#+title: Emacs setup for use with LaTeX, Org, and Python
#+author: Gerard Vermeulen
#+latex_class: article-local
#+latex_class_options: [11pt,a4paper,english,svgnames]
#+macro: kbd (eval (by-backend-kbd-org-macro $1))
#+options: ^:{}
#+property: header-args:emacs-lisp :exports code :results silent :tangle init.el
#+startup: showeverything
#+begin_src latex :noweb yes :results raw
,#+latex_header: <<latex-header-1>>
,#+latex_header: <<latex-header-2>>
,#+latex_header: <<latex-header-3>>
,#+latex_header: <<latex-header-4>>
,#+latex_header: <<latex-header-5>>
#+end_src

* Copying
:PROPERTIES:
:CUSTOM_ID: sec:copying
:END:

This README contains my Emacs setup for use with LaTeX, Org, and Python.

Copyright \copy 2021-2023 Gerard Vermeulen.

#+BEGIN_QUOTE
Permission is granted to copy, distribute and/or modify this
document under the terms of the GNU Free Documentation License,
Version 1.3 or any later version published by the Free Software
Foundation; with no Invariant Sections, with no Front-Cover Texts,
and with no Back-Cover Texts.  A copy of the license is included in
the section entitled "GNU Free Documentation License".
#+END_QUOTE

* Quick start
:PROPERTIES:
:CUSTOM_ID: sec:quick-start
:END:

Backup the =user-emacs-directory= (defaults often to =~/.emacs.d= on =Linux=,
=Unix=, or =Darwin=) and execute the commands in listing [[lst:prepare-user-emacs-directory-with-https][prepare the
=user-emacs-directory= without =ssh= access]] or in listing [[lst:prepare-user-emacs-directory-with-ssh][prepare the
=user-emacs-directory= with =ssh= access]].  After invoking Emacs interactively
(in interactive mode, neither in batch mode, nor in server mode), Emacs will ask
you to install a selected set of packages.  Quit Emacs and invoke Emacs again.

# #+caption[Prepare the user-emacs-directory]:
# #+caption: Clone and initialize the user-emacs-directory.
# #+name: lst:prepare-user-emacs-directory
# #+begin_src shell :noeval :tangle no
# cd ~
# git clone ccdr@mercury.grenoble.cnrs.fr:SERVER/emacs.d.git .emacs.d
# make --directory=.emacs.d init
# emacs &
# #+end_src

#+caption[Prepare the user-emacs-directory without =ssh= access]:
#+caption: Clone and initialize the user-emacs-directory without =ssh= access.
#+name: lst:prepare-user-emacs-directory-with-https
#+begin_src shell :noeval :tangle no
cd ~
git clone https://forge.chapril.org/gav451/emacs.d.git .emacs.d
make --directory=.emacs.d init
emacs &
#+end_src

#+caption[Prepare the =user-emacs-directory= with =ssh= access]:
#+caption: Clone and initialize the user-emacs-directory with =ssh= access.
#+name: lst:prepare-user-emacs-directory-with-ssh
#+begin_src shell :noeval :tangle no
cd ~
git clone ssh://gitea@forge.chapril.org:222/gav451/emacs.d.git .emacs.d
make --directory=.emacs.d init
emacs &
#+end_src

* Introduction
:PROPERTIES:
:CUSTOM_ID: sec:introduction
:END:

This Emacs setup aims to install automatically a minimal set of extension
packages that allows to handle my reports and presentations.  The file format of
the reports is [[https://orgmode.org/][Org Mode]] plain text with [[https://www.python.org/][Python]] source code blocks and the file
format of the presentations is [[https://www.latex-project.org/][LaTeX]].

This [[info:org#Top][org]] file (more precisely the original [[info:org#Top][org]] source file of this file)
illustrates three methods in my work-flow:
1. How to tangle (or export) source blocks from [[info:org#Top][org]] files. This file contains
   source blocks to produce the files =early-init.el=, =init.el=, =latexmkrc=,
   =org-store-link=, and =example.py= by tangling.
2. How to export [[info:org#Top][org]] files to other formats such as [[https://en.wikipedia.org/wiki/HTML][HTML]], [[https://www.latex-project.org/][LaTeX]], and [[https://en.wikipedia.org/wiki/PDF][PDF]].
3. How [[info:org#Hyperlinks][org hyperlinks (info)]] allow to link inside and outside [[info:org#Top][Org Mode]]: hover
   over or click on the links to experiment.

The [[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX - Aalborg University Center TeX]] extension package provides a
powerful [[https://en.wikipedia.org/wiki/Text-based_user_interface][Text-based User Interface (TUI)]] environment to edit the [[https://www.latex-project.org/][LaTeX]]
presentations.

The [[https://github.com/bdarcus/citar][Citar]] extension package provides quick filtering and selecting of
bibliographic entries, and the option to run different commands on those
selections.  [[https://github.com/bdarcus/citar][Citar]] requires at least [[info:org#Top][Org (info)]]-9.5 , which is already part of
Emacs-28.1.  [[https://github.com/bdarcus/citar][Citar]] exploits the enhancements of Emacs' builtin selection
mechanism provided by the extension packages [[https://github.com/minad/vertico][vertico]], [[https://github.com/oantolin/embark][embark]], [[https://github.com/minad/marginalia][marginalia]], and
[[https://github.com/minad/consult][consult]].  The [[https://github.com/andras-simonyi/citeproc-el][citeproc]] extension package provides
[[https://citationstyles.org/][CSL: citation style language]] processing
capabilities to [[https://github.com/bdarcus/citar][citar]] and [[https://orgmode.org/][Org Mode]].  The [[https://github.com/citation-style-language/styles#readme][citation style language: style
repository]] links to a curated repository of CSL styles.

The [[https://github.com/vedang/pdf-tools][pdf-tools]] extension package renders [[https://en.wikipedia.org/wiki/PDF][PDF]] file with the possibility to
annotate the file or to click on anchors in the [[https://en.wikipedia.org/wiki/PDF][PDF]] file that link back to the
original [[https://www.latex-project.org/][LaTeX]] file of the document.  An example of my work-flow are the steps
to convert this [[info:org#Top][org]] file to [[https://en.wikipedia.org/wiki/PDF][PDF]] and to see the result with [[https://github.com/vedang/pdf-tools][pdf-tools]] in Emacs:
execute the commands ~pdf-tools-install~, ~org-babel-tangle~,
~org-latex-export-latex-to-latex~, and ~compile~.  This sets up an infinite
[[https://www.latex-project.org/][LaTeX]] compilation loop to update and redisplay the [[https://en.wikipedia.org/wiki/PDF][PDF]] file after excution of
the ~org-latex-export-latex-to-latex~ command in this buffer.

Here follows a list of interesting Emacs configurations:
1. [[https://github.com/alhassy/emacs.d][Musa Al-hassy's configuration]] is an impressive example of producing the Emacs
   initialization files and other files by tangling an [[info:org#Top][org]] file. His methodology
   is impressive, as his [[https://alhassy.github.io/ElispCheatSheet/][Elisp Cheat Sheet]] and [[https://alhassy.github.io/org-special-block-extras/][org-special-block-extra package]]
   show.  To me, this is a configuration to admire, but his methodology is way
   over my head.
2. [[https://github.com/oantolin/emacs-config][Omar Antolin Camarena's configuration]] exploits built-in packages, Omar's own
   small packages, and large external packages.  Omar is the author of [[https://github.com/oantolin/orderless][orderless]]
   and [[https://github.com/oantolin/embark][embark]].  I have stolen his idea of using ~custom-set-variables~ instead
   of the customize interface although that is [[https://www.masteringemacs.org/article/bad-emacs-advice][bad Emacs advice]] for new users.
3. [[https://gitlab.com/ambrevar/dotfiles][Pierre Neirhardt's configuration]] implements lazy loading without help of
   external packages.  I have stolen his approach of using lazy loading to
   silently ignore the setup stanzas of uninstalled extension packages.
4. [[https://sachachua.com/dotemacs/][Sacha Chua's configuration]] is a practical example of producing the Emacs
   initialization files by tangling an [[info:org#Top][org]] file.  It gives me the impression
   that she is a very practical person trying to achieve her goals by the most
   efficient means.
5. [[https://github.com/purcell/emacs.d][Steve Purcell's configuration]] is well organized and a showcase of readable
   code.  Its commit and issue histories are also helpful: see for instance the
   discussion [[https://github.com/purcell/emacs.d/issues/778][The order of company candidates is incorrect in Emacs lisp mode]].

Here follows a list of links on how to use Emacs and Elisp:
1. [[https://www.youtube.com/watch?v=lkIicfzPBys][A guided tour of Emacs]] is a link to a video tour pointing how [[info:emacs#Buffers][buffers (info)]],
   [[info:emacs#Dired][dired (info)]], [[info:emacs#Help][documentation (info)]], [[info:elisp#Top][elisp (info)]], [[info:elisp#Debugging][elisp debugging (info)]],
   [[info:eshell#Top][eshell (info)]], and [[info:emacs#Keyboard Macros][keyboard macros (info)]] turn Emacs in an powerful coding
   and editing environment.
2. [[https://www.youtube.com/watch?v=6ZWp05OW1c0][Emergency Emacs]] is a link to a video on fundamental editing features and
   principles with focus on [[info:ediff#Top][ediff (info)]], [[info:emacs#Undo][undo (info)]], [[info:emacs#Moving Point][moving point (info)]],
   [[info:emacs#Erasing][erasing (info)]], and [[info:emacs#Dynamic Abbrevs][dynamic abbreviations (info)]].
2. [[https://endlessparentheses.com/][Endless Parentheses]] is a blog with many mindblowing code snippets.
3. [[https://www.murilopereira.com/how-to-open-a-file-in-emacs/][How to open a file in Emacs]] looks into [[info:elisp#Top][elisp (info)]] and
   [[info:elisp#Debugging][elisp debugging (info)]] and then compares Emacs, [[https://www.vim.org/][Vim]],
   [[https://neovim.io/][Neovim]], and [[https://code.visualstudio.com/][Visual Studio Code]] with respect to values and technology.
4. [[https://protesilaos.com/codelog/2022-01-31-learning-emacs/][Learning Emacs and Elisp]] is a link to a video tutorial with a transcript on
   the best approach to learn Emacs and Elisp.
5. [[https://www.masteringemacs.org/][Mastering Emacs]] is a link to a blog with many interesting posts that promotes
   a book on how to become a proficient Emacs user.

* [[info:emacs#Early Init File][Early Init File (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:early-init-file
:END:

Try to load [[https://github.com/emacscollective/no-littering][no-littering]] as early as possible, since it helps to keep
=~/.emacs.d= clean.

#+caption[Tangle the early-init-file]:
#+caption: Tangle the early-init-file.
#+name: lst:tangle-early-init-file
#+begin_src emacs-lisp :tangle early-init.el
;;; early-init.el --- user early-init file        -*- lexical-binding: t -*-
;;; Commentary:
;;; Code:
(setq load-prefer-newer t)

(require 'no-littering nil 'noerror)

(provide 'early-init)
;; Emacs looks for "Local variables:" after the last "?\n?\f".

;; Local Variables:
;; indent-tabs-mode: nil
;; End:
;;; earl-init.el ends here
#+end_src

In order to get help in understanding the code block above in a buffer showing
the original [[info:org#Top][Org]] source file, type {{{kbd(C-c C-c)}}} after moving
point (or cursor) to one of the items of the list:
1. src_emacs-lisp{(describe-variable #'load-prefer-newer t)}
2. src_emacs-lisp{(apropos-library "no-littering")}
3. src_emacs-lisp{(find-function #'hack-local-variables)}
to execute the code between the curly braces for access to help.  This shows
that *Emacs is a self-documenting editor.*

* [[info:emacs#Init File][Init File (info)]] header
:PROPERTIES:
:CUSTOM_ID: sec:init-file-header
:END:

The =user-init-file= header requires =cl-lib= and customizes Emacs variables.
It consists of four parts in listing [[lst:1st-custom-set-variables-call]],
[[lst:2nd-custom-set-variables-call]], [[lst:3rd-custom-set-variables-call]], and
[[lst:4th-custom-set-variables-call]] in order to limit the length of the listings
for exporting to LaTeX.

The [[info:elisp#Quoting][quoting (info)]] and the [[info:elisp#Backquote][backquote (info)]] pages explain how to understand the
~'~ (quote), ~`~ (backquote), ~,~ (substitute) and ~@,~ (splice) in the
~custom-set-variables~ function calls in listing
[[lst:1st-custom-set-variables-call]], [[lst:2nd-custom-set-variables-call]],
[[lst:3rd-custom-set-variables-call]], and [[lst:4th-custom-set-variables-call]].  A
tutorial of how to use those reader macros is the [[https://mullikine.github.io/posts/macro-tutorial/][didactic emacs-lisp macro
example]].

The [[info:emacs#Init File][init file (info)]] does not load the ~custom-file~ as [[info:emacs#Saving Customizations][saving customizations
(info)]] recommends because of the ~custom-set-variables~ function calls.

#+caption[Customize the first set of Emacs variables]:
#+caption: Customize the first set of Emacs variables.
#+name: lst:1st-custom-set-variables-call
#+begin_src emacs-lisp
;;; init.el --- user init file                    -*- lexical-binding: t -*-
;;; Commentary:
;;; Code:
(require 'cl-lib)

(custom-set-variables
 '(after-save-hook #'executable-make-buffer-file-executable-if-script-p)
 '(column-number-mode t)
 '(cursor-type 'box)
 `(custom-file ,(locate-user-emacs-file "custom.el"))
 '(epg-pinentry-mode 'loopback)
 '(global-hl-line-mode t)
 '(global-hl-line-sticky-flag t)
 '(history-delete-duplicates t)
 '(history-length 500)
 '(indent-tabs-mode nil)
 '(inhibit-startup-buffer-menu t)
 '(inhibit-startup-screen t)
 '(initial-buffer-choice t)
 '(initial-scratch-message "")
 `(insert-directory-program ,(or (executable-find "gls")
                                 (executable-find "ls")))
 '(kill-ring-max 300))
#+end_src

#+caption[Customize the second set of Emacs variables]:
#+caption: Customize the second set of Emacs variables.
#+name: lst:2nd-custom-set-variables-call
#+begin_src emacs-lisp
(custom-set-variables
 ;; See https://github.com/melpa/melpa#mirrors for official Melpa mirrors.
 '(package-archives
   '(("gnu" . "https://elpa.gnu.org/packages/")
     ("gnu-devel" . "https://elpa.gnu.org/devel/")
     ("melpa" . "https://melpa.org/packages/")
     ;; ("melpa" . "https://www.mirrorservice.org/sites/melpa.org/packages/")
     ("nongnu" . "https://elpa.nongnu.org/nongnu/")))
 ;; Pin packages to GNU ELPA for info or stability.
 '(package-pinned-packages
   `,(delq nil `((auctex . "gnu")
                 (compat . "gnu")
                 (consult . "gnu-devel")
                 ,(when (version< emacs-version "29.0.0")
                    '(eglot . "gnu-devel"))
                 (embark . "gnu-devel")
                 (embark-consult . "gnu-devel")
                 (engrave-faces . "gnu-devel")
                 (hyperbole . "gnu-devel")
                 (marginalia . "gnu-devel")
                 (org . "gnu-devel")
                 (queue . "gnu")
                 (rainbow-mode . "gnu")
                 (spinner . "gnu")
                 (xr . "gnu")
                 (vertico . "gnu-devel")))))
#+end_src

#+caption[Customize the third set of Emacs variables]:
#+caption: Customize the third set of Emacs variables.
#+name: lst:3rd-custom-set-variables-call
#+begin_src emacs-lisp
(custom-set-variables
 '(package-selected-packages
   `,(delq nil `(async              ; asynchroneous processing
                 debbugs            ; access the GNU bug tracker
                 no-littering       ; keep `user-emacs-directory' clean
                 org                ; thought organizer
                 wgrep))))          ; open a writable grep buffer
#+end_src

#+caption[Customize the fourth set of Emacs variables]:
#+caption: Customize the fourth set of Emacs variables.
#+name: lst:4th-custom-set-variables-call
#+begin_src emacs-lisp
(custom-set-variables
 '(recentf-mode t)
 '(save-place-mode t)
 '(scroll-bar-mode nil)
 '(tab-always-indent 'complete)
 '(tab-width 8)
 '(tool-bar-mode nil)
 '(url-cookie-trusted-urls nil)
 '(url-cookie-untrusted-urls '(".*"))
 '(use-dialog-box nil)
 '(view-read-only t))

(when (version< "28.0" emacs-version)
  (custom-set-variables
   '(mode-line-compact 'long)
   '(next-error-message-highlight t)
   '(use-short-answers t)))

(when (eq system-type 'darwin)
  (custom-set-variables
   '(ns-alternate-modifier nil)
   '(ns-command-modifier 'meta)
   '(ns-right-command-modifier 'super)))

(when (eq window-system 'ns)
  (add-to-list 'initial-frame-alist '(height . 51))
  (add-to-list 'initial-frame-alist '(width . 180)))
#+end_src

* [[info:emacs#Package Installation][Install the selected packages (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:install-selected-packages
:END:

[[info:emacs#Package Installation][Emacs installs packages]] from archives on the internet.  This setup uses three
archives:
1. The [[https://elpa.gnu.org/][GNU Emacs Lisp Package Archive]]
2. The [[https://elpa.nongnu.org/][NonGNU Emacs Lisp Package Archive]].
3. The [[https://melpa.org/#/][Milkypostman's Emacs Lisp Package Archive (MELPA)]] with its official
   [[https://www.mirrorservice.org/sites/melpa.org/packages/][mirror]] in case [[https://downforeveryoneorjustme.com/melpa.org][is Melpa.org down?]] tells [[https://melpa.org/#/][MELPA]] is down for everyone.
The code in listing [[lst:install-selected-packages]] assumes that the package
system is in a *virgin* state if the package [[https://github.com/emacscollective/no-littering][no-littering]] is not present:
1. It installs and loads [[https://github.com/emacscollective/no-littering][no-littering]] after ensuring refreshing of the
   contents of available packages.
2. It installs [[https://elpa.gnu.org/devel/org.html][Org (GNU-devel ELPA archive)]] early to shadow the built-in package
   while preventing collisions between the snapshot and built-in packages.
3. It calls src_emacs-lisp{(package-install-selected-packages)} to check the
   installation status of all packages in
   src_emacs-lisp{package-selected-packages} and to install the missing packages
   after the user has agreed to its prompt.
4. It defines a function to ensure the installation of packages in other source
   blocks.  This allows skipping installation in sections with a =:noexport:=
   tag by disallowing tangling.
In case of normal Emacs usage, src_emacs-lisp{(package-list-packages)} refreshes
the contents of packages and allows to update packages to the latest version.

#+caption[Install the selected packages]:
#+caption: Install the selected packages.
#+name: lst:install-selected-packages
#+begin_src emacs-lisp
(unless noninteractive
  (unless (require 'no-littering nil 'noerror)
    (unless (bound-and-true-p package-archive-contents)
      (package-refresh-contents))
    ;; Install and require `no-littering'.
    (package-install 'no-littering)
    (require 'no-littering)
    ;; https://emacs.stackexchange.com/a/45939 answers
    ;; "How to shadow automatically a built-in package by installing it?"
    (defun shadow-builtin-by-install (pkg)
      (when-let ((desc (cadr (assq pkg package-archive-contents))))
        (package-install desc 'dont-select)))
    ;; Shadow built-in `org' by installing `org'.
    (shadow-builtin-by-install 'org)
    ;; Install the selected packages.
    (package-install-selected-packages)))

(defun ensure-package-selection (package)
  "Ensure selection of PACKAGE."
  (when (and (package-installed-p package)
             (bound-and-true-p package-selected-packages))
    (cl-pushnew package package-selected-packages)))

(defun ensure-package-installation (&rest packages)
  "Ensure installation of all packages in PACKAGES."
  (let ((ok t))
    (dolist (package packages)
      (unless (package-installed-p package)
        (package-install package))
      (unless (ensure-package-selection package)
        (setq ok nil)))
    ok))
#+end_src

* [[https://git.savannah.gnu.org/cgit/emacs.git/tree/admin/notes/tree-sitter/starter-guide?h=feature/tree-sitter][Emacs Tree-sitter]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-tree-sitter
:END:

#+caption[Customize Emacs Tree-sitter]:
#+caption: Customize Emacs Tree-sitter.
#+name: lst:customize-emacs-tree-sitter
#+begin_src emacs-lisp
(when (require 'treesit nil 'noerror)
  ;; https://lists.gnu.org/archive/html/emacs-devel/2022-11/msg01372.html
  (let ((tselp (expand-file-name "~/VCS/tree-sitter-module/dist/")))
    (when (file-exists-p tselp)
      (add-to-list 'treesit-extra-load-path tselp)
      ;; Does not play nicely with eglot:
      ;; (setq major-mode-remap-alist '((python-mode . python-ts-mode)))
      ;; Plays nicely with eglot:
      (add-to-list 'auto-mode-alist
                   `(,(rx ".py" (opt (any "iw")) eos) . python-ts-mode)))))
#+end_src

* [[info:emacs#Faces][Text faces or styles (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:text-faces-or-styles
:END:

This setup does not configure [[info:emacs#Custom Themes][custom themes (info)]] in order to prevent endless
useless tweaking.  See the [[https://protesilaos.com/codelog/2020-09-05-emacs-note-mixed-font-heights/][note on mixed font heights in Emacs]] for how to setup
fonts properly.  It boils down to two rules:
1. The height of the default face must be an integer number to make the height a
   physical quantity.
2. The heights of all other faces must be real numbers to scale those heights
   with respect to the height of the face (those heights default to 1.0 for no
   scaling).
The code in listing [[lst:configure-face-attributes]] source implements those rules.
Listing [[lst:set-default-face-height]] shows that font scaling is easy in case of
proper initialization of all face heigths.  Listing
[[lst:fix-gtk-color-for-invert-default-face]], [[lst:shadow-org-font-lock-faces]], and
[[lst:shadow-org-font-lock-faces]] show a few tweaks to improve visibility without
theming:
1. Fixing the =gtk= background color of the already loaded =region= face.
2. Toggling between a dark and light background by means of
   src_emacs-lisp{(invert-default-face)}.
3. Shadowing the definition of faces before loading.  The last item in the page
   on [[https://orgmode.org/worg/org-contrib/babel/examples/fontify-src-code-blocks.html#org5c4406f][fontifying Org mode source code blocks]] describes this method.

#+caption[Configure =face-attributes=]:
#+caption: Configure =face-attributes=.
#+name: lst:configure-face-attributes
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; Set face attributes.
  (cond
   ((eq system-type 'darwin)
    (set-face-attribute 'default nil :family "Hack" :height 120)
    (set-face-attribute 'fixed-pitch nil :family "Hack")
    (set-face-attribute 'variable-pitch nil :family "FiraGo"))
   ((eq system-type 'gnu/linux)
    (set-face-attribute 'default nil :family "Hack" :height 110)
    (set-face-attribute 'fixed-pitch nil :family "Hack")
    (set-face-attribute 'variable-pitch nil :family "FiraGo"))
   (t
    (set-face-attribute 'default nil :family "Hack" :height 110)
    (set-face-attribute 'fixed-pitch nil :family "Hack")
    (set-face-attribute 'variable-pitch nil :family "DejaVu Sans"))))
#+end_src

#+caption[Implement =set-default-face-height=]:
#+caption: Implement =set-default-face-height=.
#+name: lst:set-default-face-height
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun set-default-face-height ()
    "Set the default face height in all current and future frames.

Scale all other faces with a height that is a real number."
    (interactive)
    (let* ((prompt (format "face heigth (%s): "
                           (face-attribute 'default :height)))
           (choices (mapcar #'number-to-string
                            (number-sequence 50 200 10)))
           (height (string-to-number
                    (completing-read prompt choices nil 'require-match))))
      (message "Setting the height of the default face to %s" height)
      (set-face-attribute 'default nil :height height))))
#+end_src

#+caption[Use =buffer-face-mode= to set fixed or variable pitch face]:
#+caption: Use =buffer-face-mode= to set fixed or variable pitch face.
#+name: lst:use-buffer-face-mode-for-fixed-or-variable-pitch-face
#+begin_src emacs-lisp
;; Use proportional font faces in current buffer
(defun set-buffer-variable-pitch-face ()
  "Set a variable width (proportional) font in current buffer."
  (interactive)
  (setq buffer-face-mode-face 'variable-pitch)
  (buffer-face-mode))

;; Use monospaced font faces in current buffer
(defun set-buffer-fixed-pitch-face ()
  "Set a fixed width (monospace) font in current buffer."
  (interactive)
  (setq buffer-face-mode-face 'fixed-pitch)
  (buffer-face-mode))

(add-hook 'magit-mode-hook #'set-buffer-fixed-pitch-face)
(add-hook 'prog-mode-hook #'set-buffer-fixed-pitch-face)
#+end_src

#+caption[Fix a `gtk' color and implement =invert-default-face=]:
#+caption: Fix a `gtk' color and implement =invert-default-face=.
#+name: lst:fix-gtk-color-for-invert-default-face
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun fix-gtk-region-face-background-color ()
    (when (featurep 'gtk)
      (set-face-attribute
       'region nil
       :background (cdr (assoc (face-attribute 'default :background)
                               '(("white" . "LightGoldenrod2")
                                 ("black" . "blue3")))))))

  (defun invert-default-face ()
    "Invert the default face."
    (interactive)
    (invert-face 'default)
    (fix-gtk-region-face-background-color))

  (fix-gtk-region-face-background-color))
#+end_src

#+caption[Shadow Org font-lock faces to improve the readability]:
#+caption: Shadow Org font-lock faces to improve the readability.
#+name: lst:shadow-org-font-lock-faces
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; Shadow two definitions in org-faces.el:
  (defface org-block
    ;; https://emacs.stackexchange.com/a/9604 answers:
    ;; How to override a defined face for light and dark backgrounds?
    `((((background dark))
       :inherit (fixed-pitch)
       ,@(and (>= emacs-major-version 27) '(:extend t))
       :background "#444444")
      (t
       :inherit (fixed-pitch)
       ,@(and (>= emacs-major-version 27) '(:extend t))
       :background "#FFFFD0"))
    "My face used for text inside various blocks.

It is always used for source blocks.  You can refine what face
should be used depending on the source block language by setting,
`org-src-block-faces', which takes precedence.

When `org-fontify-quote-and-verse-blocks' is not nil, text inside
verse and quote blocks are fontified using the `org-verse' and
`org-quote' faces, which inherit from `org-block'.")

  (defface org-table
    ;; https://emacs.stackexchange.com/a/9604 answers:
    ;; How to override a defined face for light and dark backgrounds?
    `((((background dark))
       :inherit (fixed-pitch)
       ,@(and (>= emacs-major-version 27) '(:extend t))
       :background "#444444")
      (t
       :inherit (fixed-pitch)
       ,@(and (>= emacs-major-version 27) '(:extend t))
       :background "#FFFFD0"))
    "My face for tables."))
#+end_src

#+caption[Shadow Emacs font-lock faces to improve the readability]:
#+caption: Shadow Emacs font-lock faces to improve the readability.
#+name: lst:shadow-emacs-font-lock-faces
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; Shadow one definition in sh-script.el:
  (defface sh-heredoc
    '((((class color) (background dark))
       (:foreground "yellow"))
      (((class color) (background light))
       (:foreground "magenta"))
      (t
       (:weight bold)))
    "My face to show a here-document."))
#+end_src

* [[info:emacs#Windows][Window management (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:window-management
:END:

Mickey Peterson's post [[https://www.masteringemacs.org/article/demystifying-emacs-window-manager][Demystifying Emacs's Window Manager]] invites to improve
window placement.  Listing [[lst:1st-window-management]], [[lst:2nd-window-management]]
and [[lst:3rd-window-management]] implement a selection of his recommendations.

#+caption[Window management functions and key bindings]:
#+caption: Window management functions and key bindings.
#+name: lst:1st-window-management
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; https://www.masteringemacs.org/article/demystifying-emacs-window-manager
  (defun split-root-below (arg)
    "Split window below from the root or from the parent with ARG."
    (interactive "P")
    (split-window (if arg (window-parent (selected-window))
                    (frame-root-window))
                  nil 'below nil))

  (defun split-root-right (arg)
    "Split window right from the root or from the parent with ARG."
    (interactive "P")
    (split-window (if arg (window-parent (selected-window))
                    (frame-root-window))
                  nil 'right nil))

   (defun toggle-window-dedication ()
    "Toggles window dedication in the selected window."
    (interactive)
    (set-window-dedicated-p
     (selected-window) (not (window-dedicated-p (selected-window)))))

   (defun make-display-buffer-matcher-function (major-modes)
    "Return a lambda function to match a list of MAJOR-MODES."
    (lambda (buffer-name action)
      (with-current-buffer buffer-name (apply #'derived-mode-p major-modes))))

   (global-set-key (kbd "M-o") #'other-window))
#+end_src

#+caption[Window management modes]:
#+caption: Window management modes.
#+name: lst:2nd-window-management
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (winner-mode +1))
#+end_src

#+caption[Window management variables]:
#+caption: Window management variables.
#+name: lst:3rd-window-management
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; https://www.masteringemacs.org/article/demystifying-emacs-window-manager
  (custom-set-variables
   '(switch-to-buffer-in-dedicated-window 'pop)
   '(switch-to-buffer-obey-display-actions t))

  (add-to-list 'display-buffer-alist
               `(,(rx (or "*Apropos*"
                          "*Help*"
                          "*info"))
                 (display-buffer-reuse-window display-buffer-pop-up-window)
                 (inhibit-same-window . nil)))
  (add-to-list 'display-buffer-alist
               `(,(rx (or "*Occur*"
                          "*grep*"
                          "*xref*"))
                 display-buffer-reuse-window
                 (inhibit-same-window . nil)))
  (add-to-list 'display-buffer-alist
               '("\\*compilation\\*"
                 display-buffer-no-window
                 (allow-no-window . t)))
  (add-to-list 'display-buffer-alist
               '("^\\*Dictionary\\*" display-buffer-in-side-window
                 (side . left)
                 (window-width . 70))))
#+end_src

* [[info:elisp#Advising Functions][Advising functions (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:advising-function
:END:

#+caption[Toggle any advice]:
#+caption: Toggle any advice.
#+name: lst:toggle-any-advice
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun advice-toggle (symbol where function &optional props)
    "Toggle between states after `advice-remove' and `advice-add'."
    (let ((how "%s `%s' advice `%s' %s `%s'"))
      (if (advice-member-p function symbol)
          (progn
            (message how "Removal of" where function "from" symbol)
            (advice-remove symbol function))
        (message how "Addition of" where function "to" symbol)
        (advice-add symbol where function props)))))
#+end_src

#+caption[Toggle specific advice]:
#+caption: Toggle specific advice.
#+name: lst:toggle-specific-advice
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
   (defun toggle-engrave-faces-attribute-values-around ()
     "Toggle `engrave-faces-attribute-values-around' advice."
     (interactive)
     (advice-toggle 'engrave-faces-attribute-values
                    :around #'engrave-faces-attribute-values-around))

   (defun toggle-engrave-faces-latex-face-apply-override ()
     "Toggle `engrave-faces-latex-face-apply' advice."
     (interactive)
     (advice-toggle 'engrave-faces-latex-face-apply
                    :override #'engrave-faces-latex-face-apply-override))

   (defun toggle-engrave-faces-latex-face-mapper-override ()
     "Toggle `engrave-faces-latex-face-mapper' advice."
     (interactive)
     (advice-toggle 'engrave-faces-latex-face-mapper
                    :override #'engrave-faces-latex-face-mapper-override))

   (defun toggle-eww-display-pdf-around ()
     "Toggle `eww-display-advice' advice."
     (interactive)
     (advice-toggle 'eww-display-pdf :around #'eww-display-pdf-as-binary))

   (defun toggle-ilog-timer-function-after ()
     "Toggle `ilog-timer-function' advice."
     (interactive)
     (advice-toggle 'ilog-timer-function :after #'ilog-ensure-ilog-buffer-window))

   (defun toggle-keycast-log-update-buffer-override ()
     "Toggle `keycast-log-update-buffer' advice."
     (interactive)
     (advice-toggle 'keycast-log-update-buffer
                    :override #'keycast-log-update-buffer-plain))

   (defun toggle-org-babel-python-format-session-value-override ()
     "Toggle `org-babel-python-format-session-value' advice."
     (interactive)
     (advice-toggle 'org-babel-python-format-session-value
                    :override #'org-babel-python-format-session-value-override)))
#+end_src

* [[info:emacs#Dired][Dired: directory editor as file manager (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:file-manager
:END:

[[info:emacs#Dired][Dired (info)]] and the [[https://github.com/ranger/ranger#readme][ranger]] file manager offer similar capabilities for copying,
deleting, opening, renaming, and viewing files and directories, but the
integration of [[info:emacs#Dired][dired (info)]] in Emacs is obviously much better than the
integration of [[https://github.com/ranger/ranger#readme][ranger]] in Emacs.

