emacs

General usage
The manual
Useful functions
Underrated functionalities
Build emacs from source
Notes
elisp
init.el

General usage

When using emacs, it is sometimes advised to launch it as a daemon with server-start and to keep it running for the entire session. This allows you to open other files from the command line through the emacsclient command. Files will open in the emacs window that is already open.

However, I prefer to start a single emacs instance and use eshell inside it. The advantage of eshell over your operating system's terminal emulator is that files can be opened directly with C-f. Other emacs keybindings are also consistent inside eshell.

The manual

The emacs manual is very good. Within emacs, it can be evoked from everywhere by executing C-h r. It this doesn't work, it's probably not installed. In debian, it can be installed through apt install emacs-common-non-dfsg.

Useful functions

emacs comes with many useful built-in functionalities, which are well-documented in the aforementioned manual. Additional functionalities can be added through external repositories. In the following, I list the ones I use.

Hippie expand

When activated, Hippie Expand provides low-overhead auto-completion, based on text in open buffers. Start typing a word, and then invoke auto-completion with M-/. Hippie Expand completes the word by cycling through different auto-completion mechanisms that can be specified in the configuration file―see below. If the correct expansion of the word has been passed by accident, use C-/ to cycle back.

Keyboard macros

emacs lets you record and re-execute any chain of commands, which are called keyboard macros. We use C-x ( to start and C-x ) to end the recording. Once recorded, the macro can be executed repeatedly through C-x e. This is useful if the same action has to be performed repeatedly throughout the text and there is no good regular expression to capture. It allows for a more general structural editing than the regular expression-based workflow in, for example, ed(1).

apply-macro-to-region-lines runs the keyboard macro on each line in the region. I also sometimes just execute the macro a specific [number] of times via C-[number] C-x e.

Sometimes it is useful to save a complicated macro with a name to use it more often. This can be accomplished through kmacro-name-last-macro, which prompts for a name once executed. If we really like the macro we created, we can navigate to a file—for example, init.el— and write it out via insert-kbd-macro.

Rectangle commands

Rectangle commands allow you to operate on several columns of text at once. In order to span a rectangle, move your cursor to the position where the left upper corner of this imaginary rectangle is supposed to be. Hit C-space to set a mark. Move your cursor to the position where the right bottom corner of this imaginary rectangle is supposed to be. Now, that the rectangle is set, rectangle commands can be executed by leading with C-x r. Following commands can be executed:

Kill the rectangle: C-x r k
Copy the rectangle: C-x r M-w
Yank the last killed rectangle: C-x r y
Replace the rectangle: C-x r t

There are more commands but these are the most useful ones for me.

Gnus

gnus is a news and email reader that ships with emacs. It lets you subscribe to email inboxes and, for example, RSS feeds.

gnus hides emails that have been read. To view these older emails, use /o, which displays all email. Login credentials are stored in $HOME/.authinfo.

De- and encryption. gnus can de- and encrypt emails using GnupPG. If the key is setup with the corresponding email address, emacs encrypts and decrypts emails without the need for further configuration. Emails are encrypted via C-c C-m c o. Decryption works automatically, if you receive an encrypted message and you have the correct key added to your keyring.

Address book. An address book to store e-mail addresses can be managed using the Insidious Big Brother Database (bbdb). The package can be installed from the gnu repository via the emacs package manager. Once it is installed, it needs to be configured in the .gnus.el and init.el files as shown in the next section.

Start the address book on its own via M-x bbdb and leave the regex field empty. This lists all entries. New entries can be added via c (create). Add all addresses you want, save with s and close bbdb with q (quit).

Now, when writing an email and filling out the address, bbdb will suggest contacts and cycle through them in another buffer.

Delay email sending. Gnus can schedule emails to be sent at a certain time. This requires the following line in init.el:

(gnus-delay-initialize)
(setq message-draft-headers '(References From))
(gnus-demon-add-handler 'gnus-delay-send-queue 60 nil)
(gnus-demon-init)

The second line ensures the correct time stamp. The last two lines set up a demon to automatically push out queued messages every 60 min. In a message buffer, press C-c C-j instead of C-c C-c. The message is put into a folder called "delayed".

Unmark email. Emails marked as important in other email programmes can be unmarked in gnus through M-u.

Continue editing a drafted email. Emails saved under draft can be edited later by pressing D e / B del.

Dired

dired is a file browser that is shipped with emacs that can be invoked through M-x dired.

Selecting multiple files. Navigate in the directory holding the files you want to search in. Using m, mark all files you want to modify.

If there are too many files to mark by hand, one can execute M-x find-dired and then provide suitable flags, such as -name "*.cpp". This opens another dired buffer with the files that match the regex. If you want to select all matches, press t, which toggles marks.

Replacing regular expression in several files. In dired, we can replace a regular expression across several files. Select multiple files as described above. Execute dired-do-find-regexp-and-replace or, alternatively, press Q. Follow the instructions. The files need to be explicitly saved—see below.

Saving multiple files. For a large number of files, one can execute M-x ibuffer. Mark all unsaved files with * u and save them via S, that is to say Shift+s.

Filtering files. In order to search by filename and open the list in a dired buffer, use M-x find-name-dired.

One can also operate on files in dired using the !-operator. The filename itself can be inserted into the command using ?.

ebib

ebib is a BibTeX reference manager for emacs, written by J. Kremers. It can be installed through melpa. It has been recommended to me by Göktuǧ Kayaalp.

ebib is very straight-forward to use. One thing I struggled with was to export individual entries. Göktuǧ provided an answer:

In the top buffer you can hit C e to copy the selected entry's bibtex. Also x is for export, it prompts for a database name (i.e. a bibtex file opened in ebib, open files with o, creates .bib file if it doesn't exist, close database with c). You can also mark with m and do bulk export. Sadly it doesn't visibly indicate marked entries by default so it's a bit difficult to work with marks.

Underrated functionalities

M-x remember saves the current selection to ".emacs.d/notes"
M-x calendar gives you calendar functionalities, where you can take notes and schedule appointments (via i d)
M-x diary show appointments
gnus provides email and rss reader functionalities
eww is a really good text-based web browser that can display images
eshell is an alternative shell with elisp support
tab-line-mode and global-tab-line-mode~ provide tab functionalities
See also the article Batteries included with emacs and the follow-up More batteries included with emacs
M-x desktop-save let's you save the current emacs session. You can reload it with M-x desktop-read.

Build emacs from source

I've come to the conclusion that the version provided by the package manager of my linux distribution (debian) is sufficient for my purposes: mainly academic reading and writing; sometimes writing R and Julia snippets, very rarely writing C, C++, and Fortran (I haven't written Fortran since 2018). But if you'd like to compile from source, use the following:

git clone https://git.savannah.gnu.org/git/emacs.git
bash autogen.sh
./configure
make

Notes

(setq default-directory (concat (getenv "HOME") "/")) sets default directory to the home directory.
(setq initial-buffer-choice "~/.emacs.d/scratch.org") sets the initial buffer when emacs starts
(set-face-attribute 'default nil :height 110) sets the font size; similarly, (set-face-attribute 'default nil :font "Liberation Sans-12") sets both the font family and the size.
(add-hook 'org-mode-hook (lambda () (variable-pitch-mode t))) activates variable pitch fonts in org buffers.
(find-file "/home/ilhan/.emacs.d/notes") opens a file at start up.
(toggle-frame-fullscreen) starts emacs in full screen.
(savehist-mode t) saves buffer history. Needs to be configured. From the emacs manual:

For example, to save the history of commands invoked via M-x, add ‘command-history’ to the list in ‘savehist-additional-variables’.
M-x visual-line-mode wraps long lines and M-x display-line-numbers-mode displays line numbers. This is nice for writing tex files.
C-M-k deletes text wrapped in certain delimiters such as parantheses, brackets, and quotes.

elisp

Some elisp fun(ctionality). I should probably learn scheme.

;; compute flow velocity from frequency measurements

(defun velocity (n)
  (+ (* 0.116 n) 0.08))

(mapcar 'velocity '(3.5 2.5 5.2 4.6 3.2))

(0.486 0.37 0.6832 0.6136 0.4512)

;; compute nth fibonacci number

(defun fibonacci (n)
(if (<= n 1)
    n
  (+ (fibonacci (- n 1)) (fibonacci (- n 2)))))

(mapcar 'fibonacci '(1 2 3 4 5 6 7 8 9 10))

(1 1 2 3 5 8 13 21 34 55)

init.el

My emacs configuration file reads like this:

  ;; -*- mode: emacs-lisp -*-

(add-to-list 'package-archives
             '("melpa" . "https://melpa.org/packages/") t)
(require 'package)
(package-initialize)
(unless package-archive-contents
  (package-refresh-contents))

(setq visible-bell t)

(setq inhibit-splash-screen t)
(scroll-bar-mode -1)
(tool-bar-mode -1)
(menu-bar-mode -1)
(tab-bar-mode t)

(load-theme 'modus-operandi t)

(custom-set-faces
 '(font-lock-comment-face ((t (:foreground "#b22222"))))
 '(font-lock-keyword-face ((t (:foreground "#b22222"))))
 '(highlight ((t (:background "orange")))))

;; dired
(put 'dired-find-alternate-file 'disabled nil)
(setq delete-by-moving-to-trash t)

;; ido
(setq ido-enable-flex-matching t)
(setq ido-everywhere t)
(ido-mode t)

;; eww
(setq browse-url-browser-function 'eww-browse-url)

;; gnus
(gnus-delay-initialize)
;; add time stamp when sending the email
(setq message-draft-headers '(References From))
;; send queued email every 60 minutes
(gnus-demon-add-handler 'gnus-delay-send-queue 60 nil)
(gnus-demon-init)

;; org mode
(setq org-image-actual-width nil)
(org-babel-do-load-languages 'org-babel-load-languages '((R . t)
                                                         (julia . t)
                                                         (shell . t)
                                                         (python . t)))
(setq org-hide-emphasis-markers t)
(font-lock-add-keywords 'org-mode
                          '(("^ *\\([-]\\) "
                             (0 (prog1 () (compose-region (match-beginning 1) (match-end 1) "•"))))))

(unless (package-installed-p 'org-bullets)
  (package-install 'org-bullets))
(require 'org-bullets)

(set-face-attribute 'org-level-1 nil
                    :height 1.5
                    :foreground "#b22222")
(set-face-attribute 'org-level-2 nil
                    :height 1.3
                    :foreground "#b22222")
(set-face-attribute 'org-level-3 nil
                    :height 1.15
                    :foreground "#b22222")
(set-face-attribute 'org-level-4 nil
                    :height 1.1
                    :foreground "#b22222")
(set-face-attribute 'org-level-5 nil
                    :height 1.05
                    :foreground "#b22222")
(set-face-attribute 'org-level-6 nil
                    :foreground "#b22222")


;; tpls

;; elpa keyring update
(unless (package-installed-p 'gnu-elpa-keyring-update)
  (package-install 'gnu-elpa-keyring-update))
(require 'gnu-elpa-keyring-update)

;; csv
(unless (package-installed-p 'csv-mode)
  (package-install 'csv-mode))

;; address book
(unless (package-installed-p 'bbdb)
  (package-install 'bbdb))
(require 'bbdb)
(setq bbdb-north-american-phone-numbers-p nil)
(setq bbdb-user-mail-names
      (regexp-opt '("i.oezgen@tu-braunschweig.de")))
;; cycling while completing email addresses
(setq bbdb-complete-name-allow-cycling t)
(setq bbdb-use-pop-up nil)

;; pdf viewer
(unless (package-installed-p 'pdf-tools)
  (package-install 'pdf-tools))
(require 'pdf-tools)
(pdf-tools-install)
(pdf-loader-install)

;; literature manager
(unless (package-installed-p 'ebib)
  (package-install 'ebib))
(require 'ebib)
(setq ebib-bib-search-dirs '("~/Dokumente/reading"))
(setq ebib-file-associations '(("pdf" . "evince") ("ps")))
(setq ebib-file-search-dirs '("~/Dokumente/reading"))
(setq ebib-notes-directory "~/Dokumente/notes/sources/")
(setq ebib-reading-list-file "~/Dokumente/notes/toread.org")
(setq ebib-preload-bib-files '("~/Dokumente/reading/bibliography.bib"))
(setq ebib-index-columns
      '(("Author/Editor" 40 t)
        ("Year" 6 t)
        ("Title" 50 t)
        ("Entry Key" 10 t)))

;; fetch by doi for ebib
(unless (package-installed-p 'biblio)
  (package-install 'biblio))
(require 'biblio)

(unless (package-installed-p 'citar)
  (package-install 'citar))
(require 'citar)
(setq citar-bibliography '("~/Dokumente/reading/bibliography.bib"))

;; R programming
(unless (package-installed-p 'ess)
  (package-install 'ess))

;; auto complete
(unless (package-installed-p 'auto-complete)
  (package-install 'auto-complete))

(ac-config-default)
(global-auto-complete-mode t)

;; own functions
;; (load "~/.emacs.d/elisp/custom-functions.el")

;; hooks
(add-hook 'dired-mode-hook (lambda () (dired-hide-details-mode t)))
(add-hook 'org-mode-hook (lambda () (org-bullets-mode 1)))
(add-hook 'org-mode-hook 'visual-line-mode)

;; custom functions

(defun il/dired-dotfiles-toggle ()
  "Show/hide dot-files"
  (interactive)
  (when (equal major-mode 'dired-mode)
    (if (or (not (boundp 'dired-dotfiles-show-p)) dired-dotfiles-show-p) ; if currently showing
        (progn 
          (set (make-local-variable 'dired-dotfiles-show-p) nil)
          (message "h")
          (dired-mark-files-regexp "^\\\.")
          (dired-do-kill-lines))
      (progn (revert-buffer) ; otherwise just revert to re-show
             (set (make-local-variable 'dired-dotfiles-show-p) t)))))

(defun il/get-bibtex-from-doi (doi)
 "Get a BibTeX entry from the DOI"
 (interactive "M > doi: ")
 (let ((url-mime-accept-string "text/bibliography;style=bibtex"))
   (with-current-buffer 
     (url-retrieve-synchronously 
       (format "http://dx.doi.org/%s" 
        (replace-regexp-in-string "http://dx.doi.org/" "" doi)))
     (switch-to-buffer (current-buffer))
     (goto-char (point-ma
x))
     (setq bibtex-entry 
          (buffer-substring 
                (string-match "@" (buffer-string))
              (point)))
     (kill-buffer (current-buffer))))
 (insert (decode-coding-string bibtex-entry 'utf-8))
 (bibtex-fill-entry))

(defun il/tex-figure-snippet (fig)
  "Create a LaTeX snippet for a figure and move cursor to the point where the width is defined."
  (interactive "s > fig: ")
  (insert "\\begin{figure}\n  \\begin{center}\n   \\includegraphics[width=\\textwidth]{" fig "}\n  \\end{center}\n  \\caption{Lorem ipsum}\n\\end{figure}")
  (search-backward "\\textwidth"))

;; key settings
(global-set-key (kbd "M-ä") 'pop-tag-mark)
(global-set-key (kbd "M-ö") 'il/get-bibtex-from-doi)
(global-set-key (kbd "C-ü d") 'ebib-biblio-import-doi)


;; AUTOMATED STUFF

(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(package-selected-packages
   '(htmlize org-bullets auto-complete gnuplot academic-phrases citar sicp csv-mode ess biblio pdf-tools gnu-elpa-keyring-update ebib bbdb)))

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