# Emacs and Org-Mode Tutorial

Ben Maughan, Room 4.19, Physics. Full contact information.

## 1 Introduction

This tutorial is intended to introduce the text editor Emacs and demonstrate some of the advanced techniques that are useful for researchers. In particular I will highlight the use of Emacs as a research notebook.

Note that to call Emacs a text editor is a bit of an understatement. It is also a web browser, news reader, email client, file manager, development environment, and the list goes on.

The structure of this tutorial is a general introduction to Emacs, with some preparatory work, and then an interactive session where I will demonstrate some techniques that you should work along with. To begin with you need to work through to the end of the Emacs basics section.

These tutorial notes were written as an org mode text document which you can download here (right click and save).

## 2 Initial setup

Here we will set up Emacs with spell checking. To get the most out of Emacs for scientific work, you'll find it useful to have a working LaTeX installation too.

### 2.1 Mac

The best way to install Emacs on the Mac is to use the homebrew package manager. Install homebrew from a terminal using the command

/usr/bin/ruby -e "(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"  Then install emacs and hunspell using brew install emacs --with-cocoa --with-gnutls --with-rsvg --with-imagemagick brew linkapps emacs brew install hunspell brew linkapps hunspell  Finally, download the hunspell dictionaries from here http://www.star.bris.ac.uk/bjm/hunspell-en_GB.zip and unzip the files into ~/Library/Spelling ### 2.2 Linux Linux machines come with emacs installed, ideally you'll need to be using the most recent version of emacs (25.1.1), but I think everything below will also work in Emacs 24 onwards. You can check your emacs version with emacs --version  On the astronomy group's linux machines you can access the latest Emacs with alias emacs /usr/local/bin/emacs  Otherwise, contact your system admin to intall the latest version, or install it yourself with a package manager, or from source. You can install the latest bleeding edge version from source following these instructions: https://www.gnu.org/software/emacs/manual/html_node/efaq/Installing-Emacs.html You will also need a spell-checking program, and my Emacs configuration assumes you use hunspell. This can be installed by your package manager and you should just need to make sure it is in your PATH. ### 2.3 Windows Download this zip file which contains Emacs and the hunspell spell checker http://www.star.bris.ac.uk/bjm/emacs-hunspell.zip and extract it somewhere sensible - I used my home directory. Now run addpm.exe in the emacs/bin directory to add emacs to your start menu. ### 2.4 All versions • Start emacs and go to the buffers menu and choose scratch • Paste this line into emacs and then put the cursor at the end of the line and press control and j (url-copy-file "http://www.star.bris.ac.uk/bjm/bjm-starter-init.el" (expand-file-name "~/.emacs.d/init.el") 1)  • Close and restart emacs and wait for it to finish installing packages • Close and restart emacs again You can check if you have the latest version by running the command C-h v bjm-init-version, and you should see version 1.7. For Windows you will need to edit the section of your init file that specifies where hunspell is. To do this, use M-x bjm/open-my-init-file and look for the section headed "CUSTOMISE - hunspell" (use C-s to search for this). ## 3 Emacs basics ### 3.1 Emacs tutorial Before we can get into some of the most useful areas of emacs and org-mode, you will need to learn the basics of how to operate emacs. The best way to do this is to work though the emacs tutorial. This is available under the help menu of emacs, and I will assume that you have worked through the tutorial, or already know the basics of emacs in the following. Note that our configuration changes some of the default emacs behaviour, but basic functions covered in the tutorial should work as described. ### 3.2 Key concepts Before we continue, make sure you are happy with the following basic concepts: • What the notation C- and M- means. e.g. C-x means hold down control and press x at the same time; C-x C-f means hold down control and press x then f; C-x f means hold down control and press x, then release control and press f. M- means the same for the meta key. This means the alt key on most keyboards, but this might be the command, option, or even escape key on a Mac. • How to open and save files (C-x C-f and C-x C-s) • How to move around a file (arrows, C-v, M-v, C-a, C-e, searching) • How to copy (M-w) kill/cut (C-w) and paste (C-y) • Deleting letters and words with C-d, M-d and BACKSPACE and M-BACKSPACE. Note also that undo and redo are set to C-z and C-Z in our configuration. • What is meant by buffers, windows, and frames, and how to switch between buffers (C-x C-b and C-x b) • How to quit out of a command (C-g) and quit emacs (C-x C-c) • How to run extended commands with M-x ## 4 Org-mode Emacs uses the concepts of modes to provide additional functionality. These are either major modes which relate to the type of file being edited (e.g. text-mode for text files, cperl-mode for perl files, nxml-mode for html, auctex-mode for latex etc), or minor modes that provide additional functionality. Major modes usually activate automatically when a file of a given type is opened, and only one major mode is active in a given buffer at a time. Minor modes also provide additional functionality, but can work across different major modes, and you can have as many active as you like. For example, flyspell-mode provides spell checking in many major modes. Additional major and minor modes can be installed using the emacs package manager (a bit like browser extensions). Org-mode is a very powerful major mode that provides the ability to create structured text documents, along with lots of other useful things. We will be using it here as a way to make a detailed notebook that includes code snippets, tables and images. Now, copy the tutorial org file your home directory by pasting the following line into your *scratch* buffer and putting the cursor at the end and hitting C-j. (url-copy-file "http://www.star.bris.ac.uk/bjm/emacs_tutorial.org" (expand-file-name "~/emacs_tutorial.org") 1)  Open the file and Emacs will automatically start that buffer in org-mode. Now let's start work through the tutorial adding our own notes as we go First we can check we have a recent version of org mode using M-x org-version and check it is newer than 8.0. I have marked points in bold where you need to add text. ### 4.1 org-mode structure Text in org is structured by headings, denoted by lines starting with one or more * so we are currently in a subsection! add a sub-subheading #### 4.1.1 my new sub-subsection njnksjvnksjbv #### 4.1.2 navigation Headings can be expanded or collapsed by moving to the (sub)heading and pressing TAB. S-TAB cycles all headings. You can jump to next and previous headings with C-c C-n and C-c C-p respectively. expand and collapse headings and move between them You can move headings up and down with M-up and M-down. Try this now. #### 4.1.3 lists 1. bullet lists • bullet lists can be created like this (start a line with one or more space and a - • pressing M-RET gives you a new bullet • we might also like nested bullets • like this one (I pressed M-RET TAB to indent it) • and another (M-RET now indents to the new level) • the nice thing is that for long lines of text, emacs wraps them so that they line up with the bullet • you can also reorder list items and change indentation using M-up or M-down just like with section headings • you can change bullet style using S-left and S-right Add an item to the list above and then move the items around and change the bullet style 2. numbered lists 1. numbered lists are also possible 2. M-RET gives me a new number 3. moving the items changes the numbering 4. new item Add an item to the list and move the items up and down 3. checklists [5/5] • [X] we can even have check lists • [X] M-S-RET gives a new item with a check box • [X] C-c C-c check/unchecks a box • [X] you can have sub items • [X] like this • [X] that can be checked off individually • [X] and you can track the number of items by adding [0/0] to the end of a line above a checklist - this updates when you check items off Add an item to the check list and check some items and sub-items off 4. definition lists definition lists these are useful sometimes word definition item 2 M-RET again gives another item, and long lines wrap in a tidy way underneath the definition Add an item to the definition list ### 4.2 org-mode tables Hopefully you can see straight away that the simple structure provided by org-mode gives a nice way to keep an electronic note book. Often it is nice to include tables in our notes - org handles this by using | to separate columns, and a line of — (inserted with C-c -) to add horizontal lines. Exercise: start typing in a copy of the table below 1. type the first line in verbatim 2. when you get to the "s" of comments, press TAB to go to the next line 3. go up to the previous line and use C-c - to add the row of dashes 4. next enter a few lines of data, using TAB to go through the cells - you should notice the columns changing width as needed ID X Y comments a 2 4 blah b 3 9 blah c 4 16 blah blah blah ID x y comments A 2 4 blah B 3 9 blah C 4 16 blah blah blah D 5 25 blah Now, you can move rows and columns around using M-arrow and insert or delete rows and columns using M-S-arrow. Try this out now. #### 4.2.1 Advanced tables 1. creating and exporting You can easily convert some text to a table - select the following text and use C-c | to convert the region to a table  ID x y A 2 4 B 3 9 C 4 16 D 5 25 You can also save tables to files by putting the cursor in the table and using M-x org-table-export 2. formulae You can use formulae to do arithmetic on tables (e.g. sum a column) and other spreadsheet-like functions - see the org manual for details ### 4.3 org-mode links and images Org mode supports links to files, URLs, and to other points in the org file. In this example let's use an image from my website. First copy it to your home directory (url-copy-file "http://www.star.bris.ac.uk/bjm/superman_cluster.png" (expand-file-name "~/superman_cluster.png") 1)  To add a link to a file use C-u C-c C-l and type the name of a file. Use tab-completion to select the image we just copied and you will then be asked for a description - you can press enter to leave this blank add a link here Since the file we have linked to is an image, we can display the image in emacs using C-c C-x C-v and use the same command to turn the image off again - try this. The structure of a link in org mode looks like this [[link address][text]]  where the link address is the URL or file name, and the text is the text that is displayed, so we can replace our superman link with something tidier like use C-u C-c C-l to add a link named "this" here but note that this will not display when we turn on images. Links to other parts of the org file are added easily using the name of a section, like this [[org-mode structure][this link]]  Type this in to make a link to the earlier section Finally, we can add a caption and a name to our image like this which means we can refer to our image later by using the name we just gave it, for example, look at my picture in Fig. 2 ### 4.4 Formatting text Later on we'll look at exporting our org document to different formats. Org does this very nicely, and translates your text and markup appropriately. There are simple things you can do like italics or bold text and underlines and literal text that org understands. Type a few examples here ### 4.5 LaTeX and source code blocks Sometimes you don't want org mode to try to do anything clever with some text and just display it as plain text. One way to do this is to use an example block. Go to a new line and type <e then press TAB [[link]]  Add an example block here syntax like superscripts x2 or symbols α β γ. Org also understands more complex latex like this \begin{align} x^2 + \left(\frac{y}{z}\right)^4 = 0 \end{align} We'll see how these look when we export this file later. It is also handy to include source code in your notes - on a new line type <s and TAB to create a source block. You can tall org what type of code is contained - in this case we'll put in some simple shell code, so well put "sh" at the top of the block. Now move the cursor inside the block and type C-c ' which will create a new temporary buffer in the major mode of the programming language you have specified. Type some code in, and then type C-c ' again to come back to this buffer echo "HelloUSER! Today is date"
exit


Add a source code block here, containing the following lines (without the example tags)

echo "Hello $USER! Today is date" exit  It is possible to have org execute the code in a block by putting the cursor in there and using C-c C-c and then giving it permission when asked. By default the output of the code is added to the org file below the code block - try this with the example code above. This feature of org (called babel) is particularly powerful. There are much more sophisticated things you can do, like have the code read data from a table elsewhere in the file and add images to the file. You can also add links to line numbers in the code and more. See the org-mode and babel online documentation for more. Here is an example where executing this shell code block… ls -Ss /homeb/bjm/docs | head -7 | grep -v total exit  generates this table… which is then used as an input for this R code block (using the :var option)… pie(files[,1], labels = files[,2])  to make this plot… ### 4.6 Tangling your code for literate programming In org mode you can "tangle" your file to extract out your code blocks into one or more file. This makes it a good way to document your code. As a trivial example, I want to write a script that will write the names of all of the files in my home directory to a file ls ~/* > /tmp/aaa  than I want my script to count the number of lines in that file wc -l /tmp/aaa  If I use C-c C-v C-t org will tangle those two code blocks into a file called filenames.sh This can be a very good way of writing and documenting code - you can effectively write a manual and your code together and then tangle the code out into a file that you can compile or run. Try tangling the script above ### 4.7 Org mode exporting One strength of org-mode is the ability to export to multiple formats. Most useful are web pages and pdf (via latex). To export this file to a web page, type C-c C-e to start the exporter and then press "h" to select html and "o" to select open. A new web page should now open in your browser. Export this file to a web page and view it Similarly, typing "l" and "o" in the exporter will convert the org file to latex and then compile it to produce a pdf and display that. Export this file to pdf and view it You can control which parts of the file are exported by adding tags to section headings. To do this, put the cursor on a heading and hit C-c C-c which will pop up a menu to select tags. Select the noexport tag and that heading will not be exported. Select the export tag and only that heading (and any other headings tagged with export) will be exported. Tags are inherited by subheadings. Tag a heading as noexport and then export the file again It is possible to add many customisations to the export process. Go to the top of the buffer (using M-<) and you can see some of the options that are used for this file. These are fine for simple pdf and html export, but see the org manual on exporting for more details. ### 4.8 Reproducible research Using the techniques here, it is possible to create a single org document that contains all of the code and notes for a project, and also the draft and final versions of the paper. This makes it extremely easy for anyone to reproduce your work. As an example, you can download the org file for a recent paper of mine here. That file doesn't contain all of the data (some of the data files were large), but does contain the code, results, code to generate plots, notes to myself, draft paper and final paper. By using the appropriate export settings at the top of the file I can export this to a latex file and pdf ready to submit to a journal. ## 5 Organising yourself with org-capture Org mode has a very powerful way of managing todo lists including clocking the length of time spent on tasks and adding deadlines etc. I've given you a basic setup, but see this page for a really detailed example. At the heart of this is org-capture. From anywhere in emacs hit C-c c t to capture a thought, link, or to-do item and then get right back to what you were doing. Hitting C-c c t will pop up a small window with a template for an todo item that looks like an org-mode headline. You'll see it has a priority (B by default), a scheduled date (today by default), and a link to the current file. Add some text to the headline to make your item, and then you can customise it by • using S-<up> and S-<down> to change the priority • putting the cursor in the date field and using shift and arrow keys to change the date • use C-c C-d to add a deadline date which will pop up a mini calendar - use shift and arrow keys to select the date. You can use C-c C-s to add a scheduled date, but we have one of those already by default. When you are happy, use C-c C-c to save this item to a file (this defaults to todo.org in your home directory). The nice thing about this method of adding items (called org-capture) is that you can use it anywhere in Emacs and carry on with what you were doing. Now we can have a look at our todo list using C-c a to launch the "agenda dispatcher", a powerful interface for selecting different ways to view your tasks. My favourite is to use n in the dispatcher (i.e. use C-c a n) to view the current fortnight of scheduled tasks followed by the list of any unscheduled tasks. This switches to the agenda buffer. In this list view, you might want to: • Cross an item off your list (the best bit!). To do this put the cursor on the corresponding line and hit $ which marks it as done and archives the item in a file called todo.org_archive getting rid of it from your todo list.
• Change the priority of an item using shift up/down.
• View the notes to go with items by hitting E.
• Edit or view an item in more detail by hitting RET with the cursor on the item that you want. This takes you to the item in your todo.org file where you can edit it or look at the notes you added to it in more detail.
• Quit back to where you were before with q

That is all there is to it, and you now have a simple but powerful todo list in emacs. Just remember C-c c t to create a todo item and C-c a n to view the todo list.

## 6 Efficient editing

Now we will turn to more general Emacs techniques - these are not specific to org mode, but we can demonstrate them in this org mode file

### 6.1 Installing packages

Most of the packages you need to get started are installed by my config file, but there are lots more out there. For example, let's install a package using the built in emacs package manager:

M-x package-list-packages


to bring up the list of available and installed packages. For example, to install the package "wrap-region", search for the name of the package in the buffer (just use C-s) and then put the cursor on that line and press i to mark the package for installation and x to actually install it.

After you install a package you will often need to edit your config file to activate the package and set options (this will be explaine don the web page of a package). To do this, open your config file with C-x C-f and then start typing ~/.emacs.d/init.el - you will see the completion options appear in the mini buffer and you can use the arrows and enter to select.

In general I recommend using use-package to install and setup packages. To do this for wrap-region, add the following to your init.el file (without the src tags!)

(use-package wrap-region
:diminish wrap-region-mode
:config
'(("*" "*" nil (org-mode))
("~" "~" nil (org-mode))
("/" "/" nil (org-mode))
("=" "=" "+" (org-mode))
("_" "_" nil (org-mode))
("$" "$" nil (org-mode latex-mode)))


Now save your work with C-x s and close emacs (C-x c) and restart it for the new package to be picked up.

