+Disclaimer: The two sections A simple "reproducible research" +emacs configuration and A stub of replicable article explain how to +set up org-mode for this MOOC. You really should follow them +carefully or you may have trouble doing the exercices later on. +
-We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information @@ -123,9 +125,9 @@ which is now deprecated.
Option 1: Install the .dmg file from Vincent Goulet:
@@ -158,9 +160,9 @@ brew install wget
Install the .exe file from Vincent Goulet:
https://vigou3.github.io/emacs-modified-windows/. It ships with recent
@@ -174,9 +176,15 @@ versions:
+++There will be a mini video illustrating these steps at some point +
+
Emacs comes with very basic default configuration and it appears like everyone has its own taste. You will for example find here several @@ -189,9 +197,9 @@ adding a few org-mode specific configurations.
The procedure we propose will wipe your already existing custom emacs configuration if you already have one. You should thus beforehand make @@ -200,7 +208,7 @@ exists).
-Then download this archive and uncompress it. It contains the +Then download this archive and uncompress it. It contains the following files and we will refer to them in the following:
@@ -212,9 +220,9 @@ rr_org/journal.org
Create an org/ directory in the top of your home:
org/ directory in the top of your home:
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 many emacs shortcuts that you
+entry of this notebook is populated with many emacs shortcuts that you
should give a try.
Copy rr_org/init.el in your ~/.emacs.d/ directory.
emacs -q -l rr_org/init.el
Open a new instance of Emacs and open a foo.org file. Copy the
following lines in this file:
@@ -274,13 +282,13 @@ 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 first entry of your labbook.
+is demonstrated in the first entry of your labbook.
In step 1, you were told to create an journal in
~org/journal.org. First you probably want to make sure this file is
@@ -291,58 +299,126 @@ forums.
++ ++There will be a mini video illustrating these steps at some point +
+
+Remember, you need a working LaTeX and R environment. If you can't
+open a terminal and run the commands R, pdflatex, and python, you will not be
+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 (article.org) and understand how it works though.
+
+Download the following archive and untar it. +
+ +
+ and simply make to generate the
+article. You should then be able to open the resulting article. This
+is summarized in the following command:
+
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 +tar zxf replicable.tgz; cd replicable; make ; evince article.pdf +
+If the make command fails (especially on Mac), it may be because emacs
+or something else is not correctly installed. In that case, open the
+article directly with the following command:
+
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org +
+and export it to pdf with the following shortcut: C-c C-e l o
+
+If it still doesn't work and emacs complains about not finding ESS, it
+may be because you installed ESS in your home instead of
+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 article.org: +
++# #+PROPERTY: header-args :eval never-export ++
+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.
+
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:
For those of you who prefer video explanations, here is a Youtube channel with many step by step emacs tutorials.
Company-mode is a text completion framework for Emacs. It allows to have smart completion in emacs for the most common languages. If you @@ -351,9 +427,9 @@ official webpage: http://company-mode.g
Magit is an emacs interface for Git. It is very powerfull and we use it on a daily basis but you should definitely understand what git does @@ -364,9 +440,9 @@ you should follow the instructions from here:
-Remember, you need a working LaTeX and R environment. If you can't
-open a terminal and run the commands R and pdflatex, you will not be
-able to generate this document. The article downloads the
-corresponding LaTeX packages so you also need to have a working wget
-command (alternatively, you can use curl). You may still read the
-source (article.org) and understand how it works though.
-
-Download the archive, untar it and simply make to generate the -article. You should then be able to open the resulting article. This -is summarized in the following command: -
-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 -tar zxf replicable.tgz; cd replicable; make ; evince article.pdf --
-If the make command fails (especially on Mac), it may be because emacs
-or something else is not correctly installed. In that case, open the
-article directly with the following command:
-
emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)" article.org --
-and export it to pdf with the following shortcut: C-c C-e l o
-
-If it still doesn't work and emacs complains about not finding ESS, it
-may be because you installed ESS in your home instead of
-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 article.org: -
--# #+PROPERTY: header-args :eval never-export --
-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.
-
