emacs.d/README.org

#+title: Emacs setup for use with LaTeX, Org, and Python
#+author: Gerard Vermeulen
#+latex_class: article-local
#+latex_class_options: [11pt,a4paper,english,svgnames,tables]
#+macro: kbd (eval (by-backend-kbd-org-macro $1))
#+property: header-args:emacs-lisp :exports code :results silent :tangle init.el
#+property: header-args:org :tangle include.org
#+startup: content
#+include: "include.org"

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

Backup your =user-emacs-directory= (defaults often to =~/.emacs.d= on =Linux=,
=Unix=, or =Darwin=) directory and execute the commands in listing
[[lst:prepare-user-emacs-directory]].  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

* 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 [[info:org#Top][Org-9.5 (info)]], 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/orderless][orderless]], [[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/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 Antolín 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.  I have stolen her idea of using [[https://github.com/quelpa/quelpa][quelpa]] to install packages
   from any source.
5. [[https://github.com/purcell/emacs.d][Steve Purcell's configuration]] is well organized, a showcase of readable code,
   as well helpful commit and issue histories.  See for instance the discussion
   on [[https://github.com/purcell/emacs.d/issues/778][the correctness of order of company candidates in Emacs lisp mode]].

Here follows a list of links on how to use Emacs and Elisp:
1. [[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.
2. [[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.
3. [[https://endlessparentheses.com/][Endless Parentheses]] is a blog with many mindblowing code snippets.

* [[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 three parts in listing [[lst:1st-custom-set-variables-call]],
[[lst:2nd-custom-set-variables-call]], and [[lst:3rd-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 reader
macros ~'~ (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]], and
[[lst:3rd-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)
   '(package-archives '(("gnu" . "https://elpa.gnu.org/packages/")
                        ("nongnu" . "https://elpa.nongnu.org/nongnu/")
                        ("melpa" . "https://melpa.org/packages/")))
   ;; Pin those packages to GNU ELPA to get the info documentation.
   '(package-pinned-packages '((consult . "gnu")
                               (marginalia . "gnu")
                               (vertico . "gnu"))))
#+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
   `(package-selected-packages
     `(,@(when (version< emacs-version "28.0")
           '(org                  ; plain text thought organizer
             python))             ; mode to edit Python code
       anaconda-mode              ; strangles python-mode
       applescript-mode           ; mode to edit AppleScript code
       async                      ; asynchroneous processing
       auctex                     ; Aalborg University Center TeX
       blacken                    ; Black Python code formatter client
       citar                      ; bibliography handling
       citeproc                   ; bibliography handling
       code-cells                 ; lightweight notebooks in Emacs
       company                    ; complete anything
       company-anaconda           ; complete anything in anaconda-mode
       consult                    ; consult completing-read
       deadgrep                   ; use ripgrep from Emacs
       eglot                      ; Emacs polyGLOT LSP client
       electric-operator          ; automatic spacing around operators
       elfeed                     ; web feed reader
       embark                     ; act on any buffer selection
       emms                       ; Emacs Multi-Media System
       htmlize                    ; convert buffer contents to HTML
       iedit                      ; simultaneous multi-entity editing
       keycast                    ; show current command with binding
       magit                      ; Git Text-based User Interface
       marginalia                 ; minibuffer margin notes
       markdown-mode              ; markdown text mode
       math-preview               ; display LaTeX math with MathJax
       no-littering               ; keep `user-emacs-directory' clean
       nov                        ; EPUB reader
       orderless                  ; Emacs completion style
       pdf-tools                  ; interactive docview replacement
       pdf-view-restore           ; add view history to pdf-tools
       quelpa                     ; install Emacs packages from source
       rainbow-mode               ; set background color to color string
       sly                        ; Sylvester the Cat's Common Lisp IDE
       smartparens                ; smart editing of character pairs
       toml-mode                  ; Tom's Obvious Minimal Language mode
       undo-tree                  ; more advanced yet simpler undo system
       vertico                    ; VERTical Interactive Completion
       wgrep                      ; open a writable grep buffer
       wordnut                    ; WordNet lexical database
       writegood-mode             ; bullshit and weasel-word detector
       ws-butler                  ; remove trailing whitespace
       xr                         ; undo rx to grok regular expressions
       yasnippet)))               ; code or text template expansion
#+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
   '(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)
   '(use-short-answer t)
   '(view-read-only 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#Faces][Text faces or look (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:text-faces-or-look
:END:

Section [[#sec:text-faces-or-styles][text faces or styles (info)]] tells that this setup does not use theming.
However, in order to improve visibility, it relies on:
1. Tweaking faces in memory after loading as in listing
   [[lst:tweak-faces-faces-after]].
2. Shadowing the definition of faces before loading as in listing
   [[lst:tweak-org-faces-before]] and [[lst:tweak-sh-script-faces-before]]. 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.
Section [[#sec:text-faces-or-styles][text faces or styles (info)]] also defines the function
src_emacs-lisp{(my-invert-default-face)} to toggle between a dark and a light
background.

#+caption[Improve the visibility of faces in =faces.el=]:
#+caption: Improve the visibility of faces in =faces.el=.
#+name: lst:tweak-faces-faces-after
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    (defun tweak-region-face-background-color ()
      (when (featurep 'gtk)
        (set-face-attribute
         'region nil
         :background (cdr (assoc (face-attribute 'default :background)
                                 '(("white" . "LightGoldenrod2")
                                   ("black" . "blue3")))))))

    (tweak-region-face-background-color))
#+end_src

#+caption[Improve the visibility of faces in =org-faces.el=]:
#+caption: Improve the visibility of faces in =org-faces.el=.
#+name: lst:tweak-org-faces-before
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    ;; Shadow the definition 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'."))
#+end_src

#+caption[Improve the visibility of faces in =sh-script.el=]:
#+caption: Improve the visibility of faces in =sh-script.el=.
#+name: lst:tweak-sh-script-faces-before
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    ;; Shadow the 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#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
    (define-key
      dired-mode-map (kbd "E")
      (defun my-dired-eww-find-file ()
        "Visit dired file with eww."
        (interactive)
        (eww-open-file (dired-get-file-for-visit))))

    ;; https://truongtx.me/tmtxt-dired-async.html
    (define-key
      dired-mode-map (kbd "Y")
      (defun my-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)))))
#+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#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)]].
In addition, the [[https://github.com/quelpa/quelpa][quelpa]] tool allows to fetch code from any source and build a
package on your computer before installation.  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 ensures installation of [[https://github.com/quelpa/quelpa][quelpa]] before ensuring installation of [[https://www.reddit.com/r/emacs/comments/l6rcqh/undotree_repositorys_new_home_gitlab/][undo-tree]].
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.
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 (require 'no-littering nil 'noerror)
    (package-refresh-contents)
    (package-install 'no-littering)
    (require 'no-littering))

  (unless (package-installed-p 'quelpa)
    (package-install 'quelpa))