### 6.2 Quick movement

A key strategy to using Emacs efficiently is to move around the buffer quickly without needing the mouse. Get in the mindset of using C-s as a movement tool to take the cursor somewhere you can see on the screen. Another way to do this is to use M-s to launch avy. You are prompted for the first character of a word. Enter one and then all words starting with that character are given a shortcut key. Type that shortcut to move to the word.

### 6.3 Abbreviations and completion

Emacs will try to complete words if you use M-/ for example try typing "comp" and then pressing M-/ multiple times to cycle through the completion options

Try this

Emacs also has a smart abbreviation system where you can define short hand for long terms to save an abbreviation, type the abbreviated text e.g. "abbr" and then use C-x a - and then type the full version e.g. abbreviation. From now on, any time you type abbr and space (or comma, enter etc) it will magically expand.

Make an abbreviation

### 6.4 Cut or copy line

If no text is selected then M-w copies the current line, and C-w cuts it.

### 6.5 Cycle case

Put your cursor on a word and pres M-c to cycle the case of the word. Also works for regions

Use M-; to comment/uncomment a line or a region. Use C-M-; to comment a line and move to the next one.

Select several lines and use C-c b b to make them into a comment box.

### 6.7 Search and replace

Use M-% to replace all occurrences of a string with a replacement string. You need to type y or n to approve the replacement or use ! to accept all replacements

Try replacing aaa with bbb in the following

aaa blah blah aaa blah aaa blaaah blah

### 6.8 Macros

In emacs you can record sequences of commands and play them back to repeat boring tasks. For example in the following text, let's delete the x's from the end of each line. Go to the h at the start of the first line and use C-x ( to start recording a macro. Then use C-s d to search ahead to the and of the word world, then C-k to kill the text to the end of the line, then C-a to move back to the start of the line and C-n or down arrow to move don to the line below. Now use C-x ) to end macro recording and C-x e to run the macro. Pressing e again will repeat the macro. Do this until you have cleaned up the text.

Clean up the text

hello worldx
hello worldxxx
hello worldxx
hello worldxxxxx
hello worldxx
hello worldxx
hello worldxxxxxxxx
hello worldxxxxx


To repeat the macro N times use M-N C-x e where N is an integer - set N to be very large and the macro will repeat until the end of the buffer. Many emacs commands accept numerical prefixes in this way to cause them to repeat N times.

### 6.9 Opening files and recent buffers

Use C-x b to switch buffers. This offers you a list of buffers that are currently open and recently used buffers, and you can type a string to narrow the results.

Use C-x C-f to open files or make a new file.

Type C-x f to activate helm-for-files to provide a powerful search for files. Start typing the name of a file and it will show a list of matches from your current buffers, recent files, current directory, and the locate database. If you are running Emacs on a Mac, you can tweak this to use spotlight instead.

Try this

### 6.10 Spell checking

Flyspell is a minor mode that checks spelling as you type. If you make a typo, press C-; to cycle through corrections of the mis-spelled word closest behind the cursor. You can also correct a particular word by putting the cursor on it and pressing M-$. You can spell check the whole buffer with M-x ispell. You can add words to your personal dictionary to stop them being flagged as typos. To do this rum M-$ on the word and hit i to add the word to your dictionary.

Mis-spell some words and then correct them

### 6.11 Shell commands

It is often useful to operate on text in emacs using standard shell commands. For example, suppose we had a text file containing columns of numbers that we wanted to manipulate to calculate a radius and unit vector from x and y coordinates:

#ID  x   y
A    2   4
B    3   2
C    4  -4
D    5   1


Select the text in the table, not including the line containing the column names, and use M-| to run shell-command-on-region. Then type

awk '{printf("%g %g %g\n",sqrt($2**2+$3**2),$2/sqrt($2**2+$3**2),$3/sqrt($2**2+$3**2))}'


The output text appears at the bottom of the screen and then disappears once you type anything else, but it is saved in a buffer called Shell Command Output - switch to that buffer with C-x b to see the output.

Now it would be nice to add this text back into our table - one way to do this is to use rectangles…

### 6.12 Rectangles

Emacs has a very nice feature of letting you select rectangular regions of text for manipulation. Recall that we use C-SPACE for normal text section; we use C-x SPACE for rectangular selection. Try that here, and then switch to the Shell Command Output buffer and highlight a rectangle containing the three columns that were created, and then use M-w to copy the rectangle

Now type in the names of the new columns in the table and put the cursor at the position of the first new value (i.e. under R) and paste (yank) the rectangle as normal with C-y. Now suppose we had wanted to add the new columns before the x and y columns; put the cursor in front of the 2 under x use C-y again and note how the text is shifted to the right.

#ID  x   y  R  xhat  yhat
A    2   4
B    3   2
C    4  -4
D    5   1


### 6.13 Expand region

Put the cursor on a word and hit C-= to select the word. Now hit = again to expand the selection and - to reduce the selection. Notice how the expansion increases by semantic units: word to sentence to paragraph.

### 6.14 Multiple Cursors

Press M-. a few times and watch new cursors appear below your original. Type a few words and move the cursors around. Press enter to leave multiple-cursors mode.

Now select the string "date1" in the first line of the Perl snippet below, and then hit M-. a few times to put a cursor on each of the following occurrences - you can now edit them as you wish. This is a bit like query-replace but more flexible.

chomp (my $date1=dmkeypar$o1evt_clean DATE-OBS echo+);
chomp (my $date2=dmkeypar$o2evt_clean DATE-OBS echo+);
&printdatnew("date1 = $date1 # date of o1\n"); &printdatnew("date2 =$date2 # date of o2\n");


Finally, use C-S and click to add cursors anywhere.

### 6.15 Paste history

Copy some text (M-w) and then paste (C-y) and then use M-y to cycle through previously copied text.

Do a search (C-s) somewhere in the buffer and then press RET to finish the search. Now use C-u C-SPACE to jump back to where you started the search. Keep pressing C-SPACE to jump to previous locations. Emacs marks points in the text for lots of reasons (searching, copying, pasting etc) so this will usually take you somewhere useful.

### 6.17 Compare files with ediff

To compare the contents of two text files, use M-x ediff-files and open the two files you want to compare. Stretch your window nice and wide so you can see both files side by side clearly. You should see blocks of text that differ between the two buffers highlighted. Press n to move to the next difference and p to move to the previous difference. Press a to copy the text from the left-hand file to the right-hand file, or press b to copy text from the right-hand file to the left-hand file.

Press q to exit ediff and then save your files if you have modified them.

### 6.18 Undo tree

Type some text and then use C-z to undo some of the typing and type something else instead. In a normal editor pressing undo won't get you back to the original text that you previously undid. In Emacs you can use C-x u to start undo-tree-visualise to give you a diagram of your undo history that you can move through to get back to the earlier text.

### 6.19 Quick calculation

Use C-c b c to open a quick calculator in the minibuffer. Type a calculation and hit return to see the result. The nice thing is that the result is automatically added to the clipboard to be pasted into your work.

### 6.20 Insert today's date

Use C-c b d to insert today's date.

### 6.21 Insert a file name

Use C-c b i to insert the name of a file.

### 6.22 Manage files with dired

Emacs has a very powerful file manager called dired. Hit C-x j to jump to the current file in dired. In dired you can do all the normal file management tasks, but a really neat trick is using C-x C-q to make the dired buffer editable. You can now edit the file names like a normal buffer, using e.g. multiple cursors to rename multiple files. Amazingly this also extends to editing links. Once you have made your edits use C-c C-c to save them and exit writeable mode in dired.

For more about dired, see my blog posts

## 7 Email in Emacs

This is a more advance topic and I'll direct the interested reader to my blog for posts on how I use mu4e and org-mode to manage my emails.

For the moment, consider a quick example of turning an email into a todo item.

## 8 Version history

Current version is $Revision: 1.2$

$Log: emacs_tutorial.org,v$
Revision 1.2  2016/11/13 21:10:19  bjm
Summary: Improved text around org-capture.

Revision 1.1  2016/11/12 22:04:22  bjm
Initial revision


Created: 2016-11-16 Wed 15:14

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