A GNU Emacs profile for using LaTeX and Org in academic research

Make writing tasks fun by disguising them as coding projects!

This repo contains a init.el file (configuration file) for using LaTeX in GNU Emacs version 29. You can adapt it to other configurations of Emacs (e.g., Spacemacs, Doom, etc). The SciMax configuration probably has similar support built-in. See latex-emacs28 and latex-emacs30 for configurations that work with Emacs version 28 and Emacs version 30, respectively.

Features include the following:

• heavily customized auto-complete for LaTeX
• AUCTeX
• atomic-chrome (GhostText)
• awesome-tabs (install from Github)
• dashboard and dashboard-hackernews (keep abreast with the latest distractions)
• org-mode
• org-agenda
• org-roam (capture templates include timestamps)
• org-roam-ui (view your zettelkasten like a mind-maps in your browser, very cool, similar to the one in Obsidian)
• pdf-tools
• pdf-noter

I built the latex-emacs profile on top of a configuration by Alvaro Ortiz Troncoso. His configuration included the auto-complete-auctex.el package of Chris Monsanto from 2012. Although the autocompletion is out of style for Emacs fans at the cutting edge of package development, it works!

I designed this configuration to support the efficient editing of academic documents in LaTeX. See the Features section below. See the related repos section below for LaTeX templates for the first manuscript submission, a writing log to accompany every writing project, a poster, a slideshow, a diary for 2022, and a diary for 2023.

This configuration is compatible with org-mode. Org-mode is an enhanced markdown that reads LaTeX code intermingled with org markup. Org-mode is very popular with Emacs users because the sections and subsections are easy to fold, and org documents are easy to export to many file formats. It evolved out of an outliner package. It greatly eases the creation of lists, so it is useful for planning and brainstorming. Org-mode also has a powerful org-agenda component for scheduling events. Many have tried to use org-mode to implement the Getting Things Done method of Jim Allen. Org-mode also powers the org-roam package, which implements electronically the zettelkasten system or slip-box system of taking smart notes.

In addition to Emacs, you can edit org-mode markdown in several other leading text editors like Visual Studio Code, so you can still use org-mode if you fear Emacs. Org-mode is responsible for the recent resurgence in the popularity of Emacs. (The median age of an Emacs user is about 33 years). The recurring annual emacsconfs reflects this surge in popularity. The two-day conference is virtual and free.

Org-mode supports literate programming with almost any programming language, although the latex-emacs init.el file is not configured for literate programming. Instead, see my complete configuration for Emacs. Unlike the above configuration written in Emacs lisp (elisp), the complete configuration is wrapped in org-mode. It is a 6000-line literature programming document. I wrote the comments in org-mode; they flank blocks of elisp code.

You can read an org-mode document into Emacs with the latex-emacs configuration, even though the latex-emacs init.el file does not call org-mode because the base distribution of Emacs now contains org-mode. See this repo for a manuscript template that can be edited in org-mode. For a writing log to be used in parallel to writing a manuscript in org-mode, see this [repo] (https://github.com/MooersLab/writingLogTemplateInOrg).

I am keeping the latex-emacs configuration isolated from my main configuration to ease the development of latex-emacs. The latex-emacs profile also serves as a backup configuration when I break my main configuration, which happens less often these days.

I use the following bash alias to start Emacs29 with the configuration stored in the folder ~/latex-emacs29. Note that I am not hiding this folder in my top directory. The hindrance of hiding the Emacs configuration folder is greater than the benefit of not accidentally deleting it once in a lifetime. With my init.el file on GitHub, I can easily restore my Emacs configuration if disaster strikes.

alias e29l='/Applications/Emacs29.0.5.app/Contents/MacOS/Emacs --init-directory ~/latex-emacs29'.

The --init-directory flag has been available as of January 2022 with Emacs version 29.0.5. This flag negates the need for the package chemacs2 and its slightly more complex setup.

I made a second variant of the above alias for debugging:

alias e29ld='/Applications/Emacs29.0.5.app/Contents/MacOS/Emacs --init-directory ~/latex-emacs29 --debug-init'.

Multiple versions of Emacs on the same computer

You can have multiple versions of Emacs on your system; however, you must match the profiles to the Emacs version because the binaries in the elpa subfolder of the latex-emacs29 folder may not run with different versions of Emacs.

No warranty is implied. Use at your own risk.

I used this configuration to prepare the presentation given to the Berlin Emacs Meetup on 31 August 2022.

Why LaTeX?

LaTeX is the gold standard markup system for technical writing.

• Combine a passion for coding with writing (e.i., make writing fun by disguising it as coding).
• Code reuse: recycle old documents.
• Precise control over the appearance of the output.
• Equation typesetting par none.
• Automated scaling and placement of figures.
• Syntax highlighting of code fragments.
• Reduced use of the mouse: More ergonomic.
• Reduced context switching: Be more productive.
• Slideshows as PDFs are immune to embarrassing font issues when presenting slides on another operating system.
• Support for multi-part documents (books).
• Precise control over typesetting of the bibliography.
• Automated table of contents and list assembly.
• Automated index generation.
• Source files are compact and easy to share by e-mail.
• You can put the source files under version control.
• Overleaf supports collaborative writing.

Most markdown variants do not support the automated generation of indices for large documents. Most literate programming projects built on top of markdown have this serious limitation.

Why Emacs?

Over the past several decades, many Emacs and package developers have developed a suite of packages to aid the writing of LaTeX documents. These features support efficient editing of LaTeX documents.

In addition, you can extend Emacs with the Emacs Lisp programming language. Elisp is a variant of LISP that was customized to ease the configuring of Emacs. Emacs is a platform for building a customized text editor. You can customize your LaTeX environment and add functions to aid your workflow.

Of course, other text editors have these features too, but Emacs is the most extensible. It is the ultimate editor: Once you become competent at Emacs, you will not make another editor your primary editor. You might still use other editors, but Emacs will meet most of your needs.

Emacs has been under development for 45 years. According to the Lindy effect, it should be available for another 45 years.

Why not Overleaf?

Overleaf is a web-based LaTeX editor. Overleaf is excellent for maintaining multiple writing projects and strongly supports collaborative editing. I find the Overleaf GUI intuitive and has good support for debugging. The GUI provides helpful tools for generating the code for tables of various sizes and for selecting images to be inserted into figure environments. It provides an outside view of the document. I use this feature to generate outline views of the slide shows I am developing in Beamer. I use this outline view to navigate to specific slides and to rearrange slides while editing the beamer file. Overleaf also has an extensive collection of attractive documentation about LaTeX, a nice supplement to TeX StackExchange.

I have over 600s writing projects on Overleaf. These projects include grant applications, manuscripts, slideshows, and posters. I often use an old project as a template to make a new project. This saves a lot of time.

I use it multiple times daily because I store my daily writing in a book document that serves as my digital laboratory notebook. I speed up navigation to active projects by storing their URLs on a private homepage (index.html).

I have subscribed to the Pro license for several years and have used Overleaf for six years. I recommend the free account to anyone trying to master LaTeX. I recommend the Pro license for anyone doing collaborative writing or managing dozens to 100s of projects. The Pro license enables you to use Git to make copies of your writing projects on your computer using Git.

The reasons not to use Overleaf include the following:

• pricey annual subscription
• poor support for Emacs key bindings
• lack of a system for storing snippets of LaTeX boilerplate
• time spent in Overleaf is not time spent in Emacs (but see workaround solution below via GhostText)

GhostText and Overleaf

Overleaf does support a small subset of Emacs keybindings. Even better, if you select the legacy mode on Overleaf, you can send the text area to Emacs for editing via the GhostText plugin for your browser and the atomic-chrome package for Emacs. You can use snippets on the Emacs side of the websocket; the inserted code will appear immediately on the Overleaf side. My configuration for atomic-chrome is below:

;; atomic-chrome, used to interact with GhostText extension for Google Chrome.
(use-package atomic-chrome)
(atomic-chrome-start-server)
(setq atomic-chrome-default-major-mode 'python-mode)
(setq atomic-chrome-extension-type-list '(ghost-text))
;;(atomic-chrome-start-httpd)
(setq atomic-chrome-server-ghost-text-port 4001)
(setq atomic-chrome-url-major-mode-alist
      '(("github\\.com" . gfm-mode)
        ("overleaf.com" . latex-mode)
        ("750words.com" . latex-mode)))
; Select the style of opening the editing buffer by atomic-chrome-buffer-open-style.
; full: Open in the selected window.
; split: Open in the new window by splitting the selected window (default).
; frame: Create a new frame and window in it. You must be using some windowing package.
(setq atomic-chrome-buffer-open-style 'split)

Advantages of using LaTeX in Emacs over Overleaf

• The availability of the yasnippets package. You can build document templates and save them as yasnippet snippets. You then insert the document template into a new file upon entering the snippet name and hitting tab.
• Powerful macros in AUCTeX support creating and editing new documents.
• Syntax checking before compiling is available. See the keybinding lists below.
• Terse and clear bug reporting during PDF compiling.
• Preview a rendered version of a select region in the buffer. You remove the preview with a key binding. The preview allows you to check an equation's typesetting without going through the longer step of compiling the file into a PDF.

Why not Org-mode

Org-mode includes support for document preparation, time management, and literate programming. Many people in the past decade were drawn to Emacs by org-mode. Org documentats can recognize LaTeX markup. It is seamless to export an org document through LaTeX to a PDF and open that PDF in your default PDF viewer.

The main drawbacks to org-mode for me are as follows:

• Most publishers do not accept org files, but they do accept tex files. (You can export the org file to a LaTeX file that might need heavy editing to get the publisher's acceptance.)
• Overleaf does not support the use of org files.
• Org markup adds another layer of abstraction on top of LaTeX.

I am already a LaTeX native. I do not need the crutch of org-mode to produce tex files.

Features of this configuration:

• Install packages from MELPA with use-package.
• Uses Protesilaos Stavrou's (Prot's) ef-themes package. Set to the ef-cyprus theme. The ef-light theme is good too.
• latex-mode and auctex-mode with an old autocompletion package that works,
• Keybindings remapped for macOS so Meta is cmd, Super is cap locks, and Hyper is Fn.
• Numerous keybindings from outline-mode to fold and unfold sections in a LaTeX file.
• Configured to cope with the minted package under compiling. It gets around the compile with -shell-escape command.
• Configured to use snippets from the snippets subfolder.
• Has hippieexpand enabled.
• Uses the awesome-tabs package to enable navigation between buffers via tabs. (The keybindings s-0, s-1, ..., s9 enable switching tabs from the keyboard.)
• Has the word count mode (wc-mode) enabled.
• Includes pomodoro-mode.
• Has minibuffer history.
• Includes ivy enabled for enhanced auto-completion selections.
• atomic-chrome configured to interact with GhostText extension for Google Chrome so you can edit in Emacs LaTeX documents on Chrome.
• Includes the texcount script with C-c w to get a more accurate word count when in latex-mode.
• Move N-selected lines up and down with the meta and the arrow keys.
• Scratch buffer retained.
• Add the itemize, enumerate, and description functions to convert selected markdown lists into LaTeX itemize, description, or enumerated lists.
• Includes configuration for changing the size of the font in the modeline. This is useful for preparing slides about using Emacs.

Installation

1. git clone https://MooersLab/github.com/latex-emacs latex-emacs in your home directory.
2. Create link to your snippets folder: ln -s snippets ~/.emacs.d/snippets. This link negates the need to maintain multiple copies of the snippet libraries.
3. Edit file paths in init.el as needed. Git clone the packages stored in manual-packages.
4. Add alias e29l='/Applications/Emacs29.0.5.app/Contents/MacOS/Emacs --init-directory ~/latex-emacs29 to your .bashrc or .zshrc file so you can open Emacs with alias e29l.
5. Add the GhostText extension to Chrome or Firefox or Safari or Edge.
6. Install LaTeX and include in your PATH.
7. Edit in init.el the file path to texcount. This Perl script comes with LaTeX. You might be able to invoke texcount without the file path if you have no previously defined aliases to do texcount.

Operation

This setup can be run in versions > 29.0.5 with emacs --init-directory ~/latex-emacs29 or the alias e29l. This command ignores your default Emacs configuration in ~/.emacs.d You can run it in isolation from your default emacs configuration. It makes a nice backup system when you break the main configuration.

Create an empty text file with touch start.tex. Start Emacs and load the file. Enter C-o C-e to create a new document using the corresponding AUCTeX macro.

Key bindings

Useful key bindings: LaTeX specific

These keybindings are active in the latex-mode or useful in this mode.