  (unless (package-installed-p 'undo-tree)
    ;; Neither GNU ELPA, nor MELPA have the latest version.
    (quelpa '(undo-tree :repo "tsc25/undo-tree" :fetcher gitlab)))

  (unless noninteractive
    (package-install-selected-packages))
#+end_src

* [[info:dir#Top][Info documentation]]
:PROPERTIES:
:CUSTOM_ID: sec:info-documentation
:END:

Listing [[lst:configure-info]] fixes what looks like a bug in Emacs-28.0.91 and adds
a path in my home directory 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
    (unless (version< emacs-version "28.0")
      ;; Why is this necessary after `package-activate-1'?
      (dolist (item package-alist)
        (let ((pkg-dir (package-desc-dir (cadr item))))
          (when (file-exists-p (expand-file-name "dir" pkg-dir))
            (cl-pushnew pkg-dir Info-directory-list :test #'equal)))))

    ;; Emacs should 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:
** [[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 my-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

* [[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 none
  # pdf previewer and update pdf previewer
  $pdf_previewer = "emacsclient -e '(find-file-other-window %S)'";
  $pdf_update_method = 4;  # 4 runs a 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' );
  $clean_ext .= " acr acn alg bbl glo gls glg ist lol run.xml";
  sub makeglossaries {
      my ($name, $path) = fileparse( $$Psource );
      return system "makeglossaries -d '$path' '$name'";
  }
  # Emacs looks for "Local variables:" after the last "?\n?\f".
  
  # 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 none
#+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
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]]

* 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:orderless#Top][Orderless (info)]] for an advanced completion style,
2. [[info:embark#Top][Embark (info)]] for minibuffer actions with context menus,
3. [[info:marginalia#Top][Marginalia (info)]] for rich annotations in the minibuffer, and
4. [[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 and [[#sec:minibuffer-history-completion][minibuffer-history-completion]] provides completion
on previous input in the minibuffer.

** [[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)
    (custom-set-variables
     '(savehist-additional-variables
       '(eww-history
         kill-ring
         regexp-search-string
         search-ring
         search-string))))
  (when (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                         | keys                | remap                              |
|---------------------------------+---------------------+------------------------------------|
| =vertico-directory-delete-char= | {{{kbd(DEL)}}}      |                                    |
| =vertico-directory-delete-word= | {{{kbd(M-DEL)}}}    |                                    |
| =vertico-directory-enter=       | {{{kbd(RET)}}}      |                                    |
| =vertico-exit=                  | {{{kbd(C-j)}}}      | =exit-minibuffer=                  |
| =vertico-exit-input=            | {{{kbd(C-RET)}}}    |                                    |
| =vertico-first=                 | {{{kbd(M-<)}}}      | =beginning-of-buffer=              |
| =vertico-first=                 | {{{kbd(M-<)}}}      | =minibuffer-beginning-of-buffer=   |
| =vertico-insert=                | {{{kbd(TAB)}}}      |                                    |
| =vertico-last=                  | {{{kbd(M->)}}}      | =end-of-buffer=                    |
| =vertico-next-group=            | {{{kbd(C-<down>)}}} | =forward-paragraph=                |
| =vertico-next=                  | {{{kbd(<down>)}}}   | =next-line-or-history-element=     |
| =vertico-next=                  | {{{kbd(C-n)}}}      | =next-line=                        |
| =vertico-previous-group=        | {{{kbd(C-<up>)}}}   | =backward-paragraph=               |
| =vertico-previous=              | {{{kbd(<up>)}}}     | =previous-line-or-history-element= |
| =vertico-previous=              | {{{kbd(C-p)}}}      | =previous-line=                    |
| =vertico-save=                  | {{{kbd(M-w)}}}      | =kill-ring-save=                   |
| =vertico-scroll-down=           | {{{kbd(M-v)}}}      | =scroll-down-command=              |
| =vertico-scroll-up=             | {{{kbd(C-v)}}}      | =scroll-up-command=                |
|---------------------------------+---------------------+------------------------------------|

** [[info:orderless#Top][Orderless (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:orderless-configuration
:END:

Listing [[lst:configure-orderless]] enables =orderless=.

#+caption[Configure =orderless=]:
#+caption: Configure =orderless=.
#+name: lst:configure-orderless
#+begin_src emacs-lisp
  (when (fboundp 'orderless-filter)
    (custom-set-variables
     ;; https://github.com/purcell/emacs.d/issues/778
     '(completion-styles '(basic completion-partial orderless))
     '(completion-category-defaults nil)
     '(completion-category-overrides
       '((file (styles partial-completion)))))
    (add-hook 'minibuffer-setup-hook
              (defun my-on-minibuffer-setup-hook()
                (setq-default completion-styles '(substring orderless)))))
#+end_src

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

Listing [[lst:configure-embark]] configures =embark= key bindings: type for instance
{{{kbd(C-x C-h)}}} or {{{kbd(C-c C-h)}}} that the initialization
src_emacs-lisp{(setq prefix-help-command #'embark-prefix-help-command)} enables
minibuffer help after a prefix key.

#+caption[Configure =embark=]:
#+caption: Configure =embark=.
#+name: lst:configure-embark
#+begin_src emacs-lisp
  (when (cl-every #'fboundp '(embark-act embark-bindings embark-dwim))
    (global-set-key (kbd "C-,") #'embark-act)
    (global-set-key (kbd "C-:") #'embark-dwim)
    (global-set-key (kbd "C-h B") #'embark-bindings)
    (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 (fboundp 'marginalia-mode)
    (marginalia-mode +1))
#+end_src

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

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


#+caption[Configure =consult=]:
#+caption: Configure =consult=.
#+name: lst:configure-consult
#+begin_src emacs-lisp
  (when (fboundp 'consult-apropos)
    (custom-set-variables
     '(consult-project-root-function #'vc-root-dir))
    ;; C-c bindings (mode-specific-map)
    (global-set-key (kbd "C-c h") #'consult-history)
    (global-set-key (kbd "C-c m") #'consult-mode-command)
    ;; 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-map (kbd "4 b") #'consult-buffer-other-window)
    (define-key ctl-x-map (kbd "5 b") #'consult-buffer-other-frame)
    (define-key ctl-x-map (kbd "r x") #'consult-register)
    (define-key ctl-x-map (kbd "r 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-project)
    (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
    (global-set-key (kbd "M-y") #'consult-yank-pop)
    (global-set-key (kbd "<help> a") #'consult-apropos)
    ;; Tweak functions
    (advice-add 'completing-read-multiple
                :override #'consult-completing-read-multiple))
#+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

** [[https://lists.gnu.org/archive/html/emacs-devel/2021-12/msg00802.html][Minibuffer history completion]]
:PROPERTIES:
:CUSTOM_ID: sec:minibuffer-history-completion
:END:

See [[https://lists.gnu.org/archive/html/emacs-devel/2021-12/msg00802.html][Juri Linkov (Emacs Developer mailing list)]] for how to allow completion on
previous input in the minibuffer. Listing
[[lst:enable-minibuffer-history-completion]] enables minibuffer history completion.