For instance, this setup allows to insert an =org-mode= link to an poorly
identified file containing a specific image into an =org-mode= buffer by means
of the facilities of [[info:emacs#Dired][dired (info)]] as follows:
1. Type {{{kbd(C-x d)}}} to open the directory containing the pooly identified
   file with the specific image in a =dired-mode= buffer.
2. Start searching for the specific image by navigating to the name of any image
   file.
3. Type {{{kbd(v)}}} to switch to view the file in an =image-mode= buffer.
4. In the =image-mode= buffer, continue searching for the specific image by
   typing:
   - {{{kbd(n)}}} to view the next image in the =dired-mode= buffer,
   - {{{kbd(p)}}} to view the previous image in the =dired-mode= buffer, and
   - {{{kbd(q)}}} to quit the =image-mode= buffer and to go back to the
     =dired-mode= buffer.
5. After finding the specific image, use {{{kbd(C-c l)}}} in the =image-mode=
   buffer or the =dired-mode= buffer to store the =org-link=.
6. Switch to the =org-mode= buffer and use {{{kbd(C-c C-l)}}} to insert the
   =org-link= into the buffer.

Listing [[lst:customize-dired]] makes the directory editor sort entries
alphabetically after grouping the directories before grouping the files by
extension.

#+caption[Customize =dired=]:
#+caption: Customize =dired=.
#+name: lst:customize-dired
#+begin_src emacs-lisp
(with-eval-after-load 'dired
  (custom-set-variables
   '(dired-dwim-target t)
   ;; | switch | action                                 |
   ;; |--------+----------------------------------------|
   ;; | -a     | also list hidden entries               |
   ;; | -l     | use a long listing format              |
   ;; | -X     | sort alphabetically by entry extension |
   ;; | -G     | skip long listing format group names   |
   ;; | -1     | list one entry per line                |
   '(dired-listing-switches "-alGX1 --group-directories-first")
   '(dired-recursive-copies 'always)
   '(dired-recursive-deletes 'always)))

(with-eval-after-load 'files
  (custom-set-variables
   ;; Ensure the use of `GNU-ls' from `coreutils' on darwin.
   '(insert-directory-program (or (executable-find "gls")
                                  (executable-find "ls")))))

(with-eval-after-load 'wdired
  (custom-set-variables
   '(wdired-allow-to-change-permissions t)))
#+end_src

Listing [[lst:extra-dired-key-bindings]] adds new key bindings to =dired-mode-map= to:
1. Open files with the [[https://en.wikipedia.org/wiki/Eww_(web_browser)][Emacs Web Wowser]] inside Emacs.
2. Let [[https://en.wikipedia.org/wiki/Rsync][rsync]] copy marked files outside Emacs to a local or remote directory.
The link [[https://truongtx.me/tmtxt-dired-async.html][asynchoronous execution library for Emacs Dired]] is the original source
for the idea of using [[https://en.wikipedia.org/wiki/Rsync][rsync]] and the blog articles [[https://oremacs.com/2016/02/24/dired-rsync/][using rsync in dired]] and
[[https://vxlabs.com/2018/03/30/asynchronous-rsync-with-emacs-dired-and-tramp/][asynchronous rsync with Emacs, dired and tramp]] are vivid recommendations written
by experienced Emacs users.

#+caption[Extra =dired= key bindings]:
#+caption: Extra =dired= key bindings.
#+name: lst:extra-dired-key-bindings
#+begin_src emacs-lisp
(with-eval-after-load 'dired
  (defun dired-eww-open-file ()
    "In Dired, open the regular file named on this line with eww"
    (interactive)
    (let ((file (dired-get-file-for-visit)))
      (if (file-regular-p file)
          (eww-open-file file)
        (error "Eww rejects `%s', since it is not a regular file" file))))

  ;; https://truongtx.me/tmtxt-dired-async.html
  (defun dired-rsync (target)
    "Copy marked files with `rsync' to TARGET directory."
    (interactive
     (list (expand-file-name
            (read-file-name "Rsync to:" (dired-dwim-target-directory)))))
    ;; Store all marked files into the `files' list and intialize
    ;; the `rsync-command'.
    (let ((files (dired-get-marked-files nil current-prefix-arg))
          (rsync-command "rsync -av --progress "))
      ;; Add all marked files as arguments to the `rsync-command'.
      (dolist (file files)
        (setq rsync-command
              (concat rsync-command
                      (if (string-match "^/ssh:\\(.*\\)$" file)
                          (format " -e ssh %s" (match-string 1 file))
                        (shell-quote-argument file)) " ")))
      ;; Append the destination directory to the `rsync-command'.
      (setq rsync-command
            (concat rsync-command
                    (if (string-match "^/ssh:\\(.*\\)$" target)
                        (format " -e ssh %s" (match-string 1 target))
                      (shell-quote-argument target))))
      ;; Run the async shell command.
      (async-shell-command rsync-command)
      ;; Finally, switch to that window.
      (other-window 1)))

  (define-key dired-mode-map (kbd "E") #'dired-eww-open-file)
  (define-key dired-mode-map (kbd "Y") #'dired-rsync))
#+end_src

* [[info:emacs#Completion Styles][Minibuffer completion styles (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:minibuffer-completion-styles
:END:

Listing [[lst:configure-minibuffer-completion-styles][configure minibuffer completion styles]] implements ideas of the post
[[https://www.masteringemacs.org/article/understanding-minibuffer-completion][Understanding minibuffer completion]].

#+caption[Configure =minibuffer= completion styles]:
#+caption: Configure =minibuffer= completion styles.
#+name: lst:configure-minibuffer-completion-styles
#+begin_src emacs-lisp
(when (require  'minibuffer nil 'noerror)
  ;; https://www.masteringemacs.org/article/understanding-minibuffer-completion
  (custom-set-variables
   '(completion-category-overrides
     '((file (styles basic substring))))
   '(completion-ignore-case nil)
   '(completion-styles '(basic flex partial-completion substring))))
#+end_src

* [[info:elisp#Processes][Processes (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:processes
:END:

Listing [[lst:process-utilities]] defines a function to run a (command-line) program
with arguments and to obtain a list with its numeric exit status as well as its
output to =stdout=.

#+caption[Process utilities]:
#+caption: Process utilities.
#+name: lst:process-utilities
#+begin_src emacs-lisp
;; https://gitlab.com/howardabrams/spacemacs.d/blob/master/layers/ha-org/funcs.el#L418
(defun shell-command-with-exit-code (program &rest args)
  "Run PROGRAM with ARGS and return exit-code and output in a list."
  (with-temp-buffer
    (list (apply 'call-process program nil (current-buffer) nil args)
          (buffer-string))))
#+end_src

* [[info:emacs#Help][Help (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:help
:END:

Table [[tab:help-key-bindings]] lists a number of key bindings to start playing with
the help facilities of Emacs.  Try {{{kbd(C-h o)}}} instead of {{{kbd(C-h f)}}}
or {{{kbd(C-h v)}}}.

#+attr_latex: :booktabs yes :float table
#+caption[Help key bindings]:
#+caption: Help key bindings.
#+name: tab:help-key-bindings
|------------------------------+----------+------------------|
| command                      | key map  | keys             |
|------------------------------+----------+------------------|
| Info-goto-emacs-command-node | help-map | {{{kbd(C-h F)}}} |
| describe-function            | help-map | {{{kbd(C-h f)}}} |
| describe-key                 | help-map | {{{kbd(C-h k)}}} |
| describe-symbol              | help-map | {{{kbd(C-h o)}}} |
| describe-variable            | help-map | {{{kbd(C-h v)}}} |
| info                         | help-map | {{{kbd(C-h i)}}} |
|------------------------------+----------+------------------|


** [[info:emacs#Name Help][Shortdoc-display-group (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:shortdoc-display-group
:END:

Listing [[lst:configure-shortdoc]] binds {{{kbd(C-h y)}}} to
=short-doc-display-group= and defines a short documentation group for functions
defined in this Org file.

#+caption[Configure =shortdoc=]:
#+caption: Configure =shortdoc=.
#+name: lst:configure-shortdoc
#+begin_src emacs-lisp
(when (fboundp 'shortdoc-display-group)
  (define-key help-map (kbd "y") #'shortdoc-display-group)
  (with-eval-after-load 'shortdoc
    ;; Ensure defining the functions before documenting them.
    (define-short-documentation-group init
      "Advice"
      (advice-toggle :no-manual t)
      (toggle-engrave-faces-attribute-values-around :no-manual t)
      (toggle-engrave-faces-latex-face-apply-override :no-manual t)
      (toggle-engrave-faces-latex-face-mapper-override :no-manual t)
      (toggle-eww-display-pdf-around :no-manual t)
      (toggle-ilog-timer-function-after :no-manual t)
      (toggle-keycast-log-update-buffer-override :no-manual t)
      (toggle-org-babel-python-format-session-value-override :no-manual t)
      "Face"
      (invert-default-face :no-manual t)
      (set-default-face-height :no-manual t)
      "Interaction"
      (enable-this-command :no-manual t)
      (narrow-or-widen-dwim :no-manual t)
      (org-narrow-to-table :no-manual t)
      "LaTeX"
      (biber-delete-cache :no-manual t)
      (update-lualatex-opentype-font-name-database :no-manual t)
      "Org"
      (by-backend :no-manual t)
      (by-backend-kbd-org-macro :no-manual t)
      (org-active-current-time-stamp :nomanual t)
      (org-babel-execute:latex-extra-header :no-manual t)
      (org-babel-execute:latex-header :no-manual t)
      (org-electric-dollar :no-manual t)
      (org-eval-emacs-lisp-setup-blocks :no-manual t)
      (org-eval-python-setup-blocks :no-manual t)
      (org-eval-infixed-blocks :no-manual t)
      (org-latex-engraved-source-block-filter :no-manual t)
      (org-inactive-current-time-stamp :nomanual t)
      (org-syntax-convert-keyword-case-to-lower :no-manual t)
      (smart-latex-engrave-org-source-blocks :no-manual t)
      (zero-all-org-src-blocks-indentation :no-manual t)
      "Python"
      (choose-common-python-interpreter :no-manual t))))
#+end_src

** [[info:info#Top][Info (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:info
:END:

Listing [[lst:configure-info]] adds the required paths to the places where =info=
looks for files.

#+caption[Configure =info=]:
#+caption: Configure =info=.
#+name: lst:configure-info
#+begin_src emacs-lisp
(with-eval-after-load 'info
  ;; Make Emacs find ALL "*.info" files in `package-user-dir' on Gentoo Linux.
  (when (eq system-type 'gnu/linux)
    (dolist (path
             (nreverse
              (mapcar
               (lambda (name)
                 (expand-file-name (file-name-directory name)))
               (directory-files-recursively package-user-dir "\\.info\\'"))))
      (add-to-list 'Info-directory-list path nil #'file-equal-p)))
  ;; Make Emacs find my "python.info" file.
  (add-to-list 'Info-directory-list
               (expand-file-name "~/.local/share/info")))
#+end_src

* [[info:emacs#Key Bindings][Key bindings (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:key-bindings
:END:

#+attr_latex: :booktabs yes :float table
#+caption[Basic key bindings]:
#+caption: Basic key bindings.
#+name: tab:basic-key-bindings
|--------------------+------------+------------------------|
| command            | key map    | keys                   |
|--------------------+------------+------------------------|
| undo               | global-map | {{{kbd(s-z)}}}         |
| backward-kill-word | global-map | {{{kbd(C-backspace)}}} |
| backward-char      | global-map | {{{kbd(C-b)}}}         |
| forward-char       | global-map | {{{kbd(C-f)}}}         |
| backward-word      | global-map | {{{kbd(M-b)}}}         |
| forward-word       | global-map | {{{kbd(M-f)}}}         |
| backward-sentence  | global-map | {{{kbd(M-a)}}}         |
| forward-sentence   | global-map | {{{kbd(M-e)}}}         |
|--------------------+------------+------------------------|

** [[info:emacs#Disabling][Disabling Commands (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:enable-disabled-commands
:END:

Execute src_emacs-lisp{(find-library "novice")} to see how Emacs prevents new
users from shooting themselves in the feet.  Listing
[[lst:configure-disabled-command-function]] enables [[https://www.emacswiki.org/emacs/DisabledCommands][disabled commands on the fly]].

#+caption[Configure the =disabled-command-function=]:
#+caption: Configure the =disabled-command-function=.
#+name: lst:configure-disabled-command-function
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (setq disabled-command-function
        (defun enable-this-command (&rest _args)
          "Called when a disabled command is executed.
Enable it and re-execute it."
          (put this-command 'disabled nil)
          (message "You typed %s.  %s was disabled until now."
                   (key-description (this-command-keys)) this-command)
          (sit-for 0)
          (call-interactively this-command))))
#+end_src

** [[https://github.com/michael-heerdegen/interaction-log.el#readme][Interaction-log]]
:PROPERTIES:
:CUSTOM_ID: sec:interaction-log
:END:

#+caption[Configure =interaction-log=]:
#+caption: Configure =interaction-log=.
#+name: lst:configure-interaction-log
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'interaction-log)
           (require 'interaction-log nil 'noerror))

  ;; https://www.skybert.net/emacs/show-shortcuts-when-giving-presentations/
  (defun ilog-ensure-ilog-buffer-window ()
    "Ensure the visibility of the `ilog' buffer, when it exists."
    (when (and (get-buffer ilog-buffer-name)
               (not (get-buffer-window ilog-buffer-name)))
      (display-buffer (get-buffer ilog-buffer-name))))

  (define-key help-map (kbd "C-l") #'interaction-log-mode)
  (advice-add 'ilog-timer-function :after #'ilog-ensure-ilog-buffer-window))
#+end_src


** [[https://github.com/tarsius/keycast#readme][Keycast]]                                                         :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:keycast
:header-args:emacs-lisp: :tangle no :eval never-export
:END:

Listing [[lst:configure-keycast]] configures =keycast=.

#+caption[Configure =keycast=]:
#+caption: Configure =keycast=.
#+name: lst:configure-keycast
#+begin_src emacs-lisp
;; Make `keycast-log-update-buffer' use a buffer similar to the
;; control buffer `ediff-setup-windows-plain' returns.
(when (and (ensure-package-installation 'keycast)
           (require 'keycast nil 'noerror))
  (custom-set-variables
   '(keycast-mode-line-window-predicate 'keycast-bottom-right-window-p))

  (defun keycast-log-update-buffer-plain ()
    (let ((buffer (get-buffer keycast-log-buffer-name)))
      (unless (buffer-live-p buffer)
        (setq buffer (get-buffer-create keycast-log-buffer-name))
        (with-current-buffer buffer
          (setq buffer-read-only t)))
      (unless (get-buffer-window buffer)
        (display-buffer buffer '(display-buffer-at-bottom
                                 (dedicated . t)
                                 (window-height . 10))))
      (when-let ((output (keycast--format keycast-log-format)))
        (with-current-buffer buffer
          (goto-char (if keycast-log-newest-first (point-min) (point-max)))
          (let ((inhibit-read-only t))
            (when (and (> keycast--command-repetitions 0)
                       (string-match-p "%[rR]" keycast-log-format))
              (unless keycast-log-newest-first
                (backward-char))
              (ignore-errors
                (delete-region (line-beginning-position)
                               (1+ (line-end-position)))))
            (insert output))
          (goto-char (if keycast-log-newest-first (point-min) (point-max)))))))

  (advice-add 'keycast-log-update-buffer
              :override #'keycast-log-update-buffer-plain))
#+end_src

* [[info:emacs#Emacs Server][Using Emacs as a server (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:using-emacs-server
:END:

Emacs can act as a server that listens to a socket to share its state (for
instance buffers and command history) with other programs by means of a shell
command =emacsclient=.  Section [[#sec:latexmk-save-compile-display-loop]] and
[[#sec:qutebrowser-userscript]] show how to use ~emacsclient~ to:
1. Install an asynchronous (or background) loop of saving a LaTeX file,
   compiling it, and redisplaying the output in Emacs.
2. Make [[https://qutebrowser.org][qutebrowser]] send html links with document titles to Emacs.
The code in listing [[lst:start-emacs-server]] starts the Emacs server.

#+caption[Start the Emacs server]:
#+caption: Start the Emacs server.
#+name: lst:start-emacs-server
#+begin_src emacs-lisp
(when window-system
  (unless (or noninteractive (daemonp))
    (add-hook 'after-init-hook #'server-start)))
#+end_src

** Latexmk save-compile-display loop
:PROPERTIES:
:CUSTOM_ID: sec:latexmk-save-compile-display-loop
:END:

The =latexmk= resource file in the next source code block shows how to use
=emacsclient= to (re)display the PDF file in Emacs after each succesful
(re)compilation on condition that the settings of the ~compile-command~ local
variable in section are compatible.  The local variable ~compile-command~ in the
[[#sec:local-variables][local variables]] section (only visible in =org= files, but not in =html= and
=pdf= files) shows how to use the =latexmkrc= file.

#+attr_latex: :options breaklines
#+caption[Tangle the =Latexmk= resource file]:
#+caption: Tangle the =Latexmk= resource file.
#+name: lst:latexmkrc
#+begin_src perl :tangle latexmkrc :comments no
# pdf creator
$pdf_mode = 4;  # 4 means lualatex
# pdf previewer and update pdf previewer
$pdf_previewer = "emacsclient -e '(find-file-other-window %S)'";
$pdf_update_method = 4;  # 4 runs $pdf_update_command to force the update
$pdf_update_command = "emacsclient -e '(with-current-buffer (find-buffer-visiting %S) (pdf-view-revert-buffer nil t))'";
# see for instance glossary.latexmkrc
add_cus_dep( 'acn', 'acr', 0, 'makeglossaries' );
add_cus_dep( 'glo', 'gls', 0, 'makeglossaries' );
# use ".=" to append to $clean_ext
$clean_ext .= " acr acn alg bbl dvi glo gls glg ist lol lst";
$clean_ext .= " nav run.xml snm synctex.gz";
sub makeglossaries {
    my ($name, $path) = fileparse( $$Psource );
    return system "makeglossaries -d '$path' '$name'";
}
# Emacs looks for "Local variables:" after the last "newline-formfeed".

# Local Variables:
# mode: perl
# End:
#+end_src

** [[https://qutebrowser.org/doc/userscripts.html][Qutebrowser userscript]]
:PROPERTIES:
:CUSTOM_ID: sec:qutebrowser-userscript
:END:

The next block contains an userscript that sends a [[info:org#The store-link protocol][store-link org-protocol]]
message with the url and the title from [[https://qutebrowser.org][qutebrowser]] to =emacsclient=.  The
function =urlencode= translates the url and the title for the message. The
[[info:python#Examples<22>][Python urllib examples]] show how to use =urlencode=.  The final =execvp= call
deals with a [[https://qutebrowser.org][qutebrowser]] userscript requirement: the =emacsclient= process must
get the PID of the userscript that must kill itself after the take-over.
Termination of the =emacsclient= process hands control back to [[https://qutebrowser.org][qutebrowser]].

On a [[https://en.wikipedia.org/wiki/POSIX][POSIX]] system, you can run the userscript from [[https://qutebrowser.org][qutebrowser]] or from a
terminal to see whether it works.  In case you try to run it from Emacs, Emacs
may hang or die.

#+caption[Tangle a qutebrowser userscript]:
#+caption: Tangle a qutebrowser userscript.
#+header: :comments no
#+header: :tangle-mode (identity #o755)
#+name: lst:qutebrowser-userscript
#+begin_src python :noeval :tangle org-store-link
#!/usr/bin/env python
from urllib.parse import urlencode
from os import environ, execvp

url = environ.get("QUTE_URL", "https://orgmode.org")
title = environ.get("QUTE_TITLE", "Org Mode")
parameters = urlencode({"url": url, "title": title})
print(payload := f"org-protocol://store-link?{parameters}")
execvp("emacsclient", ("-n", payload))
#+end_src

** TODO Look into: org-protocol handling with other browser on Darwin
:PROPERTIES:
:CUSTOM_ID: sec:org-protocol-darwin
:END:

1. [[http://rwx.io/posts/osx-uri-protocol-handler/][Patrick Goddi: macOS URI protocol handler]] and his [[https://github.com/fooqri/uri-handler][URI-Handler]].
2. [[https://www.hammerspoon.org/][Hammerspoon]]
3. [[https://vritser.github.io/posts/capture-anywhere/][Emacs Capture Anywhere]]

** [[https://en.wikipedia.org/wiki/AppleScript][AppleScript]]                                                     :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:applescript
:header-args:emacs-lisp: :tangle no
:END:

#+caption[Ensure =applescript-mode= installation]:
#+caption: Ensure =applescript-mode= installation.
#+name: lst:ensure-applescript-mode-installation
#+begin_src emacs-lisp
(when (ensure-package-installation 'applescript-mode))
#+end_src

#+caption[Applescript code to register =org-protocol= on Darwin]:
#+caption: Applescript code to register =org-protocol= on Darwin.
#+name: lst:applescript-org-protocol
#+begin_src applescript :tangle no
on emacsclient(input)
  do shell script "/usr/local/bin/emacsclient -n -c '" & input & "'"
  tell application "Emacs" to activate
end emacsclient

on open location input
  emacsclient(input)
end open location

on open inputs
  repeat with raw_input in inputs
    set input to POSIX path of raw_input
    emacsclient(input)
  end repeat
end open

on run
  do shell script emacsclient("")
end run
#+end_src

* Completion
:PROPERTIES:
:CUSTOM_ID: sec:completion
:END:

[[info:vertico#Top][Vertico (info)]] provides a performant and minimalistic vertical completion UI
based on the default completion system and behaves therefore correctly under all
circumstances.  [[https://cestlaz.github.io/post/using-emacs-80-vertico/][Using Vertico, Marginalia, Consult, and Embark]] links to a video
demonstration.  Vertico integrates well with fully supported complementary
packages to enrich the completion UI:
1. [[info:embark#Top][Embark (info)]] for minibuffer actions with context menus,
2. [[info:marginalia#Top][Marginalia (info)]] for rich annotations in the minibuffer, and
3. [[info:consult#Top][Consult (info)]] for useful search and navigation commands,
where the order is that of [[https://github.com/bdarcus/citar#installation][enhancing citar's experience]] and the configuration
steps below.

Finally, [[https://company-mode.github.io/][company: a modular complete-anything framework for Emacs]] provides
completion in any buffer.

** [[info:company#Top][Company (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:company
:END:

[[info:company#Top][Company (info)]] is a modular completion framework and the the snippet [[lst:ensure-company-installation][below]]
ensures its installation.

#+caption[Ensure =company= installation]:
#+caption: Ensure =company= installation.
#+name: lst:ensure-company-installation
#+begin_src emacs-lisp
(ensure-package-installation 'company)
#+end_src

** [[info:vertico#Top][Vertico (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:vertico-configuration
:END:

Listing [[lst:enable-vertico-mode]] configures and enables =savehist-mode= and
enables =vertico-mode=.  The documentation src_emacs-lisp{(describe-function
'savehist-mode)} why it is best to turn on =savehist-mode= in the Emacs init
file.

#+caption[Enable =savehist-mode= and =vertico-mode=]:
#+caption: Enable =savehist-mode= and =vertico-mode=.
#+name: lst:enable-vertico-mode
#+begin_src emacs-lisp
(when (fboundp 'savehist-mode)
  (savehist-mode +1))
(with-eval-after-load 'savehist-mode
  (custom-set-variables
   '(savehist-additional-variables
     '(eww-history
       kill-ring
       regexp-search-string
       search-ring
       search-string))))
(when (and (ensure-package-installation 'vertico)
           (fboundp 'vertico-mode))
  (vertico-mode +1))
(with-eval-after-load 'vertico
  (define-key vertico-map (kbd "RET") #'vertico-directory-enter)
  (define-key vertico-map (kbd "DEL") #'vertico-directory-delete-char)
  (define-key vertico-map (kbd "M-DEL") #'vertico-directory-delete-word))
#+end_src

#+attr_latex: :booktabs yes :float table
#+caption[Vertico key map bindings]:
#+caption: Vertico key map bindings.
#+name: tab:vertico-keymap-bindings
|-------------------------------+----------------------------------+---------------------|
| command                       | remap                            | keys                |
|-------------------------------+----------------------------------+---------------------|
| vertico-directory-delete-char |                                  | {{{kbd(DEL)}}}      |
| vertico-directory-delete-word |                                  | {{{kbd(M-DEL)}}}    |
| vertico-directory-enter       |                                  | {{{kbd(RET)}}}      |
| vertico-exit                  | exit-minibuffer                  | {{{kbd(C-j)}}}      |
| vertico-exit-input            |                                  | {{{kbd(C-RET)}}}    |
| vertico-first                 | beginning-of-buffer              | {{{kbd(M-<)}}}      |
| vertico-first                 | minibuffer-beginning-of-buffer   | {{{kbd(M-<)}}}      |
| vertico-insert                |                                  | {{{kbd(TAB)}}}      |
| vertico-last                  | end-of-buffer                    | {{{kbd(M->)}}}      |
| vertico-next-group            | forward-paragraph                | {{{kbd(C-<down>)}}} |
| vertico-next                  | next-line-or-history-element     | {{{kbd(<down>)}}}   |
| vertico-next                  | next-line                        | {{{kbd(C-n)}}}      |
| vertico-previous-group        | backward-paragraph               | {{{kbd(C-<up>)}}}   |
| vertico-previous              | previous-line-or-history-element | {{{kbd(<up>)}}}     |
| vertico-previous              | previous-line                    | {{{kbd(C-p)}}}      |
| vertico-save                  | kill-ring-save                   | {{{kbd(M-w)}}}      |
| vertico-scroll-down           | scroll-down-command              | {{{kbd(M-v)}}}      |
| vertico-scroll-up             | scroll-up-command                | {{{kbd(C-v)}}}      |
|-------------------------------+----------------------------------+---------------------|

** [[info:orderless#Top][Orderless (info)]]                                                :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:orderless-configuration
:header-args:emacs-lisp: :tangle no
:END:

 Listing [[lst:configure-orderless]] configures [[info:orderless#Company][orderless for company (info)]].  Note:
*Python editing is orders of magnitude faster after removal of Orderless*.

#+caption[Configure =orderless=]:
#+caption: Configure =orderless=.
#+name: lst:configure-orderless
#+begin_src emacs-lisp
(when (ensure-package-installation 'marginalia)
  (with-eval-after-load 'orderless
    (custom-set-variables
     '(orderless-component-separator " +"))

    (defun just-one-face (fn &rest args)
      (let ((orderless-match-faces [completions-common-part]))
        (apply fn args)))

    (advice-add 'company-capf--candidates :around #'just-one-face)))
#+end_src

** [[info:embark#Top][Embark (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:embark-configuration
:END:

Listing [[lst:configure-embark]] configures =embark= key bindings:
1. =embark-act= prompts the user for an action and performs it.
2. Except for highlighting of email and web URLs, =embark-dwim= englobes the
   functionality of src_emacs-lisp{(find-library "goto-addr")} that activates
   mail and web URLs to turn them into clickable buttons.  Since =embark-dwim=
   acts on a superset of target types, it renders =goto-addr= superfluous.  See:
   1. [[info:emacs#Goto Address mode][Goto Address mode (info)]].
   2. [[info:embark#The default action on a target][The default (embark-dwim) action on a target (info)]].
3. =embark-bindings= allows to explore all current command key bindings in the
   minibuffer.
4. The initialization src_emacs-lisp{(setq prefix-help-command
   #'embark-prefix-help-command)} enables minibuffer help after a prefix key
   (for instance {{{kbd(C-x)}}} or {{{kbd(C-c)}}}) as typing {{{kbd(C-x C-h)}}}
   or {{{kbd(C-c C-h)}}} shows.

#+caption[Configure =embark=]:
#+caption: Configure =embark=.
#+name: lst:configure-embark
#+begin_src emacs-lisp
(when (ensure-package-installation 'embark 'embark-consult)
  (when (fboundp 'embark-act)
    (global-set-key (kbd "C-,") #'embark-act))
  (when (fboundp 'embark-dwim)
    (global-set-key (kbd "C-:") #'embark-dwim))
  (when (fboundp 'embark-bindings)
    (global-set-key (kbd "C-h B") #'embark-bindings))
  (when (fboundp 'embark-prefix-help-command)
    (setq prefix-help-command #'embark-prefix-help-command)))
#+end_src

** [[info:marginalia#Top][Marginalia (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:marginalia-configuration
:END:

Listing [[lst:enable-marginalia-mode]] enables =marginalia-mode=.

#+caption[Enable =marginalia-mode=]:
#+caption: Enable =marginalia-mode=.
#+name: lst:enable-marginalia-mode
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'marginalia)
           (fboundp 'marginalia-mode))
  (marginalia-mode +1))
#+end_src

** [[info:consult#Top][Consult (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:consult-configuration
:END:

Consult provides practical commands based on the Emacs minibuffer completion
function [[info:elisp#Minibuffer Completion][completing-read]].  Listing [[lst:configure-consult]] configures =consult=.

#+attr_latex: :booktabs yes :float table
#+caption[Configuration specific key bindings]:
#+caption: Configuration specific key-bindings.
#+name: tab:configuration-specific-key-bindings
|-----------------------------+----------------------+---------------------|
| command                     | key map              | keys                |
|-----------------------------+----------------------+---------------------|
| consult-bookmark            | ctl-x-r-keymap       | {{{kbd(C-x r b)}}}  |
| consult-buffer-other-frame  | ctl-x-5-keymap       | {{{kbd(C-x 5 b)}}}  |
| consult-buffer-other-window | ctl-x-4-keymap       | {{{kbd(C-x 4 b)}}}  |
| consult-buffer              | ctl-x-keymap         | {{{kbd(C-x b)}}}    |
| consult-compile-error       | goto-map             | {{{kbd(M-g e)}}}    |
| consult-complex-command     | ctl-x-keymap         | {{{kbd(C-x M-:)}}}  |
| consult-find                | search-map           | {{{kbd(M-s f)}}}    |
| consult-focus-lines         | search-map           | {{{kbd(M-s u)}}}    |
| consult-git-grep            | search-map           | {{{kbd(M-s g)}}}    |
| consult-global-mark         | goto-map             | {{{kbd(M-g k)}}}    |
| consult-goto-line           | goto-map             | {{{kbd(M-g M-g)}}}  |
| consult-goto-line           | goto-map             | {{{kbd(M-g g)}}}    |
| consult-history             | global-map           | {{{kbd(C-c h)}}}    |
| consult-imenu               | goto-map             | {{{kbd(M-g i)}}}    |
| consult-keep-lines          | search-map           | {{{kbd(M-s k)}}}    |
| consult-line                | search-map           | {{{kbd(M-s l)}}}    |
| consult-mark                | goto-map             | {{{kbd(M-g m)}}}    |
| consult-mode-command        | global-map           | {{{kbd(C-c m)}}}    |
| consult-multi-occur         | search-map           | {{{kbd(M-s m)}}}    |
| consult-outline             | goto-map             | {{{kbd(M-g o)}}}    |
| consult-register            | ctl-x-r-keymap       | {{{kbd(C-x r x)}}}  |
| consult-yank-pop            | global-map           | {{{kbd(M-y)}}}      |
|-----------------------------+----------------------+---------------------|
| deadgrep                    | search-map           | {{{kbd(M-s d)}}}    |
| elfeed                      | global-map           | {{{kbd(C-x w)}}}    |
| embark-act                  | global-map           | {{{kbd(C-\,)}}}     |
| embark-bindings             | global-map           | {{{kbd(C-h B)}}}    |
| embark-dwim                 | global-map           | {{{kbd(C-:)}}}      |
| iedit-mode                  | global-map           | {{{kbd(C-;)}}}      |
| minibuffer-complete-history | minibuffer-local-map | {{{kbd(C-<tab>)}}}  |
| narrow-or-widen-dwim        | ctl-x-keymap         | {{{kbd(C-x C-n)}}}  |
| org-agenda                  | global-map           | {{{kbd(C-c a)}}}    |
| org-capture                 | global-map           | {{{kbd(C-c c)}}}    |
| org-cite                    | org-mode-map         | {{{kbd(C-c b)}}}    |
| org-insert-link-global      | global-map           | {{{kbd(C-c C-l)}}}  |
| org-narrow-to-table         | ctl-x-keymap         | {{{kbd(C-x n t)}}}  |
| org-store-link              | global-map           | {{{kbd(C-c l)}}}    |
|-----------------------------+----------------------+---------------------|


#+caption[Configure =consult=]:
#+caption: Configure =consult=.
#+name: lst:configure-consult
#+begin_src emacs-lisp
(when (ensure-package-installation 'consult)
  (custom-set-variables
   '(consult-project-function #'(lambda (_) (vc-root-dir))))
  ;; C-c bindings (current-global-map)
  (global-set-key (kbd "C-c h") #'consult-history)
  (global-set-key (kbd "C-c m") #'consult-mode-command)
  ;; C-h bindings (help-map)
  (define-key help-map (kbd "a") #'consult-apropos)
  ;; C-x bindings (ctl-x-map)
  (define-key ctl-x-map (kbd "M-:") #'consult-complex-command)
  (define-key ctl-x-map (kbd "b") #'consult-buffer)
  (define-key ctl-x-4-map (kbd "b") #'consult-buffer-other-window)
  (define-key ctl-x-5-map (kbd "b") #'consult-buffer-other-frame)
  (define-key ctl-x-r-map (kbd "x") #'consult-register)
  (define-key ctl-x-r-map (kbd "b") #'consult-bookmark)
  ;; M-g bindings (goto-map)
  (define-key goto-map (kbd "g") #'consult-goto-line)
  (define-key goto-map (kbd "M-g") #'consult-goto-line)
  (define-key goto-map (kbd "o") #'consult-outline)
  (define-key goto-map (kbd "m") #'consult-mark)
  (define-key goto-map (kbd "k") #'consult-global-mark)
  (define-key goto-map (kbd "i") #'consult-imenu)
  (define-key goto-map (kbd "e") #'consult-compile-error)
  ;; M-s bindings (search-map)
  (define-key search-map (kbd "g") #'consult-git-grep)
  (define-key search-map (kbd "f") #'consult-find)
  (define-key search-map (kbd "k") #'consult-keep-lines)
  (define-key search-map (kbd "l") #'consult-line)
  (define-key search-map (kbd "m") #'consult-multi-occur)
  (define-key search-map (kbd "u") #'consult-focus-lines)
  ;; Other bindings (current-global-map)
  (global-set-key (kbd "M-y") #'consult-yank-pop))
#+end_src

** [[https://company-mode.github.io/][Company: a modular complete anything framework for Emacs]]
:PROPERTIES:
:CUSTOM_ID: sec:company-configuration
:END:

Listing [[lst:configure-company]] configures =company=.