Key binding	Description
C-c w	Run the texcount script on the buffer. It does not count the words in the LaTeX markup.
C-c C-j	Enter at the end of a line for an item in the list. Then a new item is inserted into the next line.
M-RET	To insert an item in the middle of the list.
C-c C-e	Enter to get a prompt for the kind of environment.
C-c C-s	Enter to insert a section or subsection.
C-c C-a	Compile and open PDF in default viewer
C-c C-c	Compile document.
C-c `	Go to compile error.
C-c C-p C-s	Preview regions.
C-c =	Open navigable table of contents view of the document.
C-c C-k	Kill the text file processing.
C-c ;	Comment out a region.
C-c %	Comment out a paragraph
C-c C-a	Compile a LaTeX text file and display the PDF in the default PDF viewer.
C-j	Add a new line and indent the new line.
M-q	To fill in a paragraph (text-wrap) and indent the current paragraph.
C-c C-q C-e	Fill and indent the current environment.
C-c C-q C-s	Fill and indent the current section.
C-c C-q C-r	Fill and indent the current region.
C-c {	To insert open and close braces and position the cursor between the braces.
C-c }	To move the cursor past the right brace.
M-x tex-validate-buffer	Enter to check the entire buffer for syntax errors.
M-x tex-validate-region	Enter to check the entire region for syntax errors.
C-c C-f	To process a file.
C-c C-v	To view a DVI file.
C-c C-b	To process the buffer.
C-c TAB	To run M-x tex-bibtex-file.

Useful key bindings: General editing

If you are rusty or just starting to use Emacs, you need only these 23 key bindings to function in Emacs.

Key binding	Description
C-x C-x	Quit Emacs
C-g	Abort current command
C-x C-f	Open a file
M-!	Open a shell, perhaps to create a file to open: touch new.tex
C-SPC	Mark the beginning of a selected region.
C-x SPC	Start marking rectangular box selection.
C-x u	Undo
C-M-_	Redo undone changes.
C-x C-s	Save file.
C-x C-w	Save the current buffer to the specified filename.
C-y	Paste clipboard.
C-w	Cut
s-c	Copy (option-c). The init.el file above maps the Mac option key to s, the Super key.
C-k	Delete line and store in kill ring (i.e., clipboard). Repeat to delete the new-line character.
C-a	Move the cursor to the beginning of the line.
C-e	Move the cursor to the end of the line.
C-x d	Open dired for directory navigation.
C-h	Invoke the help menu.
M-x package-list-packages	Refresh list of packages. Emacs may prompt you to install updates: enter u x y to upgrade packages.
M-x package-install	Must run package-list-packages first.
M-\	Will join the two words by removing the whitespaces between two words.
M-d	Delete word.
C-d	Delete character.

Vim users can turn on evil mode to emulate Vim key bindings.

Uncommenting the corresponding code in the init. el file invokes CUA keybindings (C-c, C-v, and C-x for copy, paste, and cut). However, there are conflicts with the LaTeX keybindings. I recommend either using evil-mode or learning the essential Emacs key bindings; they are much easier to master than they look :).

Quizzes

The recall of key bindings fades quickly after the first encounter but improves with spaced repetitions. I have provided two sets of quizzes to improve recall: One set for each set of the above key bindings. The quizzes in the set have the same questions, but I randomized their order to break up your memory of the answers based on the context of the question in the quiz.

Related projects of possible interest

• LaTeX manuscript template
• Writing log template in LaTeX
• Slideshow template in LaTeX
• Annotated bibliography Template in LaTeX
• Diary for 2022 in LaTeX
• Diary for 2023 in LaTeX
• latex-emacs profile
• snippets for latex-mode in Emacs
• Quizzes about Emacs to improve recall of keybindings
• Slides from talk about GhostText, Data Science Workshop, July 2022
• Video link to talk about GhostText, Data Science Workshop, July 2022
• The writer's law

Funding

• NIH: R01 CA242845, R01 AI088011
• NIH: P30 CA225520 (PI: R. Mannel); P20GM103640 and P30GM145423 (PI: A. West)

Updates

Version	Changes	Date
Version 0.2	Added funding and update table. Minor edits to the README.md	2024 May 3
Version 0.2.1	Minor edits in the README.md.	2024 May 10
Version 0.2.2	More minor edits in the README.md	2024 June 27