#+caption[Enable =minibuffer-history-completion=]:
#+caption: Enable =minibuffer-history-completion=.
#+name: lst:enable-minibuffer-history-completion
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    (defun minibuffer-setup-history-completions ()
      (unless (or minibuffer-completion-table minibuffer-completion-predicate)
        (setq-local minibuffer-completion-table
                    (symbol-value minibuffer-history-variable))))

    (add-hook 'minibuffer-setup-hook 'minibuffer-setup-history-completions)

    ;; Stolen from Emacs-28.1 for Emacs-27.2:
    (unless (fboundp 'minibuffer--completion-prompt-end)
      (defun minibuffer--completion-prompt-end ()
        (let ((end (minibuffer-prompt-end)))
          (if (< (point) end)
              (user-error "Can't complete in prompt")
            end))))

    ;; Adapted from ‘minibuffer-complete’:
    (defun minibuffer-complete-history ()
      "Allow minibuffer completion on previous input."
      (interactive)
      (completion-in-region (minibuffer--completion-prompt-end) (point-max)
                            (symbol-value minibuffer-history-variable)
                            nil))

    (define-key minibuffer-local-map (kbd "C-<tab>") #'minibuffer-complete-history))
#+end_src

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

** [[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 (autoload 'deadgrep "deadgrep" nil t)
    (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

* 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:

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

#+caption[Enable =nov-mode=]:
#+caption: Enable =nov-mode=.
#+name: lst:enable-nov-mode
#+begin_src emacs-lisp
  (when (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.

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[Enable =pdf-tools=]:
#+caption: Enable =pdf-tools=.
#+name: lst:enable-pdf-tools
#+begin_src emacs-lisp
  (when (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-view
      (custom-set-variables
       '(pdf-view-display-size 'fit-page))

      (when (fboundp 'pdf-view-restore-mode)
        (add-hook 'pdf-view-mode-hook #'pdf-view-restore-mode))))
#+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]].  For instance, 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~.  Listing [[lst:require-auctex]] initializes
[[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]] properly.

#+caption[Require =AUCTeX=]:
#+caption: Require =AUCTeX=.
#+name: lst:require-auctex
#+begin_src emacs-lisp
  ;; Use `require' to make `TeX-master' a safe local variable.
  (when (require 'tex nil 'noerror)
    (custom-set-variables
     '(TeX-auto-save t)
     '(TeX-install-font-lock #'font-latex-setup)
     '(TeX-parse-self t)))
#+end_src

Listing [[lst:configure-bibtex]] configures the Emacs =bibtex= library to use the
LaTeX =BiBTeX= dialect for backwards compatibility.

#+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

Listing [[lst:configure-font-latex]] disables font scaling of section titles.

#+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

Listing [[lst:configure-latex]] configures =latex= for a full featured
=LaTeX-section-command=.  Finally, out of the box, [[https://en.wikipedia.org/wiki/AUCTeX][AUCTeX]] does not indent text
between square brackets.  The code in listing [[lst:configure-tex]] corrects this by
advising to override ~TeX-brace-count-line~ with ~my-TeX-brace-count-line~.

#+caption[Configure =latex=]:
#+caption: Configure =latex=.
#+name: lst:configure-latex
#+begin_src emacs-lisp
  (with-eval-after-load 'latex
    (custom-set-variables
     '(LaTeX-section-hook '(LaTeX-section-heading
                            LaTeX-section-title
                            LaTeX-section-toc
                            LaTeX-section-section
                            LaTeX-section-label))))
#+end_src

#+caption[Configure =TeX=]:
#+caption: Configure =TeX=.
#+name: lst:configure-tex
#+begin_src emacs-lisp
  (with-eval-after-load 'tex
    (custom-set-variables
     ;; Disable `TeX-electric-math' to prevent collisions with `smartparens'.
     '(TeX-electric-math nil))

    ;; https://emacs.stackexchange.com/questions/17396/
    ;; indentation-in-square-brackets
    (defun my-TeX-brace-count-line ()
      "Count number of open/closed braces."
      (save-excursion
        (let ((count 0) (limit (line-end-position)) char)
          (while (progn
                   (skip-chars-forward "^{}[]\\\\" limit)
                   (when (and (< (point) limit) (not (TeX-in-comment)))
                     (setq char (char-after))
                     (forward-char)
                     (cond ((eq char ?\{)
                            (setq count (+ count TeX-brace-indent-level)))
                           ((eq char ?\})
                            (setq count (- count TeX-brace-indent-level)))
                           ((eq char ?\[)
                            (setq count (+ count TeX-brace-indent-level)))
                           ((eq char ?\])
                            (setq count (- count TeX-brace-indent-level)))
                           ((eq char ?\\)
                            (when (< (point) limit)
                              (forward-char) t))))))
          count)))

    (advice-add 'TeX-brace-count-line :override #'my-TeX-brace-count-line))
#+end_src

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

#+caption[Configure =math-preview=]:
#+caption: Configure =math-preview=.
#+name: lst:configure-math-preview
#+begin_src emacs-lisp
  (with-eval-after-load 'math-preview
    (let ((command (executable-find "~/node_modules/.bin/math-preview")))
      (if command
          (custom-set-variables
           `(math-preview-command ,command)
           '(math-preview-raise 0.5)
           '(math-preview-scale 1))
        ;; https://stackoverflow.com/a/17509764 answers:
        ;; How to install an npm package from github directly?
        (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 Org files
:PROPERTIES:
:CUSTOM_ID: sec:writing-org-files
:END:

*** [[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:

The code in listing [[lst:customize-org-babel]], [[lst:customize-org]], and
[[lst:customize-org-export]] does basic customization of [[https://orgmode.org/][Org-mode]] variables.
Listing [[lst:customize-org-latex-classes]] defines [[info:org#LaTeX specific export settings][org-latex-classes (info)]] for
backward compatibility. See table [[tab:org-latex-class-tag-placeholder]] and type
{{{kbd(C-h v org-latex-classes)}}} for an explanation of the code in listing
[[lst:customize-org-latex-classes]].

#+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]            |

#+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-python
    (custom-set-variables
     '(org-babel-python-command "python -E")))

  (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))))
#+end_src

#+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 '((C . t)
                                  (calc . t)
                                  (dot . t)
                                  (emacs-lisp . t)
                                  (eshell . t)
                                  (fortran . t)
                                  (gnuplot . t)
                                  (latex . t)
                                  (lisp . t)
                                  (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 :session :async")
                                      ("v" . "verse")))))
#+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 'org
    ;; 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)))

    (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-export=]:
#+caption: Customize =org-export=.
#+name: lst:customize-org-export
#+begin_src emacs-lisp
  (with-eval-after-load 'ox-latex
    (custom-set-variables
     '(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")
     '(org-latex-listings 'minted)
     '(org-latex-minted-langs '((cc "c++")
                                (cperl "perl")
                                (diff "diff")
                                (shell-script "bash")
                                (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

*** [[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, orderless, 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.  Listing [[lst:configure-oc-cite+citar]] configures =org-cite=, =citar=,
and =org=.

#+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
    (require 'oc-biblatex)
    (require 'oc-csl)

    (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))))

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

    (define-key org-mode-map (kbd "C-c b") #'org-cite-insert))
#+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 an [[https://orgmode.org/][Org-mode]] cite link:
   1. Type {{{kbd(C-c b)}}} or {{{kbd(M-x org-cite-insert)}}}.
   2. Navigate to the bibliographic entry to insert.
   3. Select it.
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]]

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

Listing [[lst:customize-org-link]] configures =org-link= to use relative file path
links.

#+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

Listing [[lst:org-ref-like-org-link-types]] defines =org-link= types for backwards
compatibility with [[https://github.com/jkitchin/org-ref][org-ref]].  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]].  Finally, listing
[[lst:emacs-lisp-setup-patch-ol-info]] 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 (lambda (path _desc backend _info)
                     (pcase backend
                       (`latex (format "\\gls*{%s}" path))
                       (_ path))))
    (org-link-set-parameters
     "cite" :export (lambda (path _desc backend _info)
                      (pcase backend
                        (`latex (format "\\cite{%s}" path))
                        (_ path))))
    (org-link-set-parameters
     "eqref" :export (lambda (path _desc backend _info)
                       (pcase backend
                         (`latex (format "\\eqref{%s}" path))
                         (_ path))))
    (org-link-set-parameters
     "hyperlink" :export (lambda (path desc backend _info)
                           (pcase backend
                             (`latex (format "\\hyperlink{%s}{%s}" path desc))
                             (_ path))))
    (org-link-set-parameters
     "label" :export (lambda (path _desc backend _info)
                       (pcase backend
                         (`latex (format "\\label{%s}" path))
                         (_ path))))
    (org-link-set-parameters
     "ref" :export (lambda (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:emacs-lisp-setup-patch-ol-info
#+begin_src emacs-lisp :exports code :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

#+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 :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")
                      ("marginalia" . "https://github.com/minad/marginalia")
                      ("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://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 'org
    (defun org-syntax-convert-keyword-case-to-lower ()
      "Convert all #+KEYWORDS to #+keywords."
      (interactive)
      (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
  (defun my-org-eval-blocks-named (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)
                 (let ((name (org-element-property :name block)))
                   (when (and name (string-match-p infix name))
                     block))))))
        (dolist (block blocks)
          (goto-char (org-element-property :begin block))
          (org-babel-execute-src-block)))))

  ;; Emacs looks for "Local variables:" after the last "?\n?\f".
  (add-to-list 'safe-local-eval-forms
               '(apply 'my-org-eval-blocks-named '("emacs-lisp-setup")))
  (add-to-list 'safe-local-eval-forms
               '(apply 'my-org-eval-blocks-named '("python-setup")))
#+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:emacs-lisp-setup-latex-header]] 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:emacs-lisp-setup-latex-header
#+begin_src emacs-lisp :exports code :silent
  (with-eval-after-load 'org-src
    (defun prefix-all-lines (prefix body)
      (with-temp-buffer
        (insert body)
        (string-insert-rectangle (point-min) (point-max) prefix)
        (buffer-string)))

    (add-to-list 'org-src-lang-modes '("latex-header" . latex))

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

    (defun org-babel-execute:latex-header (body _params)
      "Execute a block of LaTeX preamble 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))

    (add-to-list 'org-src-lang-modes '("latex-extra-header" . latex))

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

    (defun org-babel-execute:latex-extra-header (body _params)
      "Execute a block of LaTeX preamble 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)))
#+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#Export Settings][#+INCLUDE: <FILE> (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:include-file-usage
:END:

Evaluation of the source block in listing
[[lst:make-source-block-with-export-keyword-settings]] produces the source block
that exports to listing [[lst:source-file-export-keyword-settings]] in order to show
the first nine lines of this [[file:README.org]] file.  The last line shows that
[[file:include.org][include.org]] is the argument for [[info:org#Export Settings][#+INCLUDE: <FILE>]].

#+caption[Make setup and include file export keyword settings source block]:
#+caption: The shell script to make the source block containing the export
#+caption: keyword settings.
#+name: lst:make-source-block-with-export-keyword-settings
#+begin_src shell :exports both :results drawer
  echo "#+caption[Source file export keyword settings]:"
  echo "#+caption: The first nine lines of README.org containing the export"
  echo "#+caption: keyword settings."
  echo "#+name: lst:source-file-export-keyword-settings"
  echo "#+begin_src org :tangle no"
  head -n 9 README.org
  echo -n "#+end_src"
#+end_src

#+RESULTS: lst:make-source-block-with-export-keyword-settings
:results:
#+caption[Source file export keyword settings]:
#+caption: The first nine lines of README.org containing the export
#+caption: keyword settings.
#+name: lst:source-file-export-keyword-settings
#+begin_src org :tangle no
#+title: Emacs setup for use with LaTeX, Org, and Python
#+author: Gerard Vermeulen
#+babel: :cache no
#+latex_class: article-local
#+latex_class_options: [11pt,a4paper,english,svgnames,tables]
#+macro: kbd (eval (by-backend-kbd-org-macro $1))
#+property: header-args:emacs-lisp :exports code :results silent :tangle init.el
#+property: header-args:org :tangle include.org
#+startup: content
#+end_src
:end:

Listing [[lst:by-backend-kbd-org-macro]] defines the tools for the definition of the
[[https://orgmode.org/][Org mode]] =kbd= macro on the fifth line of listing
[[lst:source-file-export-keyword-settings]].

#+caption[Define the tools of the =Org-mode= =kbd= macro]:
#+caption: Define the tools for the =Org-mode= =kbd= macro.
#+name: lst:by-backend-kbd-org-macro
#+begin_src emacs-lisp
  (with-eval-after-load 'ox
    (autoload 'htmlize-protect-string "htmlize" nil t)

    (defmacro by-backend (&rest body)
      `(cl-case org-export-current-backend ,@body))

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

Listing [[lst:use-latex-header-1]], [[lst:use-latex-header-2]], [[lst:use-latex-header-3]],
[[lst:use-latex-header-4]], and [[lst:use-latex-header-5]] tangle into the
[[file:include.org][include.org]] file in order to create the [[https://www.latex-project.org/][LaTeX]] preamble.

#+caption[LaTeX preamble: replacing the =Org-mode= default packages]:
#+caption: LaTeX preamble: replacing the =Org-mode= default packages.
#+name: lst:use-latex-header-1
#+begin_src org
  ,#+begin_src latex-header
    % LuaLaTeX-, PdfLaTeX-, or XeTeX-COMPILER COMPATIBILITY:
    % Prevent collisions by using font packages before compiler specific packages.
    \usepackage{ifthen,ifluatex,ifxetex}
    \usepackage{amsmath}
    \usepackage{amssymb}
    \usepackage{pifont}          % check mark (\ding{52}) and cross mark (\ding{56})
    \usepackage{textcomp}        % \texttimes
    \usepackage{wasysym}         % \diameter
    \ifthenelse{\boolean{luatex}}{
      \usepackage{fontspec}        % lualatex
      \usepackage{unicode-math}    % lualatex
    }{\ifthenelse{\boolean{xetex}}{
        \usepackage{mathspec}        % xetex
      }{
        \usepackage[T1]{fontenc}     % pdflatex
        \usepackage[utf8]{inputenc}  % pdflatex
      }
    }

    % Org-mode REQUIREMENTS:
    \usepackage{graphicx}
    \usepackage{longtable}
    \usepackage{wrapfig}
    \usepackage{rotating}
    \usepackage[normalem]{ulem}
    \usepackage{capt-of}
    \usepackage{hyperref}

  ,#+end_src
#+end_src

#+caption[LaTeX preamble: language, lists and floats]:
#+caption: LaTeX preamble: language, lists and floats.
#+name: lst:use-latex-header-2
#+begin_src org
  ,#+begin_src latex-header
    % 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_src
#+end_src

#+caption[LaTeX preamble: page layout]:
#+caption: LaTeX preamble: page layout.
#+name: lst:use-latex-header-3
#+begin_src org
  ,#+begin_src latex-header
    % PAGE LAYOUT:
    \usepackage{fancyhdr}
    \usepackage{lastpage}
    \usepackage[
      headheight=20mm,
      top=40mm,
      bottom=20mm,
      left=60pt,
      right=60pt,
      heightrounded,
      verbose,
    ]{geometry}

    % TECHNICS:
    \usepackage{siunitx}
    \usepackage{tikz}

  ,#+end_src
#+end_src

#+caption[LaTeX preamble: float barriers]:
#+caption: LaTeX preamble: float barriers.
#+name: lst:use-latex-header-4
#+begin_src org
  ,#+begin_src latex-header
    % 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
      }%
    }
    \makeatother

  ,#+end_src
#+end_src

#+caption[LaTeX preamble: fancy headers and footers]:
#+caption: LaTeX preamble: fancy headers and footers.
#+name: lst:use-latex-header-5
#+begin_src org
  ,#+begin_src latex-header
    % 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}}
    }
    % #+latex_header: END.
  ,#+end_src
#+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(M-x org-latex-classes)}}}, {{{kbd(M-x
org-latex-subtitle-format)}}}, {{{kbd(M-x org-latex-title-command)}}}, and
{{{kbd(M-x 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}
  \\listoftables
  \\listoffigures
  \\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/org-contrib/babel/languages/ob-doc-LaTeX.html#orgcc214c1][Worg: backend dependent execution]]
:PROPERTIES:
:CUSTOM_ID: sec:backend-dependent-execution-update
:END:

#+caption[Worg update: backend dependent header arguments]:
#+caption: Worg update: backend dependent header arguments.
#+name: lst:backend-dependent-execution-update
#+begin_src org :tangle worg-backend-dependent-execution-update.org
  ,#+latex_header: \usepackage{tikz}

  ,#+header: :file (by-backend (html "tree.svg") (latex nil))
  ,#+header: :results (by-backend (html "raw file") (latex "latex replace"))
  ,#+header: :headers '("\\usepackage{tikz}\n")
  ,#+begin_src latex
    \usetikzlibrary{trees}
    \begin{tikzpicture}
      \node [circle, draw, fill=red!20] at (0,0) {1}
      child { node [circle, draw, fill=blue!30] {2}
        child { node [circle, draw, fill=green!30] {3} }
        child { node [circle, draw, fill=yellow!30] {4} }};
    \end{tikzpicture}
  ,#+end_src

  # Setup
  ,#+begin_src emacs-lisp :exports none
    (with-eval-after-load 'ox
      (setq org-babel-latex-htlatex "htlatex")
      (defmacro by-backend (&rest body)
        `(cl-case org-export-current-backend ,@body)))
  ,#+end_src
#+end_src

This section updates the outdated [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-LaTeX.html#orgcc214c1][Worg: backend dependent execution]] example to
Emacs-27.2 and Org-9.5.2.  It shows how to export [[https://en.wikipedia.org/wiki/PGF/TikZ][PGF/TikZ]] images to:
1. [[https://en.wikipedia.org/wiki/PDF][PDF]] by embedding in [[https://www.latex-project.org/][LaTeX]].
2. [[https://en.wikipedia.org/wiki/HTML][HTML]] by passing from [[https://www.latex-project.org/][LaTeX]] by [[https://en.wikipedia.org/wiki/PDF][PDF]] and to [[https://en.wikipedia.org/wiki/Scalable_Vector_Graphics][SVG]].
Listing [[lst:backend-dependent-execution-update]] tangles to
[[file:worg-backend-dependent-execution-update.org][worg-backend-dependent-execution-update.org]] as either a standalone example or an
example for inclusion.  Finally, inclusion of
[[file:worg-backend-dependent-execution-update.org][worg-backend-dependent-execution-update.org]] produces here the figure with the
nodes 1, 2, 3, and 4:\\
#+include: worg-backend-dependent-execution-update.org
How to include such figures as floats remains an open question.

*** [[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 (autoload 'pp-display-expression "pp")
      (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

* Programming
:PROPERTIES:
:CUSTOM_ID: sec:programming
: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
  (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 :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:

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]]

** [[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 two 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://github.com/pythonic-emacs/anaconda-mode][Anaconda - code navigation, documentation lookup, and completion for Python]].
In my opinion, [[https://github.com/joaotavora/eglot][eglot]] has more potential than [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]], but [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] is
compatible with [[info:org#Editing Source Code][source code block editing]] while [[https://github.com/joaotavora/eglot][eglot]] is not.

Here are a few links covering how to integrate Emacs, Python and a Python LSP
server, before plunging into the configuring 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:configure-python]] tells the Python shell to disregard its environment
variables (in particular =PYTHONSTARTUPFILE=).  The [[https://github.com/pythonic-emacs/pythonic#readme][pythonic]] and [[https://github.com/jorgenschaefer/pyvenv#readme][pyvenv]] packages
provide support 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]]) and tweak the
environment variables and restart the relevant Python child processes (in case
of [[https://github.com/jorgenschaefer/pyvenv#readme][pyvenv]]).  Therefore, this setup replaces those packages with listing
[[lst:manage-pyenv]] to manage [[https://github.com/pyenv/pyenv#readme][pyenv]] from within Emacs and listing
[[lst:setting-python-shell-virtualenv-root]] to set
=python-shell-virtualenv-root=.

#+caption[Configure =python=]:
#+caption: Configure =python=.
#+name: lst:configure-python
#+begin_src emacs-lisp
  (with-eval-after-load 'python
    (custom-set-variables
     '(python-indent-guess-indent-offset nil)
     '(python-shell-interpreter-args "-i -E")))
#+end_src

#+caption[Manage =pyenv=]:
#+caption: Manage =pyenv=.
#+name: lst:manage-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[Setting =python-shell-virtualenv-root=]:
#+caption: Setting =python-shell-virtualenv-root=.
#+name: lst:setting-python-shell-virtualenv-root
#+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 (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

*** [[https://github.com/joaotavora/eglot][Eglot]]
:PROPERTIES:
:CUSTOM_ID: sec:eglot
:END:
Listing [[lst:configure-eglot+python-lsp-server-for-python]] tangles to
=user-init-file= and 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]].
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-rope/rope#readme][rope]],
and [[https://github.com/google/yapf#readme][yapf]].  In addition, install the [[https://github.com/emanspeaks/pyls-flake8#readme][pyls-flake8]] plugin to let [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]]
use [[https://github.com/PyCQA/flake8][flake8]].

Listing [[lst:on-hack-local-variables-hook-eglot-maybe]] defines a hook function to
launch [[https://github.com/joaotavora/eglot][eglot]] in presence of a proper [[info:emacs#Directory Variables][.dir-locals.el]] file in the root directory
of any [[https://www.python.org][Python]] project.  Listing [[lst:eglot-directory-variables-for-python]] shows
such a proper [[info:emacs#Directory Variables][.dir-locals.el]] file.

#+caption[Configure =eglot= with =python-lsp-server= for Python]:
#+caption: Configure =eglot= with =python-lsp-server= for Python.
#+name: lst:configure-eglot+python-lsp-server-for-python
#+begin_src emacs-lisp
  (with-eval-after-load 'eglot
    ;; (setq eglot-server-programs '((python-mode "pylsp")))
    (add-to-list 'eglot-server-programs '(python-mode "pylsp"))

    (setq-default
     eglot-workspace-configuration
     '(;; Disable the `:pyls_flake8' plugin to fall back to pycodestyle.
       (:pylsp . (:plugins (:pyls_flake8 (:enabled t))))
       (:pylsp . (:plugins (:jedi_completion (:cache_for ["astropy"]))))
       (:pylsp . (:plugins (:jedi (:auto_import_modules ["numpy"]))))))

    (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[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:on-hack-local-variables-hook-eglot-maybe
#+begin_src emacs-lisp
  (when (fboundp '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 'hack-local-variables-hook
              (defun on-hack-local-variables-hook-eglot-maybe ()
                (when (and (derived-mode-p 'python-mode)
                           (assoc 'eglot-workspace-configuration
                                  dir-local-variables-alist))
                  (eglot-ensure)))))
#+end_src

#+caption[Propose =directory-variables= to launch =eglot=]:
#+caption: Propose =directory-variables= in the root of any Python project to
#+caption: launch =eglot=.
#+name: lst:eglot-directory-variables-for-python
#+begin_src emacs-lisp :tangle dir-locals.el
  ;; Proposal for a .dir-locals.el file in the root of any Python project.
  ((python-mode
    . ((eglot-workspace-configuration
        . (;; Disable the `:pyls_flake8' plugin to fall back to pycodestyle.
           (:pylsp . (:plugins (:pyls_flake8 (:enabled t))))
           (:pylsp . (:plugins (:jedi (:auto_import_modules ["numpy"]))))
           (:pylsp . (:plugins (: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                   | keys             | key map          |
|---------------------------+------------------+------------------|
| =xref-find-definition=    | {{{kbd(M-.)}}}   | =global-map=     |
| =xref-pop=                | {{{kbd(M-\,)}}}  | =global-map=     |
| =flymake-goto-next-error= | {{{kbd(C-c n)}}} | =eglot-mode-map= |
| =flymake-goto-prev-error= | {{{kbd(C-c p)}}} | =eglot-mode-map= |
| =eglot-rename=            | {{{kbd(C-c r)}}} | =eglot-mode-map= |
| =eldoc-doc-buffer=        | {{{kbd(C-h .)}}} | =eglot-mode-map= |
|---------------------------+------------------+------------------|

Allthough the configuration of [[https://github.com/pythonic-emacs/blacken#readme][blacken]] is not explicit, I use it to format all
new Python code with the [[https://black.readthedocs.io/en/stable/index.html][Python Black code formatter]]. Listing
[[lst:pyproject-toml-kick-off]] and [[lst:setup-cfg-kick-off]] implement the rules in
[[https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html][using black with other tools]] in order to 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]].

#+caption[Kick starting a =pyproject.toml= file]:
#+caption: Kick starting a =pyproject.toml= file.
#+name: lst:pyproject-toml-kick-off
#+begin_src toml :tangle pyproject.toml
  [build-system]
  requires = ["setuptools", "wheel"]
  build-backend = "setuptools.build_meta"

  [tool.black]
  line-length = 88
#+end_src

#+caption[Kick starting a =setup.cfg= file]:
#+caption: Kick starting a =setup.cfg= file.
#+name: lst:setup-cfg-kick-off
#+begin_src toml :tangle setup.cfg
  [flake8]
  max-line-length = 88
  extend-ignore = E203

  [pycodestyle]
  ignore = E203
  max-line-length = 88
#+end_src

[[https://jedi.readthedocs.io/en/latest/][Jedi]] provides grammar checking and completion candidates to [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]].
Only [[https://jedi.readthedocs.io/en/latest/docs/changelog.html][jedi-0.18.1]] works with for instance [[https://numpy.org/][numpy-1.22.0]] in the sense that it does
not choke on universal functions provided that [[https://jedi.readthedocs.io/en/latest/][jedi]] does not parse but imports
[[https://numpy.org/][numpy-1.22.0]] (see [[https://github.com/davidhalter/jedi/issues/1744][jedi issue #1744]], [[https://github.com/davidhalter/jedi/issues/1745][#1745]], and [[https://github.com/davidhalter/jedi/issues/1746][#1746]]).  Since the universal
functions are neither builtin methods nor data instances but a kind of "callable
instances", the [[https://docs.python.org/3/library/inspect.html][Python inspect]] module also fails to handle the universal
functions properly.

Listing [[lst:make-pylsp-server-patch]] generates and listing
[[lst:echo-pylsp-server-patch]] echos the patch in listing
[[lst:show-pylsp-server-patch]] to make [[https://jedi.readthedocs.io/en/latest/][jedi]] import [[https://numpy.org/][numpy-1.22.2]] in order to serve
the information to [[https://github.com/python-lsp/python-lsp-server][python-lsp-server]] allowing it to handle universal functions.

#+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-auto-import-modules.patch
#+end_src

#+caption[Echo =pylsp-auto-import-modules.patch= listing]:
#+caption: Echo =pylsp-auto-import-modules.patch= listing.
#+name: lst:echo-pylsp-server-patch
#+begin_src shell :exports both :results drawer
  echo "#+attr_latex: :options breaklines"
  echo "#+caption[Show =pylsp-auto-import-modules.patch=]:"
  echo "#+caption: Show =pylsp-auto-import-modules.patch=."
  echo "#+name: lst:show-pylsp-server-patch"
  echo "#+begin_src diff :tangle no"
  cat pylsp-auto-import-modules.patch
  echo -n "#+end_src"
#+end_src

#+RESULTS: lst:echo-pylsp-server-patch
:results:
#+attr_latex: :options breaklines
#+caption[Show =pylsp-auto-import-modules.patch=]:
#+caption: Show =pylsp-auto-import-modules.patch=.
#+name: lst:show-pylsp-server-patch
#+begin_src diff :tangle no
diff --git a/pylsp/config/schema.json b/pylsp/config/schema.json
index c29d78b..4f30101 100644
--- a/pylsp/config/schema.json
+++ b/pylsp/config/schema.json
@@ -69,6 +69,14 @@
       "default": null,
       "description": "List of errors and warnings to enable."
     },
+    "pylsp.plugins.jedi.auto_import_modules": {
+      "type": "array",
+        "default": ["numpy", "gi"],
+      "items": {
+        "type": "string"
+      },
+      "description": "List of module names for jedi to import (jedi.settings.auto_import_modules)."
+    },
     "pylsp.plugins.jedi.extra_paths": {
       "type": "array",
       "default": [],
diff --git a/pylsp/workspace.py b/pylsp/workspace.py
index bf312f6..4758b53 100644
--- a/pylsp/workspace.py
+++ b/pylsp/workspace.py
@@ -14,6 +14,8 @@ from . import lsp, uris, _utils

 log = logging.getLogger(__name__)

+DEFAULT_AUTO_IMPORT_MODULES = ["numpy", "gi"]
+
 # TODO: this is not the best e.g. we capture numbers
 RE_START_WORD = re.compile('[A-Za-z_0-9]*$')
 RE_END_WORD = re.compile('^[A-Za-z_0-9]*')
@@ -252,6 +254,8 @@ class Document:

         if self._config:
             jedi_settings = self._config.plugin_settings('jedi', document_path=self.path)
+            jedi.settings.auto_import_modules = jedi_settings.get('auto_import_modules',
+                                                                  DEFAULT_AUTO_IMPORT_MODULES)
             environment_path = jedi_settings.get('environment')
             extra_paths = jedi_settings.get('extra_paths') or []
             env_vars = jedi_settings.get('env_vars')
#+end_src
:end:

*** [[https://github.com/pythonic-emacs/anaconda-mode][Anaconda]]
:PROPERTIES:
:CUSTOM_ID: sec:anaconda
:END:
Listing [[lst:configure-anaconda+company-for-python]] and
[[lst:define-my-toggle-anaconda-mode]] configure [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]]. See [[https://github.com/jorgenschaefer/elpy/blob/8d0de310d41ebf06b22321a8534546447456870c/elpy.el#L2775][elpy-module-company]]
for how to handle ~company-backends~ as a local variable in listing
[[lst:configure-anaconda+company-for-python]]. The call to [[info:elisp#Advising Functions][advice-add]] in listing
[[lst:define-my-toggle-anaconda-mode]] opens Python =org-edit-src-code= buffers in
~anaconda-mode~.

#+caption[Configure =anaconda= with =company= for Python]:
#+caption: Configure =anaconda= with =company= for Python.
#+name: lst:configure-anaconda+company-for-python
#+begin_src emacs-lisp
  (with-eval-after-load 'python
    (with-eval-after-load 'company
      (when (and (fboundp 'anaconda-mode)
                 (fboundp 'company-anaconda))
        (defun my-disable-anaconda-mode ()
          (when (derived-mode-p 'python-mode)
            (anaconda-mode -1)
            (make-variable-buffer-local 'company-backends)
            (setq company-backends
                  (delq 'company-anaconda
                        (mapcar #'identity company-backends)))
            (anaconda-eldoc-mode -1)))
        (defun my-enable-anaconda-mode ()
          (when (derived-mode-p 'python-mode)
            (anaconda-mode +1)
            (make-variable-buffer-local 'company-backends)
            (setq company-backends
                  (cons 'company-anaconda
                        (delq 'company-semantic
                              (delq 'company-capf
                                    (mapcar #'identity company-backends)))))
            (anaconda-eldoc-mode
             (if (file-remote-p default-directory) -1 1)))))))
#+end_src

#+caption[Define =my-toggle-anaconda-mode= for Python]:
#+caption: Define =my-toggle-anaconda-mode= for Python.
#+name: lst:define-my-toggle-anaconda-mode
#+begin_src emacs-lisp
  (with-eval-after-load 'python
    (unless (and (fboundp 'my-disable-anaconda-mode)
                 (fboundp 'my-enable-anaconda-mode))
      (when (fboundp 'anaconda-mode)
        (defun my-disable-anaconda-mode ()
          (when (derived-mode-p 'python-mode)
            (anaconda-mode -1)
            (anaconda-eldoc-mode -1)))
        (defun my-enable-anaconda-mode ()
          (when (derived-mode-p 'python-mode)
            (anaconda-mode +1)
            (anaconda-eldoc-mode
             (if (file-remote-p default-directory) -1 1))))))

    (when (fboundp 'my-enable-anaconda-mode)
      (advice-add 'org-edit-src-code :after #'my-enable-anaconda-mode))
    (when (and (fboundp 'my-disable-anaconda-mode)
               (fboundp 'my-enable-anaconda-mode))
      (defun my-toggle-anaconda-mode ()
        "Toggle anaconda-mode with bells and whistles."
        (interactive)
        (if (bound-and-true-p anaconda-mode)
            (my-disable-anaconda-mode)
          (my-enable-anaconda-mode)))))
#+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 and either [[https://github.com/pythonic-emacs/anaconda-mode][anaconda]] or [[https://github.com/joaotavora/eglot][eglot]] works when coding certain functions of for
instance [[https://numpy.org/][numpy]] and [[https://scipy.org/][scipy]].

#+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:jedi
: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.

*** 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/pythonic-emacs/anaconda-mode#readme][anaconda]], [[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 several packages in this Emacs
setup ([[https://github.com/pythonic-emacs/anaconda-mode#readme][anaconda]], [[https://github.com/andras-simonyi/citeproc-el#readme][citeproc]], [[https://github.com/pythonic-emacs/pythonic#readme][pythonic]]) 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 several packages in this Emacs setup ([[https://github.com/pythonic-emacs/anaconda-mode#readme][anaconda]],
[[https://github.com/andras-simonyi/citeproc-el#readme][citeproc]], [[https://github.com/bdarcus/citar#readme][citar]], and [[https://github.com/pythonic-emacs/company-anaconda][company-anaconda]]) 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
  (with-eval-after-load 'emacs
    (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 (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
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
  (with-eval-after-load 'emacs
    ;; To disables pairing of the quote character for lisp modes,
    ;; require smartparens-config instead of smartparens.
    (when (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 '(prog-mode-hook text-mode-hook))
        (add-hook hook #'smartparens-mode))

      ;; Hook on the specific `eval-expression-minibuffer-setup-hook'
      ;; and not on the general `minibuffer-setup-hook'.
      (dolist (hook '(emacs-lisp-mode-hook
                      eval-expression-minibuffer-setup-hook
                      ielm-mode-hook
                      lisp-mode-hook
                      python-mode-hook
                      sly-mrepl-mode-hook))
        (add-hook hook #'smartparens-strict-mode))

      ;; Tweak for the call to `smartparens-strict-mode' hooked on
      ;; `eval-expression-minibuffer-setup-hook'.
      (sp-with-modes '(fundamental-mode           ; first usage.
                       minibuffer-inactive-mode)  ; later usage.
        (sp-local-pair "'" nil :actions nil))

      ;; 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-mode]] 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-mode=]:
#+caption: Configure =electric-operator-mode=.
#+name: lst:configure-electric-operator-mode
#+begin_src emacs-lisp
  (when (fboundp 'electric-operator-mode)
    (add-hook 'c-mode-common #'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 (require 'yasnippet nil 'noerror)
    (custom-set-variables
     '(yas-alias-to-yas/prefix-p nil))
    (yas-global-mode +1))
#+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 tables by means of =org-narrow-to-table=.

#+caption[Configure =narrow-or-widen-dwim=]:
#+caption: Configure =narrow-or-widen-dwim=.
#+name: lst:configure-narrow-or-widen-dwim
#+begin_src emacs-lisp
  (defun org-narrow-to-table ()
    "Narrow buffer to current table."
    (interactive)
    (if (org-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-dwim otherwise.
  Dwim means: region, org-src-block, org-subtree, 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 (ignore-errors (org-edit-src-code))
               (ignore-errors (org-narrow-to-block))
               (ignore-errors (org-narrow-to-table))
               (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
** [[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.
In case of proper initialization of all face heigths, font scaling is easy as
listing [[lst:my-set-default-face-height]] shows.  Finally, the code in listing
[[lst:my-invert-default-face]] allows swapping the foreground and background colors
of the default face on all frames.

#+caption[Configure =face-attributse=]:
#+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 =my-set-default-face-height=]:
#+caption: Implement =my-set-default-face-height=.
#+name: lst:my-set-default-face-height
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    (defun my-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[Implement =my-invert-default-face=]:
#+caption: Implement =my-invert-default-face=.
#+name: lst:my-invert-default-face
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    (defun my-invert-default-face ()
      "Invert the default face."
      (interactive)
      (invert-face 'default)
      (tweak-region-face-background-color)))
#+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 (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:

#+caption[Implement =my-pulse-one-line=]:
#+caption: Implement =my-pulse-one-line=.
#+name: lst:my-pulse-one-line
#+begin_src emacs-lisp
  (with-eval-after-load 'emacs
    ;; https://karthinks.com/software/batteries-included-with-emacs/
    ;; https://www.reddit.com/r/emacs/comments/jwhr6g/batteries_included_with_emacs/
    (defun my-pulse-one-line (&rest _)
      "Pulse the current line."
      (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 #'my-pulse-one-line)))
#+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#Goto Address mode][Goto address mode (info)]]
:PROPERTIES:
:CUSTOM_ID: sec:goto-address-mode
:END:

Listing [[lst:configure-goto-address-mode]]:
1. Enables =goto-address-prog-mode= for programming modes and
 =goto-address-mode= for a selection of other modes.
2. Defines a function to toggle =goto-address-prog-mode= for programming modes
   and =goto-address-mode= for other modes.
3. Binds {{{kbd(C-c C-o)}}} to =goto-address-at-point= in
 =goto-address-highlight-keymap=.

#+caption[Configure =goto-address-mode=]:
#+caption: Configure =goto-address-mode=.
#+name: lst:configure-goto-address-mode
#+begin_src emacs-lisp
  (when (cl-every #'fboundp '(goto-address-mode goto-address-prog-mode))
    (defun toggle-goto-address-dwim-mode ()
      "Toggle `goto-address-mode' or `goto-address-prog-mode' smartly.
  In case of `prog-mode', toggle the latter, else the former."
      (interactive)
      (if (derived-mode-p 'prog-mode)
          (call-interactively #'goto-address-prog-mode)
        (call-interactively #'goto-address-mode)))

    (dolist (hook '(eshell-mode-hook shell-mode-hook org-mode-hook))
      (add-hook hook #'goto-address-mode))

    (add-hook 'prog-mode-hook #'goto-address-prog-mode)

    (with-eval-after-load 'goto-addr
      (define-key goto-address-highlight-keymap
        (kbd "C-c C-o") #'goto-address-at-point)))
#+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://github.com/skeeto/elfeed#readme][Elfeed: Emacs web feed reader]]
:PROPERTIES:
:CUSTOM_ID: sec:emacs-web-feed-reader
:END:

#+caption[Enable =elfeed=]:
#+caption: Enable =elfeed=.
#+name: lst:enable-elfeed
#+begin_src emacs-lisp
  (autoload 'elfeed "elfeed" nil t)
  (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://ambrevar.xyz/atom.xml" p-neirhardt)
         ("https://emacshorrors.com/feed.atom" v-schneidermann)
         ("https://emacsninja.com/emacs.atom" v-schneidermann)
         ("https://feeds.feedburner.com/InterceptedWithJeremyScahill" j-scahill)
         ("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://updates.orgmode.org/feed/updates" org-updates)
         ("https://www.aclu.org/taxonomy/feed-term/2152/feed" aclu)
         ("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)))))
#+end_src

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

#+caption[Enable =emms=]:
#+caption: Enable =emms=.
#+name: lst:enable-emms
#+begin_src emacs-lisp
  (custom-set-variables
   '(emms-mode-line-format "")
   '(emms-player-list '(emms-player-mpd emms-player-mpv))
   `(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)
   '(emms-playing-time-display-format " %s ")
   '(emms-playlist-mode-center-when-go t))

  (defun my-emms-print-metadata-find ()
    (require 'find-func)
    (locate-file
     "emms-print-metadata"
     (expand-file-name
      "src"
      (file-name-directory (find-library-name "emms")))
     exec-suffixes #'file-executable-p))

  (with-eval-after-load 'emms
    (require 'emms-info-libtag)
    (let ((emms-print-metadata (my-emms-print-metadata-find)))
      (when emms-print-metadata
        (custom-set-variables
         '(emms-info-functions nil)
         `(emms-info-libtag-program-name ,emms-print-metadata))
        (add-hook 'emms-info-functions #'emms-info-libtag))))

  (with-eval-after-load 'elfeed-show
    (when (require 'emms-setup nil 'noerror)
      (emms-all)))

  (autoload 'emms-streams "emms-streams" nil 'interactive)
  (with-eval-after-load 'emms-streams (emms-all))
#+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 "?\n?\f".
  
  ;; Local Variables:
  ;; indent-tabs-mode: nil
  ;; End:
  ;;; init.el ends here
#+end_src

* 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.

\printbibliography

# Emacs looks for "Local variables:" after the last "\?n\?f".

# Local Variables:
# compile-command: "latexmk -interaction=nonstopmode -lualatex -pvc -shell-escape README.tex"
# eval: (apply 'my-org-eval-blocks-named '("emacs-lisp-setup"))
# fill-column: 80
# End: