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mooc-rr-ressources
Commit 0859d634 authored by Konrad Hinsen's avatar Konrad Hinsen
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Revision of emacs/org-mode resources

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module2/ressources/emacs_orgmode.org
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......@@ -19,7 +19,7 @@ The next section provides information on how to install emacs.
* Installing emacs, org-mode, ess, and auctex.
** Linux (Debian, Ubuntu)
We provide here only instructions for debian-based distributions. Feel
We provide here only instructions for Debian-based distributions. Feel
free to contribute to this document to provide up-to-date information
for other distributions (e.g.n redhat, fedora).
......@@ -97,28 +97,21 @@ versions:
- Emacs 26.1
- Org-mode 9.1.13
- ESS 17.11
To have code pretty printing when exporting to html, it appears like
you should install the =htmlize= package, which is done by opening emacs
and typing the following command:
#+BEGIN_EXAMPLE
M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" key
#+END_EXAMPLE
*** Directory naming conventions
In all the following instructions, it is common to refer to your home
In the following instructions, we refer to your home
directory through the (UNIX) =~/= notation. On Windows, your home
directory should be something like =C:\Users\yourname=. Therefore,
whenever we mention the =~/org/= (resp. the =~/.emacs.d/=) directory this
means we are referring to =C:\Users\yourname\org= (resp.
=C:\Users\yourname\.emacs.d\=).
*** Making R and Python available to the console
When running a command, windows will look for the command in the
When running a command, Windows will look for the command in the
directories indicated in the =PATH= environment variable. If none of
these directories contains the command, Windows will stop and indicate
the command does not exist. To make sure R (, which may be in
something like =C:/Program Files/R/R-3.5.1/bin/x64/=) and Python (,
which may be in something like =C:/Program Files/Python/Python37/=) can
easily be run from emacs, you should thus configure the =PATH= variable
the command does not exist. To make sure R (which may be in
something like =C:/Program Files/R/R-3.5.1/bin/x64/=) and Python (which may be in something like =C:/Program Files/Python/Python37/=) can
easily be run from Emacs, you should thus configure the =PATH= variable
accordingly.
This requires to go through the "Environment Variable" editor as
......@@ -142,6 +135,14 @@ matplotlib.matplotlib_fname()
Open the =matplotlibrc= file and add a =#= at the beginning of the line
starting with =backend=, which amounts to use the default =Agg= value.
** All platforms: pretty code in HTML export
To have code pretty printing when exporting to HTML, you should
install the =htmlize= package, which is done by opening emacs and
typing the following command:
#+BEGIN_EXAMPLE
M-x package-install RET htmlize RET # where M-x means pressing the "Esc" key then the "x" 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
Emacs/Orgmode"/ in French). Watching it before following the
......@@ -157,10 +158,10 @@ minimalist one that is rather "/reproducible research/" oriented by
adding a few org-mode specific configurations.
** Step 0: Backup and download our configuration
The procedure we propose will wipe your already existing custom emacs
configuration if you already have one. *You should thus beforehand make
a backup of =~/.emacs= and of =~/.emacs.d/init.el=* (if these file
exists).
The procedure we propose will wipe your already existing custom Emacs
configuration if you have one. *You should thus beforehand make
a backup of =~/.emacs= and of =~/.emacs.d/init.el=* (if these files
exist).
#+begin_src shell :results output :exports none
export FILE_LIST="rr_org/init.el rr_org/journal.org"
......@@ -187,7 +188,7 @@ 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 [[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://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.
......@@ -231,10 +232,10 @@ is demonstrated in the [[https://app-learninglab.inria.fr/gitlab/learning-lab/mo
** Step 5: 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
backed up in a revision control system like git. We leave it up to you
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 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
réplicable avec Emacs/Orgmode"/ in French). Watching it before
following the instructions given in this section may help.
......@@ -262,7 +263,7 @@ tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
*Possible issues*:
- If the =make= command fails (especially on Mac), it may be because
emacs or something else is not correctly installed. In that case,
Emacs or something else is not correctly installed. In that case,
open the article directly with the following command:
#+begin_src sh :results output :exports both
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org
......@@ -282,16 +283,16 @@ If you remove the =# = in the beginning of the line, it will not be a
comment anymore and will indicate org-mode to stop evaluating every
chunk of code when exporting.
* Emacs Tips and tricks
* Emacs tips and tricks
** Cheat-sheets
Learning emacs and org-mode can be difficult as there is an inordinate
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
- [[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://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]].
- 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]].
*** 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://orgmode.org/worg/orgcard.html][The official org-mode refcard]]
......@@ -306,12 +307,12 @@ have smart completion in emacs for the most common languages. If you
feel this is needed, you should follow the instructions from the
official Web page: http://company-mode.github.io/
*** 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]] (/"Utilisation
Emacs/git"/ in French).
It is very powerful and we use it on a daily basis but you should
definitely understand what git does behind the scene beforehand. If
definitely understand what git does behind the scenes beforehand. If
you feel this would be useful for you, you should follow [[https://magit.vc/screenshots/][this visual
walk-through]] or [[https://www.emacswiki.org/emacs/Magit][this really short "crash course"]]. If you installed the
previous "/reproducible research/" emacs configuration, you can easily
......
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