#+caption[Configure =company=]:
#+caption: Configure =company=.
#+name: lst:configure-company
#+begin_src emacs-lisp
(when (fboundp 'company-mode)
  (custom-set-variables
   ;; https://github.com/purcell/emacs.d/issues/778
   '(company-transformers '(company-sort-by-occurrence)))
  (dolist (hook '(LaTeX-mode-hook
                  org-mode-hook
                  emacs-lisp-mode-hook
                  lisp-interaction-mode-hook
                  lisp-mode-hook
                  python-mode-hook
                  ielm-mode-hook
                  sly-mrepl-mode-hook))
    (add-hook hook #'company-mode)))
#+end_src

* [[info:emacs#Search][Search and replace (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:search-replace
:END:

** [[info:emacs#Regexp Replace][Regexp Replace (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:regexp-replace
:END:

Executing {{{kbd(M-x replace-regexp)}}} prompts fo a regular expression =REGEXP=
and a substitution =NEWSTRING= to replace =REGEXP= with =NEWSTRING=.  The tools
in section [[#sec:narrowing][Narrowing]] allow to limit the scope of {{{kbd(M-x replace-regexp)}}}.
A list pointing to relevant documentation is:
1. [[info:emacs#Regexp Replace][Regexp Replace (info)]] explains how the substitution handles references to
   regular expression groups and lisp expressions.
2. [[info:emacs#Regexps][Syntax of Regular Expressions (info)]] describes regular expression features
   for users.
3. [[info:elisp#Regular Expressions][Emacs Lisp Regular Expressions (info)]] describes regular expression features
   for programmers.
4. [[https://www.emacswiki.org/][Emacs Wiki]] has an article on [[https://www.emacswiki.org/emacs/ReplaceRegexpWithLispExpressions][replacing regexp with lisp expressions]].
Table [[tab:replace-regexp-tranform]] tabulates how to perfom example tasks by means
of {{{kbd(M-x replace-regexp)}}} using =(regular-expression transform)= pairs.

#+attr_latex: :booktabs yes :float table
#+caption[Example =replace-regexp= (regular-expression substitution) pairs]:
#+caption: Example =replace-regexp= (regular-expression substitution) pairs.
#+name: tab:replace-regexp-tranform
| task                        | regular expression              | substitution  |
|-----------------------------+---------------------------------+---------------|
| move dot two digits forward | =0\.\([[:digit:]][[:digit:]]\)= | =0\1.=        |
| move dot two digits forward | =0\.\([0-9][0-9]\)=             | =0\1.=        |
| renumber grep/occur matches | =\(.+:\)=                       | =\,(1+ \#)._= |
|-----------------------------+---------------------------------+---------------|

** [[https://github.com/Wilfred/deadgrep#readme][Deadgrep]]
:PROPERTIES:
:CUSTOM_ID: sec:deadgrep
:END:

[[https://github.com/Wilfred/deadgrep#readme][Deadgrep]] uses [[https://github.com/BurntSushi/ripgrep#readme][ripgrep]] for superfast text searching in the default directory or
the current [[https://en.wikipedia.org/wiki/Version_control][VCS]] directory tree.  Listing [[lst:configure-deadgrep]] binds =deadgrep=
to {{{kbd(M-s d)}}} and =deadgrep-edit-mode= to {{{kbd(C-c C-w)}}}.

#+caption[Configure =deadgrep=]:
#+caption: Configure =deadgrep=.
#+name: lst:configure-deadgrep
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'deadgrep)
           (fboundp 'deadgrep))
  (define-key search-map (kbd "d") #'deadgrep)
  (with-eval-after-load 'deadgrep
    (define-key deadgrep-mode-map (kbd "C-c C-w") #'deadgrep-edit-mode)))
#+end_src

** [[https://www.genivia.com/get-ugrep.html][Ugrep]]
:PROPERTIES:
:CUSTOM_ID: sec:ugrep
:END:

[[https://www.genivia.com/get-ugrep.html][Ugrep]] is an ultra fast grep with interactive query UI and fuzzy search.  The
pages [[https://github.com/Genivia/ugrep#emacs][Using ugrep within Emacs]] and [[https://manueluberti.eu/emacs/2022/08/07/emacs-ugrep/][Ugrep in Emacs]] show how to make Emacs use it
with [[info:emacs#Grep Searching][lgrep]] and [[info:emacs#Xref][xref]].  Listing [[lst:use-ugrep]] shows my implementation of the
suggestions on those pages.

#+caption[Use =ugrep= when available]:
#+caption: Use =ugrep= when available.
#+name: lst:use-ugrep
#+begin_src emacs-lisp
(when (executable-find "ugrep")
  (with-eval-after-load 'grep
    (custom-set-variables
     `(grep-template ,(string-join '("ugrep"
                                     "--color=always"
                                     "--decompress"
                                     "--ignore-binary"
                                     "--ignore-case"
                                     "--include=\"<F>\""
                                     "--line-number"
                                     "--null"
                                     "--recursive"
                                     "--regexp=<R>")
                                   " "))))
  (with-eval-after-load 'xref
    (custom-set-variables
     '(xref-search-program-alist
       '((grep
          . "xargs -0 grep <C> --null -snHE -e <R>")
         (ripgrep
          . "xargs -0 rg <C> --null -nH --no-heading --no-messages -g '!*/' -e <R>")
         (ugrep
          . "xargs -0 ugrep <C> --null -ns -e <R>")))
     '(xref-search-program 'ugrep))))
#+end_src

** [[https://github.com/mattiase/xr#readme][XR - Emacs regexp parser and analyzer]]
:PROPERTIES:
:CUSTOM_ID: sec:ensure-xr-installation
:END:

[[https://github.com/mattiase/xr#readme][XR]] converts Emacs regular expressions to the structured =rx= form, thus being an
inverse of =rx=. It can also find mistakes and questionable constructs inside
regexp strings.

#+caption[Ensure =xr= installation]:
#+caption: Ensure =xr= installation.
#+name: lst:ensure-xr-installation
#+begin_src emacs-lisp
(when (ensure-package-installation 'xr))
#+end_src

* [[info:emacs#Version Control][Version Control (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:version-control
:END:

** [[info:ediff#Top][Ediff (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:ediff
:END:

Video links to complete the [[info:ediff#Top][ediff (info)]] manual are:
1. [[https://www.youtube.com/watch?v=6ZWp05OW1c0][Emergency Emacs]].
2. [[https://protesilaos.com/codelog/2020-04-10-emacs-smerge-ediff/][Use =smerge= and =ediff= to resolve file conflicts]].
Listing [[lst:configure-ediff]] configures =ediff= to display all its buffers in a
single frame and to make all text visible prior to ediffing Org buffers.

#+caption[Configure =ediff=]:
#+caption: Configure =ediff=.
#+name: lst:configure-ediff
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (custom-set-variables
   '(ediff-merge-split-window-function #'split-window-horizontally)
   '(ediff-split-window-function #'split-window-horizontally)
   '(ediff-window-setup-function #'ediff-setup-windows-plain)))
(with-eval-after-load 'org
  ;; https://github.com/oantolin/emacs-config#readme
  (defun ediff-with-org-show-all ()
    "Expand all headings prior to ediffing org buffers."
    (add-hook 'ediff-prepare-buffer-hook #'org-show-all nil t))
  (add-hook 'org-mode-hook #'ediff-with-org-show-all))
#+end_src

** [[https://git-scm.com/book/en/v2][Git]]
:PROPERTIES:
:CUSTOM_ID: sec:git
:END:

[[https://www.theserverside.com/blog/Coffee-Talk-Java-News-Stories-and-Opinions/git-push-new-branch-remote-github-gitlab-upstream-example][How to push new branches to remote repositories on Github or Gitlab]] explains how
to do this from the command line.  Listing
[[lst:forking-and-branching-remote-repositories]] shows an example work flow of
command line =git= and =nano= invocations.  I did yet not figure out how to do
this by means of [[info:magit#Top][Magit (info)]]: I still have to understand [[info:magit#Pushing][Magit pushing (info)]]
and to figure out how to use src_emacs-lisp{(magit-push-current-to-pushremote)}
or src_emacs-lisp{(magit-push-current-to-upstream)}.

#+caption[Forking and branching on Github or Gitlab]:
#+caption: Forking and branching on Github or Gitlab.
#+name: lst:forking-and-branching-remote-repositories
#+begin_src shell :noeval
# Clone the repository
git clone git@github.com:gav451/engrave-faces engrave-faces-fork
cd engrave-face-fork
# Handle 1st branch:
# - Create and switch to a new branch with either:
git switch -c latex-engrave-symbolic-color-names
#   or: git checkout -b latex-engrave-symbolic-color-names
# - Use "--set-upstream origin" as a 1st-time branch push:
git push --set-upstream origin latex-engrave-symbolic-color-names
# - Create, add, and commit, and push changes in this branch:
nano engrave-faces-latex.el
git add engrave-faces-latex.el
git commit -m 'Commit latex-engrave-dont-symbolic-color-names changes'
git push
# - Switch to master branch:
git checkout master
# Handle 2nd branch:
# - Create and switch to a new branch with either:
git switch -c latex-engrave-dont-wrap-white-space
#   - or: git checkout -b latex-engrave-dont-wrap-white-space
# - Use "--set-upstream origin" as a 1st-time branch push:
git push --set-upstream origin latex-engrave-dont-wrap-white-space
# - Create, add, commit, and push changes in this branch:
nano engrave-faces-latex.el
git add engrave-faces-latex.el
git commit -m 'Commit latex-engrave-dont-wrap-white-space changes'
git push
# - Switch to master branch:
git checkout master
#+end_src

*** [[https://www.theserverside.com/blog/Coffee-Talk-Java-News-Stories-and-Opinions/git-push-new-branch-remote-github-gitlab-upstream-example][List all Git branches]]
:PROPERTIES:
:CUSTOM_ID: sec:list-all-git-branches
:END:

#+caption[List all =git= branches]:
#+caption: List all =git= branches.
#+name: lst:list-all-git-branches
#+begin_src shell :exports both :results verbatim
git -C ~/VCS/engrave-faces-fork branch -a
#+end_src

#+RESULTS: lst:list-all-git-branches
: * gav
:   latex-engrave-dont-wrap-white-space
:   latex-engrave-symbolic-color-names
:   master
:   remotes/origin/HEAD -> origin/master
:   remotes/origin/gav
:   remotes/origin/latex-engrave-dont-wrap-white-space
:   remotes/origin/latex-engrave-symbolic-color-names
:   remotes/origin/master

*** [[info:magit#Top][Magit (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:magit
:END:

[[info:magit#Top][Magit (info)]] is an Emacs interface to the version control system [[https://git-scm.com/book/en/v2][Git]] and the
snippet [[lst:ensure-magit-installation][below]] ensures its installation.

#+caption[Ensure =Magit= installation]:
#+caption: Ensure =Magit= installation
#+name: lst:ensure-magit-installation
#+begin_src emacs-lisp
(ensure-package-installation 'magit)
#+end_src

* Reading
:PROPERTIES:
:CUSTOM_ID: sec:reading
:END:

** Reading [[https://en.wikipedia.org/wiki/DjVu][DjVu]] files
:PROPERTIES:
:CUSTOM_ID: sec:reading-djvu-files
:END:

This setup relies on [[info:emacs#Document View][Document View (info)]] to facilitate reading [[https://en.wikipedia.org/wiki/DjVu][DjVu]] files.
Reading the code shown by src_emacs-lisp{(find-function
'doc-view-djvu->tiff-converter-ddjvu)} shows that reading [[https://en.wikipedia.org/wiki/DjVu][DjVu]] files requires
the command line [[https://en.wikipedia.org/wiki/DjVu][DjVu]] decoder =ddjvu= from the [[http://djvu.sourceforge.net/][DjVuLibre]] utilities.

** Reading EPUB files
:PROPERTIES:
:CUSTOM_ID: sec:reading-epub-files
:END:

The package [[https://depp.brause.cc/nov.el/][nov.el]] provides a major mode for reading EPUB files in Emacs.
Listing [[lst:configure-nov]] configures [[https://depp.brause.cc/nov.el/][nov.el]].

#+caption[Configure =nov=]:
#+caption: Configure =nov=.
#+name: lst:configure-nov
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'nov)
           (fboundp 'nov-mode))
  (add-to-list 'auto-mode-alist `(,(rx ".epub" eos) . nov-mode)))
#+end_src

** Reading PDF files
:PROPERTIES:
:CUSTOM_ID: sec:reading-pdf-files
:END:

The [[https://github.com/vedang/pdf-tools][pdf-tools]] package exploits the [[https://github.com/freedesktop/poppler][poppler]] library to render and to let you
annotate [[https://en.wikipedia.org/wiki/PDF][PDF]] files.  It also exploits the [[https://wiki.contextgarden.net/SyncTeX][SyncTeX]] library to link anchors in [[https://en.wikipedia.org/wiki/PDF][PDF]]
files produced with LaTeX to the original LaTeX sources.  The [[https://github.com/nicolaisingh/saveplace-pdf-view#readme][saveplace-pdf-view]]
package saves =pdf-view= and =doc-view= places.

In order to use [[https://github.com/vedang/pdf-tools][pdf-tools]], you have to type {{{kbd(M-x pdf-tools-install)}}} after
installation of [[https://github.com/vedang/pdf-tools][pdf-tools]] from [[https://melpa.org/][MELPA]] or after each update of [[https://github.com/freedesktop/poppler][poppler]] to build or
rebuild the =epdfinfo= executable that serves the [[https://en.wikipedia.org/wiki/PDF][PDF]] files to Emacs.

#+caption[Configure =pdf-tools=]:
#+caption: Configure =pdf-tools=.
#+name: lst:configure-pdf-tools
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'pdf-tools 'saveplace-pdf-view)
           (fboundp 'pdf-loader-install))
  ;; `pdf-loader-install' is the lazy equivalent of `pdf-tools-install':
  ;; see the README file.
  (pdf-loader-install)

  (with-eval-after-load 'pdf-outline
    ;; Unmask the `image-save' key binding in `pdf-view-mode-map' and
    ;; in `image-mode-map' (by parenthood).
    (define-key pdf-outline-minor-mode-map (kbd "o") nil)
    (define-key pdf-outline-minor-mode-map (kbd "O") #'pdf-outline))

  (with-eval-after-load 'pdf-view
    (custom-set-variables
     '(pdf-view-display-size 'fit-page)
     `(pdf-view-use-scaling ,(eq system-type 'darwin)))
    (require 'saveplace-pdf-view nil 'noerror)))
#+end_src

* Writing
:PROPERTIES:
:CUSTOM_ID: sec:writing
:END:

** Writing LaTeX files
:PROPERTIES:
:CUSTOM_ID: sec:writing-latex-files
:END:

Loading =tex.el= immediately instead of lazily ensures proper initialization of
[[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]].  In particular, the ~TeX-master~ safe local variable in the =tex.el=
elisp library file has no autoload cookie.  Without prior loading of =tex.el=,
Emacs will complain that ~TeX-master~ is no safe local variable in case it reads
a LaTeX file that sets ~TeX-master~.  The list below summarizes the main [[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]]
configuration objectives:
1. Listing [[lst:require-tex]] ensures installation of [[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]] and initializes [[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]]
   properly for =LuaTeX= or =LuaLaTeX=.
2. Listing [[lst:require-tex]] also enables [[https://git.savannah.gnu.org/cgit/auctex.git/patch/?id=f464242eab092e610dda6b654e6fd197ef649d3eAA][indenting between square brackets]]
   which is a recent feature.
3. Listing [[lst:update-lualatex-opentype-font-name-database]] defines a function to
   update the =OpenType Font= name database for =LuaLaTeX= when the output of
   =LuaLaTeX= shows missing fonts.
4. Listing [[lst:configure-bibtex]] configures the Emacs =bibtex= library to use the
   LaTeX =BiBTeX= dialect for backwards compatibility.
5. Listing [[lst:configure-font-latex]] disables font scaling of section titles.
6. Listing [[lst:configure-latex]] configures =latex= for a full featured
   =LaTeX-section-command=.

#+caption[Require and configure =TeX=]:
#+caption: Require and configure =TeX=.
#+name: lst:require-tex
#+begin_src emacs-lisp
(when (ensure-package-installation 'auctex)
  ;; Use `require' to make `TeX-master' a safe local variable.
  (when (require 'tex nil 'noerror)
    (custom-set-variables
     '(TeX-auto-save t)
     '(TeX-engine 'luatex)
     '(TeX-indent-close-delimiters "]")
     '(TeX-indent-open-delimiters "[")
     '(TeX-install-font-lock #'font-latex-setup)
     '(TeX-parse-self t)
     ;; Disable `TeX-electric-math' to prevent collisions with `smartparens'.
     '(TeX-electric-math nil))))
#+end_src

#+caption[Update the =LuaLaTeX OpenType Font=  name database]:
#+caption: Update the =LuaLaTeX= =OpenType Font= name database.
#+name: lst:update-lualatex-opentype-font-name-database
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun update-lualatex-opentype-font-name-database ()
    "Update the \"OpenType Font\" name database for \"LuaLaTeX\"."
    (interactive)
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code
         "luaotfload-tool" "-vv" "--update" "--force")
      (if (= 0 exit-code)
          (message "%s" (string-trim output))
        (error "%s" (string-trim output))))))
#+end_src

#+caption[Configure =bibtex=]:
#+caption: Configure =bibtex=.
#+name: lst:configure-bibtex
#+begin_src emacs-lisp
(with-eval-after-load 'bibtex
  (custom-set-variables '(bibtex-dialect 'BibTeX)))
#+end_src

#+caption[Configure =font-latex=]:
#+caption: Configure =font-latex=.
#+name: lst:configure-font-latex
#+begin_src emacs-lisp
(with-eval-after-load 'font-latex
  (custom-set-variables
   '(font-latex-fontify-sectioning 1.0)))
#+end_src

#+caption[Configure =latex=]:
#+caption: Configure =latex=.
#+name: lst:configure-latex
#+begin_src emacs-lisp
(with-eval-after-load 'latex
  (custom-set-variables
   '(LaTeX-electric-left-right-brace t)
   '(LaTeX-section-hook '(LaTeX-section-heading
                          LaTeX-section-title
                          LaTeX-section-toc
                          LaTeX-section-section
                          LaTeX-section-label))))
#+end_src

*** [[https://gitlab.com/matsievskiysv/math-preview/-/blob/master/README.md][Math-preview]]
:PROPERTIES:
:CUSTOM_ID: sec:math-preview
:END:

[[https://gitlab.com/matsievskiysv/math-preview/-/blob/master/README.md][Math-preview]] uses [[https://docs.mathjax.org/en/latest/][Mathjax-3]] to display [[https://www.latex-project.org/][LaTeX]], [[https://www.w3.org/Math/][MathML]],and [[http://asciimath.org/][asciimath]] in Emacs
buffers with help of an external [[https://nodejs.org][node.js]] program.

#+caption[Configure =math-preview=]:
#+caption: Configure =math-preview=.
#+name: lst:configure-math-preview
#+begin_src emacs-lisp
(when (ensure-package-installation 'math-preview)
  (with-eval-after-load 'math-preview
    ;; https://docs.mathjax.org/en/latest/input/tex/extensions/physics.html
    (let ((physics (split-string "
abs absolutevalue acomm acos acosecant acosine acot acotangent
acsc admat anticommutator antidiagonalmatrix arccos arccosecant
arccosine arccot arccotangent arccsc arcsec arcsecant arcsin
arcsine arctan arctangent asec asecant asin asine atan atangent
bmqty bqty Bqty bra braket comm commutator cos cosecant cosh
cosine cot cotangent coth cp cross crossproduct csc csch curl dd
derivative det determinant diagonalmatrix diffd differential div
divergence dmat dotproduct dv dyad erf ev eval evaluated exp
expectationvalue exponential expval fderivative fdv flatfrac
functionalderivative grad gradient gradientnabla hypcosecant
hypcosine hypcotangent hypsecant hypsine hyptangent
identitymatrix Im imaginary imat innerproduct ip ket ketbra
laplacian ln log logarithm matrixdeterminant matrixel
matrixelement matrixquantity mdet mel mqty naturallogarithm norm
op order outerproduct partialderivative paulimatrix pb
pderivative pdv pmat pmqty Pmqty poissonbracket pqty Pr
principalvalue Probability pv PV qall qand qas qassume qc qcc
qcomma qelse qeven qfor qgiven qif qin qinteger qlet qodd qor
qotherwise qq qqtext qsince qthen qty quantity qunless qusing
rank Re real Res Residue sbmqty sec secant sech sin sine sinh
smallmatrixquantity smdet smqty spmqty sPmqty svmqty tan tangent
tanh tr Tr trace Trace va var variation vb vdot vectorarrow
vectorbold vectorunit vmqty vnabla vqty vu xmat xmatrix
zeromatrix zmat")))
      (cl-pushnew `("physics" . ,physics)
                  math-preview-tex-packages-autoload-packages))
    (setq math-preview-raise 0.5
          math-preview-scale 1
          math-preview-tex-default-packages '("autoload" "ams" "physics"))
    (let ((command (executable-find "~/node_modules/.bin/math-preview")))
      (if command
          (setq math-preview-command command)
        ;; https://stackoverflow.com/a/17509764 answers:
        ;; How to install an npm package from github directly?
        (unless (file-directory-p "~/node_modules")
          (make-directory "~/node_modules"))
        (cl-destructuring-bind (exit-code output)
            (shell-command-with-exit-code
             "npm" "install"
             "git+https://gitlab.com/matsievskiysv/math-preview.git")
          (if (= 0 exit-code)
              (message "%s" (string-trim output))
            (error "%s" (string-trim output))))))))
#+end_src

*** TODO Improve the AUCTeX configuration slowly
:PROPERTIES:
:CUSTOM_ID: sec:configure-auctex-slowly
:END:

[[https://github.com/thisirs/dotemacs/blob/master/lisp/init-auctex.el][AUCTeX setup of an experienced user]]

** Writing [[https://www.markdownguide.org/][Markdown]] files
:PROPERTIES:
:CUSTOM_ID: sec:writing-markdown-files
:END:

#+caption[Configure =markdown-mode=]:
#+caption: Configure =markdown-mode=.
#+name: lst:configure-markdown-mode
#+begin_src emacs-lisp
(when (ensure-package-installation 'markdown-mode))
#+end_src

** Writing [[info:org#Top][Org (info)]] files
:PROPERTIES:
:CUSTOM_ID: sec:writing-org-files
:END:

The [[https://org-babel.readthedocs.io/en/latest/][Org Babel reference card]] complements section [[info:org#Working with Source Code][Working with Source Code (info)]]
of the [[info:org#Top][Org (info)]] manual.

*** [[info:org#Activation][Org activation (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:activate-org
:END:

#+caption[Activate =Org=]:
#+caption: Activate =Org=.
#+name: lst:activate-org
#+begin_src emacs-lisp
(when (cl-every #'fboundp '(org-agenda org-capture))
  (global-set-key (kbd "C-c a") #'org-agenda)
  (global-set-key (kbd "C-c c") #'org-capture)
  (with-eval-after-load 'ol
    (global-set-key (kbd "C-c l") #'org-store-link)
    (global-set-key (kbd "C-c C-l") #'org-insert-link-global)))
#+end_src

*** Org customization
:PROPERTIES:
:CUSTOM_ID: sec:customize-org
:END:

I have split the initial customization of [[https://orgmode.org/][Org-mode]] over several listings.  Here,
follows a list detailing and motivating each listing:
1. Listing [[lst:customize-org]] handles basic customization of [[https://orgmode.org/][Org-mode]] variables
2. Listing [[lst:customize-org-babel]] handles basic customization of [[https://orgmode.org/][Org-mode]]
   variables specific to [[info:org#Working with Source Code][working with source code (info)]] and it selects the
   Python interpreter by means of
   src_emacs-lisp{(choose-common-python-interpreter)} defined in listing
   [[lst:choose-common-python-interpreter]].
3. Listing [[lst:customize-org-link]] handle basic customization of [[https://orgmode.org/][Org-mode]]
   variables specific to [[info:org#Hyperlinks][hyperlinks (info)]].
4. Listing [[lst:configure-org-mode-map]] extends the =org-mode-map= with useful
   key-bindings.
5. Listing [[lst:customize-org-src]] facilitates [[info:org#Editing Source Code][editing Python source code blocks]],
   and it provides a function to remove the indentation of all =org-src-mode=
   blocks without =-i= switch.
6. Listing [[lst:customize-ob-python]] allows to pretty-print Python session source
   block values with [[https://github.com/psf/black#readme][black]] instead of [[https://docs.python.org/3/library/pprint.html][pprint]].
7. Listing [[lst:customize-org-export-ui]] selects the =non-intrusive= expert user
   interface for export dispatching.
8. Listing [[lst:customize-org-for-lualatex-export]] and
   [[lst:customize-ox-latex-for-lualatex-export]] configure [[https://orgmode.org/][Org-mode]] to generate
   output for the LuaLaTeX compiler.
9. Listing [[lst:customize-org-latex-classes]] defines [[info:org#LaTeXspecificexportsettings][org-latex-classes (info)]] for
   backward compatibility. See table [[tab:org-latex-class-tag-placeholder]] and
   type {{{kbd(C-hv org-latex-classes)}}} for an explanation of the code in
   listing [[lst:customize-org-latex-classes]].

#+caption[Customize =Org=]:
#+caption: Customize =Org=.
#+name: lst:customize-org
#+begin_src emacs-lisp
(with-eval-after-load 'org
  (custom-set-variables
   `(org-babel-load-languages
     (delq nil '((C . t)
                 (calc . t)
                 ,(when (fboundp 'grapviz-dot-mode) '(dot . t))
                 (emacs-lisp . t)
                 (eshell . t)
                 ,(when (fboundp 'fennel-mode) '(fennel . t))
                 (fortran . t)
                 ,(when (fboundp 'gnuplot-mode) '(gnuplot . t))
                 (js . t)
                 (latex . t)
                 (lisp . t)
                 ,(when (fboundp 'lua-mode) '(lua . t))
                 ,(when (fboundp 'maxima-mode) '(maxima . t))
                 (org . t)
                 (perl . t)
                 (python . t)
                 (shell . t))))
   '(org-export-backends '(ascii beamer html icalendar latex odt texinfo))
   '(org-file-apps '((auto-mode . emacs)
                     (directory . emacs)
                     ("\\.mm\\'" . default)
                     ("\\.x?html?\\'" . default)
                     ("\\.pdf\\'" . emacs)))
   '(org-modules '(ol-bibtex
                   ol-doi
                   ol-eww
                   ol-info
                   org-id
                   org-protocol
                   org-tempo))
   '(org-structure-template-alist '(("a" . "export ascii")
                                    ("c" . "center")
                                    ("C" . "comment")
                                    ("e" . "example")
                                    ("E" . "export")
                                    ("h" . "export html")
                                    ("l" . "export latex")
                                    ("q" . "quote")
                                    ("s" . "src")
                                    ("p" . "src python -i :session")
                                    ("v" . "verse")))))
#+end_src

#+caption[Customize =org-babel=]:
#+caption: Customize =org-babel=.
#+name: lst:customize-org-babel
#+begin_src emacs-lisp
(with-eval-after-load 'ob-core
  (custom-set-variables
   '(org-confirm-babel-evaluate nil)))

(with-eval-after-load 'ob-latex
  (custom-set-variables
   '(org-babel-latex-preamble
     (lambda (_)
       "\\documentclass[preview]{standalone}\n"))
   '(org-babel-latex-begin-env
     (lambda (_)
       "\\begin{document}\n"))
   '(org-babel-latex-end-env
     (lambda (_)
       "\\end{document}\n"))))

(with-eval-after-load 'ob-lisp
  (with-eval-after-load 'sly
    (custom-set-variables
     '(org-babel-lisp-eval-fn #'sly-eval))))

(with-eval-after-load 'ob-python
  (choose-common-python-interpreter 'python))
#+end_src

#+caption[Customize =org-link=]:
#+caption: Customize =org-link=.
#+name: lst:customize-org-link
#+begin_src emacs-lisp
(with-eval-after-load 'ol
  (custom-set-variables
   '(org-link-file-path-type 'relative)))
#+end_src

#+caption[Configure =org-mode-map=]:
#+caption: Configure =org-mode-map=.
#+name: lst:configure-org-mode-map
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; From: "Nicolas Richard" <theonewiththeevillook@yahoo.fr>
  ;; Date: Fri, 08 Mar 2013 16:23:02 +0100	[thread overview]
  ;; Message-ID: <87vc913oh5.fsf@yahoo.fr> (raw)
  (defun org-electric-dollar ()
    "When called once, insert \\(\\) and leave point in between.
When called twice, replace the previously inserted \\(\\) by one $."
    (interactive)
    (if (and (looking-at "\\\\)") (looking-back "\\\\(" (- (point) 2)))
        (progn (delete-char 2)
               (delete-char -2)
               (insert "$"))
      (insert "\\(\\)")
      (backward-char 2)))

  (defun org-active-current-time-stamp ()
    "Insert an active date-time stamp of the current time."
    (interactive)
    (if (fboundp 'org-insert-time-stamp)
        (org-insert-time-stamp (current-time) 'with-hm)
      (let ((stamp (format-time-string "<%Y-%m-%d %a %H:%M>" (current-time))))
        (insert stamp)
        stamp)))

  (defun org-inactive-current-time-stamp ()
    "Insert an inactive date-time stamp of the current time."
    (interactive)
    (if (fboundp 'org-insert-time-stamp)
        (org-insert-time-stamp (current-time) 'with-hm 'inactive)
      (let ((stamp (format-time-string "[%Y-%m-%d %a %H:%M]" (current-time))))
        (insert stamp)
        stamp)))

  (with-eval-after-load 'org
    (define-key org-mode-map
      (kbd "C-c <SPC>") #'org-inactive-current-time-stamp)
    (define-key org-mode-map
      (kbd "C-c C-<SPC>") #'org-active-current-time-stamp)
    (define-key org-mode-map (kbd "$") #'org-electric-dollar)
    (define-key org-mode-map (kbd "M-q") #'org-fill-paragraph)))
#+end_src

#+caption[Customize =org-src=]:
#+caption: Customize =org-src=.
#+name: lst:customize-org-src
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (with-eval-after-load 'org-src
    (custom-set-variables
     '(org-src-preserve-indentation t)))

  (declare-function org-babel-map-src-blocks "ext:ob-core" (file &rest body))
  (declare-function org-do-remove-indentation "ext:org-macs" (n skip-fl))

  (defun zero-all-org-src-blocks-indentation ()
    "Remove the indentation of all `org-src-mode' blocks without `-i' switch."
    (interactive)
    (when (derived-mode-p 'org-mode)
      (save-excursion
        (org-babel-map-src-blocks
            nil
          (unless (or (string-match "-i " switches)
                      (string-match (rx (or bos bol) graph) body))
            (when-let ((new (with-temp-buffer
                              (insert body)
                              (org-do-remove-indentation)
                              (buffer-string))))
              (goto-char beg-body)
              (delete-region beg-body end-body)
              (insert new))))))))
#+end_src

