# -*- mode: org -*-
#+TITLE:     Emacs/org-mode
#+DATE: June, 2018
#+STARTUP: overview indent
#+OPTIONS: num:nil toc:t
#+PROPERTY: header-args :eval never-export

*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 [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][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 [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4]["emacs and git" video tutorial available at the same place]].

The next section provides information on how to install emacs.

* Table of Contents                                                     :TOC:
- [[#installing-emacs][Installing Emacs]]
  - [[#linux-debian-ubuntu][Linux (Debian, Ubuntu)]]
  - [[#macos][macOS]]
  - [[#windows][Windows]]
- [[#a-simple-reproducible-research-emacs-configuration][A simple "reproducible research" emacs configuration]]
  - [[#step-0-backup-and-remove-your-previous-configuration][Step 0: Backup and remove your previous configuration]]
  - [[#step-1-download-our-configuration][Step 1: Download our configuration]]
  - [[#step-2-prepare-your-journal][Step 2: Prepare your journal]]
  - [[#step-3-put-the-emacs-configuration-file-in-the-right-place][Step 3: Put the Emacs configuration file in the right place]]
  - [[#step-4-adapt-the-configuration-to-your-specific-needs-if-required][Step 4: Adapt the configuration to your specific needs if required]]
  - [[#step-5-check-whether-the-installation-is-working-or-not][Step 5: Check whether the installation is working or not]]
  - [[#step-6-open-and-play-with-your-journal][Step 6: Open and play with your journal:]]
- [[#a-stub-of-a-replicable-article][A stub of a replicable article]]
- [[#emacs-tips-and-tricks][Emacs tips and tricks]]
  - [[#cheat-sheets][Cheat-sheets]]
  - [[#video-tutorials][Video tutorials]]
  - [[#additional-useful-emacs-packages][Additional useful emacs packages]]
  - [[#other-resources][Other resources]]

* Installing Emacs
In the following we describe for each platform the installation method that we consider most convenient. There are other options that may be preferable in particular situations, so you may want to look at the [[https://www.gnu.org/software/emacs/download.html][Emacs Web site]] for details, but we strongly suggest you first try the method we recommend.

At the end of the installation procedure, you should have one of

 1. Emacs 26 (the latest version)
 2. Emacs 25 plus Org-Mode 9

Emacs 25 comes with Org-Mode 8, which is not compatible with our examples. So if you use Emacs 25, you must separately install Org-Mode 9. Emacs 26 already includes Org-Mode 9.

Our MOOC also requires a few extra Emacs packages: [[https://ess.r-project.org/][ESS]] (for working with the R language) and [[https://www.gnu.org/software/auctex/][AUCTeX]] (for editing LaTeX). They will be installed automatically the first time you start Emacs if you use the configuration described under [[#a-simple-reproducible-research-emacs-configuration][A simple "reproducible research" emacs configuration]].

** 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).

These are the versions of Emacs that various distributions provide:
- Debian (stretch) ships with [[https://packages.debian.org/stretch/emacs25][emacs 25.1]] and [[https://packages.debian.org/stretch/org-mode][org-mode 9.0.3]]
- Ubuntu (bionic 18.04) ships with [[https://packages.ubuntu.com/bionic/emacs25][emacs 25.2]] and [[https://packages.ubuntu.com/bionic/org-mode][org-mode 9.1.6]]
- Ubuntu (artful 17.04) ships with [[https://packages.ubuntu.com/artful/emacs25][emacs 25.2]] and [[https://packages.ubuntu.com/artful/org-mode][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):
#+begin_src sh :results output :exports both
apt-get update ; apt-get install emacs25 org-mode
#+end_src

Then verify that you have a sufficiently recent version of Emacs.
#+begin_src sh :results output :exports both
emacs --version 2>&1 | head -n 1
#+end_src

#+RESULTS:
: GNU Emacs 25.2.2

Likewise, you'll want to check you have a recent version of Org-Mode:
#+begin_src sh :results output :exports both
emacs -batch --funcall "org-version" 2>&1 | grep version
#+end_src

#+RESULTS:
: 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.

The Web site https://emacsformacosx.com/ proposes precompiled Emacs versions for macOS. Download the latest version (the one that figures prominently on the page) and install it like you would install any other macOS application, by copying =Emacs.app= from the downloaded disk image to a convenient location on your computer.

If you like working in a terminal (the =Terminal.app= from macOS, or an enhanced one such as [[https://iterm2.com/][iTerm2]]), the standard macOS way of opening a file in Emacs is =open -a Emacs.app /path/to/my/file.txt=. This will launch Emacs, unless it is already running, and then ask Emacs to open the file. Note that this is different from the Unix/Linux way of running Emacs, which is what you see in the videos. Under Linux, you type "emacs /path/to/my/file.txt" in the terminal, which always starts a fresh copy of Emacs.

*** Advanced topics - not required for following the MOOC
For advanced uses of Emacs, such as calling Emacs from a Makefile to automate document processing, you have to adopt the Unix way also under macOS, because this is the only way to provide parameters other than filenames. However, you have to enter the full path to the executable. Assuming that you have copied =Emacs.app= to =/path/to/emacs=, this is =/path/to/emacs/Emacs.app/Contents/MacOS/Emacs=. If you just type =emacs=, you will use the prehistoric command-line-only version at =/usr/bin/emacs= provided by Apple. You can of course make the Emacs executable more easily accessible using a shell alias, or by putting =/path/to/emacs/Emacs.app/Contents/MacOS/= on your =$PATH=. See the [[https://www.gnu.org/software/bash/manual/bashref.html][bash manual]] for details and explanation.

Be aware that running Emacs the Unix way implies some subtle differences compared to running Emacs the macOS way. In particular, Emacs will inherit the shell's environment variables when run the Unix way, but the user session's environment variables when run the macOS way.
** Windows
Download the [[https://ftp.gnu.org/gnu/emacs/windows/emacs-26/emacs-26.1-i686.zip][precompiled Emacs 26.1]] and unzip the zip file preserving the directory structure, and run =bin\runemacs.exe=.

Alternatively, create a desktop shortcut to =bin\runemacs.exe=, and start Emacs by double-clicking on that shortcut's icon. See [[https://www.gnu.org/software/emacs/manual/html_node/emacs/Windows-Startup.html][here]] for an explanation of this and other methods for launching Emacs under Windows.
*** 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 [[http://sametmax.com/ajouter-un-chemin-a-la-variable-denvironnement-path-sous-windows/][here]].
*** Installing and configuring Matplotlib (graphic python library)
Open an DOS console and type the following command:
#+begin_src shell :results output :exports both
python -m pip install -U matplotlib
#+end_src
[[file:emacs_orgmode_images/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:
#+begin_src python :results output :exports both
import matplotlib
matplotlib.matplotlib_fname()
#+end_src
[[file:emacs_orgmode_images/matplotlib.png]]

Open the =matplotlibrc= file and modify the line starting with =backend=
to make it =backend : Agg=.
* Python and R
Computational documents contain code, which in the case of our MOOC use the languages Python and R. So you must install Python and R in addition to Emacs, unless of course they are already installed on your computer. Note that when we say Python, we mean the Python 3 language, not its predecessors Python 1 and Python 2, which are similar but not quite compatible. More precisely, the examples in the MOOC require Python 3.6 or later, the current official version being 3.7.3. For R, we have used version 3.4, but somewhat older versions are probably fine as well.

Like for Emacs, there are many ways to install Python and R. Worse, there are good reasons for there being many ways, because there is no single best one for everybody. The following guidelines should help you pick a good one for you.

*Linux users* should start by checking the packages provided by their Linux distribution. It almost certainly contains Python and R, but the versions may not be sufficiently recent. For example, Debian 9 (named "stretch"), the current stable release, proposes Python 3.5. The exact names of the packages you need to install unfortunately varies among distributions, but they should be similar to =python3= and =r-base=.

*macOS* users who already use one of the package managers for macOS, i.e. one of [[https://brew.sh/][Homebrew]], [[https://www.macports.org/][MacPorts]], or [[http://www.finkproject.org/][fink]], should also look for Python and R in their distributions. However, it's not worth installing any of these package managers just for Python and R.

Users of *Windows*, as well as *Linux* and *macOS* users who don't find sufficiently recent versions in their package manager's distributions, should consider the [[https://www.anaconda.com/distribution/][Anaconda distribution]] that contains both Python and R plus a huge collection of add-on packages for both languages. Anaconda is particularly recommended for those who plan to use Python more regularly, as it is the most convenient approach to managing Python environments.

Finally, you can follow the installation procedures proposed by the development teams of [[https://www.python.org/][Python]] and [[https://www.r-project.org/][R]] for their respective languages. Compared to the approaches described above, the main inconvenience is the absence of simple strategies for updating and for installing add-on packages. But if you install Python and/or R just for the MOOC, this is not much of an issue.
* LaTeX (optional)
If you want to work with the replicable article stub (shown in [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][this video]]), you also need an installation of LaTeX. This is a rather big piece of software (several GB), so you may prefer to skip its installation. It is not required to follow the MOOC, but if you end up producing real-life computational documents with Emacs, you will have to install it eventually.

As for Python and R, *Linux* users, and also *macOS* users with a package manager, should start by checking their distribution's package list for packages called =tex=, =latex=, or better yet =texlive= or =miktex=, the two main TeX distributions that already contain almost everything you are likely to need.

Otherwise, pick one of [[https://tug.org/texlive/][TeX Live]] or  [[https://miktex.org/][MiKTeX]] and follow the installation instructions they provide. [[https://www.tug.org/mactex/][MacTeX]] for macOS is TeX Live plus a few macOS-specific add-ons. The differences between MiKTeX and TeX Live are not very important, so if you don't know which one to pick, toss a coin!
* A simple "reproducible research" emacs configuration 
This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/jump_to_id/9cfc7500f0ef46d288d2317ec7b037b4][video tutorial]] (/"Mise en place
Emacs/Orgmode"/ in French). Watching it before following the
instructions given in this section may help.

Emacs comes with a very basic default configuration, so almost
everyone wants to personalize it. Given the flexibility of Emacs, a
configuration can become quite complex and in fact include what would
otherwise be considered complete software packages. In the context of
this MOOC, we propose a relatively minimalist configuration oriented
towards "/reproducible research/" with Org-Mode. If you are new to
Emacs, we strongly recommended that you use it with as little
modification as possible, by following the instructions in this
section. If you are a more experienced Emacs user, you can go through
the instructions and adopt the pieces that you consider useful for
you.

It is unfortunately rather probable that some of you will run into
unforeseen problems with this configuration. If that is your case, ask
a question on the forum. We will do our best to help you.
** Step 0: Backup and remove your previous configuration
If you have used Emacs before, you may already have a personal
configuration. And even if not, you may have Emacs configuration files
without being aware of them, since some software packages create or
modify Emacs configuration files. In order to avoid trouble, remove
prior configurations, after making a backup elsewhere.

The files that you should backup and then remove (if they exist) are:

  1. =~/.emacs=
  2. =~/.emacs.el=
  3. =~/.emacs.elc=

There is also a directory that you should backup and then remove (if
it exists), with everything it might contain:

  4. =~/.emacs.d=

In the above filenames, =~/= stands for your home directory. Windows
users should replace it by =C:\Users\MyName=, replacing MyName by
their user name.
** Step 1: Download our configuration

#+begin_src shell :results output :exports none
export FILE_LIST="rr_org/init.el rr_org/journal.org rr_org/init.org"
tar zcf rr_org_archive.tgz $FILE_LIST
#+end_src

Download [[file:rr_org_archive.tgz][this archive]] and uncompress it. It contains the
following files and we will refer to them in the following:

#+begin_src shell :results output :exports results
tar tzf rr_org_archive.tgz
#+end_src

#+RESULTS:
: rr_org/init.el
: rr_org/journal.org
: rr_org/init.org

Alternatively, [[file:rr_org/][the files you are looking for are available here]]. As
you may notice, the configuration (=init.el= in emacs lisp) is hard to
follow, which is why we manage it through an =init.org=, file, which is
really nice for readability. This is a trick you may want to adopt
too (i.e., modify the =init.org= and regenerate the =init.el= by simply
/tangling/ the file --with =M-x org-babel-tangle=, see instructions in the
beginning of =init.org=).

If you use Windows, and if you use a desktop shortcut to start Emacs,
you must include the path to the file =init.el= in the command for the
shortcut. For example, if you installed Emacs as
=C:\Users\MyName/emacs=, your desktop shortcut should execute the
command =C:\Users\MyName\emacs\bin\runemacs.exe -l .emacs.d/init.el=.

** Step 2: Prepare your journal
Create an =org/= directory in the top of your home:
#+begin_src sh :results output :exports both
mkdir -p ~/org/
#+end_src
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://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.
** Step 3: Put the Emacs configuration file in the right place
Create the directory =~/.emacs.d/= and copy =rr_org/init.el= into it.
** Step 4: 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 5: Check whether the installation is working or not
Quit Emacs if it is running, and start it again. This first start will
take a bit of time because Emacs will download a few add-on
packages. For that reason, please make sure that you have a working
internet connection for this step. Note also that the download can
fail for other reasons, such as the package servers being overloaded.
Such situations do not last very long, so we recommend that you just
quit Emacs (=C-x C-c=, meaning =Ctrl + x= followed by =Ctrl + c=) and
restart it. At worst, repeat this until you get no more errors on
startup.

Next, open a file =foo.org=. Copy the following lines into 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 [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/rr_org/journal.org][first entry of your labbook]].
** Step 6: Open and play with your journal:
In step 2, you were told to create a journal in
=~org/journal.org=. 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
MOOC forum.
* A stub of a replicable article
This section is illustrated in a [[https://www.fun-mooc.fr/courses/course-v1:inria+41016+session02/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.

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 ([[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
make -C replicable_article/ all ../replicable_article.tgz
#+end_src

#+RESULTS:

Download the following [[file:replicable_article.tgz][archive]], uncompress it and simply =make= to generate the
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
is summarized in the following command:
#+begin_src sh :results output :exports both
wget --no-check-certificate -O replicable_article.tgz https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/replicable_article.tgz
tar zxf replicable_article.tgz; cd replicable_article; make ; evince article.pdf
#+end_src

*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:
  #+begin_src sh :results output :exports both
  emacs -q --eval "(setq enable-local-eval t)" --eval "(setq enable-local-variables t)"  article.org
  #+end_src
  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 [[https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/ressources/replicable_article/article.org][article.org]]:
#+BEGIN_EXAMPLE
# #+PROPERTY: header-args :eval never-export
#+END_EXAMPLE
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
- [[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]] 
  # French version: https://www.gnu.org/software/emacs/refcards/pdf/fr-refcard.pdf
- 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://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://www.gnu.org/software/emacs/refcards/pdf/orgcard.pdf][in pdf]]).
- [[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]].
** Video tutorials
For those of you who prefer video explanations, here is a [[https://www.youtube.com/playlist?list=PL9KxKa8NpFxIcNQa9js7dQQIHc81b0-Xg][Youtube
channel with many step by step emacs tutorials]].

For general information about a number of packages you could also
check the [[https://cestlaz.github.io/stories/emacs/][Using Emacs]], series of blogposts / videos.
** Additional useful emacs packages
*** Company-mode
[[http://company-mode.github.io/][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/][http://company-mode.github.io/]]
*** Magit
[[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+session02/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 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
invoke magit by using ~C-x g~.
** Other resources
- [[https://orgmode.org/orgguide.pdf][The compact Org-mode Guide]]
- A huge ressource of emacs/org-mode magic is Bernt Hansen's «[[http://doc.norang.ca/org-mode.html][Organize
  your life in plain text]]», whose source is obviously itself an
  [[http://doc.norang.ca/org-mode.org][org-mode document]].
- [[https://github.com/dfeich/org-babel-examples][Many examples illustrating the use of different languages in
  org-mode]]


