Then copy =rr_org/journal.org= file in your =~/org/= directory. This
Then copy =rr_org/journal.org= file in your =~/org/= directory. This
file will be your laboratory notebook and all the notes you will
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
capture with =C-c c= will go automatically go in this file. The first
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
entry of this notebook is populated with [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][many Emacs shortcuts]] that you
should give a try.
should give a try.
** Step 2: Set up Emacs configuration
** Step 2: Set up Emacs configuration
Copy =rr_org/init.el= in your =~/.emacs.d/= directory.
Copy =rr_org/init.el= in your =~/.emacs.d/= directory.
...
@@ -249,7 +249,7 @@ worked.
...
@@ -249,7 +249,7 @@ worked.
In the video, we already have demonstrated the main features and
In the video, we already have demonstrated the main features and
shortcuts of emacs/org-mode that will help you maintain a document and
shortcuts of emacs/org-mode that will help you maintain a document and
benefit from literate programming. The list of features and shortcuts
benefit from literate programming. The list of features and shortcuts
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]].
is demonstrated in the [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][first entry of your labbook]].
** Step 5: Open and play with your journal:
** Step 5: Open and play with your journal:
In step 1, you were told to create an journal in
In step 1, you were told to create an journal in
=~org/journal.org=. First you probably want to make sure this file is
=~org/journal.org=. First you probably want to make sure this file is
...
@@ -266,7 +266,7 @@ open a terminal and run the commands =R=, =pdflatex=, and =python=, you will not
...
@@ -266,7 +266,7 @@ 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
able to generate this document. When being compiled, the article downloads the
corresponding LaTeX packages so you also need to have a working =wget=
corresponding LaTeX packages so you also need to have a working =wget=
command (alternatively, it uses =curl=). Once downloaded, you may still read the
command (alternatively, it uses =curl=). Once downloaded, you may still read the
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.
source ([[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org]]) and understand how it works though.
#+begin_src shell :results output :exports none
#+begin_src shell :results output :exports none
make -C replicable_article/ all ../replicable_article.tgz
make -C replicable_article/ all ../replicable_article.tgz
...
@@ -275,7 +275,7 @@ make -C replicable_article/ all ../replicable_article.tgz
...
@@ -275,7 +275,7 @@ make -C replicable_article/ all ../replicable_article.tgz
#+RESULTS:
#+RESULTS:
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
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://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.pdf][resulting article]]. This
@@ -296,7 +296,7 @@ tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
...
@@ -296,7 +296,7 @@ tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
command line to load your personal emacs configuration.
command line to load your personal emacs configuration.
Finally, when you'll be tired of always re-executing all the source
Finally, when you'll be tired of always re-executing all the source
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]]:
code when exporting, just look for the following line in [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]:
#+BEGIN_EXAMPLE
#+BEGIN_EXAMPLE
# #+PROPERTY: header-args :eval never-export
# #+PROPERTY: header-args :eval never-export
#+END_EXAMPLE
#+END_EXAMPLE
...
@@ -310,12 +310,12 @@ Learning Emacs and Org-Mode can be difficult as there is an inordinate
...
@@ -310,12 +310,12 @@ Learning Emacs and Org-Mode can be difficult as there is an inordinate
amount of shortcuts. Many people have thus come up with
amount of shortcuts. Many people have thus come up with
cheat-sheats. Here is a selection in case it helps:
cheat-sheats. Here is a selection in case it helps:
*** Emacs
*** Emacs
- [[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://gitlab.inria.fr/learninglab/mooc-rr/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]]
- [[https://www.gnu.org/software/emacs/refcards/pdf/refcard.pdf][The official GNU emacs refcard]]
- Two graphical cheat-sheats by Sacha Chua on [[http://sachachua.com/blog/wp-content/uploads/2013/05/How-to-Learn-Emacs-v2-Large.png][how to learn Emacs]] and on
- Two graphical cheat-sheats by Sacha Chua 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]].
[[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
*** Org-mode
- [[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://gitlab.inria.fr/learninglab/mooc-rr/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/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]].
- [[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]].