#+caption[Customize =ob-python=]:
#+caption: Customize =ob-python=.
#+name: lst:customize-ob-python
#+begin_src emacs-lisp
(with-eval-after-load 'ob-python
  (defun org-babel-python-format-session-value-override
      (src-file result-file result-params)
    "Return Python code to evaluate SRC-FILE and write result to RESULT-FILE.
Use `black' instead of `pprint' when \"pp\" is a member of RESULT-PARAMS."
    (format "\
import ast
with open('%s') as __org_babel_python_tmpfile:
    __org_babel_python_ast = ast.parse(__org_babel_python_tmpfile.read())
__org_babel_python_final = __org_babel_python_ast.body[-1]
if isinstance(__org_babel_python_final, ast.Expr):
    __org_babel_python_ast.body = __org_babel_python_ast.body[:-1]
    exec(compile(__org_babel_python_ast, '<string>', 'exec'))
    __org_babel_python_final = eval(
        compile(ast.Expression(__org_babel_python_final.value), '<string>', 'eval')
    )
    with open('%s', 'w') as __org_babel_python_tmpfile:
        if %s:
            import black
            __org_babel_python_tmpfile.write(
                black.format_str(repr(__org_babel_python_final), mode=black.Mode())
            )
        else:
            __org_babel_python_tmpfile.write(str(__org_babel_python_final))
else:
    exec(compile(__org_babel_python_ast, '<string>', 'exec'))
    __org_babel_python_final = None"
            (org-babel-process-file-name src-file 'noquote)
            (org-babel-process-file-name result-file 'noquote)
            (if (member "pp" result-params) "True" "False")))

  (advice-add 'org-babel-python-format-session-value
              :override #'org-babel-python-format-session-value-override))
#+end_src

#+caption[Customize =org-export=]:
#+caption: Customize =org-export=.
#+name: lst:customize-org-export-ui
#+begin_src emacs-lisp
(with-eval-after-load 'ox
  (custom-set-variables
   '(org-export-dispatch-use-expert-ui t)))
#+end_src

#+caption[Customize =org= for export to LuaLaTeX]:
#+caption: Customize =org= for export to LuaLaTeX.
#+name: lst:customize-org-for-lualatex-export
#+begin_src emacs-lisp
(with-eval-after-load 'org
  ;; https://list.orgmode.org/87o84fd4oi.fsf@posteo.net/
  (add-to-list
   'org-preview-latex-process-alist
   '(luamagick
     :programs ("lualatex" "convert")
     :description "pdf > png"
     :message "you need to install lualatex and imagemagick."
     :image-input-type "pdf"
     :image-output-type "png"
     :image-size-adjust (1.0 . 1.0)
     :post-clean nil
     :latex-header nil
     :latex-compiler ("lualatex -interaction nonstopmode -output-directory %o %f")
     :image-converter ("convert -density %D -trim -antialias %f -quality 100 %O")))
  (custom-set-variables
   '(org-preview-latex-default-process 'luamagick)
   '(org-latex-default-packages-alist '(("" "fontspec" t ("lualatex"))
                                        ("AUTO" "inputenc" t ("pdflatex"))
                                        ("T1" "fontenc" t ("pdflatex"))
                                        ("" "graphicx" t)
                                        ("" "longtable" nil)
                                        ("" "wrapfig" nil)
                                        ("" "rotating" nil)
                                        ("normalem" "ulem" t)
                                        ("" "amsmath" t)
                                        ("" "amssymb" t)
                                        ("" "capt-of" nil)
                                        ("" "hyperref" nil)))))
#+end_src

#+caption[Customize =ox-latex= for export to LuaLaTeX]:
#+caption: Customize =ox-latex= for export to LuaLaTeX.
#+name: lst:customize-ox-latex-for-lualatex-export
#+begin_src emacs-lisp
(with-eval-after-load 'ox-latex
  (custom-set-variables
   '(org-latex-pdf-process
     ;; https://tecosaur.github.io/emacs-config/#compiling
     `(,(concat "latexmk -f -pdf -%latex"
                " -interaction=nonstopmode -shell-escape -outdir=%o %f")))
   '(org-latex-compiler "lualatex")
   '(org-latex-hyperref-template "\\hypersetup{
  pdfauthor={%a},
  pdftitle={%t},
  pdfkeywords={%k},
  pdfsubject={%d},
  pdfcreator={%c},
  pdflang={%L},
  citecolor=blue,
  colorlinks=true,
  filecolor=blue,
  hyperfootnotes=false,
  linkcolor=blue,
  unicode=true,
  urlcolor=blue,
}\n")
   `,(if (version< emacs-version "29.0.0")
         '(org-latex-listings 'minted)
       '(org-latex-src-block-backend 'minted))
   '(org-latex-minted-langs '((cc "c++")
                              (conf "text")
                              (cperl "perl")
                              (diff "diff")
                              (shell-script "bash")
                              (json "json")
                              (org "text")
                              (toml "toml")))
   '(org-latex-minted-options '(("bgcolor" "LightGoldenrodYellow")))
   `(org-latex-logfiles-extensions
     ',(cl-union '("lof" "lot") org-latex-logfiles-extensions :test #'equal))
   '(org-latex-prefer-user-labels t)
   '(org-latex-subtitle-separate t)))
#+end_src

#+caption[Customize =org-latex-classes= for backwards compatibility]:
#+caption: Customize =org-latex-classes= for backwards compatibility.
#+name: lst:customize-org-latex-classes
#+begin_src emacs-lisp
(with-eval-after-load 'ox-latex
  (mapc (function (lambda (element)
                    (add-to-list 'org-latex-classes element)))
        (nreverse
         (quote (("elsarticle-1+2+3"	; Elsevier journals
                  "\\documentclass{elsarticle}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
                  ("\\section{%s}" . "\\section*{%s}")
                  ("\\subsection{%s}" . "\\subsection*{%s}")
                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                 ("article-1+2+3"
                  "\\documentclass{article}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
                  ("\\section{%s}" . "\\section*{%s}")
                  ("\\subsection{%s}" . "\\subsection*{%s}")
                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                 ("report-1+2+3"
                  "\\documentclass[11pt]{report}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
                  ("\\part{%s}" . "\\part*{%s}")
                  ("\\chapter{%s}" . "\\chapter*{%s}")
                  ("\\section{%s}" . "\\section*{%s}")
                  ("\\subsection{%s}" . "\\subsection*{%s}")
                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
                 ("book-1+2+3"
                  "\\documentclass[11pt]{book}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
                  ("\\part{%s}" . "\\part*{%s}")
                  ("\\chapter{%s}" . "\\chapter*{%s}")
                  ("\\section{%s}" . "\\section*{%s}")
                  ("\\subsection{%s}" . "\\subsection*{%s}")
                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))))))
#+end_src

#+attr_latex: :booktabs yes :float table
#+caption[The relation tag-placeholder in listing [[lst:customize-org-latex-classes]]]:
#+caption: The relation tag-placeholder in listing [[lst:customize-org-latex-classes]].
#+name: tab:org-latex-class-tag-placeholder
| tag | placeholder           |
|-----+-----------------------|
|  +1 | [DEFAULT-PACKAGES]    |
|  +2 | [PACKAGES]            |
|  +3 | [EXTRA]               |
|  -1 | [NO-DEFAULT-PACKAGES] |
|  -2 | [NO-PACKAGES]         |
|  -3 | [NO-EXTRA]            |

*** [[https://github.com/bdarcus/citar][Citar: citing bibliography]] with [[https://orgmode.org/][Org Mode]]
:PROPERTIES:
:CUSTOM_ID: sec:citing-bibliography
:END:

[[https://github.com/bdarcus/citar][Citar]] is a completing-read front-end to browse and act on BibTeX, BibLaTeX, as
well as CSL JSON bibliographic data with LaTeX, markdown, and org-cite editing
support.  In combination with vertico, embark, marginalia, and consult, [[https://github.com/bdarcus/citar][Citar]]
provides quick filtering and selecting of bibliographic entries from the
minibuffer, as well as the option to run different commands on those
selections. The article [[https://kristofferbalintona.me/posts/202206141852/][Citations in org-mode: Org-cite and Citar]] tries to walk
you from understanding the general context (bibliography producer, text
processor, text to product convertor) to an Emacs setup.  Listing
[[lst:configure-oc-cite+citar]] shows my =org-cite=, =citar=, and =org=
configuration.

#+caption[Configure =org-cite= with =citar=]:
#+caption: Configure =oc-cite= with =citar=.
#+name: lst:configure-oc-cite+citar
#+begin_src emacs-lisp
(with-eval-after-load 'oc
  ;; Org-9.5 needs the requirements, but Org-9.6 does not.
  (when (version< (org-version) "9.5.99")
    (require 'oc-biblatex)
    (require 'oc-csl)))

(with-eval-after-load 'org
  (define-key org-mode-map (kbd "C-c b") #'org-cite-insert))

(when (ensure-package-installation 'citar 'citar-embark)
  (with-eval-after-load 'embark
    (when (fboundp 'citar-embark-mode)
      (citar-embark-mode +1)))

  (when (require 'citar nil 'noerror)
    (custom-set-variables
     '(citar-bibliography '("~/VCS/research/refs.bib"))
     '(citar-library-file-extensions '("djvu" "pdf"))
     '(citar-library-paths '("~/VCS/research/papers/"))))

  (with-eval-after-load 'oc
    (custom-set-variables
     '(org-cite-export-processors '((latex biblatex)
                                    (t csl)))
     '(org-cite-global-bibliography '("~/VCS/research/refs.bib")))

    (when (require 'citar nil 'noerror)
      (custom-set-variables
       '(org-cite-activate-processor 'citar)
       '(org-cite-follow-processor 'citar)
       '(org-cite-insert-processor 'citar)))))
#+end_src

Ref. [cite:@Schulte.MCSE.2011.41] shows that [[https://orgmode.org/][Org-mode]] is a simple, plain-text
markup language for hierarchical documents allowing intermingling of data, code,
and prose.  It serves as an example link to to show how to use [[https://github.com/bdarcus/citar][Citar]] within this
setup, provided that =citar-bibliography= and =citar-library-paths= point to
valid directories and files.  In an [[https://orgmode.org/][Org-mode]] buffer this setup allows to:
1. Insert one or more [[https://orgmode.org/][Org-mode]] cite links:
   1. Type {{{kbd(C-c b)}}} or {{{kbd(M-x org-cite-insert)}}}.
   2. Navigate to a bibliographic entry to insert:
      1. Select it with {{{kbd(TAB)}}} to select more entries.
      2. Select it with {{{kbd(RET)}}} to select the last entry.
2. View an electronic copy of an [[https://orgmode.org/][Org-mode]] cite link:
   1. Move point to the [[https://orgmode.org/][Org-mode]] cite link.
   2. Type {{{kbd(C-:)}}} or {{{kbd(M-x embark-dwim)}}}.
   3. Navigate to the corresponding library file.
   4. Select it.
3. Open the DOI of an [[https://orgmode.org/][Org-mode]] cite link:
   1. Move point to the [[https://orgmode.org/][Org-mode]] cite link.
   2. Type {{{kbd(C-:)}}} or {{{kbd(M-x embark-dwim)}}}.
   3. Navigate to the corresponding link.
   4. Select it.

*** TODO Compare bibtex and biblatex
1. [[https://www.economics.utoronto.ca/osborne/latex/BIBTEX.HTM][Using bibtex: a short guide]]
2. [[https://www.tug.org/texlive//devsrc/Master/texmf-dist/doc/latex/biblatex/biblatex.pdf][The biblatex package]]
3. [[https://github.com/yuchenlin/rebiber][Rebiber: A tool for normalizing bibtex with official info]]
4. [[https://github.com/josephwright/biblatex-phys][A biblatex implementation of the AIP and APS bibliography style]]

#+caption[Delete =Biber= cache when =Biber= fails to make a bibliography]:
#+caption: Delete =Biber= cache when =Biber= fails to make a bibliography.
#+name: lst:delete-biber-cache
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; https://tex.stackexchange.com/a/579356 answers
  ;; "How to solve Biber exiting with error code 2 but no error messages?"
  (defun biber-delete-cache ()
    "Delete the `Biber' cache to get rid of `Biber' exit code 2."
    (interactive)
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code "rm" "-rf" "$(biber --cache)")
      (if (= 0 exit-code)
          (message "%s" (string-trim output))
        (error "%s" (string-trim output))))))
#+end_src

*** [[https://github.com/tecosaur/engrave-faces#readme][Engrave Faces]]
:PROPERTIES:
:CUSTOM_ID: sec:engrave-faces
:END:

This package has a front-end that processes fontified buffers and pipes its
output into one of three back-ends for export to LaTeX, HTML and text with ANSI
escape codes.  It is an alternative to =minted= in case of LaTeX export or to
=htmlized= in case of HTML export.

The listings below work around two issues with spacing in the =pdf= output
resulting from use of the =engraved= source block back-end during =LaTeX=
export, and one isssue with symbolic color names in faces.  They increase the
quality of the export results of this [[file:README.org][README.org]] and the user-friendliness of
this facility to a level acceptable for my workflow:
1. The default Org export configuration for engraving listings produces =pdf=
   output with a non-equidistant interline spacing in floating listings (those
   with captions) and equidistant interline spacing in non-floating =tcolorbox=
   environments (those without captions).  I have traced the non-equidistant
   interline spacing back to the =breakable= option of =Code= environments
   inside =listing= environments.  However, =tcolorbox= requires =breakable= for
   listings that do not fit on a page.  The filter
   =org-latex-engraved-source-block-filter= in listing
   [[lst:org-latex-engraved-source-block-filter]] and the
   =org-latex-engraved-preamble= customization in listing
   [[lst:smart-latex-engrave-org-source-blocks]] allow to engrave =org-mode= source
   blocks to "floating unbreakable with caption" or "non-floating breakable
   without caption" LaTeX environments.  This is a partial work-around, but part
   of my workflow.
2. Listing [[lst:ensure-engrave-faces-with-latex-face-apply-fix]] makes
   =engrave-faces-latex-face-apply= handle symbolic color name strings (in
   addition to the hexadecimal strings).  Since faces in for instance
   src_emacs-lisp{(find-library "org-faces")} and src_emacs-lisp{(find-library
   "faces")} have symbolic color names (beware: Emacs themes may replace the
   symbolic color names with hexadecimal strings), this fix allows to engrave
   for instance org-mode source blocks during LaTeX export without any
   customization of =engrave-faces-themes=.  Listing
   [[lst:ensure-engrave-faces-with-attribute-values-fix]] proposes another method to
   obtain the same result.  Currently, I prefer to tangle listing
   [[lst:ensure-engrave-faces-with-attribute-values-fix]] to the =user-init-file=
   instead of listing [[lst:ensure-engrave-faces-with-latex-face-apply-fix]].
3. Listing [[lst:ensure-engrave-faces-with-latex-face-mapper-fix]] makes
   =engrave-faces-latex-face-mapper= handle horizontal and vertical spacing in
   multiple line documentation strings correctly. For instance, without this fix
   the mishandling of vertical and horizontal spacing destroys the indentation
   in Python documentation strings.  An Emacs lisp example of the bug is the
   disappearance of the empty line in the documentation string of
   =org-latex-engraved-source-block-filter= of listing
   [[lst:org-latex-engraved-source-block-filter]] in exported =pdf= files.  The idea
   of the fix is to let the LaTeX face mapper wrap only groups of "words joined
   by blank characters" in LaTeX commands and pass "newlines and other
   whitespace between those groups" on without wrapping.
4. Listing [[lst:ox-engraved-emacs-lisp-setup]] shows how to use this configuration.

#+caption[Engrave to floating unbreakable or non-floating breakable environments]:
#+caption: Define an =org-export= filter function to engrave =org-src-mode=
#+caption: blocks to floating unbreakable LaTeX environments or non-floating
#+caption: breakable LaTeX environments.
#+name: lst:org-latex-engraved-source-block-filter
#+begin_src emacs-lisp :results silent
(ensure-package-installation 'engrave-faces)

(defun org-latex-engraved-source-block-filter (data _backend _info)
  "Replace \"Code\" with \"Breakable\" in non-floating environments.

Customize `org-latex-engraved-preamble' to define a Breakable (non-floating)
environment and an unbreakable Code (floating) environment."
  (unless (string-match "^\\\\DeclareTColorBox\\[\\]{Breakable}"
                        org-latex-engraved-preamble)
    (user-error "`org-latex-engraved-preamble' defines no `Breakable' environment"))
  (when (eq org-latex-src-block-backend 'engraved)
    (let ((enter "^\\\\begin{Code}\n\\\\begin{Verbatim}")
          (leave "^\\\\end{Verbatim}\n\\\\end{Code}"))
      ;; Transform only blocks matching the enter regexp at position 0.
      ;; Do not transform blocks that are listing environments.
      (when (and (string-match enter data) (eql 0 (match-beginning 0)))
        (setq data (replace-match
                    "\\begin{Breakable}\n\\begin{Verbatim}" t t data))
        (when (string-match leave data (match-end 0))
          (setq data (replace-match
                      "\\end{Verbatim}\n\\end{Breakable}" t t data))
          (when (string-match enter data)
            (user-error "The `enter' regexp `%s' should not match" enter))
          (when (string-match leave data)
            (user-error "The `leave' regexp `%s' should not match" leave))
          data)))))
#+end_src

#+caption[Smart LaTeX engraving of =org-src-mode= blocks]:
#+caption: Smart LaTeX engraving of =org-src-mode= blocks.
#+name: lst:smart-latex-engrave-org-source-blocks
#+begin_src emacs-lisp
(defun smart-latex-engrave-org-source-blocks ()
  "Enable smart LaTeX engraving of `org-src-mode' blocks.

Sets backend and preamble locally to support floating unbreakable LaTeX
environments and non-floating breakable LaTeX environments by means of
`org-latex-engraved-source-block-filter'."
  (interactive)
  (when (require 'ox-latex nil 'noerror)
    (setq-local org-latex-src-block-backend 'engraved
                org-latex-engraved-preamble "\\usepackage{fvextra}
[FVEXTRA-SETUP]

% Make code and line numbers normalsize. Make line numbers grey.
\\renewcommand\\theFancyVerbLine{
  \\normalsize\\color{black!40!white}\\arabic{FancyVerbLine}}
% In case engrave-faces-latex-gen-preamble has not been run.
\\providecolor{EfD}{HTML}{f7f7f7}
\\providecolor{EFD}{HTML}{28292e}
% To use \\DeclareTColorBox from the tcolorbox package:
\\usepackage[breakable,xparse]{tcolorbox}
% Define a Breakable environment to fontify code outside floats.
\\DeclareTColorBox[]{Breakable}{o}{
  colback=EfD, colframe=EFD, colupper=EFD,
  fontupper=\\normalsize\\setlength{\\fboxsep}{0pt},
  IfNoValueTF={#1}{
    boxsep=1pt, arc=1pt, outer arc=1pt, boxrule=0.5pt,
  }{
    boxsep=1pt, arc=0pt, outer arc=0pt, boxrule=0pt, leftrule=1pt
  },
  left=2pt, right=2pt, top=1pt, bottom=1pt, breakable
}
% Define an unbreakable Code environment to fontify code inside floats.
\\DeclareTColorBox[]{Code}{o}{
  colback=EfD, colframe=EFD, colupper=EFD,
  fontupper=\\normalsize\\setlength{\\fboxsep}{0pt},
  IfNoValueTF={#1}{
    boxsep=1pt, arc=1pt, outer arc=1pt, boxrule=0.5pt
  }{
    boxsep=1pt, arc=0pt, outer arc=0pt, boxrule=0pt, leftrule=1pt
  },
  left=2pt, right=2pt, top=1pt, bottom=1pt,
}

[LISTINGS-SETUP]")))
#+end_src

#+caption[Fix engraving of symbolic color names in =engrave-faces-latex=]:
#+caption: Fix engraving of symbolic colors names in =engrave-faces-latex=.
#+name: lst:ensure-engrave-faces-with-latex-face-apply-fix
#+begin_src emacs-lisp :tangle no
(when (require 'engrave-faces-latex nil t)
  (defun engrave-faces-latex--color (color)
    "Convert COLOR loosely to a string of six hexadecimal digits."
    (if (char-equal ?# (aref color 0))
        (substring color 1 7)
      (apply 'format "%02x%02x%02x"
             (mapcar (lambda (c) (ash c -8))
                     (color-values color)))))

  (defun engrave-faces-latex-face-apply-override (faces content)
    "Convert attributes of FACES to LaTeX commands applied to CONTENT."
    (let ((attrs (engrave-faces-merge-attributes faces)))
      (let ((bg (plist-get attrs         :background))
            (fg (plist-get attrs         :foreground))
            (it (eql (plist-get attrs    :slant) 'italic))
            (bl (member (plist-get attrs :weight) '(bold extra-bold)))
            (st (plist-get attrs         :strike-through)))
        (concat
         (when bg (concat "\\colorbox[HTML]{"
                          (engrave-faces-latex--color bg) "}{"))
         (when fg (concat "\\textcolor[HTML]{"
                          (engrave-faces-latex--color fg) "}{"))
         (when st "\\sout{") (when bl "\\textbf{") (when it "\\textit{")
         content
         (when bg "}") (when fg "}") (when st "}") (when bl "}") (when it "}")))))

  (advice-add 'engrave-faces-latex-face-apply
              :override #'engrave-faces-latex-face-apply-override))
#+end_src

#+caption[Fix engraving of symbolic color names in =engrave-faces=]:
#+caption: Fix engraving of symbolic colors names in =engrave-faces=.
#+name: lst:ensure-engrave-faces-with-attribute-values-fix
#+begin_src emacs-lisp
(when (require 'engrave-faces nil t)
  (defun engrave-faces-attribute-values-around (efav-fun &rest args)
    (let ((values (apply efav-fun args))
          (attribute (cadr args)))
      (if (not (member attribute '(:foreground :background)))
          values
        (mapcar (lambda (color)
                  (if (char-equal ?# (aref color 0))
                      color)
                  (apply 'format "#%02x%02x%02x"
                         (mapcar (lambda (c) (ash c -8))
                                 (color-values color))))
                values))))

  (advice-add 'engrave-faces-attribute-values
              :around #'engrave-faces-attribute-values-around))
#+end_src

#+caption[Fix engraving of horizontal/vertical spacing in multiline docstrings]:
#+caption: Fix engraving of horizontal and vertical spacing in multiple line
#+caption: documentation strings.
#+name: lst:ensure-engrave-faces-with-latex-face-mapper-fix
#+begin_src emacs-lisp
(when (require 'engrave-faces-latex nil t)
  (defun engrave-faces-latex-face-mapper-override (faces content)
    "Create a LaTeX representation of CONTENT with FACES applied."
    (let* ((style (engrave-faces-preset-style faces))
           (protected-content
            (funcall
             (if (and engrave-faces-latex-mathescape
                      (eq 'font-lock-comment-face (car style)))
                 #'engrave-faces-latex--protect-content-mathescape
               #'engrave-faces-latex--protect-content)
             content)))
      ;; Wrap groups of "words joined by blank characters" in LaTeX commands.
      ;; Do not wrap newlines and other whitespace between those groups.
      (let ((regexp (rx (or (group-n 1 (+ graph ) (* (+ blank) (+ graph)))
                            (group-n 2 (+ (any "\n" space))))))
            (slug (when (and style
                             (eq engrave-faces-latex-output-style 'preset))
                    (plist-get (cdr style) :slug)))
            (start 0) (stack))
        (while (string-match regexp protected-content start)
          (setq start (match-end 0))
          (when-let ((pc (match-string 1 protected-content)))
            (if (stringp slug)
                (push (concat "\\EF" slug "{" pc "}") stack)
              (push (engrave-faces-latex-face-apply faces pc) stack)))
          (when-let ((pc (match-string 2 protected-content)))
            (push pc stack)))
        (apply #'concat (nreverse stack)))))

  (advice-add 'engrave-faces-latex-face-mapper
              :override #'engrave-faces-latex-face-mapper-override))
#+end_src

#+caption[Emacs setup to use =engrave-faces-latex= in =org-mode= smartly]:
#+caption: Emacs setup to use =engrave-faces-latex= in =org-mode= smartly.
#+name: lst:ox-engraved-emacs-lisp-setup
#+begin_src emacs-lisp :tangle no
(with-eval-after-load 'ox
  (make-variable-buffer-local 'org-export-filter-src-block-functions)
  (add-to-list 'org-export-filter-src-block-functions
               'org-latex-engraved-source-block-filter)
  (when (fboundp 'smart-latex-engrave-org-source-blocks)
    (smart-latex-engrave-org-source-blocks)))
#+end_src

*** [[info:org#Adding Hyperlink Types][Making Org hyperlink types (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:make-org-hyperlink-types
:END:

The listings below implement or reimplement three groups of =org-link= types:
1. Listing [[lst:org-ref-like-org-link-types]] defines =org-link= types for
   backwards compatibility with [[https://github.com/jkitchin/org-ref][org-ref]].
2. Listing [[lst:define-org-pdfview-link-type]] uses ideas from the definition of
   =docview-org-link= and =doi-org-link= types to define an =pdfview-org-link=
   type for use with [[https://github.com/vedang/pdf-tools][pdf-tools]].
3. Listing [[lst:patch-org-info-link-type]] patches the function =org-info-export=
   and listing [[lst:emacs-lisp-setup-buffer-local-ol-info]] sets the constants
   ~org-info-emacs-documents~ and ~org-info-other-documents~ as buffer local
   variables in order to export the =info-org-link= types in this document to
   =html= and LaTeX correctly.

#+caption[Define =org-link= types for backwards compatibility with =org-ref=]:
#+caption: Define =org-link= types for backwards compatibility with =org-ref=.
#+name: lst:org-ref-like-org-link-types
#+begin_src emacs-lisp
(with-eval-after-load 'ol
  (org-link-set-parameters "ac*" :export #'org-ref-ac*-export)
  (org-link-set-parameters "cite" :export #'org-ref-cite-export)
  (org-link-set-parameters "eqref" :export #'org-ref-eqref-export)
  (org-link-set-parameters "hyperlink" :export #'org-ref-hyperlink-export)
  (org-link-set-parameters "label" :export #'org-ref-label-export)
  (org-link-set-parameters "ref" :export #'org-ref-ref-export)

  (defun org-ref-ac*-export (path _desc backend _info)
    (pcase backend
      (`latex (format "\\gls*{%s}" path))
      (_ path)))

  (defun org-ref-cite-export (path _desc backend _info)
    (pcase backend
      (`latex (format "\\cite{%s}" path))
      (_ path)))

  (defun org-ref-eqref-export (path _desc backend _info)
    (pcase backend
      (`latex (format "\\eqref{%s}" path))
      (_ path)))

  (defun org-ref-hyperlink-export (path desc backend _info)
    (pcase backend
      (`latex (format "\\hyperlink{%s}{%s}" path desc))
      (_ path)))

  (defun org-ref-label-export (path _desc backend _info)
    (pcase backend
      (`latex (format "\\label{%s}" path))
      (_ path)))

  (defun org-ref-ref-export (path _desc backend _info)
    (pcase backend
      (`latex (format "\\ref{%s}" path))
      (_ path))))
#+end_src

#+caption[Define an =org-link= type for =pdf-tools=]:
#+caption: Define an =org-link= type for =pdf-tools=.
#+name: lst:define-org-pdfview-link-type
#+begin_src emacs-lisp
(with-eval-after-load 'ol
  (autoload 'pdf-view-goto-page "pdf-view" nil t)
  (org-link-set-parameters "pdfview"
                           :follow #'org-pdfview-open
                           :export #'org-pdfview-export
                           :store #'org-pdfview-store-link)

  (defun org-pdfview-export (link description backend _)
    "Export a \"pdfview\" type link.
The paths of the links export as file relative paths in order to
facilate moving single directories or whole directory trees."
    (let ((path (if (string-match "\\(.+\\)::.+" link)
                    (match-string 1 link)
                  link))
          (desc (or description link)))
      (when (stringp path)
        (setq path (file-relative-name path))
        (pcase backend
          (`html (format "<a href=\"%s\">%s</a>" path desc))
          (`latex (format "\\href{%s}{%s}" path desc))
          (`ascii (format "%s (%s)" desc path))
          (_ path)))))

  (defun org-pdfview-open (link _)
    "Open a \"pdfview\" type link."
    (string-match "\\(.*?\\)\\(?:::\\([0-9]+\\)\\)?$" link)
    (let ((path (match-string 1 link))
          (page (and (match-beginning 2)
                     (string-to-number (match-string 2 link)))))
      ;; Let Org mode open the file (in-emacs = 1) to ensure
      ;; org-link-frame-setup is respected.
      (org-open-file path 1)
      (when page (pdf-view-goto-page page))))

  (defun org-pdfview-store-link ()
    "Store a \"pdfview\" type link."
    (when (eq major-mode 'pdf-view-mode)
      (let* ((path buffer-file-name)
             (page (pdf-view-current-page))
             (link (concat "pdfview:" path "::" (number-to-string page))))
        (org-link-store-props
         :type "pdfview"
         :link link
         :description path)))))
#+end_src

#+caption[Patch =ol-info=]:
#+caption: Patch =ol-info=.
#+name: lst:patch-org-info-link-type
#+begin_src emacs-lisp :exports code :results silent
(with-eval-after-load 'ol-info
  (defun org-info-export (path desc format)
    "Export an info link.
See `org-link-parameters' for details about PATH, DESC and FORMAT."
    (let* ((parts (split-string path "#\\|::"))
           (manual (car parts))
           (node (or (nth 1 parts) "Top")))
      (pcase format
        (`html
         (format "<a href=\"%s#%s\">%s</a>"
                 (org-info-map-html-url manual)
                 (org-info--expand-node-name node)
                 (or desc path)))
        (`latex
         (format "\\href{%s\\#%s}{%s}"
                 (org-info-map-html-url manual)
                 (org-info--expand-node-name node)
                 (or desc path)))
        (`texinfo
         (let ((title (or desc "")))
           (format "@ref{%s,%s,,%s,}" node title manual)))
        (_ nil)))))
#+end_src

#+attr_latex: :options breaklines
#+caption[Patch buffer local =ol-info=]:
#+caption: Patch buffer local =ol-info=.
#+name: lst:emacs-lisp-setup-buffer-local-ol-info
#+begin_src emacs-lisp :exports code :results silent :tangle no
(with-eval-after-load 'ol-info
  (make-variable-buffer-local 'org-info-emacs-documents)
  (setq org-info-emacs-documents (delete "org" org-info-emacs-documents))
  (make-variable-buffer-local 'org-info-other-documents)
  (setq org-info-other-documents
        (cl-union
         '(("consult" . "https://github.com/minad/consult")
           ("embark" . "https://github.com/oantolin/embark")
           ("magit" . "https://magit.vc/manual/magit.html")
           ("marginalia" . "https://github.com/minad/marginalia")
           ("maxima" .
            "https://maxima.sourceforge.io/docs/manual/maxima_singlepage.html")
           ("org" . "https://orgmode.org/org.html")
           ("orderless" . "https://github.com/oantolin/orderless")
           ("sly" . "https://joaotavora.github.io/sly/")
           ("vertico" . "https://github.com/minad/vertico"))
         org-info-other-documents :test #'equal)))
#+end_src

*** [[https://bitspook.in/blog/extending-org-mode-to-handle-youtube-links/][Extending org-mode to handle YouTube links]]
:PROPERTIES:
:CUSTOM_ID: sec:make-org-yt-link-type
:END:

Listing [[lst:define-org-yt-link-type][define org-yt-link type]] implements code to open the link to the
following YouTube video [[yt:eaZUZCzaIgw#6s#10s][Extending org-mode to handle YouTube links.]]

The following posts provide programming information:
1. [[https://developers.google.com/youtube/v3/docs][YouTube API reference]].
2. [[https://developers.google.com/youtube/iframe_api_reference][YouTube Player API reference for iframe embeds]].
3. [[https://www.alphr.com/how-to-link-specific-timestamp-youtube/][How to link to a specific timestamp in a YouTube video]].

