# Emacs/org-mode

## Table of Contents

- Installing emacs, org-mode, ess, and auctex.
  - OS-specific installation procedure
    - Linux (Debian, Ubuntu)
    - Mac OS X
    - Windows
  - TODO A simple "reproducible research" emacs configuration
    - Step 0: Backup and download our configuration
    - Step 1: Prepare your journal
    - Step 2: Set up Emacs configuration
    - Step 3: Check whether the installation is working or not
    - Step 4: Open and play with your journal:
  - TODO A stub of replicable article
- Emacs Tips and tricks
  - Cheat-sheets
    - Emacs
    - Org-mode
  - Video tutorials
  - Additional useful emacs packages
    - Company-mode
    - Magit
  - Other resources

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.

## Installing emacs, org-mode, ess, and auctex.

### OS-specific installation procedure

#### 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:

- Debian (stretch) ships with emacs 25.1 and org-mode 9.0.3
- Ubuntu (bionic 18.04) ships with emacs 25.2 and org-mode 9.1.6
- Ubuntu (artful 17.04) ships with emacs 25.2 and org-mode 9.0.9

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.

#### Mac OS X

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

  - Emacs 26.1
  - Org-mode 9.1.13
  - ESS 17.11

  In that case you may have several versions of emacs installed on your machine and launching emacs from a terminal may not run the one you just installed. If anyone know how to get rid of this…

- Option 2: If you already use `brew`, simply do the following

      brew update
      brew install emacs [--with-cocoa]
      brew linkapps emacs
      brew tap homebrew/science
      brew install ess
      brew install auctex # The name may be slightly more complicated here
      brew install wget

#### Windows

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

- Emacs 26.1
- Org-mode 9.1.13
- ESS 17.11

### TODO A simple "reproducible research" emacs configuration

> 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 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 minimalistic 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).

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

#### 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: 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
    #+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 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 backed up in a revision control system like git. We leave it up to set this up but if you have any trouble, feel free to ask on the FUN forums.

### TODO A stub of replicable article

> 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.

## 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:

#### Emacs

- Common and step-by-step emacs shortcuts for our reproducible research configuration
- The official GNU emacs refcard
- Two graphical cheat-sheats by Sacha Hua on how to learn emacs and on how to learn emacs shortcuts.

#### Org-mode

- Common and step-by-step org-mode shortcuts for our reproducible research configuration
- The official org-mode refcard
- The official description of the org-mode syntax and a relatively concise description of the org-mode syntax.

### 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 webpage: http://company-mode.github.io/

#### Magit

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 behind the scene beforehand. If you feel this would be useful for you, you should follow the instructions from here: https://www.emacswiki.org/emacs/Magit

### Other resources

- The compact Org-mode Guide
- Many examples illustrating the use of different languages in org-mode