Emacs/org-mode

Table of Contents

Disclaimer: The two sections A simple "reproducible research" emacs configuration and A stub of replicable article explain how to set up emacs/org-mode for this MOOC. These are very important sections in the context of this MOOC. These sections are illustrated in two out of the three video tutorials of this sequence, and which you really should follow carefully. Otherwise, you may have trouble doing the exercises later on. Likewise, I strongly encourage you to watch the "emacs and git" video tutorial available at the same place.

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 free to contribute to this document to provide up-to-date information for other distributions (e.g.n redhat, fedora).

Today, the stable versions of the most common distributions provide recent enough versions of emacs and org-mode:

If your distribution is older than this, well, it may be a good time for upgrading…

Simply run (as root): 

apt-get update ; apt-get install emacs25 org-mode ess r-base auctex

Then make sure you have a sufficiently recent version of emacs. 

emacs --version 2>&1 | head -n 1

GNU Emacs 25.2.2

Likewise, you'll want to check you have a recent version of org-mode: 

emacs -batch --funcall "org-version" 2>&1 | grep version

Org mode version 9.1.11 (9.1.11-dist @ /usr/share/emacs/25.2/site-lisp/elpa/org-9.1.11/)

The version numbers you get will depend on the distribution you are running. You really want to make sure you do not rely on org-mode 8, which is now deprecated.

macOS

Note: macOS comes with a prehistoric command-line-only version of Emacs located at /usr/bin/emacs. It's best to forget about it.

  • Option 1: Install the .dmg file from Vincent Goulet: https://vigou3.gitlab.io/emacs-modified-macos/. It ships with recent versions:

    • Emacs 26.1
    • Org-mode 9.1.13
    • ESS 17.11

    If you install this version of Emacs, or in fact any other version of Emacs distributed as a clickable application in a .dmg file, you must type the full path to the executable if you want to run Emacs from a terminal. For example, if your clickable application is at /Applications/Emacs.app, then the executable is at /Applications/Emacs.app/Contents/MacOS/Emacs

  • Option 2: If you use Homebrew, do the following: 

    brew update
brew install emacs --with-cocoa
brew linkapps emacs
brew install wget
brew tap dunn/emacs
brew install auctex
brew tap brewsci/science
brew install ess

    This provides an emacs command for use from the command line, plus a clickable application at Cellar/emacs/26.1_1/Emacs.app inside your Homebrew directory. If you installed Homebrew at the default location /usr/local, then this is /usr/local/Cellar/emacs/26.1_1/Emacs.app. If you installed Homebrew on an account with administrator privileges, you can add 

    brew linkapps emacs

    in order to make Emacs accessible directly from /Applications.

Windows

Install the .exe file from Vincent Goulet: https://vigou3.gitlab.io/emacs-modified-windows/. It ships with recent versions:

  • Emacs 26.1
  • Org-mode 9.1.13
  • ESS 17.11

Directory naming conventions

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 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 accordingly.

This requires to go through the "Environment Variable" editor as explained here.

Installing and configuring Matplotlib (graphic python library)

Open an DOS console and type the following command: 

python -m pip install -U matplotlib

install_matplotlib.png

Then you will want to deactivate interactive plots in matplotlib. To this end, you first need to know where the matplotlib configuration is located. Open a python console the type the following code: 

import matplotlib
matplotlib.matplotlib_fname()

matplotlib.png

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: 

M-x package-install RET htmlize RET    # where M-x means pressing the "Esc" key then the "x" key

A simple "reproducible research" emacs configuration

This section is illustrated in a video tutorial ("Mise en place Emacs/Orgmode" in French). Watching it before following the instructions given in this section may help.

Emacs comes with very basic default configuration and it appears like everyone has its own taste. You will for example find here several default Emacs configurations that reflect the preferences of their creators. Likewise the configuration of Org-Mode is incredibly flexible (see for example the org-mode website for more references). In the context of this MOOC, we propose you a relatively 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 have one. You should thus beforehand make a backup of ~/.emacs and of ~/.emacs.d/init.el (if these files exist).

Then download this archive and uncompress it. It contains the following files and we will refer to them in the following: 

rr_org/init.el
rr_org/journal.org

Alternatively, the files you are looking for are available here.

Step 1: Prepare your journal

Create an org/ directory in the top of your home: 

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 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.

Alternatively, if you do not want to mess with your already existing emacs configuration, you may launch emacs with this specific configuration with the following command: emacs -q -l rr_org/init.el.

Step 3: Adapt the configuration to your specific needs if required

There are two situations in which it might be necessary to modify init.el:

  1. Your network environment forces you to use a proxy for access to Web sites (HTTP(S) protocol).

  2. You have multiple installations of Python or R on your computer, or they are in unusual places and not fully configured. If you can run

    • "python3" and "R" under Linux and macOS
    • "Python" and "R" under Windows

    in a terminal without getting an error message, then you should not have to do anything.

If you do have to modify init.el, check the comments at the beginning of the file for instructions.

Step 4: Check whether the installation is working or not

Open a new instance of Emacs and open a foo.org file. Copy the following lines in this file: 

#+begin_src shell :session foo :results output :exports both
ls -la # or dir under windows
#+end_src

Put your cursor inside this code block and execute it with the following command: C-c C-c (If you are not familiar with Emacs commands, this one means 'Ctrl + C' twice)

A #+RESULTS: block with the result of the command should appear if it 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.

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 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 a replicable article

This section is illustrated in a video tutorial ("Écrire un article réplicable avec Emacs/Orgmode" in French). Watching it before following the instructions given in this section may help.

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, uncompress 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_article.tgz https://app-learninglab.inria.fr/gitlab/learning-lab/mooc-rr-ressources/raw/master/module2/ressources/replicable_article.tgz
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, 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 re-executing 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.

Emacs tips and tricks

Cheat-sheets

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:

Video tutorials

For those of you who prefer video explanations, here is a Youtube channel with many step by step emacs tutorials.

Additional useful emacs packages

Company-mode

Company-mode is a text completion framework for Emacs. It allows to 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

Magit is an Emacs interface for Git. Its usage is briefly illustrated in the context of this MOOC in a 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 scenes beforehand. If you feel this would be useful for you, you should follow this visual walk-through or this really short "crash course". If you installed the previous "reproducible research" emacs configuration, you can easily invoke magit by using C-x g.