#+begin_src emacs-lisp :exports none :tangle no
;; https://www.youtube.com/embed/M03bTkQxVUg?start=30&end=120

(org-yt-seconds-to-hms (+ (* 3600 120) (* 60 9) 7))
(org-yt-seconds-to-hms 3661)

(org-yt-time-to-seconds "")
(org-yt-time-to-seconds "1")
(org-yt-time-to-seconds "1:1")
(org-yt-time-to-seconds "1:1:1")
(org-yt-time-to-seconds "1h1m1s")
(org-yt-time-to-seconds "1mX")
(org-yt-time-to-seconds "1h")
(org-yt-time-to-seconds "1H1m")
(org-yt-time-to-seconds "1h1s")
(org-yt-time-to-seconds "1m1s")
(org-yt-time-to-seconds "1h1s")
(org-yt-time-to-seconds "1h1M1s")

(org-yt-format-open-url "WKwZHSbHmPg" "")
(org-yt-format-open-url "WKwZHSbHmPg" nil)
(org-yt-format-open-url "WKwZHSbHmPg" '("1m1s"))
(org-yt-format-open-url "WKwZHSbHmPg" '("0:2:44" "0:2:50"))

(org-yt-open "WKwZHSbHmPg#0:2:44#0:2:50" t)

(org-yt-export "WKwZHSbHmPg#0:2:44#0:2:50" "Title" 'html nil)
(org-yt-export "WKwZHSbHmPg#0h2m40s#0h2m50s" "Title" 'html nil)
(org-yt-export "WKwZHSbHmPg#2M40S#2M50S" "Title" 'html nil)

(org-yt-export "WKwZHSbHmPg#0:2:44#0:2:50" "Title" 'latex nil)
(org-yt-export "WKwZHSbHmPg#0h2m40s#0h2m50s" "Title" 'latex nil)
(org-yt-export "WKwZHSbHmPg#2M40S#2M50S" "Title" 'latex nil)
#+end_src

#+caption[Parsing function for the =org-yt= link type]:
#+caption: Parsing function for the =org-yt= link type.
#+name: lst:org-yt-parsing
#+begin_src emacs-lisp
(defun org-yt-time-to-seconds (text)
  "Convert TEXT of the form `12:34:56' or `12h34m56s' to seconds as integers."
  (let* ((case-fold-search t)
         (hms (< (length (split-string text "[:]"))
                 (length (split-string text "[HhMmSs]"))))
         (regexp (if hms
                     (rx (opt (group (+ digit) "h"))
                         (opt (group (+ digit) "m"))
                         (opt (group (+ digit) "s")))
                   (rx (opt (group (+ digit)))
                       (opt ":" (group (+ digit)))
                       (opt ":" (group (+ digit))))))
         (_ (string-match regexp text))
         (md (match-data))
         (found (substring text (pop md) (pop md)))
         (seconds 0)
         lot)
    (if (string< found text)
        (user-error "Found `%s' which is a prefix of `%s'" found text)
      (if hms
          (while md
            (setq lot (substring text (or (pop md) 0) (or (pop md) 0)))
            (cond
             ((or (string-suffix-p "h" lot) (string-suffix-p "H" lot))
              (setq seconds (+ seconds (* 3600 (string-to-number lot)))))
             ((or (string-suffix-p "m" lot) (string-suffix-p "M" lot))
              (setq seconds (+ seconds (* 60 (string-to-number lot)))))
             ((or (string-suffix-p "s" lot) (string-suffix-p "S" lot))
              (setq seconds (+ seconds (string-to-number lot))))))
        (while md (push (string-to-number
                         (substring text (or (pop md) 0) (or (pop md) 0)))
                        lot))
        (cond
         ((length= lot 1) (setq seconds (car lot)))
         ((length= lot 2) (setq seconds (+ (* 60 (cadr lot))
                                           (car lot))))
         ((length= lot 3) (setq seconds (+ (* 3600 (caddr lot))
                                           (* 60 (cadr lot))
                                           (car lot)))))))
    seconds))
#+end_src

#+caption[Formatting functions to open =org-yt= links]:
#+caption: Formatting functions to open =org-yt= links.
#+name: lst:org-yt-open-formatting
#+begin_src emacs-lisp
(defun org-yt-seconds-to-hms (seconds)
  "Convert seconds as integers to text of the form `12h34m56s'."
  (let ((h (/ seconds 3600))
        (m (/ (% seconds 3600) 60))
        (s (% seconds 60)))
    (concat (and (> h 0) (format "%dh" h))
            (if (> h 0)
                (format "%02dm" m)
              (and (> m 0) (format "%dm" m)))
            (if (or (> h 0) (> m 0))
                (format "%02ds" s)
              (format "%ds" s)))))

(defconst org-yt-start
  "https://www.youtube.com/watch?v=%s&t=%s"
  "Format string for `org-yt-format-open-url' to fill in ID and TIMING.")

(defconst org-yt-chunk
  "https://www.youtube.com/embed/%s?autoplay=1&start=%d&end=%d"
  "Format string for `org-yt-format-open-url' to fill in ID and TIMING.")

(defun org-yt-format-open-url (id timing)
  "Convert an \"yt\" type link to an URL for opening."
  (cond
   ((not timing)
    (format org-yt-start id "0s"))
   ((length= timing 1)
    (format org-yt-start id
            (org-yt-seconds-to-hms (org-yt-time-to-seconds (car timing)))))
   ((length= timing 2)
    (format org-yt-chunk id
            (org-yt-time-to-seconds (car timing))
            (org-yt-time-to-seconds (cadr timing))))))
#+end_src

#+caption[Formatting function for HTML export of =org-yt= links]:
#+caption: Formatting function for HTML export of =org-yt= links.
#+name: lst:org-yt-html-export-formatting
#+begin_src emacs-lisp
(defconst org-yt-iframe
  "<iframe
  frameborder=\"0\" width=\"600\" height=\"450\"
  src=\"https://www.youtube.com/embed/%s%s\"
  title=\"%s\"
  allowfullscreen></iframe>"
  "Format string for `org-yt-iframe' to fill in ID, TIMING, and TITLE.")

(defun org-yt-format-iframe (id timing title)
  "Convert an \"yt\" type link to an inline frame element for export to HTML."
  (format org-yt-iframe id
          (cond
           ((not timing) "")
           ((length= timing 1)
            (format "?start=%d" id (org-yt-time-to-seconds (car timing))))
           ((length= timing 2)
            (format "?start=%d&end=%d"
                    (org-yt-time-to-seconds (car timing))
                    (org-yt-time-to-seconds (cadr timing)))))
           title))
#+end_src

#+caption[Define an =org-link= type for =YouTube=]:
#+caption: Define an =org-link= type for =YouTube=.
#+name: lst:define-org-yt-link-type
#+begin_src emacs-lisp
(defun org-yt-open (path prefix)
  "Open an \"yt\" type link with `browse-url', `emms', or \"mpv\".
PATH is a string containing the video ID and optional timing information.
Open the link with `browse-url' if PREFIX else with `emms' or \"mpv\"."
  (let* ((parts (split-string path "[#]+" t))
         (id (car parts))
         (timing (cdr parts))
         (url (org-yt-format-open-url id timing)))
    (cond
     (prefix
      (browse-url url))
     ((require 'emms nil 'noerror)
      (emms-add-url url)
      (with-current-emms-playlist
        (save-excursion
          (emms-playlist-last)
          (emms-playlist-mode-play-current-track))))
     ((executable-find "mpv")
      (let ((display-buffer-alist
             `((,shell-command-buffer-name-async . (display-buffer-no-window)))))
        (async-shell-command (format "\"%s\" \"%s\"" url)))
      (message "Launched mpv with \"%s\"" url))
     (t
      (user-error "Can't open `%s': install `emms' and/or `mpv'" url)))))

(defun org-yt-export (path desc backend _)
  "Export an \"yt\" type link."
  (let* ((parts (split-string path "[#]+" t))
         (id (car parts))
         (timing (cdr parts)))
    (pcase backend
      (`html
       (org-yt-format-iframe id timing desc))
      (`latex
       (format "\\href{%s}{%s}" (org-yt-format-open-url id timing) desc))
      (_ id))))

(with-eval-after-load 'ol
  ;; https://bitspook.in/blog/extending-org-mode-to-handle-youtube-paths/
  (org-link-set-parameters "yt"
                           :follow #'org-yt-open
                           :export #'org-yt-export))
#+end_src

*** [[https://tecosaur.github.io/emacs-config/#translate-capital-keywords][Translate capital keywords (old) to lower case (new)]]
:PROPERTIES:
:CUSTOM_ID: sec:convert-upper-to-lower-case-keywords
:END:

#+caption[Convert upper to lower case keywords]:
#+caption: Convert upper to lower case keywords.
#+name: lst:convert-upper-to-lower-case-keywords
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  ;; https://tecosaur.github.io/emacs-config/#translate-capital-keywords
  (defun org-syntax-convert-keyword-case-to-lower ()
    "Convert all #+KEYWORDS to #+keywords."
    (interactive)
    (when (derived-mode-p 'org-mode)
      (save-excursion
        (goto-char (point-min))
        (let ((count 0)
              (case-fold-search nil))
          (while (re-search-forward "^[ \t]*#\\+[A-Z_]+" nil t)
            (unless (s-matches-p "RESULTS" (match-string 0))
              (replace-match (downcase (match-string 0)) t)
              (setq count (1+ count))))
          (message "Replaced %d keywords" count))))))
#+end_src

*** [[https://lists.gnu.org/archive/html/emacs-orgmode/2016-07/msg00394.html][Evaluate specific source blocks at load-time]]
:PROPERTIES:
:CUSTOM_ID: sec:load-time-specific-source-block-evaluation
:END:

[[https://emacs.stackexchange.com/questions/12938/how-can-i-evaluate-elisp-in-an-orgmode-file-when-it-is-opened][How to do load time source block evaluation]]

#+caption[Evaluate specific source blocks at load-time]:
#+caption: Evaluate specific source blocks at load-time.
#+name: lst:load-time-specific-source-block-evaluation
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun org-eval-named-blocks-with-infix (infix)
    "Evaluate all source blocks having INFIX in their name."
    (when (eq major-mode 'org-mode)
      (let ((blocks
             (org-element-map
                 (org-element-parse-buffer 'greater-element nil) 'src-block
               (lambda (block)
                 (when-let ((name (org-element-property :name block)))
                   (when (string-match-p infix name) block))))))
        (dolist (block blocks)
          (goto-char (org-element-property :begin block))
          (org-babel-execute-src-block)))))

  (defun org-eval-emacs-lisp-setup-blocks ()
    "Evaluate all source blocks having \"emacs-lisp-setup\" in their name."
    (interactive)
    (org-eval-named-blocks-with-infix "emacs-lisp-setup"))

  (defun org-eval-python-setup-blocks ()
    "Evaluate all source blocks having \"python-setup\" in their name."
    (interactive)
    (org-eval-named-blocks-with-infix "python-setup"))

  ;; Emacs looks for "Local variables:" after the last "newline-formfeed".
  (add-to-list 'safe-local-eval-forms '(org-eval-emacs-lisp-setup-blocks))
  (add-to-list 'safe-local-eval-forms '(org-eval-python-setup-blocks)))
#+end_src

*** [[info:org#LaTeX header and sectioning][Easy LaTeX preamble editing]]
:PROPERTIES:
:CUSTOM_ID: sec:easy-latex-preamble-editing
:END:

There are at least two ways (new and old) to edit the LateX preamble
=latex_header= and =latex-extra_header= export options easily in LaTeX source or
export blocks.  This [[info:org#Top][Org (info)]] file uses the new way, but keeps the old way for
backwards compatibility.

The new way -- exploiting an idea of [[https://www.matem.unam.mx/~omar/][Omar Antolin Camarena]] -- is to code new
[[info:org#Editing Source Code][<LANGUAGE>-modes]] allowing to edit in LaTeX mode and to export to LaTeX code with
[[info:org#LaTeX specific export settings][correct LaTeX preamble export setting prefixes]].  Here, are links to three posts
exposing his idea:
1. [[https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_for_use_in_both/][Export LaTeX macros to LaTeX and HTML/MathJax preambles (reddit)]],
2. [[https://www.reddit.com/r/orgmode/comments/5bi6ku/tip_for_exporting_javascript_source_block_to/][Export JavaScript source blocks to script tags in HTML (reddit)]],
3. [[https://emacs.stackexchange.com/questions/28301/export-javascript-source-block-to-script-tag-in-html-when-exporting-org-file-to][Export JavaScript source blocks to script tags in HTML (SX)]].
Listing [[lst:org-babel-latex-header-blocks]] implements this way by means of two
new [[info:org#Editing Source Code][<LANGUAGE>-modes]]: =latex-header= and =latex-extra-header=.

#+caption[New =<LANGUAGE>-modes= to edit the LaTeX preamble easily]:
#+caption: Add =latex-header= and =latex-extra-header=  language modes to edit
#+caption: LaTeX preamble =latex_header= and =latex_extra_header= export options
#+caption: easily.
#+name: lst:org-babel-latex-header-blocks
#+begin_src emacs-lisp :exports code :results silent
(with-eval-after-load 'emacs
  (defun prefix-all-lines (prefix body)
    (with-temp-buffer
      (insert body)
      (string-insert-rectangle (point-min) (point-max) prefix)
      (buffer-string)))

  (defun org-babel-execute:latex-extra-header (body _params)
    "Execute a block of LaTeX extra header lines with org-babel.
This function is called by `org-babel-execute-src-block' and
prefixes all lines with \"#+latex_extra_header: \"."
    (prefix-all-lines "#+latex_extra_header: " body))

  (defun org-babel-execute:latex-header (body _params)
    "Execute a block of LaTeX header lines with org-babel.
This function is called by `org-babel-execute-src-block' and
prefixes all lines with \"#+latex_header: \"."
    (prefix-all-lines "#+latex_header: " body))

  (defvar org-babel-default-header-args:latex-extra-header
    '((:exports . "results") (:results . "raw")))

  (defvar org-babel-default-header-args:latex-header
    '((:exports . "results") (:results . "raw")))

  (with-eval-after-load 'org-src
    (custom-set-variables
     '(org-src-window-setup 'current-window))

    (add-to-list 'org-src-lang-modes '("toml" . conf-toml))
    (add-to-list 'org-src-lang-modes '("latex-header" . latex))
    (add-to-list 'org-src-lang-modes '("latex-extra-header" . latex))))
#+end_src

The old way is to use a special export attribute as in the function
=org-latex-header-blocks-filter= in [[https://git.sr.ht/~bzg/org-contrib/tree/master/item/lisp/ox-extra.el][ox-extra.el]].  Apparently, nobody is using
this broken function (broken, since it relies on support only in org-mode before
=2014-11-11=).  Listing [[lst:org-latex-header-blocks-filter]] proposes a fix for
=org-latex-header-blocks-filter=.

#+caption[Convert marked LaTeX export blocks to LaTeX header lines]:
#+caption: Convert marked LaTeX export blocks to LaTeX header lines.
#+name: lst:org-latex-header-blocks-filter
#+begin_src emacs-lisp
(with-eval-after-load 'ox
  (defun org-latex-header-blocks-filter (backend)
    "Convert marked LaTeX export blocks to \"#+latex_header: \" lines.
The marker is a line \"#+header: :header yes\" preceding the block.

For instance, the LaTeX export block

,#+header: :header yes
,#+begin_export latex
% This line converts to a LaTeX header line.
,#+end_export

converts to

\"#+latex_header: % This line converts to a LaTeX header line.\"."
    (when (org-export-derived-backend-p backend 'latex)
      (let ((blocks
             (org-element-map
                 (org-element-parse-buffer 'greater-element nil) 'export-block
               (lambda (block)
                 (let ((type (org-element-property :type block))
                       (header (org-export-read-attribute :header block :header)))
                   (when (and (string= type "LATEX") (string= header "yes"))
                     block))))))
        (mapc (lambda (block)
                ;; Set point to where to insert LaTeX header lines
                ;; after deleting the block.
                (goto-char (org-element-property :post-affiliated block))
                (let ((lines
                       (split-string (org-element-property :value block) "\n")))
                  (delete-region (org-element-property :begin block)
                                 (org-element-property :end block))
                  (dolist (line lines)
                    (insert (concat "#+latex_header: "
                                    (replace-regexp-in-string "\\` *" "" line)
                                    "\n")))))
              ;; Reverse to go upwards to avoid wrecking the list of
              ;; block positions in the file that would occur in case
              ;; of going downwards.
              (reverse blocks)))))

  ;; Push the filter on the hook.
  (cl-pushnew #'org-latex-header-blocks-filter
              org-export-before-parsing-hook))
#+end_src

This file uses the new way, while keeping the old way for backwards
compatibility, because the new way feels less hackish than the old way.  A
practical difference is that new way source blocks (contrary to old way export
blocks) do not work in [[info:org#Export Settings][#+SETUPFILE: <FILE>]], but only in [[info:org#Export Settings][#+INCLUDE: <FILE>]] files.

*** [[info:org#Macro Replacement][Org-mode macro utilities]]
:PROPERTIES:
:CUSTOM_ID: sec:org-macro-utilities
:END:

Listing [[lst:by-backend-kbd-org-macro]] defines the Emacs Lisp utilities to
define the [[https://orgmode.org/][Org mode]] =kbd= macro in listing
[[lst:source-file-export-keyword-settings]].

#+attr_latex: :options breaklines
#+caption[Define Emacs Lisp utilities to define the =Org-mode= =kbd= macro]:
#+caption: Define Emacs Lisp utilities to define the =Org-mode= =kbd= macro.
#+name: lst:by-backend-kbd-org-macro
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (when (ensure-package-installation 'htmlize)
    (autoload 'htmlize-protect-string "htmlize" nil t))

  ;; https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html
  (defmacro by-backend (&rest body)
    "Help for org-export backend dependent execution."
    `(cl-case ',(bound-and-true-p org-export-current-backend) ,@body))

  (defun by-backend-kbd-org-macro (keys)
    "Help for an org-export backend dependent \"#+macro: kbd\"."
    (by-backend
     (html (format "@@html:<kbd>%s</kbd>@@" (htmlize-protect-string keys)))
     (latex (format "@@latex:\\colorbox{PowderBlue}{\\texttt{%s}}@@" keys)))))
#+end_src

*** [[info:org#Export Settings][File inclusion (info)]] and [[info:org#Noweb Reference Syntax][Noweb (info)]] trickery
:PROPERTIES:
:CUSTOM_ID: sec:file-inclusion-and-noweb
:END:

Note: [[https://list.orgmode.org/87sfisf31o.fsf@posteo.net/][How to include LaTeX packages in a LaTeX export block]].

Listing [[lst:source-file-export-keyword-settings]] shows the preamble lines of this
[[file:README.org]] file.  It lists the export keyword settings, the definition of
the [[https://orgmode.org/][Org mode]] =kbd= macro and the source block that generates part of the LaTeX
preamble.  Listing [[lst:latex-header-1]], [[lst:latex-header-2]], [[lst:latex-header-3]],
[[lst:latex-header-4]], and [[lst:latex-header-5]] show the LaTeX source blocks that
generate the LaTeX preamble.  All listings in this section exists thanks to [[info:org#Export Settings][file
inclusion (info)]] and [[info:org#Noweb Reference Syntax][noweb (info)]] trickery.

#+caption[Source file export keyword settings]:
#+caption: The preamble lines of README.org containing the export keyword
#+caption: settings, the definition of the Org-mode =kbd= macro, and the
#+caption: source block that generates part of the LaTeX preamble.
#+name: lst:source-file-export-keyword-settings
#+include: "README.org" src org :lines "1-17"

#+name: latex-header-1
#+begin_src latex :exports none
% Begin of the LaTeX preamble:
% See: https://list.orgmode.org/87o807r7fr.fsf@posteo.net/
% From: "Juan Manuel Macías" <maciaschain@posteo.net>
% To: orgmode <emacs-orgmode@gnu.org>
% Subject: [tip] Insert arbitrary LaTeX code at the beginning of any float environment
% Date: Sun, 08 May 2022 22:22:16 +0000
% Message-ID: <87o807r7fr.fsf@posteo.net>
% LuaLaTeX-, PdfLaTeX-, or XeTeX-COMPILER COMPATIBILITY:
% Prevent collisions by using font packages before compiler specific packages.
\usepackage{ifthen,ifluatex,ifxetex}
\ifthenelse{\boolean{luatex}}{
  \usepackage{fontspec}        % lualatex
}{\ifthenelse{\boolean{xetex}}{
    \usepackage{mathspec}        % xetex
  }{
    \usepackage[T1]{fontenc}     % pdflatex
    \usepackage[utf8]{inputenc}  % pdflatex
  }
}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{pifont}          % check mark (\ding{52}) and cross mark (\ding{56})
\usepackage{textcomp}        % \texttimes
\usepackage{wasysym}         % \diameter

% Org-mode REQUIREMENTS:
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{capt-of}
\usepackage{hyperref}
% End of the 1st LaTeX header block.
#+end_src

#+caption[LaTeX preamble: replacing the =Org-mode= default packages]:
#+caption: LaTeX preamble: replacing the =Org-mode= default packages.
#+name: lst:latex-header-1
#+begin_src latex :exports code :noweb yes
<<latex-header-1>>
#+end_src

#+name: latex-header-2
#+begin_src latex :exports none
% LANGUAGE:
\usepackage{babel}
\usepackage{fvextra}
\usepackage{csquotes}

% LISTS:
\usepackage{enumitem}
\setlist{noitemsep}

% LISTINGS:
% Section 2.6 of caption-eng.pdf (texdoc caption) explains that the sign
% of "skip" depends on the assumption "position=above" or "position=below".
% The assumption should match the real caption position in the LaTeX code.
\usepackage{caption}
\usepackage[newfloat]{minted}
\captionsetup[listing]{position=below,skip=0em}
\usemintedstyle{xcode}

% TABLES:
% https://tex.stackexchange.com/questions/341205/
% what-is-the-difference-between-tabular-tabular-and-tabularx-environments
% https://emacs.stackexchange.com/questions/26179/
% change-org-mode-table-style-just-for-latex-export
% https://tex.stackexchange.com/questions/468585/
% table-formatting-using-siunitx
\usepackage{booktabs}
\usepackage{colortbl}
\usepackage{tabularx}  % DANGER: beware of Org table :width and :align options!
% End of the 2nd LaTeX header block.
#+end_src

#+caption[LaTeX preamble: language, lists and floats]:
#+caption: LaTeX preamble: language, lists and floats.
#+name: lst:latex-header-2
#+begin_src latex :exports code :noweb yes
<<latex-header-2>>
#+end_src

#+name: latex-header-3
#+begin_src latex :exports none
% PAGE LAYOUT:
\usepackage{fancyhdr}
\usepackage{lastpage}
\usepackage[
  headheight=20mm,
  top=40mm,
  bottom=20mm,
  left=0.1\paperwidth,
  right=0.1\paperwidth,
  heightrounded,
  verbose,
]{geometry}

% TECHNICS:
\usepackage{siunitx}
\usepackage{tikz}
% End of the 3rd LaTeX header block.
#+end_src

#+caption[LaTeX preamble: page layout and technics]:
#+caption: LaTeX preamble: page layout.
#+name: lst:latex-header-3
#+begin_src latex :exports code :noweb yes
<<latex-header-3>>
#+end_src

#+name: latex-header-4
#+begin_src latex :exports none
% FLOAT BARRIERS:
% https://tex.stackexchange.com/questions/118662/use-placeins-for-subsections
% Make section an implicit float barrier:
\usepackage[section]{placeins}
% Make subsection an implicit float barrier:
\makeatletter
\AtBeginDocument{%
  \expandafter\renewcommand\expandafter\subsection\expandafter{%
    \expandafter\@fb@secFB\subsection
  }%
}
\makeatother
% Make subsubsection an implicit float barrier:
\makeatletter
\AtBeginDocument{%
  \expandafter\renewcommand\expandafter\subsubsection\expandafter{%
    \expandafter\@fb@secFB\subsubsection
  }%
}
% End of the 4th LaTeX header block.
#+end_src

#+caption[LaTeX preamble: float barriers]:
#+caption: LaTeX preamble: float barriers.
#+name: lst:latex-header-4
#+begin_src latex :exports code :noweb yes
<<latex-header-4>>
#+end_src

#+name: latex-header-5
#+begin_src latex :exports none
% FANCY HEADERS AND FOOTERS:
% Add fancy headers and footers to normal pages.
\pagestyle{fancy}
\fancyhf{}
\renewcommand{\footrulewidth}{0.4pt}
\fancyfoot[C]{\emph{
    Emacs setup for use with \LaTeX{}, Org, and Python -- Gerard Vermeulen
  }
}
\renewcommand{\headrulewidth}{0.4pt}
\fancyhead[L]{\includegraphics[height=1.8cm]{Org-mode-unicorn.png}}
\fancyhead[C]{
  Page: \thepage/\pageref{LastPage} \\
  \text{ } \\
  \text{ } \\
  DRAFT
}
\fancyhead[R]{\includegraphics[height=1.8cm]{Emacs-logo.png}}

% Add fancy header and footer to custom titlepage.
% https://tex.stackexchange.com/questions/506102/
% adding-header-and-footer-to-custom-titlepage
\fancypagestyle{titlepage}{%
  \fancyhf{}
  \renewcommand{\footrulewidth}{0.4pt}
  \fancyfoot[C]{\emph{
      Emacs setup for use with \LaTeX{}, Org, and Python -- Gerard Vermeulen}}
  \renewcommand{\headrulewidth}{0.4pt}
  \fancyhead[L]{\includegraphics[height=1.8cm]{Org-mode-unicorn.png}}
  \fancyhead[C]{
    \pageref{LastPage} pages \\
    \text{ } \\
    \text{ } \\
    DRAFT
  }
  \fancyhead[R]{\includegraphics[height=1.8cm]{Emacs-logo.png}}
}
% End of the 5th and last LaTeX header block.
#+end_src

#+caption[LaTeX preamble: fancy headers and footers]:
#+caption: LaTeX preamble: fancy headers and footers.
#+name: lst:latex-header-5
#+begin_src latex :exports code :noweb yes
<<latex-header-5>>
#+end_src

*** [[info:org#LaTeX specific export settings][Advanced LaTeX export settings]]
:PROPERTIES:
:CUSTOM_ID: sec:advanced-latex-export-settings
:END:

Listing [[lst:ox-latex-emacs-lisp-setup]] initializes the buffer local variables
=org-latex-classes=, =org-latex-title-command=, =org-latex-toc-command=, and
=org-latex-subtitle-format=.  Listing [[lst/title-page]] is a template to initialize
=org-latex-title-command=.  Type {{{kbd(C-h v org-latex-classes)}}}, {{{kbd(C-h
v org-latex-subtitle-format)}}}, {{{kbd(C-h v org-latex-title-command)}}}, and
{{{kbd(C-h v org-latex-toc-command)}}} to read how those variables control
exporting from Org-mode to LaTeX.

#+caption[Define buffer local =ox-latex= variables]:
#+caption: Define buffer local =ox-latex= variables.
#+header: :var title-page=lst/title-page
#+name: lst:ox-latex-emacs-lisp-setup
#+begin_src emacs-lisp :results silent :tangle no
(when (require 'ox-latex nil 'noerror)
  ;; https://emacs.stackexchange.com/questions/47347/
  ;; customizing-org-latex-title-command-to-edit-title-page
  (make-variable-buffer-local 'org-latex-classes)
  (cl-pushnew '("article-local"
                "\\documentclass[11pt]{article}
[NO-DEFAULT-PACKAGES]
[PACKAGES]
[EXTRA]"
                ("\\section{%s}" . "\\section*{%s}")
                ("\\subsection{%s}" . "\\subsection*{%s}")
                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                ("\\paragraph{%s}" . "\\paragraph*{%s}")
                ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
              org-latex-classes :key #'car :test #'equal)

  (make-variable-buffer-local 'org-latex-title-command)
  (setq org-latex-title-command (concat title-page))

  (make-variable-buffer-local 'org-latex-toc-command)
  (setq org-latex-toc-command "
\\tableofcontents\\label{toc}
\\listoflistings
\\listoftables
\\newpage
")

  (make-variable-buffer-local 'org-latex-subtitle-format)
  (setq org-latex-subtitle-format ""))
#+end_src

#+caption[Show a title-page example for =org-latex-title-command=]:
#+caption: Show a title-page example for =org-latex-title-command=.
#+name: lst/title-page
#+begin_src latex :exports code :results silent :tangle no
\begin{titlepage}
  %% https://tex.stackexchange.com/questions/506102/
  %% adding-header-and-footer-to-custom-titlepage
  \thispagestyle{titlepage}
  \begin{center}
    %% Title
    \begin{Huge}
      {\bf %t} \\
      \vspace{1em}
    \end{Huge}
    %% Author
    \begin{Large}
      {\bf %a} \\
      \vspace{1em}
    \end{Large}
  \end{center}
\end{titlepage}
#+end_src

*** [[https://orgmode.org/worg/dev/org-syntax-edited.html][Org Syntax]]
:PROPERTIES:
:CUSTOM_ID: sec:org-syntax
:END:

Two tools to grok how [[https://orgmode.org/worg/dev/org-element-api.html][Org mode parsing]] works are the [[https://orgmode.org/worg/dev/org-syntax-edited.html][Org Syntax]] specification
and the [[http://xahlee.info/emacs/emacs/elisp_parse_org_mode.html][Org mode parser tutorial]]. The [[https://orgmode.org/worg/dev/org-element-api.html][Org element parsing API]] boils down to three
functions:
1. The function [[https://orgmode.org/worg/dev/org-element-api.html#global][~org-element-parse-buffer~]] implements a fully recursive buffer
   parser that returns an abstract syntax tree.
2. The functions [[https://orgmode.org/worg/dev/org-element-api.html#local][~org-element-at-point~ and ~org-element-context~]] return
   information on the document structure around point either at the element
   level or at the object level in case of ~org-element-context~.
Listing [[lst:grok-org-element-tree]] improves the [[http://xahlee.info/emacs/emacs/elisp_parse_org_mode.html][Org mode parser tutorial]] by
defining interactive wrappers that pretty print the results of those
non-interactive =org-element= functions to an =Emacs-lisp= buffer.

#+caption[Grok how =org-element= parses your document]:
#+caption: Grok how =org-element= parses your document.
#+name: lst:grok-org-element-tree
#+begin_src emacs-lisp
(with-eval-after-load 'org-element
  (when (require 'pp nil 'noerror)
    (defconst grok-org-output
      "*Grok Org Element Output*"
      "Grok Org output buffer name.")

    (defun grok-org-element-at-point ()
      (interactive)
      (pp-display-expression
       (org-element-at-point) grok-org-output))

    (defun grok-org-element-context ()
      (interactive)
      (pp-display-expression
       (org-element-context) grok-org-output))

    (defun grok-org-element-parse-buffer ()
      (interactive)
      (let ((what (completing-read
                   "granularity: "
                   '(headline element greater-element object)
                   nil 'require-match)))
        (pp-display-expression
         (org-element-parse-buffer what) grok-org-output)))

    (defun grok-org-heading-components ()
      (interactive)
      (pp-display-expression
       (org-heading-components) grok-org-output))))
#+end_src

** Grammar, spelling, and style tools
:PROPERTIES:
:CUSTOM_ID: sec:writing-tools
:END:

*** [[info:emacs#Abbrevs][Abbrevs (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:writing-abbreviations
:END:

[[https://www.masteringemacs.org/][Mickey Peterson]] has posted [[https://www.masteringemacs.org/article/correcting-typos-misspellings-abbrev][Correcting Typos and Misspellings with Abbrev]] showing
how to use [[info:emacs#Keyboard Macros][Keyboard Macros (info)]] to exploit [[https://en.wikipedia.org/wiki/Wikipedia:Lists_of_common_misspellings/For_machines][Wikipedia's list of common
misspellings for machines]].  Listing [[lst:misspellings-abbrev]] defines his
keyboard macro under the name =misspellings-abrev=.  I have used those
directions to define src_emacs-lisp{global-abbrev-table} and to store it in
src_emacs-lisp{abbrev-file-name} for git management.  I can change the
abbreviation definitions in this file by means of:
1. Execute src_emacs-lisp{(edit-abbrevs)} to alter abbreviation definitions by
   editing an =*Abbrevs*= buffer.
2. Add, edit, or remove definitions of the form ="source" 1 "target"= under the
   global or a mode-specific table.
3. Execute src_emacs-lisp{(abbrev-edit-save-buffer)} to save all user
   abbreviation definitions in the current buffer.

#+caption[Definition of the =misspellings-abbrev= keyboard macro]:
#+caption: Definition of the =misspellings-abbrev= keyboard macro.
#+name: lst:misspellings-abbrev
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (defun browse-common-misspellings ()
    "Open the Wikipedia page of common misspellings for machines in EWW."
    (interactive)
    (eww (concat "https://en.wikipedia.org/wiki/Wikipedia"
                 ":Lists_of_common_misspellings/For_machines")))

  (fset 'misspellings-abbrev
        (kmacro-lambda-form
         [?\C-s ?- ?> return backspace backspace ?\C-k ?\C-x ?a ?i ?g ?\C-y return]
         0 "%d"))

  (setq-default abbrev-mode t))
#+end_src

Listing [[lst:word-games]] defines the =anagram-p= function that migth be used games.

