src
+*** Template definitions that work with the old and new templating systems
+#+begin_src emacs-lisp :tangle init.el
+(require 'subr-x)
+(defun rrmooc/add-org-template (old-style-template)
+  (add-to-list 'org-structure-template-alist
+	       (if rrmooc/new-org-templates
+		   (cons
+		    (first old-style-template)
+		    (string-trim-right (substring (second old-style-template) 8 -9)))
+		 old-style-template)))
 #+end_src
 *** With capital letters:
 To use this type <s and then TAB
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
-        '("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>"))
+(unless rrmooc/new-org-templates
+  ;; this template is predefined in the new templating system
+  (rrmooc/add-org-template
+   '("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>")))
 #+end_src
 *** Emacs-elisp code:
 To use this type <m and then TAB
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
-        '("m" "#+begin_src emacs-lisp :tangle init.el\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
+(rrmooc/add-org-template
+ '("m" "#+begin_src emacs-lisp\n\n#+end_src" "<src lang=\"emacs-lisp\">\n\n</src>"))
 #+end_src
 
 *** R code:
 To use this type <r and then TAB. This creates an R block for textual output.
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("r" "#+begin_src R :results output :session *R* :exports both\n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 #+end_src
 
 To use this type <R and then TAB. This creates an R block for graphics
 that are stored in the =/tmp/=.
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("R" "#+begin_src R :results output graphics :file (org-babel-temp-file \"figure\" \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 #+end_src
 
@@ -399,23 +414,23 @@ To use this type <RR and then TAB. This creates an R block for
 graphics that are stored in the directory of the current file.
 
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("RR" "#+begin_src R :results output graphics :file  (org-babel-temp-file (concat (file-name-directory (or load-file-name buffer-file-name)) \"figure-\") \".png\") :exports both :width 600 :height 400 :session *R* \n\n#+end_src" "<src lang=\"R\">\n\n</src>"))
 #+end_src
 *** Python code
 To use this type <p and then TAB
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("p" "#+begin_src python :results output :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 #+end_src
 
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("P" "#+begin_src python :results output :session :exports both\n\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 #+end_src
 
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("PP" "#+begin_src python :results file :session :var matplot_lib_filename=(org-babel-temp-file \"figure\" \".png\") :exports both\nimport matplotlib.pyplot as plt\n\nimport numpy\nx=numpy.linspace(-15,15)\nplt.figure(figsize=(10,5))\nplt.plot(x,numpy.cos(x)/x)\nplt.tight_layout()\n\nplt.savefig(matplot_lib_filename)\nmatplot_lib_filename\n#+end_src" "<src lang=\"python\">\n\n</src>"))
 #+end_src
 *** Bash "sh" code:
@@ -424,28 +439,28 @@ To use this type <b and then TAB
 (if (memq system-type '(windows-nt ms-dos))
     ;; Non-session shell execution does not seem to work under Windows, so we use
     ;; a named session just like for B.
-    (add-to-list 'org-structure-template-alist
+    (rrmooc/add-org-template
      '("b" "#+begin_src shell :session session :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
-  (add-to-list 'org-structure-template-alist
+  (rrmooc/add-org-template
    '("b" "#+begin_src shell :results output :exports both\n\n#+end_src" "<src lang=\"sh\">\n\n</src>")))
 #+end_src
 
 To use this type <B and then TAB. This comes with a session argument
 (e.g., in case you want to keep ssh connexions open).
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("B" "#+begin_src shell :session *shell* :results output :exports both \n\n#+end_src" "<src lang=\"sh\">\n\n</src>"))
 #+end_src
 *** Graphviz
 #+begin_src emacs-lisp :tangle init.el
-(add-to-list 'org-structure-template-alist
+(rrmooc/add-org-template
  '("g" "#+begin_src dot :results output graphics :file \"/tmp/graph.pdf\" :exports both
-   digraph G {
-      node [color=black,fillcolor=white,shape=rectangle,style=filled,fontname=\"Helvetica\"];
-      A[label=\"A\"]
-      B[label=\"B\"]
-      A->B
-   }\n#+end_src" "<src lang=\"dot\">\n\n</src>"))
+digraph G {
+node [color=black,fillcolor=white,shape=rectangle,style=filled,fontname=\"Helvetica\"];
+A[label=\"A\"]
+B[label=\"B\"]
+A->B
+}\n#+end_src" "<src lang=\"dot\">\n\n</src>"))
 #+end_src
 ** Evaluating whole subtree:                                          :LUKA:
 #+begin_src emacs-lisp :tangle init.el

module2/ressources/rstudio.org

@@ -89,8 +89,8 @@ 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+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+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["git/GitLab configuration" tutorial]]* (in French).
+). Before proceeding, make sure you also have followed the
+*[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85]["git/GitLab configuration" tutorial]]*.
 
 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

module2/ressources/rstudio_fr.org

@@ -93,11 +93,11 @@ 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+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).
+[[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/7508aece244548349424dfd61ee3ba85][configurer Git pour Gitlab]] et le document
+[[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/gitlab_fr.org][Git et Gitlab]] correspondant.
 
 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+session02/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]] 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