diff --git a/module2/ressources/emacs_orgmode.org b/module2/ressources/emacs_orgmode.org index 28ebe3bfc30e4ccf146e8e43f36cdb3f86f3818e..de1bdca1b4a0fc050144703e228479fd81ffc61b 100644 --- a/module2/ressources/emacs_orgmode.org +++ b/module2/ressources/emacs_orgmode.org @@ -112,7 +112,7 @@ mkdir -p ~/org/ Then copy =rr_org/journal.org= file in your =~/org/= directory. This file will be your laboratory notebook and all the notes you will capture with =C-c c= will go automatically go in this file. The first -entry of this notebook is populated with [[file:rr_org/journal.org::*Org-mode][many emacs shortcuts]] that you +entry of this notebook is populated with [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][many emacs shortcuts]] that you should give a try. *** Step 2: Set up Emacs configuration Copy =rr_org/init.el= in your =~/.emacs.d/= directory. @@ -137,7 +137,7 @@ worked. In the video, we already have demonstrated the main features and shortcuts of emacs/org-mode that will help you maintain a document and benefit from literate programming. The list of features and shortcuts -is demonstrated in the [[file:rr_org/journal.org::*Emacs%20shortcuts][first entry of your labbook]]. +is demonstrated in the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][first entry of your labbook]]. *** Step 4: Open and play with your journal: In step 1, you were told to create an journal in =~org/journal.org=. First you probably want to make sure this file is @@ -150,7 +150,7 @@ open a terminal and run the commands =R=, =pdflatex=, and =python=, you will not able to generate this document. When being compiled, the article downloads the corresponding LaTeX packages so you also need to have a working =wget= command (alternatively, it uses =curl=). Once downloaded, you may still read the -source ([[file:replicable_article/article.org][article.org]]) and understand how it works though. +source ([[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]) and understand how it works though. #+begin_src shell :results output :exports none make -C replicable_article/ all replicable_article.tgz @@ -160,7 +160,7 @@ make -C replicable_article/ all replicable_article.tgz Download the following [[file:replicable_article/replicable_article.tgz][archive]] and untar it. and simply =make= to generate the -article. You should then be able to open the [[file: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: #+begin_src sh :results output :exports both wget --no-check-certificate -O replicable.tgz https://github.com/alegrand/RR_webinars/raw/master/1_replicable_article_laboratory_notebook/replicable/replicable.tgz ### Fix the broken URL @@ -181,7 +181,7 @@ system-wide. In that case, try to remove the =-q= in the previous command line to load your personal emacs configuration. Finally, when you'll be tired of always reexecuting all the source -code when exporting, just look for the following line in [[file:replicable_article/article.org][article.org]]: +code when exporting, just look for the following line in [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]: #+BEGIN_EXAMPLE # #+PROPERTY: header-args :eval never-export #+END_EXAMPLE @@ -195,12 +195,12 @@ 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: *** Emacs -- [[file:org/journal.org::*Emacs%20shortcuts][Common and step-by-step emacs shortcuts for our /reproducible research/ configuration]] +- [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step emacs shortcuts for our /reproducible research/ configuration]] - [[https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf][The official GNU emacs refcard]] - Two graphical cheat-sheats by Sacha Hua on [[http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png][how to learn emacs]] and on [[http://sachachua.com/blog/wp-content/uploads/2013/08/20130830-Emacs-Newbie-How-to-Learn-Emacs-Keyboard-Shortcuts.png][how to learn emacs shortcuts]]. *** Org-mode -- [[file:org/journal.org::*Org-mode][Common and step-by-step org-mode shortcuts for our /reproducible research/ configuration]] +- [[https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][Common and step-by-step org-mode shortcuts for our /reproducible research/ configuration]] - [[https://orgmode.org/worg/orgcard.html][The official org-mode refcard]] - [[https://orgmode.org/worg/dev/org-syntax.html][The official description of the org-mode syntax]] and a [[https://gist.github.com/hoeltgman/3825415][relatively concise description of the org-mode syntax]]. ** Video tutorials