#+caption[Word games]:
#+caption: Word games.
#+name: lst:word-games
#+begin_src emacs-lisp
;; https://funcall.blogspot.com/2022/07/lets-play-wordle.html
;; https://github.com/tabatkins/wordle-list
(defun anagram-p (evil vile)
  "Check whether strings EVIL and VILE are anagrams of each other."
  (if (string= evil vile)
      nil
    (string= (cl-sort evil #'<) (cl-sort vile #'<))))

;; https://funcall.blogspot.com/2020/01/palindromes-redux-and-sufficiently.html
;; https://irreal.org/blog/?p=8570
(defun palindrome-p (word)
  "Check whether the string WORD is a palindrome."
  (cl-do ((head 0 (1+ head))
          (tail (1- (length word)) (1- tail))
          (ok t))
      ((or (not ok) (>= head tail) ok)
    (setq ok (= (aref word head) (aref word tail))))))
#+end_src

*** [[https://dict.org/bin/Dict][DICT.org]]
:PROPERTIES:
:CUSTOM_ID: sec:writing-dict
:END:

Evaluating src_emacs-lisp{(dictionary)} connects to a local or remote =dictd=
server.  The following links explain how to configure and use =dictd=:
1. [[https://jpmens.net/2020/03/08/looking-up-words-with-dict/][Looking up words with DICT]]
2. [[https://www.rfc-editor.org/rfc/rfc2229.html][RFC 2229: A Dictionary Server Protocol]]
3. [[https://www.masteringemacs.org/article/wordsmithing-in-emacs][Wordsmithing in Emacs]]

I am using the following Debian Bullseye dictionaries on Darwin and Gentoo:
1. [[http://ftp.fr.debian.org/debian/pool/main/d/dict-devil/dict-devil_1.0-13.1_all.deb][dict-devil_1.0-13.1_all.deb]]
2. [[http://ftp.fr.debian.org/debian/pool/main/d/dict-foldoc/dict-foldoc_20201018-1_all.deb][dict-foldoc_20201018-1_all.deb]]
3. [[http://ftp.fr.debian.org/debian/pool/main/d/dict-gcide/dict-gcide_0.48.5+nmu1_all.deb][dict-gcide_0.48.5+nmu1_all.deb]]
4. [[http://ftp.fr.debian.org/debian/pool/main/d/dict-jargon/dict-jargon_4.4.7-3.1_all.deb][dict-jargon_4.4.7-3.1_all.deb]]
5. [[http://ftp.fr.debian.org/debian/pool/main/v/vera/dict-vera_1.24-1_all.deb][dict-vera_1.24-1_all.deb]]
6. [[http://ftp.fr.debian.org/debian/pool/main/w/wordnet/dict-wn_3.0-36_all.deb][dict-wn_3.0-36_all.deb]]

#+caption[Resource file for =dict= on =Darwin=]:
#+caption: Resource file for =dict= on =Darwin=.
#+name: lst:darwin-dict-resource-file
#+header: :tangle (if (eq 'darwin system-type) "~/.dictrc" "no")
#+begin_src conf
# https://jpmens.net/2020/03/08/looking-up-words-with-dict/
server 127.0.0.1 {
   port 2628
}
# Local Variables:
# mode: conf-unix
# End:
#+end_src

#+caption[Make a configuration file for =dictd= on =Darwin=]:
#+caption: Make a configuration file for =dictd= on =Darwin=.
#+name: lst:dictd-configuration-file
#+begin_src shell :eval (if (eq 'darwin system-type) "yes" "never") :results silent
cat > ~/.dictd.conf <<EOF
# https://www.masteringemacs.org/article/wordsmithing-in-emacs
database devil {
   data "${HOME}/.local/share/dictd/devil.dict.dz"
   index "${HOME}/.local/share/dictd/devil.index"
}
database foldoc {
   data "${HOME}/.local/share/dictd/foldoc.dict.dz"
   index "${HOME}/.local/share/dictd/foldoc.index"
}
database gcide {
   data "${HOME}/.local/share/dictd/gcide.dict.dz"
   index "${HOME}/.local/share/dictd/gcide.index"
}
database jargon {
   data "${HOME}/.local/share/dictd/jargon.dict.dz"
   index "${HOME}/.local/share/dictd/jargon.index"
}
database vera {
   data "${HOME}/.local/share/dictd/vera.dict.dz"
   index "${HOME}/.local/share/dictd/vera.index"
}
database wn {
   data "${HOME}/.local/share/dictd/wn.dict.dz"
   index "${HOME}/.local/share/dictd/wn.index"
}
EOF
#+end_src

#+caption[Run =dictd= in debug mode on =Darwin=]:
#+caption: Run =dictd= in debug mode on =Darwin=.
#+name: lst:darwin-dictd-launch
#+begin_src shell :eval never :tangle no
# https://jpmens.net/2020/03/08/looking-up-words-with-dict/
/usr/local/sbin/dictd \
    --config .dictd.conf \
    --verbose \
    --logfile .dictd.log \
    -d nodetach
#+end_src

*** [[https://github.com/tecosaur/lexic#readme][Emacs LEXICal information viewer]]                               :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:writing-lexic
:header-args:emacs-lisp: :tangle no
:END:

The [[https://github.com/tecosaur/lexic#readme][Emacs LEXICal information viewer]] is a front-end for offline dictionary,
etymology, or thesaurus back-ends (currently limited to [[https://en.wikipedia.org/wiki/Sdcv][sdcv]]).  Listing
[[lst:configure-lexic]] configures [[https://github.com/tecosaur/lexic#readme][lexic]].

#+attr_latex: :options breaklines
#+caption[Configure =lexic=]:
#+caption: Configure =lexic=.
#+name: lst:configure-lexic
#+begin_src emacs-lisp
(when (ensure-package-installation 'lexic)
  ;; http://download.huzheng.org/fr/
  ;; https://polyglotte.tuxfamily.org/doku.php?id=donnees:dicos_bilingues
  ;; http://download.huzheng.org/dict.org/stardict-dictd-web1913-2.4.2.tar.bz2
  ;; http://download.huzheng.org/dict.org/stardict-dictd_www.dict.org_gcide-2.4.2.tar.bz2
  (with-eval-after-load 'lexic
    (if-let ((lpp (executable-find "sdcv")))
        (custom-set-variables
         '(lexic-program-path lpp)
         '(lexic-dictionary-alist '(("full" . t)))
         ;; sdcv --data-dir .local/share -l
         '(lexic-dictionary-list
           '("Webster's Revised Unabridged Dictionary (1913)"
             "dictd_www.dict.org_gcide"))
         '(lexic-dictionary-path "~/.local/share"))
    (message "`lexic' fails to find the `sdcv' executable"))))
#+end_src

*** [[https://wordnet.princeton.edu/][Wordnet]]                                                        :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:writing-wordnet
:END:

The [[https://github.com/gromnitsky/wordnut#readme][wordnut]] package is a major mode interface to [[https://wordnet.princeton.edu/][Wordnet]], a lexical database for
the English language.  Listing [[lst:check-wordnut]] checks whether the system meets
the [[https://github.com/gromnitsky/wordnut#readme][wordnut]] prerequisites.

#+caption[System check for =wordnut=]:
#+caption: System check for =wordnut=.
#+name: lst:check-wordnut
#+begin_src emacs-lisp :tangle no
(when (ensure-package-installation 'wordnut)
  (with-eval-after-load 'wordnut
    (if-let ((wn (executable-find "wn")))
        (custom-set-variables
         '(wordnut-cmd wn))
      (message "`wordnut' fails to find the `wn' executable"))))
#+end_src

*** [[https://github.com/bnbeckwith/writegood-mode#readme][Writegood mode]]
:PROPERTIES:
:CUSTOM_ID: sec:writing-writegood-mode
:END:

[[https://github.com/bnbeckwith/writegood-mode#readme][Writegood mode]] is a minor mode to aid in finding common writing problems.  The post
[[http://matt.might.net/articles/shell-scripts-for-passive-voice-weasel-words-duplicates/][Matt Might's "My Ph.D. advisor rewrote himself in bash" scripts]] inspired this mode.
Listing [[lst:configure-writegood-mode]] configures [[https://github.com/bnbeckwith/writegood-mode#readme][writegood mode]].

#+caption[Configure =writegood-mode=]:
#+caption: Configure =writegood-mode=.
#+name: lst:configure-writegood-mode
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'writegood-mode)
           (fboundp 'writegood-mode))
  (global-set-key (kbd "C-c g") #'writegood-mode))
#+end_src

* Programming Tools
:PROPERTIES:
:CUSTOM_ID: sec:programming-tools
:END:

** [[info:eglot#Top][Eglot (info)]] or [[https://github.com/joaotavora/eglot][Eglot]]
:PROPERTIES:
:CUSTOM_ID: sec:eglot
:END:

[[https://github.com/joaotavora/eglot#readme][Emacs polyGLOT (Eglot)]] is an Emacs language-server-protocol client that stays
out of the way.  The following listings contribute to a programming language
mode independent [[https://github.com/joaotavora/eglot][Eglot]] configuration:
1. Listing [[lst:minimal-eglot-setup][minimal Eglot setup]] ensures installation of [[https://github.com/joaotavora/eglot][Eglot]], shows how to get
   debug information from the [[https://github.com/python-lsp/python-lsp-server][Python LSP server]], and adds key bindings to
   =eglot-mode-keymap=.
2. Listing [[lst:help-setup-org-src-mode-for-eglot]] and
   [[lst:setup-python-org-src-mode-for-eglot]] try to prepare any =org-src-mode=
   buffers for use with [[https://github.com/joaotavora/eglot][Eglot]].  They are a refactored implementation of the post
   [[https://www.reddit.com/r/emacs/comments/w4f4u3/using_rustic_eglot_and_orgbabel_for_literate/][Using rustic, eglot, and org-babel with LSP support in Emacs]] for my use with
   Python.
3. Listing [[lst:narrow-format-all-python]] defines a function to format only the
   narrowed region of Python =org-src-mode= blocks prepared by means of the code
   in listing [[lst:setup-python-org-src-mode-for-eglot]]. *Do not use*
   =format-all-buffer= *on such buffers*, since =format-all-buffer= does not
   handle the narrowing.
4. Listing [[lst:eglot-maybe-ensure]] starts [[https://github.com/joaotavora/eglot][Eglot]] in case of proper programming
   modes and proper directory local variables (meaning in presence of a proper
   file [[info:emacs#Directory Variables][.dir-locals.el]] in the root directory of any project using proper
   programming modes).

#+caption[Ensure =eglot= installation with minimal setup]:
#+caption: Ensure =eglot= installation with minimal setup.
#+name: lst:minimal-eglot-setup
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (when (version< emacs-version "29.0.0")
    (ensure-package-installation 'eglot))

  ;; Replace `nil' with `t' for debugging.
  (when nil
    (when (require 'eglot nil t)
      (setq eglot-server-programs
            `(((python-ts-mod python-mode)
               . ,(eglot-alternatives
                   '(("pylsp" "-vv")
                     ("ruff-lsp"))))))))

  (with-eval-after-load 'eglot
    (define-key eglot-mode-map (kbd "C-c n") 'flymake-goto-next-error)
    (define-key eglot-mode-map (kbd "C-c p") 'flymake-goto-prev-error)
    (define-key eglot-mode-map (kbd "C-c r") 'eglot-rename)))
#+end_src

#+caption[Help to setup any =org-src-mode= buffers for =eglot=]:
#+caption: Help to setup any =org-src-mode= buffers for =eglot=.
#+name: lst:help-setup-org-src-mode-for-eglot
#+begin_src emacs-lisp
(when (fboundp 'eglot-ensure)
  (defcustom eglot-maybe-ensure-modes '(python-mode)
    "Modes where maybe `eglot-ensure' should be or has been called.
This may be in the case of proper directory local variables or in
the case of proper `org-src-mode' buffers.")

  ;; https://www.reddit.com/r/emacs/comments/w4f4u3
  ;; /using_rustic_eglot_and_orgbabel_for_literate/
  (defun eglot-org-babel-edit-prep (info)
    "Try to setup an `org-mode-src' buffer to make `eglot-ensure' succeed.
INFO has a form similar to the return value of
`org-babel-get-src-block-info'.  Try to load the tangled file
into the `org-src-mode' buffer as well as to narrow the region to
the Org-mode source block code before calling `eglot-ensure'."
    (unless (bound-and-true-p org-src-mode)
      (user-error "Buffer %s is no `org-src-mode' buffer" (buffer-name)))
    (let ((mark (point))
          (body (nth 1 info))
          (filename (cdr (assq :tangle (nth 2 info)))))
      (when (string= filename "no")
        (user-error "Org source block has no tangled file"))
      (setq filename (expand-file-name filename))
      (unless (file-readable-p filename)
        (user-error "Tangled file %s is not readable" filename))
      (with-temp-buffer
        (insert-file-contents filename 'visit nil nil 'replace)
        (unless (search-forward body nil 'noerror)
          (user-error "Org source block does not occur in tangled file %s"
                      filename))
        (when (search-forward body nil 'noerror)
          (user-error "Org source block occurs twice or more in tangled file %s"
                      filename)))
      (goto-char (point-min))
      (insert-file-contents filename 'visit nil nil 'replace)
      (let ((max-point (search-forward body))
            (min-point (search-backward body)))
        (narrow-to-region min-point max-point))
      (goto-char mark)
      (eglot-ensure))))
#+end_src

#+caption[Setup Python =org-src-mode= buffers for =eglot=]:
#+caption: Setup Python =org-src-mode= buffers for =eglot=.
#+name: lst:setup-python-org-src-mode-for-eglot
#+begin_src emacs-lisp
(when (fboundp 'eglot-ensure)
  ;; https://www.reddit.com/r/emacs/comments/w4f4u3
  ;; /using_rustic_eglot_and_orgbabel_for_literate/
  (defun undo-eglot-org-babel-edit-prep()
    "Undo the `eglot' setup by deleting the text hidden by narrowing.
This is to advice `org-edit-src-exit' and `org-edit-src-save'."
    (when (and (bound-and-true-p org-src-mode)
               (buffer-file-name)
               (apply #'derived-mode-p eglot-maybe-ensure-modes))
      (save-excursion
        (goto-char (point-min))
        (save-restriction
          (widen)
          (delete-region (point-min) (point)))
        (goto-char (point-max))
        (save-restriction
          (widen)
          (delete-region (point) (point-max))))))

  (defun org-babel-edit-prep:python (info)
    (eglot-org-babel-edit-prep info))

  (advice-add 'org-edit-src-exit :before #'undo-eglot-org-babel-edit-prep)
  (advice-add 'org-edit-src-save :before #'undo-eglot-org-babel-edit-prep))
#+end_src

#+caption[Experimental =narrow-format-all:python=]:
#+caption: Experimental =narrow-format-all:python=.
#+name: lst:narrow-format-all-python
#+begin_src emacs-lisp
(when (and (fboundp 'eglot-ensure)
           (fboundp 'format-all-buffer))
  (defun narrow-format-all:python ()
    "Format narrowed Python `org-src-mode' buffers correctly.
Use this function instead of `format-all-buffer' on `org-babel-edit-prep:python'
prepared buffers."
    (interactive)
    (when (eq major-mode 'python-mode)
      (let ((source-min (point-min))
            (source-max (point-max))
            (source (current-buffer))
            (target (get-buffer-create "*narrow-format-all:python*")))
        (with-current-buffer target
          (barf-if-buffer-read-only)
          (erase-buffer)
          (save-excursion
            (insert-buffer-substring-no-properties
             source source-min source-max))
          (python-mode)
          (setq-local format-all-formatters '(("Python" black)))
          (format-all-buffer)
          (let ((target-min (point-min))
                (target-max (point-max)))
            (with-current-buffer source
              (erase-buffer)
              (save-excursion
                (insert-buffer-substring-no-properties
                 target target-min target-max)))))))))
#+end_src

#+caption[Start =eglot= in case of a proper =dir-local-variables-alist=]:
#+caption: Start =eglot= in case of a proper =dir-local-variables-alist=.
#+name: lst:eglot-maybe-ensure
#+begin_src emacs-lisp
(when (fboundp 'eglot-ensure)
  (defun eglot-maybe-ensure ()
    (when (and (apply #'derived-mode-p eglot-maybe-ensure-modes)
               (assoc 'eglot-workspace-configuration dir-local-variables-alist))
      (eglot-ensure)))

  ;; The two hooks `after-change-major-mode-hook' and
  ;; `hack-local-variables-hook' are OK, but language mode hooks like
  ;; `python-mode-hook' are not.
  (add-hook 'after-change-major-mode-hook #'eglot-maybe-ensure))
#+end_src

** [[https://github.com/lassik/emacs-format-all-the-code#readme][Format-all]]
:PROPERTIES:
:CUSTOM_ID: sec:format-all
:END:

Listing [[lst:configure-format-all]]:
1. Configures [[https://github.com/lassik/emacs-format-all-the-code#readme][format-all]] which is a package that provides an universal interface
   to code formatters of more than 60 computer languages.
2. Adds =format-all-org-babel-post-tangle= to =org-babel-post-tangle-hook= to
   format tangled Python code.

#+caption[Configure =format-all=]:
#+caption: Configure =format-all=.
#+name: lst:configure-format-all
#+begin_src emacs-lisp
;; https://github.com/lassik/emacs-format-all-the-code#readme
;; https://ianyepan.github.io/posts/format-all/
;; https://jamesaimonetti.com/posts/formatting-tangled-output-in-org-mode/
(when (ensure-package-installation 'format-all)
  ;; (with-eval-after-load 'prog-mode
  ;;   (when (autoload 'format-all-ensure-formatter "format-all")
  ;;     (add-hook 'prog-mode-hook #'format-all-ensure-formatter)))
  (with-eval-after-load 'ob-tangle
    (add-hook
     'org-babel-post-tangle-hook
     (defun format-all-org-babel-post-tangle ()
       (when (derived-mode-p 'python-mode)
         (setq-local format-all-formatters '(("Python" black)))
         (format-all-buffer)
         (save-buffer)
         (message "Saved reformatted tangled buffer `%s'" (buffer-file-name)))))))
#+end_src

** [[info:flymake#Top][Flymake (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:flymake
:END:

Flymake is an universal on-the-fly syntax checker for Emacs. It is a requirement
of [[https://github.com/joaotavora/eglot][eglot]], but you can use it without [[https://github.com/joaotavora/eglot][eglot]] for instance in [[https://git.savannah.gnu.org/cgit/emacs.git/tree/lisp/progmodes/python.el][python-mode]] buffers
that do not visit a file.

* Programming Modes
:PROPERTIES:
:CUSTOM_ID: sec:programming-languages
:END:

** [[https://dept-info.labri.fr/~strandh/Teaching/PFS/Common/Strandh-Tutorial/Dir-symbolic.html][Common Lisp programming]]
:PROPERTIES:
:CUSTOM_ID: sec:common-lisp-programming
:END:

Listing [[lst:configure-sly]] configures the [[info:sly#Top][Sly (info)]] Common Lisp IDE for Emacs
for use with [[http://www.sbcl.org/][Steel Bank Common Lisp (sbcl)]]:
1. It configures =sly-default-lisp= and =sly-lisp-implementations= as in the
   ~sly~ documentation string instead of in the [[info:sly#Multiple Lisps][multiple lisps (info)]] manual.
2. It ensures the [[info:sly#Auto-SLY][automatic connection to the lisp server (info)]] when opening a
   Common Lisp file.
3. It configures searching documentation in the [[http://www.lispworks.com/documentation/HyperSpec/Front/][Common Lisp HyperSpec]] according
   to the [[info:sly#Basic customization][basic customization (info)]] manual.
Finally, listing [[lst:configure-sly]] uses a technique to [[info:sly#Loading Slynk faster][load Slynk faster (info)]]
by means of a custom core file in src_emacs-lisp{no-littering-var-directory}.
Listing [[lst:sbcl-core-for-sly]] tangles to a script to dump such a [[http://www.sbcl.org/][SBCL]] core.

#+caption[Configure =sly=]:
#+caption: Configure =sly=.
#+name: lst:configure-sly
#+begin_src emacs-lisp
(when (ensure-package-installation 'sly)
  (with-eval-after-load 'sly
    (custom-set-variables
     ;; Customize `sly-default-lisp' instead of `inferior-lisp-program',
     ;; because `sly' uses `inferior-lisp-program' only as a backwards
     ;; compatibility fallback option.
     '(sly-default-lisp 'sbcl)
     `(sly-lisp-implementations
       '((sbcl (,(executable-find "sbcl")
                "--core"
                ,(no-littering-expand-var-file-name "sbcl.core-for-sly"))))))

    (add-hook 'sly-mode-hook
              (defun on-sly-mode-hook ()
                (unless (sly-connected-p)
                  (save-excursion (sly)))))

    (cond
     ((eq system-type 'darwin)
      (setq common-lisp-hyperspec-root
            "file:///usr/local/share/doc/hyperspec/HyperSpec/")
      (setq common-lisp-hyperspec-symbol-table
            (concat common-lisp-hyperspec-root "Data/Map_Sym.txt")))
     ((eq system-type 'gnu/linux)
      (setq common-lisp-hyperspec-root
            "file:///usr/share/doc/hyperspec-7.0/HyperSpec/"))
     (t (message "Default Common Lisp HyperSpec access")))

    (define-key sly-prefix-map (kbd "M-h") #'sly-documentation-lookup)))
#+end_src

#+caption[Script to dump a SBCL core for the Sly Common Lisp IDE]:
#+caption: Script to dump a SBCL core for the Sly Common Lisp IDE.
#+header: :tangle-mode (identity #o755)
#+name: lst:sbcl-core-for-sly
#+begin_src shell :noeval :tangle ~/bin/sbcl.core-for-sly
#!/bin/sh

sbcl <<EOF
(mapc 'require '(sb-bsd-sockets sb-posix sb-introspect sb-cltl2 asdf))
(save-lisp-and-die "sbcl.core-for-sly")
EOF

# Local Variables:
# mode: shell-script
# sh-indentation: 2
# sh-basic-offset: 2
# End:
#+end_src

*** [[https://courses.cs.northwestern.edu/325/][CS 325 AI Programming]]
:PROPERTIES:
:CUSTOM_ID: sec:cs-325-ai-programming
:END:

The [[https://courses.cs.northwestern.edu/325/][CS 325 AI Programming]] course allows to learn Common Lisp by self-study and
the page [[https://courses.cs.northwestern.edu/325/admin/lisp-setup.php][CS 325: Setting up Lisp]] gives instructions how to:
1. [[https://courses.cs.northwestern.edu/325/admin/lisp-setup.php#lisp][Download and install common lisp]].
2. [[https://courses.cs.northwestern.edu/325/admin/lisp-setup.php#quicklisp][Install Quicklisp]].
3. [[https://courses.cs.northwestern.edu/325/admin/lisp-setup.php#install-325][Install the CS325 library]].

*** [[https://www.quicklisp.org/][Quicklisp]]
:PROPERTIES:
:CUSTOM_ID: sec:quicklisp
:END:

[[https://www.quicklisp.org/][Quicklisp]] is a library manager for Common Lisp.  Listing
[[lst:download+verify-quicklisp]] downloads the [[https://www.quicklisp.org/][Quicklisp]] file and verifies its
signature to prevent tampering.  Listing [[lst:bootstrap-quicklisp]] tangles to a
shell script allowing to bootstrap [[https://www.quicklisp.org/][Quicklisp]] with [[http://www.sbcl.org/][SBCL]].  Listing
[[lst:quicklisp-sbclrc-file]] tangles to the a [[http://www.sbcl.org/][SBCL]] resource file with [[https://www.quicklisp.org/][Quicklisp]]
support.

#+caption[Download and verify =quicklisp=]:
#+caption: Download and verify =quicklisp=.
#+name: lst:download+verify-quicklisp
#+begin_src shell :dir ~ :results none :tangle no
curl -sS -O https://beta.quicklisp.org/quicklisp.lisp
curl -sS -O https://beta.quicklisp.org/quicklisp.lisp.asc
curl -sS -O https://beta.quicklisp.org/release-key.txt
gpg --import release-key.txt
gpg --verify quicklisp.lisp.asc quicklisp.lisp
#+end_src

#+caption[Bootstrap =quicklisp=]:
#+caption: Bootstrap =quicklisp=.
#+header: :tangle-mode (identity #o755)
#+name: lst:bootstrap-quicklisp
#+begin_src shell :noeval :tangle ~/bin/quicklisp-sbcl-bootstrap
#!/bin/sh

sbcl --load ~/quicklisp.lisp <<EOF
(quicklisp-quickstart:install)
(quit)
EOF

# Local Variables:
# mode: shell-script
# sh-indentation: 2
# sh-basic-offset: 2
# End:
#+end_src

#+caption[A =quicklisp= sbclrc file]:
#+caption: A =quicklisp= sbclrc file.
#+name: lst:quicklisp-sbclrc-file
#+begin_src lisp :eval never-export :tangle ~/.sbclrc
;;; Hey Emacs, this is my -*- lisp -*- .sbclrc file.
#-quicklisp
(let ((quicklisp-init (merge-pathnames "quicklisp/setup.lisp"
                                       (user-homedir-pathname))))
  (when (probe-file quicklisp-init)
    (load quicklisp-init)))
#+end_src

** [[info:eintr#Top][Emacs Lisp Programming (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-lisp-programming
:END:

Here is a list of links describing how to program and debug [[info:elisp#Top][Emacs Lisp (info)]] code:
1. [[https://www.masteringemacs.org/article/evaluating-elisp-emacs][Evaluating Elisp in Emacs]]
2. [[https://endlessparentheses.com/debugging-emacs-lisp-part-1-earn-your-independence.html][Debugging Elisp Part 1: Earn your independence]]
3. [[https://endlessparentheses.com/debugging-elisp-part-2-advanced-topics.html][Debugging Elisp Part 2: Advanced topics]]
4. [[http://xahlee.info/talk_show/xah_talk_show_2022-01-20.html][Xah talk show: Elisp coding: xah-add-space-after-comma]]
5. [[http://xahlee.info/talk_show/xah_talk_show_2022-01-22.html][Xah talk show: Elisp coding: narrow-to-region, sort-lines, hilight-unicode]]

Ref. [cite:@Monnier.ACM-PL.4.1] exposes the evolution of Emacs Lisp and explains
many Emacs Lisp idioms.

Listing [[lst:setup-ielm][setup ielm]] customizes the [[https://wikemacs.org/wiki/IELM][Interactive Emacs Lisp Mode]] for better
interoperability with [[https://smartparens.readthedocs.io/en/latest/][Smartparens]]: get help on the key bindings by means of
src_emacs-lisp{(describe-function 'inferior-emacs-lisp-mode)}.

#+caption[Setup =ielm=]:
#+caption: Setup =ielm=.
#+name: lst:setup-ielm
#+begin_src emacs-lisp
(with-eval-after-load 'ielm
  (if (version< "29.0.0" emacs-version)
      (setopt ielm-dynamic-return nil)
    (custom-set-variables
     '(ielm-dynamic-return nil))))
#+end_src

** [[https://fennel-lang.org/][Fennel Programming]]
:PROPERTIES:
:CUSTOM_ID: sec:fennel-programming
:END:

Here is a list of links describing how to install and setup [[https://fennel-lang.org/][Fennel]] and how to
install and use [[https://gitlab.com/andreyorst/ob-fennel][ob-fennel]] with the [[https://love2d.org/][LÖVE 2D game engine]]:
1. [[https://fennel-lang.org/][The Fennel Programming Language]]
2. [[https://fennel-lang.org/setup][Setting up Fennel]]
3. [[https://gitlab.com/andreyorst/ob-fennel][Org Babel support for the Fennel language: ob-fennel]]
4. [[https://andreyorst.gitlab.io/posts/2022-09-26-reproducible-research-with-org-mode-fennel-and-love/][Reproducible Research with Org Mode, Fennel, and LÖVE]]

#+caption[Install =fennel-mode= and =ob-fennel= when =fennel= is an executable]:
#+caption: Install =fennel-mode= and =ob-fennel= when =fennel= is an executable.
#+name: lst:install-ob-fennel-mode
#+begin_src emacs-lisp
(when (and (executable-find "fennel")
           (ensure-package-installation 'fennel-mode 'quelpa))
  (unless (package-installed-p 'ob-fennel)
    (quelpa '(ob-fennel :repo "andreyorst/ob-fennel" :fetcher gitlab)))
  (ensure-package-selection 'ob-fennel))
#+end_src

#+caption[Fennel example]:
#+caption: Fennel example.
#+header: :var x=10 y=20
#+name: lst:fennel-example
#+begin_src fennel :eval never-export :results silent :session fennel
(+ x y)
#+end_src

#+caption[Install =Fennel= with luarocks on Darwin]:
#+caption: Install =Fennel= with luarocks on Darwin.
#+name: lst:install-fennel-on-darwin
#+begin_src shell :eval never :results silent :tangle no
luarocks \
    install --local readline \
    HISTORY_INCDIR=/usr/local/opt/readline/include \
    HISTORY_DIR=/usr/local/opt/readline/lib
#+end_src

** [[https://www.lua.org/][Lua Programming]]
:PROPERTIES:
:CUSTOM_ID: sec:lua-programming
:END:

#+caption[Install =lua-mode= in case of =Lua=]:
#+caption: Install =lua-mode= in case of =Lua=.
#+name: lst:install-lua-mode
#+begin_src emacs-lisp
(when (and (executable-find "lua")
           (ensure-package-installation 'company-lua 'lua-mode)))
#+end_src

#+caption[Lua example]:
#+caption: Lua example.
#+name: lst:lua-example
#+begin_src lua :results silent :var x=10 y=20
return (x+y)
#+end_src

** [[info:maxima#Top][Maxima Programming (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:maxima-programming
:END:

Listing [[lst:configure-maxima]] configures [[https://gitlab.com/sasanidas/maxima][Maxima Mode]]. The following list contains
more information:
1. [[https://gitlab.com/sasanidas/maxima][Maxima Mode]] is an Emacs interface to the computer algebra system [[https://en.wikipedia.org/wiki/Maxima_(software)][Maxima]].
2. [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-maxima.html][Maxima Source Code Blocks in Org Mode]] shows how to use [[https://en.wikipedia.org/wiki/Maxima_(software)][Maxima]] in [[https://orgmode.org/][Org Mode]].
3. [[https://home.csulb.edu/~woollett/mbe.html][Maxima By Example]] is a tutorial for [[https://en.wikipedia.org/wiki/Maxima_(software)][Maxima]].
Listing [[lst:maxima-example]] is a minimal example of how to use how to use [[https://en.wikipedia.org/wiki/Maxima_(software)][Maxima]]
in [[https://orgmode.org/][Org Mode]].

#+caption[Configure =maxima=]:
#+caption: Configure =maxima=.
#+name: lst:configure-maxima
#+begin_src emacs-lisp
(when (ensure-package-installation 'maxima 'company-maxima)
  (add-hook 'maxima-mode-hook #'maxima-hook-function)
  (add-hook 'maxima-inferior-mode-hook #'maxima-hook-function)
  (add-to-list 'auto-mode-alist
               (cons "\\.mac\\'" 'maxima-mode))
  (add-to-list 'interpreter-mode-alist
               (cons "maxima" 'maxima-mode)))
#+end_src

#+caption[Maxima example]:
#+caption: Maxima example.
#+name: lst:maxima-example
#+begin_src maxima :exports code :results silent
print(1+1);
#+end_src

** [[https://www.seas.upenn.edu/~chaoliu/2017/09/01/python-programming-in-emacs/][Python programming]]
:PROPERTIES:
:CUSTOM_ID: sec:python-programming
:END:
The [[https://www.emacswiki.org/emacs/PythonProgrammingInEmacs][Python Programming in Emacs]] wiki page lists options to enhance Emacs's
built-in ~python-mode~. Here, the focus is on three packages:
1. [[https://github.com/joaotavora/eglot][Eglot - Emacs polyGLOT: an Emacs LSP client that stays out of your way]].  The
   maintainer also contributes to Emacs itself and has a deep understanding of
   [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]].  He refuses to add new features without seeing how they fit
   into [[https://sheer.tj/the_way_of_emacs.html][the Way of Emacs]] as this discussion on [[https://github.com/joaotavora/eglot/issues/523][org-mode source code blocks]]
   shows.
2. [[https://jedi.readthedocs.io/en/latest/][Jedi]] is a static analysis tool for Python that is typically used in plugins
   for editors or integrated development environments.  Jedi has a focus on
   autocompletion and object definition lookup functionality.
3. [[https://github.com/astoff/code-cells.el#readme][Code-cells]] allows to edit [[https://ipython.org/notebook.html][IPython or Jupyter notebooks]] in Emacs with help
   from either [[https://github.com/mwouts/jupytext][Jupytext]] or [[https://pandoc.org/][Pandoc]].

Here are links covering how to integrate Emacs, Python and a Python LSP
server, before plunging into the configuration steps:
1. [[https://taingram.org/blog/emacs-lsp-ide.html][Building Your Own Emacs IDE with LSP]]
2. [[https://rgoswami.me/posts/emacs-lang-servers/][Doom Emacs and Language Servers]]
3. [[https://ddavis.io/posts/eglot-python-ide/][Eglot based Emacs Python IDE]]
4. [[https://www.mattduck.com/lsp-python-getting-started.html][Getting started with lsp-mode for Python]]
5. [[https://ddavis.io/posts/python-emacs-3/][Python & Emacs, Take 3]]
6. [[https://ddavis.io/posts/emacs-python-lsp/][Python with Emacs: py(v)env and lsp-mode]]

*** [[https://git.savannah.gnu.org/cgit/emacs.git/tree/lisp/progmodes/python.el][Python-mode]]
:PROPERTIES:
:CUSTOM_ID: sec:python-mode
:END:

Listing [[lst:setup-python-mode][setup Python mode]] and [[lst:choose-common-python-interpreter][choose common Python interpreter]] select a common
Python interpreter in a virtual environment for use in =python-mode= and
=ob-python= by means of src_emacs-lisp{(choose-common-python-interpreter)}.  The
[[https://github.com/pythonic-emacs/pythonic#readme][pythonic]], [[https://github.com/jorgenschaefer/pyvenv#readme][pyvenv]], and [[https://github.com/jorgenschaefer/pyvenv#readme][pyvenv]] packages allow to handle Python virtual
environments within Emacs.  The [[https://github.com/pyenv/pyenv][pyenv]] package provides support to work with
[[https://github.com/pyenv/pyenv#readme][pyenv]] (eventually with [[https://github.com/pyenv/pyenv-virtualenv#readme][pyenv-virtualenv]]) to select between different python
versions (eventually each with different environments).  In the end, all those
packages do is to set =python-shell-virtualenv-root= (in case of [[https://github.com/pyenv/pyenv#readme][pyenv]] and
[[https://github.com/pythonic-emacs/pythonic#readme][pythonic]]) or tweak the environment variables and restart the relevant Python
child processes (in case of [[https://github.com/jorgenschaefer/pyvenv#readme][pyvenv]]).  Therefore, I replace those packages with
listing [[lst:access-pyenv][access pyenv]] and [[lst:select-python-virtual-environment][select a Python interpreter in a virtual environment]] to
set =python-shell-virtualenv-root= from within Emacs.

Listing [[lst:setup-python-mode][setup Python mode]] and [[lst:choose-common-python-linter][choose common Python linter]] select a common Python
linter for the =python-check-command= and the =python-flymake-command= by means
of src_emacs-lisp{(choose-common-python-linter)} from:
1. [[https://github.com/PyCQA/pyflakes][Pyflakes - simple tool which checks Python source files for errors]].
2. [[https://flake8.pycqa.org/en/latest/][Flake8 - your tool for style guide enforcement]].
3. [[https://github.com/charliermarsh/ruff][Ruff - an extremely fast Python linter written in Rust]].
I use [[https://pypi.org/project/ruff/][Ruff]] to replace [[https://pypi.org/project/flake8/][Flake8]] with a variety of its plugins. [[https://notes.crmarsh.com/][Charlie Marsh]]
explains why he started [[https://pypi.org/project/ruff/][Ruff]] in the post [[https://notes.crmarsh.com/python-tooling-could-be-much-much-faster][Python tooling could be much faster]].

Listing [[lst:pyproject-toml-kickoff][kickoff pyproject.toml proposal]] facilitates dropping a [[https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml][pyproject.toml]]
file into Python projects which anyhow should switch to using a [[https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml][pyproject.toml]]
file as explained in the post [[https://bbc.github.io/cloudfit-public-docs/packaging/this_way_up.html][This Way Up: A Bottom-Up Look At Python Packaging]].
The [[https://packaging.python.org/en/latest/tutorials/packaging-projects/][packaging Python projects tutorial]] and the [[https://github.com/pypa/sampleproject][Python sample project]] walk you
through the process of writing a [[https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml][pyproject.toml]] file.  [[https://github.com/charliermarsh/ruff#does-ruff-support-numpy--or-google-style-docstrings][Ruff docstring setup]]
explains how to setup documentation string checking in the [[https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml][pyproject.toml]] file.

Listing [[lst:setup-cfg-kickoff][kickoff setup.cfg proposal]] implements the [[https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html][using black with other tools]]
rules which make [[https://flake8.pycqa.org/en/latest/][flake8]] or [[https://pycodestyle.pycqa.org/en/latest/][pycodestyle]] agree with [[https://black.readthedocs.io/en/stable/index.html][black's uncompromising style]].

Finally, listing [[lst:flake8-nocolor][flake8-nocolor]] and [[lst:ruff-nocolor][ruff-nocolor]] pipe the =stdout= output of the
[[https://pypi.org/project/flake8/][flake8]] and [[https://pypi.org/project/ruff/][ruff]] executables through =cat= to remove escape sequences.

#+caption[Setup Python mode]:
#+caption: Setup Python mode.
#+name: lst:setup-python-mode
#+begin_src emacs-lisp
(with-eval-after-load 'python
  (custom-set-variables
   '(python-indent-guess-indent-offset nil)
   '(python-shell-completion-native-disabled-interpreters '("ipython3" "pypy")))
  (choose-common-python-interpreter 'python)
  (choose-common-python-linter 'ruff-nocolor))
#+end_src

#+caption[Choose a common Python interpreter]:
#+caption: Choose a common Python interpreter for =ob-python= and =python-mode=.
#+name: lst:choose-common-python-interpreter
#+begin_src emacs-lisp
(defun choose-common-python-interpreter (&optional interpreter)
  "Let `ob-python' and `python-mode' use the same Python INTERPRETER."
  (interactive)
  (let* ((prompt (format "Choose Python (%s): "
                          (bound-and-true-p python-shell-interpreter)))
         (choices '(ipython python))
         (choice (if (member interpreter choices)
                     (symbol-name interpreter)
                   (completing-read prompt choices nil t))))
    (when (boundp 'org-babel-python-command)
      (pcase choice
        ("python"
         (custom-set-variables
          `(org-babel-python-command
            ,(concat (or (executable-find "python3")
                         (executable-find "python"))
                     " -E"))))
        ("ipython"
         (custom-set-variables
          `(org-babel-python-command
            ,(concat (or (executable-find "ipython3")
                         (executable-find "ipython"))
                     " --simple-prompt --HistoryAccessor.enabled=False")))))
      (message "Now `org-babel-python-command' equals %S"
               org-babel-python-command))
    (when (boundp 'python-shell-interpreter)
      (pcase choice
        ("python"
         (custom-set-variables
          `(python-shell-interpreter
            ,(or (executable-find "python3") (executable-find "python")))
          '(python-shell-interpreter-args "-E -i")))
        ("ipython"
         (custom-set-variables
          `(python-shell-interpreter
            ,(or (executable-find "ipython3") (executable-find "ipython"))))
         (setq python-shell-interpreter-args
               "--simple-prompt --HistoryAccessor.enabled=False")))
      (message "Now `python-shell-interpreter' equals %S"
               python-shell-interpreter))))
#+end_src

#+caption[Choose a common Python linter]:
#+caption: Choose a common Python linter for =python-check-command= and
#+caption: =python-flymake-command=.
#+name: lst:choose-common-python-linter
#+begin_src emacs-lisp
(defun choose-common-python-linter (&optional linter)
  "Let `python-check-command' and `python-flymake-command' use the same LINTER."
  (interactive)
  (let* ((prompt (format "Choose Python checker (%s): "
                         (bound-and-true-p python-check-command)))
         (choices '(flake8-nocolor pyflakes ruff-nocolor))
         (choice (if (member linter choices)
                     (symbol-name linter)
                   (completing-read prompt choices nil t))))
    (when (and (boundp 'python-check-command) (boundp 'python-flymake-command))
      (pcase choice
        ("flake8-nocolor"
         (custom-set-variables
          `(python-check-command ,(executable-find choice))
          `(python-flymake-command (list ,(executable-find choice) "-"))))
        ("pyflakes"
         (custom-set-variables
          `(python-check-command ,(executable-find choice))
          `(python-flymake-command `(,(executable-find choice)))))
        ("ruff-nocolor"
         (custom-set-variables
          `(python-check-command ,(executable-find choice))
          `(python-flymake-command
            (list ,(executable-find choice) "--stdin-filename" "stdin" "-")))))
      (when (bound-and-true-p python-check-custom-command)
        (setq python-check-custom-command nil))
      (message "Python checker commands are %S and %S"
               python-check-command python-flymake-command))))
#+end_src

#+caption[Access =pyenv=]:
#+caption: Access =pyenv=.
#+name: lst:access-pyenv
#+begin_src emacs-lisp
(when (executable-find "pyenv")
  (defun pyenv-full-path (version)
    "Return the full path for VERSION."
    (unless (string= version "system")
      (concat (pyenv-root) (file-name-as-directory "versions") version)))

  (defun pyenv-root ()
    "Return \"pyenv root\" as a directory."
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code "pyenv" "root")
      (if (= 0 exit-code)
          (file-name-as-directory (string-trim output))
        (error "%s" (string-trim output)))))

  (defun pyenv-version-name ()
    "Return \"pyenv version-name\"."
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code "pyenv" "version-name")
      (if (= 0 exit-code)
          (string-trim output)
        (error "%s" (string-trim output)))))

  (defun pyenv-versions ()
    "Return \"pyenv versions --bare --skip-aliases\" as a list.
Complete the result with \"system\"."
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code
         "pyenv" "versions" "--bare" "--skip-aliases")
      (if (= 0 exit-code)
          (cons "system" (split-string output))
        (error "%s" (string-trim output)))))

  (defun pyenv-virtualenvs ()
    "Return \"pyenv virtualenvs --bare --skip-aliases\" as a list."
    (cl-destructuring-bind (exit-code output)
        (shell-command-with-exit-code
         "pyenv" "virtualenvs" "--bare" "--skip-aliases")
      (if (= 0 exit-code)
          (split-string output)
        (error "%s" (string-trim output))))))
#+end_src

#+caption[Select the Python virtual environment]:
#+caption: Select the Python virtual environment.
#+name: lst:select-python-virtual-environment
#+begin_src emacs-lisp
(with-eval-after-load 'python
  (when (cl-every #'fboundp '(pyenv-full-path
                              pyenv-version-name
                              pyenv-versions
                              pyenv-virtualenvs))
    (setq python-shell-virtualenv-root
          (pyenv-full-path (or (pyenv-version-name)
                               (car (pyenv-virtualenvs))
                               (car (pyenv-versions)))))
    (message "Now `python-shell-virtualenv-root' equals %S"
             python-shell-virtualenv-root)

    (defun set-python-shell-virtualenv-root-to-pyenv-version ()
      "Set `python-shell-virtual-env-root' to a pyenv version."
      (interactive)
      (let* ((version-name (pyenv-version-name))
             (prompt (format "pyenv version (%s): " version-name))
             (choices (pyenv-versions))
             (version (completing-read prompt choices nil 'require-match)))
        (unless (string= version-name version)
          (setq python-shell-virtualenv-root (pyenv-full-path version))
          (setenv "PYENV_VERSION" version))
        (message "Now `python-shell-virtualenv-root' equals %S"
                 python-shell-virtualenv-root)))

    (defun set-python-shell-virtualenv-root-to-pyenv-virtualenv ()
      "Set `python-shell-virtual-env-root' to a pyenv virtualenv."
      (interactive)
      (let* ((version-name (pyenv-version-name))
             (prompt (format "pyenv virtualenv (%s): " version-name))
             (choices (pyenv-virtualenvs))
             (version (completing-read prompt choices nil 'require-match)))
        (unless (string= version-name version)
          (setq python-shell-virtualenv-root (pyenv-full-path version))
          (setenv "PYENV_VERSION" version))
        (message "Now `python-shell-virtualenv-root' equals %S"
                 python-shell-virtualenv-root)))))
#+end_src

#+caption[Kickoff =pyproject.toml= proposal]:
#+caption: Kickoff =pyproject.toml= proposal.
#+name: lst:pyproject-toml-kickoff
#+begin_src toml :tangle pyproject.toml
# Use for instance "hatch new" to create or initialize a project.
# See: https://pypi.org/project/hatch

[tool.black]
line-length = 88

[tool.ruff]
line-length = 88
select = [
  "ARG", # flake8-unused-arguments
  "B",   # flake8-bugbear
  "C",   # mccabe
  "C4",  # flake8-comprehensions
  "E",   # pycodestyle
  "D",   # pydocstyle
  "F",   # pyflakes
  "UP",  # pyupgrade
  "W",   # pycodestyle
]
ignore = [
  "B905", # `zip()` without an explicit `strict=` parameter
  # https://www.pydocstyle.org/en/stable/error_codes.html#default-conventions
  # pydocstyle numpy convention:
  # "D107", # missing docstring in __init__
  # "D203", # single blank line required before class docstring
  # "D212", # multi-line docstring summary should start at the first line
  # "D213", # multi-line docstring summary should start at the second line
  # "D402", # first line should not be the function signature
  # "D413", # missing blank line after last section
  # "D415", # 1st line should end with a ".", "?", or "?"
  # "D416", # section name should end with a ":"
  # "D417", # missing argument descriptions in the docstring
]

[tool.ruff.mccabe]
max-complexity = 15

[tool.ruff.pydocstyle]
convention = "numpy"

# Local Variables:
# mode: conf-toml-mode
# End:
#+end_src

#+caption[Kickoff =setup.cfg= proposal]:
#+caption: Kickoff =setup.cfg= proposal.
#+name: lst:setup-cfg-kickoff
#+begin_src toml :tangle setup.cfg
[flake8]
docstring-convention = numpy
extend-select = B,F,W
extend-ignore = W503
max-complexity = 15
max-line-length = 88

[pycodestyle]
ignore = W503
max-line-length = 88

# Local Variables:
# mode: conf-toml
# End:
#+end_src

#+caption[Wrap =flake8= to remove color from text output]:
#+caption: Wrap =flake8= to remove color from text output.
#+header: :tangle-mode (identity #o755)
#+name: lst:flake8-nocolor
#+begin_src shell :noeval :tangle ~/bin/flake8-nocolor
#!/bin/sh

flake8 "$@" | cat

# Local Variables:
# mode: shell-script
# sh-indentation: 2
# sh-basic-offset: 2
# End:
#+end_src

#+caption[Wrap =ruff= to remove color from text output]:
#+caption: Wrap =ruff= to remove color from text output.
#+header: :tangle-mode (identity #o755)
#+name: lst:ruff-nocolor
#+begin_src shell :noeval :tangle ~/bin/ruff-nocolor
#!/bin/sh

ruff "$@" | cat

# Local Variables:
# mode: shell-script
# sh-indentation: 2
# sh-basic-offset: 2
# End:
#+end_src

*** [[https://github.com/joaotavora/eglot][Eglot]] for [[https://git.savannah.gnu.org/cgit/emacs.git/tree/lisp/progmodes/python.el][python-mode]]
:PROPERTIES:
:CUSTOM_ID: sec:eglot-python
:END:

Listing [[lst:configure-eglot+pylsp-ruff]] configures [[https://github.com/joaotavora/eglot][eglot]] for [[https://www.python.org][Python]] using the
[[https://github.com/python-lsp/python-lsp-server][python-lsp-server]] with the [[https://github.com/python-lsp/python-lsp-ruff#readme][pylsp-ruff]] plugin for the easiest way to let
[[https://github.com/python-lsp/python-lsp-server][python-lsp-server]] use [[https://pypi.org/project/ruff/][Ruff]].  The latest [[https://github.com/python-lsp/python-lsp-server#readme][python-lsp-server]] documentation tells to
configure it for [[https://github.com/PyCQA/flake8][flake8]] as in listing [[lst:configure-eglot+pylsp+flake8]]. In order
to enable all builtin [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]] capabilities, ensure installation of the
Python packages [[https://github.com/hhatto/autopep8#readme][autopep8]], [[https://github.com/PyCQA/flake8][flake8]], [[https://github.com/PyCQA/pydocstyle#readme][pydocstyle]], [[https://github.com/PyCQA/pylint#readme][pylint]], [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]], [[https://github.com/python-rope/rope#readme][rope]],
and [[https://github.com/google/yapf#readme][yapf]].  This method is under investigation (it feels flaky since it shows
some error messages twice).

Listing [[lst:eglot-directory-variables-for-python]] shows a proper [[info:emacs#Directory Variables][.dir-locals.el]]
file in the root directory of any [[https://www.python.org][Python]] project to start [[https://github.com/joaotavora/eglot][eglot]] automatically
according to the configuration in listing [[lst:eglot-maybe-ensure]].  Type
{{{kbd(M-x eglot-show-workspace-configuration)}}} to dump a =JSON=
representation of src_emacs-lisp{eglot-workspace-configuration} for debugging.
The comment in listing [[lst:minimal-eglot-setup][minimal Eglot setup]] also shows how to decrease
or to increase the verbosity of [[https://github.com/python-lsp/python-lsp-server][Python LSP server]] log output for debugging.

#+caption[Configure =eglot= with =python-lsp-ruff=]:
#+caption: Configure =eglot= with =python-lsp-ruff=.
#+name: lst:configure-eglot+pylsp-ruff
#+begin_src emacs-lisp
(with-eval-after-load 'eglot
  (setq-default
   eglot-workspace-configuration
   ;; Enable the `:pylsp_ruff' plugin and ensure to disable the
   ;; `:flake8', `:mccabe', and `:pycodestye' plugins.
   '(:pylsp (:plugins
             (:pylsp_ruff
              (:enabled t)
              :flake8
              (:enabled :json-false)
              :mccabe
              (:enabled :json-false)
              :pycodestyle
              (:enabled :json-false)
              :jedi
              (:auto_import_modules ["numpy"])
              :jedi_completion
              (:cache_for ["astropy"]))))))
#+end_src

#+caption[Configure =eglot= with =python-lsp-server= and the =flake8= plugin]:
#+caption: Configure =eglot= with =python-lsp-server= and the =flake8= plugin.
#+name: lst:configure-eglot+pylsp+flake8
#+begin_src emacs-lisp :tangle no
(with-eval-after-load 'eglot
  (setq-default
   eglot-workspace-configuration
   ;; How to use flake8 instead of pycodestyle or ruff, see:
   ;; https://github.com/python-lsp/python-lsp-server#configuration
   '(:pylsp (:configurationSources
             ["flake8"]
             :plugins
             (:flake8
              (:enabled t)
              :mccabe
              (:enabled :json-false)
              :pycodestyle
              (:enabled :json-false)
              :pyflakes
              (:enabled :json-false)
              :pylsp-ruff
              (:enabled :json-false)
              :jedi
              (:auto_import_modules ["numpy"])
              :jedi_completion
              (:cache_for ["astropy"]))))))
#+end_src

#+caption[A =.dir-locals.el= proposal to launch =eglot= automatically]:
#+caption: A =.dir-locals.el= file proposal for Python projects or Org-mode
#+caption: projects tangling Python files to launch =eglot= automatically.
#+name: lst:eglot-directory-variables-for-python
#+begin_src emacs-lisp :tangle dir-locals.el
;; A .dir-locals.el file proposal in the root of any
;; Python project or Org-mode project tangling Python files
;; to launch eglot automatically.
((nil  ;; nil, since Emacs-29.1 filters out irrelevant variable names.
  . ((eglot-workspace-configuration
      ;; Enable the `:pylsp_ruff' plugin and ensure to disable the
      ;; `:flake8', `:mccabe', and `:pycodestye' plugins.
      . (:pylsp (:plugins
                 (:pylsp_ruff
                  (:enabled t)
                  :flake8
                  (:enabled :json-false)
                  :mccabe
                  (:enabled :json-false)
                  :pycodestyle
                  (:enabled :json-false)
                  :jedi
                  (:auto_import_modules ["numpy"])
                  :jedi_completion
                  (:cache_for ["astropy"]))))))))
#+end_src

#+attr_latex: :booktabs yes :float table
#+caption[Eglot related key bindings]:
#+caption: Eglot related key-bindings.
#+name: tab:eglot-related-key-bindings
|-------------------------+----------------+------------------|
| command                 | key map        | keys             |
|-------------------------+----------------+------------------|
| xref-find-definition    | global-map     | {{{kbd(M-.)}}}   |
| xref-pop                | global-map     | {{{kbd(M-\,)}}}  |
| flymake-goto-next-error | eglot-mode-map | {{{kbd(C-c n)}}} |
| flymake-goto-prev-error | eglot-mode-map | {{{kbd(C-c p)}}} |
| eglot-rename            | eglot-mode-map | {{{kbd(C-c r)}}} |
| eldoc-doc-buffer        | eglot-mode-map | {{{kbd(C-h .)}}} |
|-------------------------+----------------+------------------|

Listing [[lst:make-pylsp-server-patch]] is useful to propagate eventual patches of
a local fork of [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]].

#+caption[Make =pylsp-auto-import-modules.patch= listing]:
#+caption: Make =pylsp-auto-import-modules.patch= listing.
#+name: lst:make-pylsp-server-patch
#+begin_src shell :exports code :results none
  git -C $HOME/VCS/python-lsp-server diff >pylsp.patch
#+end_src

*** [[https://jedi.readthedocs.io/en/latest/][Jedi]]
:PROPERTIES:
:CUSTOM_ID: sec:jedi
:END:

Listing [[lst:example-py]] is a [[https://www.python.org][Python]] example to test whether [[https://jedi.readthedocs.io/en/latest/][jedi]] in combination
with [[https://github.com/joaotavora/eglot][eglot]] works when coding for instance [[https://numpy.org/][numpy]] universal functions.

#+caption[Tangle the =example.py= file]:
#+caption: Tangle the =example.py= file.
#+name: lst:example-py
#+begin_src python :tangle example.py
import numpy
import astropy.units as apu

a = numpy.arange(0, 11)
a = numpy.linspace(0, 10, num=11)
a = numpy.arccos(a)
q = apu.Quantity(a, apu.meter)
print(q)
#+end_src

*** [[https://github.com/astoff/code-cells.el#readme][Code-cells]]
:PROPERTIES:
:CUSTOM_ID: sec:code-cells
:END:

[[https://github.com/astoff/code-cells.el#readme][Code-cells]] allows to edit [[https://ipython.org/notebook.html][IPython or Jupyter notebooks]] in Emacs with help from
either [[https://github.com/mwouts/jupytext][Jupytext]] or [[https://pandoc.org/][Pandoc]] to translate between the [[https://nbformat.readthedocs.io/en/latest/][ipynb]] format and different
plain text formats.  Sofar, I have used [[https://github.com/astoff/code-cells.el#readme][code-cells]] to open [[https://nbformat.readthedocs.io/en/latest/][ipynb]] notebooks with
{{{kbd(C-x C-f)}}} in Emacs for viewing.  Listing [[lst:configure-code-cells]]
configures =code-cells=.

#+caption[Configure =code-cells=]:
#+caption: Configure =code-cells=.
#+name: lst:configure-code-cells
#+begin_src emacs-lisp
(when (ensure-package-installation 'code-cells)
  (with-eval-after-load 'code-cells
    (let ((map code-cells-mode-map))
      (define-key map (kbd "M-p") #'code-cells-backward-cell)
      (define-key map (kbd "M-n") #'code-cells-forward-cell)
      (define-key map (kbd "C-c C-c") #'code-cells-eval))))
#+end_src

*** TODO Look into: editing facilities
1. [[https://github.com/douglasdavis/numpydoc.el/blob/main/numpydoc.el][Emacs extension to insert numpy style docstrings in function definitions]]

* [[https://github.com/emacs-tw/awesome-emacs#library][Libraries]]
:PROPERTIES:
:CUSTOM_ID: sec:libraries
:END:

** [[info:dash.info#Top][Library dash.el (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:dash-library
:END:

The library [[info:dash.info#Top][dash.el (info)]] positions itself as a modern alternative for the list
processing API of [[info:cl#Top][cl]].  It is a requirement of several important packages in this
Emacs setup (for instance [[https://github.com/andras-simonyi/citeproc-el#readme][citeproc]], [[https://github.com/magit/magit#readme][magit]], and [[https://github.com/Fuco1/smartparens#readme][smartparens]]).  Listing
[[lst:configure-dash]] enables fontification of =dash= macros and makes
=info-lookup-symbol= take into account the =dash= macros.

#+caption[Configure =dash= fontification and info lookup]:
#+caption: Configure =dash= fontification and info lookup.
#+name: lst:configure-dash
#+begin_src emacs-lisp
(when (fboundp #'global-dash-fontify-mode)
  (global-dash-fontify-mode))

(when (fboundp #'dash-register-info-lookup)
  (with-eval-after-load 'info-look
    (dash-register-info-lookup)))
#+end_src

** [[https://github.com/rejeep/f.el][Library f.el]]
:PROPERTIES:
:CUSTOM_ID: sec:f-library
:END:

The library [[https://github.com/rejeep/f.el][f.el]] positions itself as a modern API for working with files and
directories in Emacs.  It is a requirement of the [[https://github.com/andras-simonyi/citeproc-el#readme][citeproc]] package in this Emacs
setup and requires no configuration.

** [[https://github.com/magnars/s.el][Library s.el]]
:PROPERTIES:
:CUSTOM_ID: sec:s-library
:END:
The library [[https://github.com/magnars/s.el][s.el]] positions itself as the long lost Emacs string manipulation
library.  It is a requirement of the [[https://github.com/andras-simonyi/citeproc-el#readme][citeproc]] and [[https://github.com/bdarcus/citar#readme][citar]] packages in this Emacs
setup and requires no configuration.

* [[info:emacs#Minor Modes][Minor Modes (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:minor-modes
:END:

** [[https://github.com/victorhge/iedit#readme][Synchronal multiple-region editing]]
:PROPERTIES:
:CUSTOM_ID: sec:synchronal-multiple-region-editing
:END:

#+caption[Enable =iedit=]:
#+caption: Enable =iedit=.
#+name: lst:enable-iedit
#+begin_src emacs-lisp
(when (ensure-package-installation 'iedit)
  (require 'iedit nil 'noerror))
#+end_src

** [[https://github.com/lewang/ws-butler#readme][Unobtrusive whitespace trimming]]
:PROPERTIES:
:CUSTOM_ID: sec:unobtrusive-whitespace-trimming
:END:

#+caption[Configure =ws-butler=]:
#+caption: Configure =ws-butler=.
#+name: lst:configure-ws-butler
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'ws-butler)
           (require 'ws-butler nil 'noerror))
  (custom-set-variables
   '(ws-butler-keep-whitespace-before-point nil))
  (add-hook 'prog-mode-hook #'ws-butler-mode)
  (add-hook 'text-mode-hook #'ws-butler-mode))
#+end_src

** [[https://countvajhula.com/2021/09/25/the-animated-guide-to-symex/][Structural editing]]
:PROPERTIES:
:CUSTOM_ID: sec:structural-editing
:END:

Structural editing keeps character pairs (for instance parentheses, curly and
square brackets as well as single and double quotes) balanced to leave code (for
instance Lisp and Python) and text (for instance LaTeX and Org) structure
intact.  I use [[https://github.com/Fuco1/smartparens][smartparens]] which offers a normal mode (=smartparens-mode=) and a
strict mode (=smartparens-strict-mode=).  Although both modes insert character
pairs, the normal mode allows to delete one of the paired characters easily
while the strict mode does not.  Therefore, the strict mode is more for code
editing since it never breaks programming language rules and the normal mode is
more for text editing where structure is a matter of convention instead of
programming language rules.

For instance, the strict mode in Python allows to delete entire lists, tuples,
or the arguments after the cursor (what Emacs calls =point=) in a function call
without breaking the character pair balance.  In order to repair a broken
character pair balance, insert a single character by prefixing it with "C-q"
bound to =quoted-insert=.

The [[https://smartparens.readthedocs.io/en/latest/index.html][smartparens documentation]] targets experienced Emacs users.  The
following links show how to put the documentation to practical use:
1. [[https://gist.github.com/oantolin][Omar Antolin's gist "my-smartparens-config.el"]] is the first place to look for
   how to tweak [[https://github.com/Fuco1/smartparens][smartparens]].  However, the gist may be partially obsolete, since
   it is not part of his current [[https://github.com/oantolin/emacs-config][Emacs configuration]].
2. [[https://lists.gnu.org/archive/html/help-gnu-emacs/2014-07/msg00135.html][How to enable smartparens in the minibuffer after eval-expression]] explains
   how the machinery after the first and after later usages of =eval-expression=
   differ and discusses options how to handle those differences.
Listing [[lst:configure-smartparens]] aims to configure [[https://github.com/Fuco1/smartparens][smartparens]] for Elisp,
LaTeX, Org, and Python.

Despite the provocative post [[https://andreyorst.gitlab.io/posts/2022-02-20-what-if-structural-editing-was-a-mistake/]["What if structural editing was a mistake?"]],
[[https://github.com/Fuco1/smartparens][smartparens]] is one of my favorite packages. In particular, [[https://github.com/Fuco1/smartparens][smartparens]] handles
matching pairs in Org-mode files with export and source blocks for multiple
formats and languages correctly.  Therefore, [[https://smartparens.readthedocs.io/en/latest/index.html?highlight=show-smartparens-mode#getting-started][show-smartparens-mode]] highlights
matching pairs immediately in front or after point in such files correctly,
contrary to for instance [[https://github.com/Fanael/rainbow-delimiters#readme][rainbow-delimiters]].

#+caption[Configure =smartparens=]:
#+caption: Configure =smartparens=.
#+name: lst:configure-smartparens
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'smartparens)
           ;; Require `smartparens-config' instead of `smartparens' to
           ;; disable pairing of the quote character for lisp modes.
           (require 'smartparens-config nil 'noerror))
  (custom-set-variables
   '(sp-base-key-bindings 'sp)
   '(sp-override-key-bindings '(("C-(" . sp-backward-barf-sexp)
                                ("C-)" . sp-forward-slurp-sexp))))

  (dolist (hook '(conf-toml-mode-hook prog-mode-hook text-mode-hook))
    (add-hook hook #'smartparens-mode))

  (dolist (hook '(emacs-lisp-mode-hook
                  ielm-mode-hook
                  lisp-data-mode-hook
                  lisp-mode-hook
                  python-mode-hook
                  sly-mrepl-mode-hook))
    (add-hook hook #'smartparens-strict-mode))

  ;; https://xenodium.com/emacs-smartparens-auto-indent/index.html
  (defun indent-between-pair (&rest _ignored)
    (newline)
    (indent-according-to-mode)
    (forward-line -1)
    (indent-according-to-mode))

  (dolist (left '("(" "[" "{"))
    (sp-local-pair 'prog-mode left
                   nil :post-handlers '((indent-between-pair "RET"))))

  (show-smartparens-global-mode +1))
#+end_src

** [[https://github.com/davidshepherd7/electric-operator#readme][Electric operators]]
:PROPERTIES:
:CUSTOM_ID: sec:electric-operators
:END:

Listing [[lst:configure-electric-operator]] configures =electric-operator-mode=
to add spaces around operators for compatibility with for instance the [[https://black.readthedocs.io/en/stable/][Black
code formatter for Python]].

#+caption[Configure =electric-operator=]:
#+caption: Configure =electric-operator=.
#+name: lst:configure-electric-operator
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'electric-operator)
           (fboundp 'electric-operator-mode))
  (add-hook 'c-mode-common-hook #'electric-operator-mode)
  (add-hook 'python-mode-hook #'electric-operator-mode))
#+end_src

** [[https://joaotavora.github.io/yasnippet/][Smart snippets]]
:PROPERTIES:
:CUSTOM_ID: sec:smart-snippets
:END:

#+caption[Enable =yas-global-mode=]:
#+caption: Enable =yas-global-mode=.
#+name: lst:enable-yas-global-mode
#+begin_src emacs-lisp
(when (ensure-package-installation 'yasnippet)
  (custom-set-variables
   ;; Set `yas-alias-to-yas/prefix-p' before loading `yasnippet'.
   '(yas-alias-to-yas/prefix-p nil))
  (when (require 'yasnippet nil 'noerror)
    (yas-global-mode +1)))
#+end_src

** [[info:autotype#Tempo][Tempo (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:tempo
:END:

The official [[info:autotype#Tempo][tempo (info)]] documentation is very short and the following links
are obsolete or do not reveal the full power of [[info:autotype#Tempo][tempo (info)]] after its
adaptation to =lexical-binding=:
1. [[https://www.emacswiki.org/emacs/TempoMode][Tempo (Emacs Wiki)]]
2. [[https://www.lysator.liu.se/~davidk/elisp/][David Kågedal’s elisp]]
3. [[https://github.com/yilkalargaw/emacs-native-snippets][Emacs's Native Snippets]], [[https://www.reddit.com/r/emacs/comments/wdbk34/emacss_native_templating_and_snippet_fuctionality/][Emacs's native templating and snippet functionality]]
Listing [[lst:configure-tempo-ui]] provide a function to define local keybindings
and the tools to add =tempo-tags= to abbreviation tables.  Listing
[[lst:configure-tempo-latex-completing-read]] shows how to combine =tempo=, =latex=
and =completing-read= for the builtin =tempo= package that is part of Emacs-28.1
and later.  Listing [[lst:setup-python-tempo]] configures =tempo= for =python-mode=.

#+caption[Configure =tempo= user interface]:
#+caption: Configure =tempo= user-interface.
#+name: lst:configure-tempo-ui
#+begin_src emacs-lisp
(with-eval-after-load 'tempo
  (custom-set-variables
   '(tempo-interactive t))

  (defun setup-local-tempo-key-bindings ()
    "Initialize local `tempo' key bindings."
    (local-set-key (kbd "M-n") #'tempo-forward-mark)
    (local-set-key (kbd "M-p") #'tempo-backward-mark))

  (defun abbrev-tempo-expand-if-complete ()
    "Hook function for `define-abbrev' with `no-self-insert' property `t'."
    (tempo-expand-if-complete))

  (put 'abbrev-tempo-expand-if-complete 'no-self-insert t)

  (defun add-tempo-tags-to-abbrev-table (tempo-tags abbrev-table)
    "Add the tags in TEMPO-TAGS to ABBREV-TABLE.
Allows `tempo' expansion by typing <SPC> after a complete `tempo' tag."
    (dolist (tag tempo-tags)
      (unless (abbrev-symbol (car tag) abbrev-table)
        (define-abbrev abbrev-table
          (car tag) 1 'abbrev-tempo-expand-if-complete)))))
#+end_src

#+caption[Configure =tempo= for =latex= with =completing-read=]:
#+caption: Configure =tempo= for =latex= with =completing-read=.
#+name: lst:configure-tempo-latex-completing-read
#+begin_src emacs-lisp
(with-eval-after-load 'latex
  (unless (featurep 'tempo)
    (require 'tempo))

  (defun tempo-latex-environment-handler (element)
    (when-let ((ok (eq element 'latex-environment))
               (environment
                (completing-read "LaTeX environment: "
                                 (LaTeX-environment-list)
                                 #'always 'require-match)))
      `(l "\\begin{" ,environment "}" > n > r n "\\end{" ,environment "}" >)))

  (cl-pushnew 'tempo-latex-environment-handler tempo-user-elements)

  (defun setup-tempo-latex ()
    (setup-local-tempo-key-bindings)
    (defvar latex-tempo-tags nil)

    (tempo-define-template
     "LaTeX-environment"
     '('latex-environment)
     "env"
     "Insert a LaTeX environment"
     'latex-tempo-tags)

    (tempo-use-tag-list 'latex-tempo-tags)
    (add-tempo-tags-to-abbrev-table latex-tempo-tags latex-mode-abbrev-table))

  (add-hook 'LaTeX-mode-hook 'setup-tempo-latex))
#+end_src

#+caption[Configure =tempo= for =python-mode=]:
#+caption: Configure =tempo= for =python-mode=.
#+name: lst:setup-python-tempo
#+begin_src emacs-lisp
(with-eval-after-load 'python
  (unless (featurep 'tempo)
    (require 'tempo))

  (defun setup-tempo-python ()
    (defvar python-tempo-tags nil)
    (tempo-define-template
     "python-base-class"
     '("class " p ":" n >)
     "clsb" "Define a base class" 'python-tempo-tags)
    (tempo-define-template
     "python-derived-class"
     '("class " p "(" p "):" n >)
     "clsd" "Define a derived class" 'python-tempo-tags)
    (tempo-define-template
     "python-class-method"
     '("@classmethod" > n > "def " p "(cls, " p "):" n >)
     "defc" "Define a class method" 'python-tempo-tags)
    (tempo-define-template
     "python-function"
     '("def " p "(" p "):" n >)
     "deff" "Define a function" 'python-tempo-tags)
    (tempo-define-template
     "python-normal-method"
     '("def " p "(self, " p "):" n >)
     "defm" "Define a normal method" 'python-tempo-tags)
    (tempo-define-template
     "python-static-method"
     '("@staticmethod" > n > "def " p "(" p "):" n >)
     "defs" "Define a static method" 'python-tempo-tags)

    (tempo-use-tag-list 'python-tempo-tags)
    (add-tempo-tags-to-abbrev-table python-tempo-tags python-mode-abbrev-table)
    (setup-local-tempo-key-bindings))

  (add-hook 'python-mode-hook 'setup-tempo-python))
#+end_src

* [[info:emacs#Display][Display (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:display
:END:

** [[info:emacs#Narrowing][Narrowing]]
:PROPERTIES:
:CUSTOM_ID: sec:narrowing
:END:

Narrowing means focusing in on some portion of the buffer and widening means
focussing out on the whole buffer.  This allows to concentrate temporarily on
for instance a particular function or paragraph by removing clutter. The "Do
What I Mean" [[https://endlessparentheses.com/emacs-narrow-or-widen-dwim.html][narrow-or-widen-dwim]] function allows to toggle between narrowed and
widened buffer states.  Here, the function =narrow-or-widen-dwim= operates also
on any Org table, Org source block, Org block, or Org subtree.

#+caption[Configure =narrow-or-widen-dwim=]:
#+caption: Configure =narrow-or-widen-dwim=.
#+name: lst:configure-narrow-or-widen-dwim
#+begin_src emacs-lisp
(with-eval-after-load 'emacs
  (autoload 'org-at-table-p "org-table")

  (defun org-narrow-to-table ()
    "Narrow buffer to table at point."
    (interactive)
    (if (org-at-table-p)
        (narrow-to-region (org-table-begin) (org-table-end))
      (user-error "Not in a table")))

  (defun narrow-or-widen-dwim (p)
    "Widen if buffer is narrowed, narrow \"Do What I Mean\" otherwise.
DWIM means: region, Org table, Org source block, Org block, Org
subtree, LaTeX environment, TeX group, or defun, whichever
applies first.  Narrowing to org-src-block actually calls
`org-edit-src-code'.

With prefix P, don't widen, just narrow even if buffer is already
narrowed."
    (interactive "P")
    (declare (interactive-only))
    (cond ((and (buffer-narrowed-p) (not p))
           (widen))
          ((and (bound-and-true-p org-src-mode) (not p))
           (org-edit-src-exit))
          ((region-active-p)
           (narrow-to-region (region-beginning) (region-end)))
          ((derived-mode-p 'org-mode)
           (or (with-demoted-errors "DWIM: %S" (org-narrow-to-table) t)
               (with-demoted-errors "DWIM: %S" (org-edit-src-code) t)
               (with-demoted-errors "DWIM: %S" (org-narrow-to-block) t)
               (org-narrow-to-subtree)))
          ((derived-mode-p 'latex-mode)
           (LaTeX-narrow-to-environment))
          ((derived-mode-p 'tex-mode)
           (TeX-narrow-to-group))
          (t
           (narrow-to-defun))))

  (define-key ctl-x-map (kbd "n t") #'org-narrow-to-table)
  (define-key ctl-x-map (kbd "C-n") #'narrow-or-widen-dwim))
#+end_src

** [[https://jblevins.org/log/rainbow-mode][Visualize color codes and names]]
:PROPERTIES:
:CUSTOM_ID: sec:rainbow-mode
:END:

Listing [[lst:enable-rainbow-mode]] enables =rainbow-mode= to colorize color codes
and names in buffers for debugging.

#+caption[Enable =rainbow-mode=]:
#+caption: Enable =rainbow-mode=.
#+name: lst:enable-rainbow-mode
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'rainbow-mode)
           (fboundp 'rainbow-mode))
  (custom-set-variables
   '(rainbow-x-colors-major-mode-list
     '(c++-mode
       c-mode
       emacs-lisp-mode
       inferior-emacs-lisp-mode
       java-mode
       lisp-interaction-mode
       org-mode
       python-mode)))
  (rainbow-mode +1))
#+end_src

** [[https://karthinks.com/software/batteries-included-with-emacs/][Flash the line around point for visual feedback]]
:PROPERTIES:
:CUSTOM_ID: sec:flash-line-around-point
:END:

Listing [[lst:flash-line-around-point]] implements flashing of the line around point
for visual feedback after a selection of commands that make it hard to track
point movements visually.

#+caption[Implement =flash-line-around-point=]:
#+caption: Implement =flash-line-around-point=.
#+name: lst:flash-line-around-point
#+begin_src emacs-lisp
;; Ensure loading `pulse' with the dynamic variables `pulse-delay' and
;; `pulse-iterations' before masking them lexically instead of after
;; to prevent the warning triggered by lazy loading.
(when (require 'pulse nil 'noerror)
  ;; https://karthinks.com/software/batteries-included-with-emacs/
  ;; https://github.com/karthink/.emacs.d/blob/master/init.el#L2077
  (defun flash-line-around-point (&rest _)
    "Flash the line around point."
    (let ((pulse-iterations 16)
          (pulse-delay 0.1))
      (pulse-momentary-highlight-one-line (point))))

  (dolist (command '(scroll-up-command
                     scroll-down-command
                     recenter-top-bottom
                     other-window))
    (advice-add command :after #'flash-line-around-point)))
#+end_src

* Applications
:PROPERTIES:
:CUSTOM_ID: sec:applications
:END:

** [[info:emacs#Hyperlinking][Hyperlinking and Web Navigation Features (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:hyperlinking-web-navigating
:END:

*** [[info:emacs#Browse-URL][Browse URL (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:browse-url
:END:

Listing [[lst:configure-browse-url]] configures =browse-url=.

#+attr_latex: :options breaklines
#+caption[Configure =browse-url=]:
#+caption: Configure =browse-url=.
#+name: lst:configure-browse-url
#+begin_src emacs-lisp
(with-eval-after-load 'browse-url
  (defun browse-url-mpv (url &optional _)
    (start-process "mpv" nil "mpv" url))

  (defconst browse-url-mpv-regexp
    (rx bos "http" (opt "s") "://"
        (or (seq "youtu.be/")
            (seq "www.youtube.com/" (or "embed/" "watch?"))
            (seq (+? nonl) (or ".mp4" ".webm") eos)))
    "Match hyperlinks to open with mpv.")

  (custom-set-variables
   `(browse-url-generic-program ,(or (when (eq system-type 'darwin) "open")
                                     (executable-find "firefox")))
   '(browse-url-handlers
     `((,browse-url-mpv-regexp . browse-url-mpv)
       ("." . eww-browse-url)))))
#+end_src

*** [[https://en.wikipedia.org/wiki/Eww_(web_browser)][Emacs Web Wowser]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-web-wowser
:END:

#+caption[Configure =eww= URLs]:
#+caption: Configure =eww= URLs.
#+name: lst:configure-eww-urls
#+begin_src emacs-lisp
(when (fboundp 'eww-browse-url)
  (defun eww-subreddit ()
    "Read a subreddit in Emacs."
    (interactive)
    (eww-browse-url (format "www.reddit.com/r/%s/.mobile"
                            (completing-read "subreddit: "
                                             '("emacs"
                                               "i3wm"
                                               "orgmode")
                                             nil t)))))
#+end_src

#+caption[Rename =eww= buffers and display =pdf= links properly]:
#+caption: Rename =eww= buffers and display =pdf= links properly.
#+name: lst:rename-eww-buffer-display-pdf-links
#+begin_src emacs-lisp
(with-eval-after-load 'eww
  (defun eww-display-pdf-as-binary (fn &rest args)
    (let ((buffer-file-coding-system 'binary))
      (apply fn args)))

  (defun eww-rename-buffer ()
    "Rename the buffer using title or url."
    (let* ((title (plist-get eww-data :title))
           (name (or (and (eq "" title) (plist-get eww-data :url)) title)))
      (rename-buffer (format "*%s # eww*" name) t)))

  (add-hook 'eww-after-render-hook #'eww-rename-buffer)
  (advice-add 'eww-display-pdf :around #'eww-display-pdf-as-binary))
#+end_src

*** [[https://www.gnu.org/software/hyperbole/][GNU Hyperbole]]                                                  :noexport:
:PROPERTIES:
:CUSTOM_ID: sec:ensure-hyperbole-installation
:header-args:emacs-lisp: :tangle no :eval never-export
:END:

Listing [[lst:ensure-hyperbole-installation][ensure Hyperbole installation]] works around two [[https://www.gnu.org/software/hyperbole/][GNU Hyperbole]] quirks:
1. The [[https://elpa.gnu.org/elpa/hyperbole.html][GNU ELPA Hyperbole]] and [[https://elpa.gnu.org/devel/hyperbole.html][GNU ELPA Hyperbole developer]] packages ship their
   own =hyperbole-autoloads= and =kotl-autoloads= files which are incompatible
   with Emacs Lisp packages from "package archives".  Consequently, Emacs can
   neither autoload nor load the =hyperbole-autoloads= and =kotl-autoloads=
   files.  Therefore, the predicate loading the =kotl-autoloads= file in the
   first =unless= form of listing [[lst:ensure-hyperbole-installation][ensure Hyperbole installation]] will fail and
   the body of this form will overwrite the =hyperbole-autoloads= file to fix
   =load-path= *and* load the =hyperbole-autoloads= and =kotl-autoloads= files.
   A next time, Emacs will be able to autoload the new =hyperbole-autoloads=
   file but not the =kotl-autoloads= file.  However, Emacs will now be able to
   load the =kotl-autoloads= file which the predicate in the first =unless= form
   of listing [[lst:ensure-hyperbole-installation][ensure Hyperbole installation]] does.
2. [[https://www.gnu.org/software/hyperbole/][GNU Hyperbole]] and [[info:vertico#Top][Vertico (info)]] do not play well together, since the
   =vertico-mode= preselection of the first candidate out of the full candidate
   completion list interferes with =hyperbole-mode= expectations where it must
   handle a full candidate list.  Therefore, the function call
   src_emacs-lisp{(either-hyperbole-or-vertico-mode)} handles this conflict by
   toggling between =hyperbole-mode= and =vertico-mode=.

#+caption[Ensure Hyperbole installation]:
#+caption: Ensure Hyperbole installation and address two Hyperbole quirks.
#+name: lst:ensure-hyperbole-installation
#+begin_src emacs-lisp
(when (ensure-package-installation 'hyperbole)
  (unless (load "kotl-autoloads.el" 'noerror nil nil 'must-suffix)
    ;; See `package-generate-autoloads' for `loaddefs-generate' usage.
    (unless (bound-and-true-p package-archive-contents)
      (package-read-all-archive-contents))
    (let* ((pkg-desc (cadr (assq 'hyperbole package-archive-contents)))
           (pkg-dir (expand-file-name
                     (package-desc-full-name pkg-desc) package-user-dir))
           (hpbl-alf (expand-file-name "hyperbole-autoloads.el" pkg-dir))
           (kotl-alf (expand-file-name
                      (file-name-concat "kotl" "kotl-autoloads.el") pkg-dir))
           (extra-data
            (concat
             (prin1-to-string
              '(add-to-list
                'load-path
                (or (and load-file-name (file-name-directory load-file-name))
                    (car load-path))))
             "\n"
             (prin1-to-string
              '(add-to-list
                'load-path
                (expand-file-name
                 "kotl"
                 (or (and load-file-name (file-name-directory load-file-name))
                     (car load-path)))))))
           (autoload-timestamps nil)
           (version-control 'never))
      (loaddefs-generate pkg-dir hpbl-alf nil extra-data nil 'generate-full)
      (dolist (alf (list hpbl-alf kotl-alf))
        (let ((buf (find-buffer-visiting hpbl-alf)))
          (when buf (kill-buffer buf)))
        (load alf nil nil nil 'must-suffix))))

  (defun either-hyperbole-or-vertico-mode ()
    "Toggle between either `hyperbole-mode' or `vertico-mode'."
    (interactive)
    (when (and (boundp hyperbole-mode) (boundp vertico-mode))
      (if hyperbole-mode
          (progn
            (hyperbole-mode -1)
            (vertico-mode +1))
        (hyperbole-mode +1)
        (vertico-mode -1)))))
#+end_src

*** [[https://en.wikipedia.org/wiki/Media_type#Mailcap][Mailcap]]
:PROPERTIES:
:CUSTOM_ID: sec:mailcap
:END:

Extension packages as [[info:emacs#EWW][EWW (info)]], [[info:emacs#Gnus][Gnus (info)]], and [[info:org#Top][Org (info)]] rely on a [[https://en.wikipedia.org/wiki/Media_type#Mailcap][mailcap]]
file to know what application should open a specific media file type.  Listing
[[lst:tangle-mailcap-file]] specifies =emacsclient= as the application to open PDF
files.

#+caption[Tangle =mailcap= file]:
#+caption: Tangle =mailcap= file.
#+name: lst:tangle-mailcap-file
#+begin_src org :tangle ~/.mailcap
# https://emacs.stackexchange.com/a/24502 answers the question:
# How to use pdf-tools (pdf-view-mode) in emacs?
application/pdf; emacsclient %s
#+end_src

*** [[https://www.emacswiki.org/emacs/WebJump][Webjump]]
:PROPERTIES:
:CUSTOM_ID: sec:webjump
:END:

Listing [[lst:configure-webjump]] binds {{{kbd(C-c j)}}} to =webjump= and
initializes a list of =webjump-sites=.

#+attr_latex: :options breaklines
#+caption[Configure =webjump=]:
#+caption: Configure =webjump=.
#+name: lst:configure-webjump
#+begin_src emacs-lisp
(when (fboundp 'webjump)
  (global-set-key (kbd "C-c j") 'webjump)
  (with-eval-after-load 'webjump
    (custom-set-variables
     '(webjump-sites
       '(("CS 325 AI Programming" . "courses.cs.northwestern.edu/325")
         ("Emacs News" . "sachachua.com/blog/category/emacs-news")
         ("Mastering Emacs" . "www.masteringemacs.org")
         ("Planet Emacs Life" . "planet.emacslife.com")
         ("Real Python" . "realpython.com")
         ("Worg - Org Mode Community" . "orgmode.org/worg")
         ("Git: Emacs" . "git.savannah.gnu.org/cgit/emacs.git")
         ("Git: Emacs Core Python Mode" .
          "git.savannah.gnu.org/cgit/emacs.git/log/lisp/progmodes/python.el")
         ("Git: GNU ELPA" . "git.savannah.gnu.org/cgit/emacs/elpa.git")
         ("Git: NonGNU ELPA" . "git.savannah.gnu.org/cgit/emacs/nongnu.git")
         ("Git: Org Mode" . "git.savannah.gnu.org/cgit/emacs/org-mode.git")
         ("List: Org Mode" . "list.orgmode.org")
         ("List: Emacs Developer Archives" .
          "lists.gnu.org/archive/html/emacs-devel/")
         ("List: Help GNU Emacs Archives" .
          "lists.gnu.org/archive/html/help-gnu-emacs/")
         ("Asian Pacific Journal Japan Focus" . "apjjf.org")
         ("Counterpunch" . "www.counterpunch.org")
         ("Dictionary FR" . [simple-query "www.cnrtl.fr"
                                          "www.cnrtl.fr/definition/" ""])
         ("Dictionary NL" . [simple-query "www.woorden.org"
                                          "www.woorden.org/woord/" ""])
         ("Le Figaro" . "www.lefigaro.fr")
         ("Le Monde" . "www.lemonde.fr")
         ("Libération" . "www.liberation.fr")
         ("Monde Diplomatique" . "www.monde-diplomatique.fr")
         ("NRC". "www.nrc.nl")
         ("The Guardian" . "www.theguardian.com/international")
         ("Trouw" . "www.trouw.nl")
         ("Volkskrant" . "www.volkskrant.nl"))))))
#+end_src

** [[info:gnus#Top][Reading News and Mail (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:reading-news-mail
:END:

1. [[https://www.maketecheasier.com/emacs-usenet-reader-with-gnus/][How to use Emacs as a USENET reader with Gnus]]
2. [[https://github.com/redguardtoo/mastering-emacs-in-one-year-guide/blob/master/gnus-guide-en.org][A practical guide to Gnus]]
3. [[https://jao.io/blog/2021-05-17-reading-and-searching-gmane-with-gnus-fast.html][Fast reading and searching of Gmane.io with Gnus]]
4. [[https://www.brautaset.org/posts/leafnode-nntp-os-x.html][Setting up Leafnode on macOS]]
5. [[https://blog.bitside.pl/posts/gnus/][Gnus]]
6. [[http://www.bobnewell.net/publish/35years/gmailhacks.html][Stupid GMail hacks for Gnus]]
7. [[http://www.bobnewell.net/publish/35years/gnuhacks.html][More stupid Gnus hacks]]
8. [[https://config.phundrak.com/emacs.html][See Mu4e section of Phundrak's Emacs configuration]]

1. [[https://www.passwordstore.org/][Pass: the standard unix password manager]]
1. [[https://www.howtogeek.com/devops/how-to-use-pass-a-command-line-password-manager-for-linux-systems/][How to use Pass, a command-line password manager for Unix systems]]
2. [[https://vitalyparnas.com/guides/pass/][Clever uses of pass, the Unix password manager]]

#+attr_latex: :booktabs yes :float table
#+caption[Gnus key bindings]:
#+caption: Gnus key bindings.
#+name: tab:gnus-key-bindings
| command                        | map                 | keys           |
|--------------------------------+---------------------+----------------|
| gnus-group-list-active         | gnus-group-list-map | {{{kbd(A-A)}}} |
| gnus-group-list-all-groups     | gnus-group-mode-map | {{{kbd(L)}}}   |
| gnus-group-toggle-subscription | gnus-group-mode-map | {{{kbd(U)}}}   |
|--------------------------------+---------------------+----------------|

#+caption[Configure =gnus=]:
#+caption: Configure =gnus=.
#+name: lst:configure-gnus
#+begin_src emacs-lisp
(with-eval-after-load 'gnus
  (custom-set-variables
   '(gnus-select-method '(nntp "news.gmane.io"))))

(with-eval-after-load 'gnus-start
  (custom-set-variables
   '(gnus-check-bogus-newsgroups nil)
   '(gnus-check-new-newsgroups 'ask-server)
   '(gnus-read-newsrc-file t)
   '(gnus-read-active-file 'some)
   '(gnus-save-killed-list t)
   '(gnus-save-newsrc-file t)
   '(gnus-use-dribble-file t)))

(with-eval-after-load 'gnus-sum
  (custom-set-variables
   '(gnus-thread-hide-subtree t)))
#+end_src

** [[info:emacs#Sending Mail][Sending Mail (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:sending-mail
:END:

1. [[https://macowners.club/posts/email-emacs-mu4e-macos/][Email setup in Emacs with Mu4e on macOS]]
2. [[https://www.bounga.org/tips/2020/05/03/multiple-smtp-accounts-in-gnus-without-external-tools/][Setting up multiple IMAP and SMTP accounts in Gnus]]
3. [[https://jherrlin.github.io/posts/emacs-on-macos-monterey/][Emacs on Macos Monterey]]
4. [[https://github.com/00riddle00/dotfiles/blob/master/.msmtprc][Msmtp resource file for posteo.net]]
5. [[https://www.devdungeon.com/content/gpg-tutorial][GPG tutorial]]
6. [[https://en.wikipedia.org/wiki/Key_server_(cryptographic)#Keyserver_examples][Cryptographic key server examples]]
7. [[https://rakhim.org/fastmail-setup-with-emacs-mu4e-and-mbsync-on-macos/][Fastmail setup with Emacs, mu4e and mbsync on macOS]]

#+caption[Configure =message=]:
#+caption: Configure =message=.
#+name: lst:configure-message
#+begin_src emacs-lisp
(custom-set-variables
 '(user-full-name "Gerard Vermeulen")
 '(user-mail-address "gerard.vermeulen@posteo.net"))
(with-eval-after-load 'message
  (custom-set-variables
   '(message-sendmail-envelope-from 'header)))
#+end_src

#+caption[Configure =sendmail=]:
#+caption: Configure =sendmail=.
#+name: lst:configure-sendmail
#+begin_src emacs-lisp
(with-eval-after-load 'sendmail
  (custom-set-variables
   '(mail-specify-envelope-from t)
   '(mail-envelope-from 'header)
   '(send-mail-function #'sendmail-send-it)
   `(sendmail-program ,(executable-find "msmtp"))))
#+end_src

#+attr_latex: :options breaklines
#+caption[Resource file for =msmtp= on =Darwin=]:
#+caption: Resource file for =msmtp= on =Darwin=.
#+name: lst:darwin-msmpt-resource-file
#+header: :tangle (if (eq 'darwin system-type) "~/.msmtprc" "no")
#+begin_src conf
# Set default values for all accounts.
defaults
auth on
tls on
logfile ~/.msmtp.log

# CNRS on Darwin
# security add-generic-password -s cnrs -a gerard.vermeulen@neel.cnrs.fr -w
account cnrs
host smtps.grenoble.cnrs.fr
port 465
tls_starttls off
from gerard.vermeulen@neel.cnrs.fr
user gerard.vermeulen@neel.cnrs.fr
passwordeval security find-generic-password -s cnrs -w

# https://notmuchmail.org/emacstips/#index11h2
# https://wiki.debian.org/msmtp
# https://tushartyagi.com/blog/configure-mu4e-and-msmtp/
# https://www.emacswiki.org/emacs/GnusMSMTP
# https://www.ying-ish.com/essay/emacs-notmuch-mbsync-msmtp-email/

# Local Variables:
# mode: conf-unix
# End:
#+end_src

#+attr_latex: :options breaklines
#+caption[Resource file for =msmtp= on =Linux=]:
#+caption: Resource file for =msmtp= on =Linux=.
#+name: lst:linux-msmpt-resource-file
#+header: :tangle (if (eq 'gnu/linux system-type) "~/.msmtprc" "no")
#+begin_src conf
# Set default values for all accounts.
defaults
auth on
tls on
tls_trust_file /etc/ssl/certs/ca-certificates.crt
logfile ~/.msmtp.log

# CNRS on Linux
# secret-tool store --label=msmtp host smtps.grenoble.cnrs.fr service smtp user gerard.vermeulen@neel.cnrs.fr
account cnrs
host smtps.grenoble.cnrs.fr
port 465
tls_starttls off
from gerard.vermeulen@neel.cnrs.fr
user gerard.vermeulen@neel.cnrs.fr

# https://notmuchmail.org/emacstips/#index11h2
# https://wiki.debian.org/msmtp
# https://tushartyagi.com/blog/configure-mu4e-and-msmtp/
# https://www.emacswiki.org/emacs/GnusMSMTP
# https://www.ying-ish.com/essay/emacs-notmuch-mbsync-msmtp-email/

# Local Variables:
# mode: conf-unix
# End:
#+end_src

** [[https://github.com/skeeto/elfeed#readme][Elfeed: Emacs web feed reader]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-web-feed-reader
:END:

Listing [[lst:configure-elfeed]] configures =elfeed= and makes a minimal attempt to
enable =emms=.

#+attr_latex: :options breaklines
#+caption[Configure =elfeed=]:
#+caption: Configure =elfeed=.
#+name: lst:configure-elfeed
#+begin_src emacs-lisp
(when (and (ensure-package-installation 'elfeed)
           (fboundp 'elfeed))
  (global-set-key (kbd "C-x w") #'elfeed)

  (with-eval-after-load 'elfeed
    (custom-set-variables
     '(elfeed-feeds
       '(("http://www.howardism.org/index.xml" h-abrams)
         ("https://bitspook.in/archive/feed.xml" c-singh)
         ("https://emacshorrors.com/feed.atom" v-schneidermann)
         ("https://emacsninja.com/emacs.atom" v-schneidermann)
         ("https://feeds.feedburner.com/InterceptedWithJeremyScahill"
          j-scahill)
         ("https://frame.work/fr/fr/blog.rss" framework)
         ("https://nullprogram.com/feed/" c-wellons)
         ("https://oremacs.com/atom.xml" o-krehel)
         ("https://planet.emacslife.com/atom.xml" planet-emacs)
         ("https://protesilaos.com/codelog.xml" p-stavrou)
         ("https://sachachua.com/blog/category/emacs/feed" s-chua)
         ("https://sciencescitoyennes.org/feed/" sciences)
         ("https://tdodge.consulting/blog/rss.xml" t-dodge)
         ("https://talkpython.fm/episodes/rss" talk-python)
         ("https://updates.orgmode.org/feed/updates" org-updates)
         ("https://www.bof.nl/rss/" bof)
         ("https://www.democracynow.org/podcast-video.xml" dn)
         ("https://www.laquadrature.net/fr/rss.xml" lqdn)
         ("https://www.lemonde.fr/blog/huet/feed/" sciences)))))

  (with-eval-after-load 'elfeed-show
    (when (fboundp 'emms-all)
      (emms-all))))
#+end_src

** [[info:emms#Top][Emacs Multimedia System (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-multimedia-system
:END:

The link [[https://sqrtminusone.xyz/posts/2021-09-07-emms/][my emms and elfeed setup]] is a nice introduction to configuring and
using =emms= with =elfeed=.  Listing [[lst:configure-emms]] configures =emms=.

#+caption[Configure =emms=]:
#+caption: Configure =emms=.
#+name: lst:configure-emms
#+begin_src emacs-lisp
(when (ensure-package-installation 'emms)
  (with-eval-after-load 'emms
    (custom-set-variables
     '(emms-player-list '(emms-player-mpd emms-player-mpv)))
    (emms-all))

  (with-eval-after-load 'emms-mode-line
    (custom-set-variables
     '(emms-mode-line-format "")))

  (with-eval-after-load 'emms-player-mpd
    (custom-set-variables
     `(emms-player-mpd-music-directory ,(expand-file-name "~/Music"))
     '(emms-player-mpd-server-name "localhost")
     '(emms-player-mpd-server-port "6600")
     '(emms-player-mpd-verbose t)))

  (with-eval-after-load 'emms-player-mpv
    (custom-set-variables
     '(emms-player-mpv-ipc-method 'ipc-server)
     '(emms-player-mpv-update-metadata t)))

  (with-eval-after-load 'emms-playing-time
    (custom-set-variables
     '(emms-playing-time-display-format " %s ")))

  (with-eval-after-load 'emms-playlist-mode
    (custom-set-variables
     '(emms-playlist-mode-center-when-go t)))

  (with-eval-after-load 'emms-streams
    (custom-set-variables
     `(emms-streams-file
       ,(no-littering-expand-etc-file-name "emms/streams.emms")))))
#+end_src

*** Hiding spurious buffers
:PROPERTIES:
:CUSTOM_ID: sec:hiding-spurious-buffers
:END:

When =emms-player-mpd= opens a connection to =mpd= and =mpd= is not running,
=mpd= responds with a message of the form "OK MPD 0.23.5".  Neither
=emms-player-mpd= nor its support library =tq= anticipate the "OK MPD 0.23.5"
message, but send such messages to a new intrusive buffer called =*spurious*=.
Listing [[lst:hiding-spurious-buffers]] hides those =*spurious*= buffers, but you
can always switch to them.  See:
1. [[info:elisp#The Zen of Buffer Display][The Zen of Buffer Display (info)]]
2. [[https://e17i.github.io/articles-emacs-display-1/][Configuring the Emacs display system]]
3. [[https://www.masteringemacs.org/article/demystifying-emacs-window-manager][Demystifying Emacs's Window Manager]]
for technical information.

#+caption[Hiding =*spurious*= buffers]:
#+caption: Hiding =*spurious*= buffers.
#+name: lst:hiding-spurious-buffers
#+begin_src emacs-lisp
(with-eval-after-load 'emms-player-mpd
  ;; https://www.masteringemacs.org/article/demystifying-emacs-window-manager
  ;; Hide `*spurious*' buffers, but you can always switch to them:
  (add-to-list 'display-buffer-alist
               '("\\*spurious\\*.*" display-buffer-no-window
                 (allow-no-window . t))))
#+end_src

*** [[https://www.musicpd.org/][Music Player Daemon]] configuration
:PROPERTIES:
:CUSTOM_ID: sec:mpd-configuration-file
:END:

Listing [[lst:darwin-mpd-conf]] proposes a [[https://www.musicpd.org/][Music Player Daemon]] configuration file on
Darwin that keeps each new connection for a day in order to reduce the rate of
=*spurious*= generation.

#+caption[A Music Player Daemon configuration file on Darwin]:
#+caption: A Music Player Daemon configuration file on Darwin.
#+name: lst:darwin-mpd-conf
#+begin_src conf :tangle (if (eq 'darwin system-type) "~/.mpd/mpd.conf" "no")
music_directory         "~/Music"
playlist_directory      "~/.mpd/playlists"
db_file                 "~/.mpd/mpd.db"
log_file                "~/.mpd/mpd.log"
pid_file                "~/.mpd/mpd.pid"
state_file              "~/.mpd/mpdstate"
follow_outside_symlinks "yes"
follow_inside_symlinks  "yes"

bind_to_address         "localhost"
port                    "6600"
connection_timeout      "86400"

audio_output {
  type                  "osx"
  name                  "CoreAudio"
  mixer_type            "software"
}
#+end_src

* [[info:emacs#Init File][Init File (info)]] footer
:PROPERTIES:
:CUSTOM_ID: sec:user-init-file-footer
:END:

#+caption[Tangle the =user-init-file= footer]:
#+caption: Tangle the =user-init-file= footer.
#+name: lst:tangle-user-init-file-footer
#+begin_src emacs-lisp
(provide 'init)

;; Emacs looks for "Local variables:" after the last "newline-formfeed".

;; Local Variables:
;; indent-tabs-mode: nil
;; End:
;;; init.el ends here
#+end_src

* GNU Free Documentation License
:PROPERTIES:
:CUSTOM_ID: sec:gnu-fdl
:END:

#+include: fdl.org

* Local variables linking to [[#sec:latexmk-save-compile-display-loop][Latexmk save-compile-display-loop]]
:PROPERTIES:
:CUSTOM_ID: sec:local-variables
:END:

Only the [[info:org#Top][Org]] source file shows the local variables footer.

#+print_bibliography:

# Emacs looks for "Local variables:" after the last "newline-formfeed".

# Local Variables:
# compile-command: "latexmk -interaction=nonstopmode -lualatex -pvc -shell-escape README.tex"
# eval: (org-eval-emacs-lisp-setup-blocks)
# fill-column: 80
# End: