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init.el
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init.el
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;;; init.el -*- lexical-binding: t; -*-
;; DO NOT EDIT THIS FILE DIRECTLY
;; This is a file generated from a literate programing source file located at
;; https://github.com/christophe-gouel/dotemacs/blob/master/README.org
;; You should make any changes there and regenerate it from Emacs org-mode
;; using org-babel-tangle (C-c C-v t)
(defconst is-mswindows (equal window-system 'w32)
"Boolean indicating whether Emacs is excuted within MS Windows.")
(use-package package
:ensure nil
:config
(add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/"))
(package-initialize))
(use-package use-package
:ensure nil
:custom
;; Always download packages if not available
(use-package-always-ensure t))
(use-package dashboard
:custom
(dashboard-projects-switch-function 'project-switch-project)
(dashboard-set-navigator t) ; raccourcis de rubrique
(dashboard-center-content t)
(dashboard-items '((recents . 6)
(projects . 6)
(bookmarks . 6)))
(dashboard-set-heading-icons t)
(dashboard-set-file-icons t)
:config
(dashboard-setup-startup-hook))
(menu-bar-mode 0)
(scroll-bar-mode 0)
(tool-bar-mode 0)
(tooltip-mode 0)
(setq blink-cursor-blinks 0 ; curseur clignote indéfiniment
custom-safe-themes t ; consider all themes as safe
display-time-24hr-format t ; Affichage de l'heure format 24h
column-number-mode t ; affichage du numéro de la colonne
prettify-symbols-unprettify-at-point t
show-trailing-whitespace t
pixel-scroll-precision-mode t)
(global-hl-line-mode +1) ; Highlight the current line
(add-hook 'text-mode-hook 'prettify-symbols-mode)
(add-hook 'prog-mode-hook (lambda ()
(display-fill-column-indicator-mode)))
(when (display-graphic-p)
;; Cursor (in terminal mode, to be set in terminal options)
(setq-default cursor-type 'bar) ; curseur étroit
(set-face-background 'cursor "#CC0000") ; curseur rouge foncé
;; Fonts and unicode characters
;; Main font
(add-to-list 'default-frame-alist '(font . "JetBrainsMono NF-11"))
;; Additional font for some unicode characters missing in prettify symbols
(set-fontset-font t 'unicode (font-spec :name "XITS Math") nil 'prepend))
(use-package rainbow-mode
:hook (prog-mode . rainbow-mode))
(use-package nerd-icons
:custom
(nerd-icons-font-family "JetBrainsMono NF"))
(use-package nerd-icons-dired
:hook
(dired-mode . nerd-icons-dired-mode))
(use-package nerd-icons-ivy-rich
:after counsel
:init
(nerd-icons-ivy-rich-mode 1)
(ivy-rich-mode 1))
(use-package nerd-icons-ibuffer
:hook (ibuffer-mode . nerd-icons-ibuffer-mode))
(use-package nerd-icons-completion
:config
(nerd-icons-completion-mode))
(use-package ligature
:config
;; Enable all JetBrains Mono ligatures in programming modes
(defconst jb-ligatures
'("-|" "-~" "---" "-<<" "-<" "--" "->" "->>" "-->" "///" "/=" "/==" "/>"
"//" "/*" "*>" "***" ",*/" "<-" "<<-" "<=>" "<=" "<|" "<||" "<|||" "<|>"
"<:" "<>" "<-<" "<<<" "<==" "<<=" "<=<" "<==>" "<-|" "<<" "<~>" "<=|"
"<~~" "<~" "<$>" "<$" "<+>" "<+" "</>" "</" "<*" "<*>" "<->" "<!--" ":>"
":<" ":::" "::" ":?" ":?>" ":=" "::=" "=>>" "==>" "=/=" "=!=" "=>" "==="
"=:=" "==" "!==" "!!" "!=" ">]" ">:" ">>-" ">>=" ">=>" ">>>" ">-" ">="
"&&&" "&&" "|||>" "||>" "|>" "|]" "|}" "|=>" "|->" "|=" "||-" "|-" "||="
"||" ".." ".?" ".=" ".-" "..<" "..." "+++" "+>" "++" "[||]" "[<" "[|" "{|"
"??" "?." "?=" "?:" "##" "###" "####" "#[" "#{" "#=" "#!" "#:" "#_(" "#_"
"#?" "#(" ";;" "_|_" "__" "~~" "~~>" "~>" "~-" "~@" "$>" "^=" "]#"))
(ligature-set-ligatures 'prog-mode jb-ligatures)
(ligature-set-ligatures 'text-mode jb-ligatures)
(ligature-set-ligatures 'comint-mode jb-ligatures)
(ligature-set-ligatures 'special-mode jb-ligatures)
;; Enables ligature checks globally in all buffers. You can also do it
;; per mode with `ligature-mode'.
(global-ligature-mode t))
(use-package doom-modeline
:hook (after-init . doom-modeline-mode))
(use-package rainbow-delimiters
:hook ((prog-mode yaml-mode) . rainbow-delimiters-mode)
:custom-face
(rainbow-delimiters-depth-1-face ((t (:foreground "red"))))
(rainbow-delimiters-depth-2-face ((t (:foreground "orange"))))
(rainbow-delimiters-depth-3-face ((t (:foreground "cyan"))))
(rainbow-delimiters-depth-4-face ((t (:foreground "green"))))
(rainbow-delimiters-depth-5-face ((t (:foreground "blue"))))
(rainbow-delimiters-depth-6-face ((t (:foreground "violet"))))
(rainbow-delimiters-depth-7-face ((t (:foreground "purple"))))
(rainbow-delimiters-depth-8-face ((t (:foreground "black"))))
(rainbow-delimiters-unmatched-face ((t (:background "yellow")))))
(use-package modus-themes
:ensure t
:config
(setq modus-themes-italic-constructs t)
(setq modus-themes-bold-constructs t)
(setq modus-themes-to-toggle '(modus-operandi-deuteranopia modus-vivendi-deuteranopia))
;; Remove the mode-line border
(setq modus-themes-common-palette-overrides
'((border-mode-line-active unspecified)
(border-mode-line-inactive unspecified)))
(load-theme 'modus-vivendi-deuteranopia)
(define-key global-map (kbd "S-<f5>") #'modus-themes-toggle))
(set-language-environment "UTF-8")
(prefer-coding-system 'utf-8)
;; (setq locale-coding-system 'utf-8) ; Mess up dired buffer under windows
(set-selection-coding-system 'utf-8)
(set-default-coding-systems 'utf-8)
(set-terminal-coding-system 'utf-8)
(set-keyboard-coding-system 'utf-8)
(setq default-buffer-file-coding-system 'utf-8-unix
x-select-request-type '(UTF8_STRING COMPOUND_TEXT TEXT STRING))
(if is-mswindows ;; MS Windows clipboard is UTF-16LE
(set-clipboard-coding-system 'utf-16le-dos))
(setq user-full-name "Christophe Gouel"
user-mail-address "[email protected]")
(setq
;; initial-major-mode 'org-mode
initial-scratch-message nil)
(use-package comint
:ensure nil
:defer t
:custom
(comint-scroll-to-bottom-on-input 'this)
(comint-scroll-to-bottom-on-output t)
(comint-move-point-for-output t))
(setq show-paren-mode t ; coupler les parenthèses
auth-sources '("~/.authinfo") ; Define file that stores secrets
backup-directory-alist '(("." . "~/.emacs.d/backup"))
default-major-mode 'text-mode ; mode par défaut
delete-by-moving-to-trash t ; Sent deleted files to trash
comment-column 0 ; Prevent indentation of lines starting with one comment
next-line-add-newlines t
jit-lock-chunk-size 50000
;; set large file threshold at 100 megabytes
large-file-warning-threshold 100000000
;; Options to make lsp usable in emacs (from
;; https://emacs-lsp.github.io/lsp-mode/page/performance/)
gc-cons-threshold (* 10 800000)
read-process-output-max (* 1024 1024))
(setq-default mouse-yank-at-point t ; coller avec la souris
case-fold-search t) ; recherche sans égard à la casse
(delete-selection-mode t) ; entrée efface texte sélectionné
(fset 'yes-or-no-p 'y-or-n-p) ; Replace yes or no with y or n
(auto-compression-mode t)
(when is-mswindows
(setq tramp-default-method "plink"))
(use-package server
:ensure nil
:defer 1
:config
(when (and (display-graphic-p) (not (server-running-p)))
(server-start)))
(use-package dictionary
:ensure nil
:defer t
:custom
(dictionary-server "dict.org"))
(use-package autorevert
:ensure nil
:custom
(auto-revert-verbose nil)) ; Prevent autorevert from generating messages
(use-package dired
:ensure nil
:commands (dired dired-jump)
:custom
(dired-listing-switches "-agho --group-directories-first")
:hook
(dired-mode . (lambda ()
(dired-hide-details-mode)))
(dired-mode . auto-revert-mode))
(use-package diredfl
:hook
(dired-mode . diredfl-mode))
(use-package compile
:ensure nil
:bind (:map compilation-mode-map ("r" . recompile))
:hook
;; Get proper coloring of compile buffers (does not seem to work under Windows, probably because cmd does not support ANSI colors)
(compilation-filter . ansi-color-compilation-filter)
:custom
;; compilation buffer automatically scrolls and stops at first error
(compilation-scroll-output 'first-error))
(use-package expand-region
:bind ("C-!" . er/expand-region))
(use-package ibuffer-project
:hook
(ibuffer .
(lambda ()
(setq ibuffer-filter-groups (ibuffer-project-generate-filter-groups))
(unless (eq ibuffer-sorting-mode 'project-file-relative)
(ibuffer-do-sort-by-project-file-relative)))))
(use-package imenu
:ensure nil
:defer t
:custom
(imenu-auto-rescan t))
(use-package imenu-list
:bind
(("C-c =" . imenu-list-smart-toggle)
:map imenu-list-major-mode-map
("M-<return>" . my-imenu-list-goto-entry))
:custom
(imenu-list-focus-after-activation t)
(imenu-list-position 'right)
:config
(defun my-imenu-list-goto-entry ()
"Goto entry and exit imenu"
(interactive)
(imenu-list-goto-entry)
(imenu-list-smart-toggle)))
(use-package flimenu
:after imenu
:config
(flimenu-global-mode))
(use-package doc-view
:ensure nil
:if (display-graphic-p)
:defer t
:custom
(doc-view-ghostscript-program (executable-find "rungs")))
(use-package pdf-tools
:if (display-graphic-p)
:mode ("\\.pdf\\'" . pdf-view-mode)
:bind (:map pdf-view-mode-map
("C-s" . isearch-forward))
;; :init
;; (pdf-tools-install) ; Standard activation command
;; (pdf-loader-install) ; On demand loading, leads to faster startup time
:custom
(pdf-view-display-size 'fit-page)
:config
(pdf-tools-install)
;; (setq TeX-view-program-selection '((output-pdf "PDF Tools"))
;; TeX-view-program-list '(("PDF Tools" TeX-pdf-tools-sync-view))
;; TeX-source-correlate-start-server t)
;; (add-hook 'TeX-after-compilation-finished-functions
;; #'TeX-revert-document-buffer)
)
(use-package proced
:ensure nil
:defer t
:custom
(proced-enable-color-flag t))
(use-package recentf
:custom
(recentf-max-saved-items 50))
(use-package grep
:ensure nil
:defer t
:config
(if is-mswindows
(setq find-program "\"C:\\Program Files\\Git\\usr\\bin\\find.exe\"")))
(use-package ripgrep
:bind
("C-c f" . my-ripgrep-in-same-extension)
:config
(defun my-ripgrep-in-same-extension (expression)
"Search for EXPRESSION in files with the same extension as the
current buffer within the project or the current directory if not in a project."
(interactive
(list
(read-from-minibuffer "Ripgrep search for: " (thing-at-point 'symbol))))
(let* ((extension (file-name-extension (buffer-file-name)))
(glob (if extension (concat "*." extension) "*"))
;; Check if we are inside a project. If not, use `nil`.
(project (if (ignore-errors (project-current)) (project-current) nil))
;; Use project root if in a project, otherwise use `default-directory`.
(root (if project (project-root project) default-directory)))
(ripgrep-regexp expression
root
(list (format "-g %s" glob))))))
(use-package outline
:ensure nil
:hook ((prog-mode text-mode) . outline-minor-mode)
:custom
(outline-minor-mode-use-buttons 'in-margins) ; add in-margin buttons to fold/unfold
:config
(unbind-key "RET" outline-overlay-button-map))
(use-package bicycle
:after outline
:bind (:map outline-minor-mode-map
([C-tab] . bicycle-cycle)
([S-tab] . my-bibycle-cycle-global)
([backtab] . my-bibycle-cycle-global))
:config
;; bicycle-cycle-global should not be used in org-mode, hence this function
(defun my-bibycle-cycle-global ()
(interactive)
(if (derived-mode-p 'org-mode)
(org-cycle-global)
(bicycle-cycle-global))))
(use-package outline-minor-faces
:after outline
:hook
(outline-minor-mode . outline-minor-faces-mode))
(use-package windmove
:ensure nil
:config
(windmove-default-keybindings))
(put 'downcase-region 'disabled nil)
(put 'upcase-region 'disabled nil)
;; Remove a bug appearing on Linux GTK and preventing the use of S-space (https://lists.gnu.org/archive/html/bug-gnu-emacs/2021-07/msg00071.html)
(when (equal window-system 'pgtk)
(setq pgtk-use-im-context-on-new-connection nil))
(keymap-global-set "C-x C-b" 'ibuffer)
(keymap-global-set "C-<apps>" 'menu-bar-mode)
(keymap-global-set "C-<menu>" 'menu-bar-mode) ; For Linux
(keymap-global-set "<f5>" 'revert-buffer)
(global-set-key [remap dabbrev-expand] 'hippie-expand)
(use-package keycast)
(use-package greek-unicode-insert
:vc (:fetcher github :repo Malabarba/greek-unicode-insert)
:bind ("²" . greek-unicode-insert-map))
(use-package smartparens
:ensure smartparens ;; install the package
:hook (prog-mode markdown-mode yaml-mode)
:config
;; load default config
(require 'smartparens-config))
(use-package which-key
:diminish which-key-mode
:init
(setq which-key-sort-uppercase-first nil
max-mini-window-height 15)
;; On va utiliser une fenêtre dédiée plutôt que le minibuffer
(which-key-setup-side-window-bottom)
;; On l'active partout, tout le temps
(which-key-mode t))
(use-package prescient
:config
(prescient-persist-mode))
(use-package company
:hook (after-init . global-company-mode)
:custom
(company-show-numbers t)
(company-idle-delay 0)
;; company configuration from
;; <https://github.com/radian-software/radian/blob/develop/emacs/radian.el>
:bind (;; Replace `completion-at-point' and `complete-symbol' with
;; `company-manual-begin'. You might think this could be put
;; in the `:bind*' declaration below, but it seems that
;; `bind-key*' does not work with remappings.
([remap completion-at-point] . company-manual-begin)
([remap complete-symbol] . company-manual-begin)
("C-c y" . company-yasnippet)
;; The following are keybindings that take effect whenever
;; the completions menu is visible, even if the user has not
;; explicitly interacted with Company.
:map company-active-map
;; Make TAB always complete the current selection. Note that
;; <tab> is for windowed Emacs and TAB is for terminal Emacs.
("<tab>" . company-complete-selection)
("TAB" . company-complete-selection)
;; Prevent SPC from ever triggering a completion.
("SPC" . nil)
;; The following are keybindings that only take effect if the
;; user has explicitly interacted with Company.
:map company-active-map
:filter (company-explicit-action-p)
;; Make RET trigger a completion if and only if the user has
;; explicitly interacted with Company. Note that <return> is
;; for windowed Emacs and RET is for terminal Emacs.
("<return>" . company-complete-selection)
("RET" . company-complete-selection))
;; :bind* (;; The default keybinding for `completion-at-point' and
;; ;; `complete-symbol' is M-TAB or equivalently C-M-i. Here we
;; ;; make sure that no minor modes override this keybinding.
;; ("M-TAB" . company-manual-begin))
)
(use-package company-math
:custom
(company-math-allow-latex-symbols-in-faces t)) ; use LaTeX symbols everywhere (avoid unicode symbols to dominate outside LaTeX mode)
(use-package company-reftex)
(use-package company-jedi)
(setq company-backends
(append
'((:separate
;; deactivate company-reftex-labels because it is too slow
;; company-reftex-labels
company-reftex-citations
company-math-symbols-latex
company-math-symbols-unicode
company-latex-commands))
company-backends))
(use-package company-box
:hook (company-mode . company-box-mode)
:custom
(company-box-doc-enable nil))
(use-package company-prescient
:config
(company-prescient-mode))
(use-package counsel
:config
(counsel-mode))
(use-package ivy
:demand
:custom
(ivy-use-virtual-buffers t)
(ivy-count-format "%d/%d ")
:config
(ivy-mode)
(ivy-configure 'counsel-imenu
:update-fn 'auto))
(use-package swiper
:bind ("C-s" . my-search-method-according-to-numlines)
:config
;; swiper is slow for large files so it is replaced by isearch for large files
(defun my-search-method-according-to-numlines ()
"Determine the number of lines of current buffer and chooses a
search method accordingly."
(interactive)
(if (< (count-lines (point-min) (point-max)) 20000)
(swiper)
(isearch-forward))))
(use-package ivy-xref
:init
(setq xref-show-definitions-function #'ivy-xref-show-defs))
(use-package ivy-prescient
:after counsel
:config
(ivy-prescient-mode))
(use-package ivy-rich
:after nerd-icons-ivy-rich
:init (ivy-rich-mode +1))
(use-package magit
:init
;; this binds `magit-project-status' to `project-prefix-map' when project.el is loaded.
(require 'magit-extras)
:bind ("C-x g" . magit-status)
:custom
(magit-diff-refine-hunk (quote all))
:config
; Do not diff when committing
(remove-hook 'server-switch-hook 'magit-commit-diff)
(remove-hook 'with-editor-filter-visit-hook 'magit-commit-diff))
(use-package magit-delta
:hook (magit-mode . magit-delta-mode))
(use-package diff-hl
:defer t
:after magit
:hook
(prog-mode . diff-hl-mode)
(latex-mode . diff-hl-mode)
(dired-mode . diff-hl-dired-mode)
(magit-post-refresh . diff-hl-magit-post-refresh))
(use-package git-modes
:mode ("/.dockerignore\\'" . gitignore-mode)) ; works also with other ignore files
(use-package chatgpt-shell
:defer t
:commands chatgpt-shell-prompt-compose
:custom
(chatgpt-shell-openai-key
(auth-source-pick-first-password :host "api.openai.com")))
(use-package gptel
:defer t
:custom
(gptel-use-curl nil)
:config
(add-to-list 'gptel-directives '(academic . "You are an editor specialized in academic paper in economics. You are here to help me generate the best text for my academic articles. I will provide you texts and I would like you to review them for any spelling, grammar, or punctuation errors. Do not stop at simple proofreading, if it is useful, propose to refine the content's structure, style, and clarity. Once you have finished editing the text, provide me with any necessary corrections or suggestions for improving the text.")))
(use-package eshell-git-prompt
:defer t
:config
(eshell-git-prompt-use-theme 'powerline))
(add-hook 'shell-mode-hook
(lambda ()
(face-remap-set-base 'comint-highlight-prompt :inherit nil)))
(use-package citar
:after (org nerd-icons)
:hook
(org-mode . citar-capf-setup)
:bind
(:map org-mode-map :package org ("C-c b" . #'org-cite-insert))
:config
;; Configuration to use nerd-icons in citar
(defvar citar-indicator-files-icons
(citar-indicator-create
:symbol (nerd-icons-faicon
"nf-fa-file_o"
:face 'nerd-icons-green
:v-adjust -0.1)
:function #'citar-has-files
:padding " " ; need this because the default padding is too low for these icons
:tag "has:files"))
(defvar citar-indicator-links-icons
(citar-indicator-create
:symbol (nerd-icons-faicon
"nf-fa-link"
:face 'nerd-icons-orange
:v-adjust 0.01)
:function #'citar-has-links
:padding " "
:tag "has:links"))
(defvar citar-indicator-notes-icons
(citar-indicator-create
:symbol (nerd-icons-codicon
"nf-cod-note"
:face 'nerd-icons-blue
:v-adjust -0.3)
:function #'citar-has-notes
:padding " "
:tag "has:notes"))
(defvar citar-indicator-cited-icons
(citar-indicator-create
:symbol (nerd-icons-faicon
"nf-fa-circle_o"
:face 'nerd-icon-green)
:function #'citar-is-cited
:padding " "
:tag "is:cited"))
(setq citar-indicators
(list citar-indicator-files-icons
citar-indicator-links-icons
citar-indicator-notes-icons
citar-indicator-cited-icons))
:custom
(org-cite-insert-processor 'citar)
(org-cite-follow-processor 'citar)
(org-cite-activate-processor 'citar)
(citar-bibliography org-cite-global-bibliography)
(citar-library-paths
(list (substitute-in-file-name "${DROPBOX}/Bibliography/Papers")))
(citar-notes-paths
(list (substitute-in-file-name "${DROPBOX}/Bibliography/notes")))
(citar-templates
'((main . "${author editor:30%sn} ${date year issued:4} ${title:48}")
(suffix . " ${=key= id:7} ${=type=:12} ${journal journaltitle}")
(preview . "${author editor:%etal} (${year issued date}) ${title}, ${journal journaltitle publisher container-title collection-title}.\n")
(note . "Notes on ${author editor:%etal}, ${title}"))))
(use-package csv-mode
:hook
(csv-mode . csv-guess-set-separator))
(use-package tex
:defer t
:ensure auctex
:hook
(TeX-mode . latex-math-mode)
(TeX-mode . turn-on-reftex)
(TeX-mode . TeX-fold-buffer)
(TeX-mode . flymake-mode)
:hook
(TeX-mode . TeX-fold-mode)
:custom
(TeX-auto-save t)
(TeX-save-query nil) ; don't ask to save the file before compiling
(TeX-parse-self t)
(LaTeX-item-indent 0)
(LaTeX-default-options "12pt")
;; (LaTeX-math-abbrev-prefix "²")
(TeX-PDF-mode t)
(TeX-electric-sub-and-superscript 1)
(LaTeX-math-list
'(
(?\) "right)")
(?\( "left(")
(?/ "frac{}{}")
))
;; View PDF
(TeX-view-program-selection '((output-pdf "PDF Tools")))
(TeX-view-program-list '(("PDF Tools" TeX-pdf-tools-sync-view)))
(TeX-source-correlate-mode t)
(TeX-source-correlate-start-server t)
;; (TeX-source-correlate-method (quote synctex))
;; Preview
(preview-auto-cache-preamble t)
(preview-default-option-list '("displaymath" "graphics" "textmath"))
(preview-auto-reveal t)
;; Fold-mode
(TeX-fold-auto-reveal t)
;; Personalize the list of commands to be folded
(TeX-fold-macro-spec-list
'(("[f]"
("footnote" "marginpar"))
("[c]"
("citeyear" "citeauthor" "citep" "citet" "cite"))
("[l]"
("label"))
("[r]"
("ref" "pageref" "eqref" "footref" "fref" "Fref"))
("[i]"
("index" "glossary"))
("[1]:||*"
("item"))
("..."
("dots"))
("(C)"
("copyright"))
("(R)"
("textregistered"))
("TM"
("texttrademark"))
(1
("part" "chapter" "section" "subsection" "subsubsection" "
paragraph" "subparagraph" "part*" "chapter*" "section*" "
subsection*" "subsubsection*" "paragraph*" "subparagraph*" "emph" "
textit" "textsl" "textmd" "textrm" "textsf" "texttt" "textbf" "
textsc" "textup"))))
;; Prevent folding of math to let prettify-symbols do the job
(TeX-fold-math-spec-list-internal nil)
(TeX-fold-math-spec-list nil)
(LaTeX-fold-math-spec-list nil)
:config
(setq-default TeX-auto-parse-length 200
TeX-master nil)
(add-hook 'TeX-after-compilation-finished-functions
#'TeX-revert-document-buffer)
(defun my-tex-compile ()
"Save and compile TeX document"
(interactive)
(save-buffer)
(TeX-command-menu "latex"))
;; Beamer
(defun my-tex-frame ()
"Run pdflatex on current frame. Frame must be declared as an environment."
(interactive)
(let (beg)
(save-excursion
(search-backward "\\begin{frame}")
(setq beg (point))
(forward-char 1)
(LaTeX-find-matching-end)
(TeX-pin-region beg (point))
(cl-letf (( (symbol-function 'TeX-command-query) (lambda (x) "LaTeX")))
(TeX-command-region)))))
:bind
(:map TeX-mode-map
("C-c e" . TeX-next-error)
("M-RET" . latex-insert-item)
("S-<return>" . my-tex-frame)
("<f9>" . my-tex-compile)))
(use-package reftex
:bind (:map reftex-mode-map
("C-c f" . reftex-fancyref-fref)
("C-c F" . reftex-fancyref-Fref))
:custom
(reftex-bibpath-environment-variables (quote ("BIBINPUTS")))
(reftex-default-bibliography '("References.bib"))
(reftex-cite-format (quote natbib))
(reftex-sort-bibtex-matches (quote author))
(reftex-plug-into-AUCTeX t)
(reftex-label-alist '(AMSTeX)) ; Use \eqref by default instead of \ref
;; Increase reftex speed (especially on Windows)
(reftex-enable-partial-scans t)
(reftex-save-parse-info t)
(reftex-use-multiple-selection-buffers t))
(use-package cdlatex
:hook
(LaTeX-mode . turn-on-cdlatex)
(LaTeX-mode . my-slow-company)
(org-mode . my-slow-company)
(cdlatex-tab . my-cdlatex-indent-maybe)
:config
;; Prevent cdlatex from defining LaTeX math subscript everywhere
(define-key cdlatex-mode-map "_" nil)
;; Allow tab to be used to indent when the cursor is at the beginning of the line
(defun my-cdlatex-indent-maybe ()
"Indent in TeX when CDLaTeX is active"
(when (or (bolp) (looking-back "^[ \t]+"))
(LaTeX-indent-line)))
(defun my-slow-company ()
"Slow down company for a better use of CDLaTeX"
(make-local-variable 'company-idle-delay)
(setq company-idle-delay 0.3))
:custom
(cdlatex-command-alist
'(("equ*" "Insert equation* env" "" cdlatex-environment ("equation*") t nil)
("frd" "Insert \\frac{\\partial }{\\partial }" "\\frac{\\partial ?}{\\partial }" cdlatex-position-cursor nil nil t)
("su" "Insert \\sum" "\\sum?" cdlatex-position-cursor nil nil t)))
(cdlatex-math-symbol-prefix ?\262)) ; correspond to key "²"
(use-package markdown-mode
:mode ("README\\.md\\'" . gfm-mode)
:custom
(markdown-command
(concat "pandoc"
" --from=markdown --to=html"
" --standalone --mathjax"
;; " --citeproc --bibliography="
;; (shell-quote-argument (substitute-in-file-name "${BIBINPUTS}\\References.bib"))
))
(markdown-enable-math t)
(markdown-enable-prefix-prompts nil)
(markdown-header-scaling nil)
(markdown-hide-markup nil)
(markdown-hide-urls t)
(markdown-fontify-code-blocks-natively t)
(markdown-enable-highlighting-syntax t)
:config
;; Code to import screenshots in markdown files
;; from <https://www.nistara.net/post/2022-11-14-emacs-markdown-screenshots> and
;; <https://stackoverflow.com/questions/17435995/paste-an-image-on-clipboard-to-emacs-org-mode-file-without-saving-it/31868530#31868530>
(defun my-markdown-screenshot ()
"Copy a screenshot into a time stamped unique-named file in the
same directory as the working and insert a link to this file."
(interactive)
(setq filename
(concat
(make-temp-name
(concat (file-name-nondirectory (buffer-file-name))
"_screenshots/"
(format-time-string "%Y-%m-%d_%a_%kh%Mm_")) ) ".png"))
(unless (file-exists-p (file-name-directory filename))
(make-directory (file-name-directory filename)))
;; copy the screenshot to file
(shell-command
(concat "powershell -command \"Add-Type -AssemblyName System.Windows.Forms;if ($([System.Windows.Forms.Clipboard]::ContainsImage())) {$image = [System.Windows.Forms.Clipboard]::GetImage();[System.Drawing.Bitmap]$image.Save('" filename "',[System.Drawing.Imaging.ImageFormat]::Png); Write-Output 'clipboard content saved as file'} else {Write-Output 'clipboard does not contain image data'}\""))
;; insert into file if correctly taken
(if (file-exists-p filename)
(insert (concat "![](" filename ")")))
(markdown-display-inline-images)
(newline))
;; Code to use RefTeX to input references in markdown
;; from https://gist.github.com/kleinschmidt/5ab0d3c423a7ee013a2c01b3919b009a
(defvar markdown-cite-format
'(
(?\C-m . "@%l")
(?p . "[@%l]")
(?t . "@%l")
(?y . "[-@%l]"))
"Markdown citation formats")
(defun my-markdown-reftex-citation ()
"Wrap reftex-citation with local variables for markdown format"
(interactive)
(let ((reftex-cite-format markdown-cite-format)
(reftex-cite-key-separator "; @"))
(reftex-citation)))
;; :hook
;; (markdown-mode . (lambda () (math-preview-all)))
:bind (:map markdown-mode-map
("C-c [" . my-markdown-reftex-citation)))
(use-package pandoc-mode
:hook
(markdown-mode . pandoc-mode)
(pandoc-mode . pandoc-load-default-settings))
(use-package org
:ensure nil
:mode ("\\.org\\'" . org-mode)
:hook
(org-mode . turn-on-org-cdlatex)
:custom
;; (org-export-with-LaTeX-fragments t) ; Export LaTeX fragment to HTML
(org-edit-src-content-indentation 0)
(org-todo-keywords '((type "TODO(t)" "STARTED(s)" "WAITING(w)" "|" "DONE(d)")))
(org-tag-alist '(("OFFICE" . ?o) ("COMPUTER" . ?c) ("HOME" . ?h) ("PROJECT" . ?p) ("CALL" . ?a) ("ERRANDS" . ?e) ("TASK" . ?t)))
(org-confirm-babel-evaluate nil)
(org-refile-targets '((nil :maxlevel . 3)))
;; Appareance
(org-pretty-entities 1) ; equivalent of prettify symbols for org
(org-cycle-hide-drawer-startup t) ; fold drawers at startup
; remove some prettification for sub- and superscripts because it makes editing difficult
(org-pretty-entities-include-sub-superscripts nil)
(org-hide-emphasis-markers t) ; remove markup markers
(org-ellipsis " [+]")
(org-highlight-latex-and-related '(native))
(org-startup-indented t) ; Indent text relative to section
(org-startup-with-inline-images t)
(org-startup-with-latex-preview t)
(org-cycle-inline-images-display t)
(org-imenu-depth 4)
(org-blank-before-new-entry '((heading . auto) (plain-list-item . nil))) ; Control the insertion of blank line after M-Ret
(org-fold-core-style 'overlays) ; Slower folding style to prevent some bugs when unfolding
:config
(org-defkey org-cdlatex-mode-map "²" 'cdlatex-math-symbol)
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . t)
(python . t)
(R . t)
(shell . t)))
:bind (:map org-mode-map
("C-c o" . org-open-at-point)
("C-c =" . imenu-list)))
(use-package org-appear
:hook
(org-mode . org-appear-mode))
(use-package org-modern
:hook
(org-mode . global-org-modern-mode))
(use-package org-fragtog
:hook
(org-mode . org-fragtog-mode))
(use-package oc
:ensure nil
:after org
:custom
(org-cite-global-bibliography
(list (substitute-in-file-name "${BIBINPUTS}/References.bib")))
(org-cite-csl-styles-dir (substitute-in-file-name "${DROPBOX}/Bibliography/csl"))
:bind (:map org-mode-map ("C-c [" . org-cite-insert)))
(use-package oxr
:after org
:vc (:fetcher github :repo bdarcus/oxr)
:bind (:map org-mode-map ("C-c ]" . oxr-insert-ref)))
(use-package ox
:ensure nil
:defer t
:custom
(org-odt-preferred-output-format "docx")) ; require soffice to be on the PATH
(use-package ox-reveal
:after ox
:ensure htmlize) ; required for the fontification of code blocks
(use-package texfrag
:hook
(eww-mode . texfrag-mode))
(use-package math-preview
:bind
("C-c m d" . math-preview-all)
("C-c m p" . math-preview-at-point)
("C-c m r" . math-preview-region)
("C-c m c d" . math-preview-clear-all)
("C-c m c p" . math-preview-clear-at-point)
("C-c m c r" . math-preview-clear-region))
(use-package flyspell
:hook (text-mode . flyspell-mode)
:config
(setq ispell-program-name (executable-find "hunspell")
flyspell-issue-welcome-flag nil
ispell-really-hunspell t
ispell-dictionary "en_US"
ispell-local-dictionary "en_US"
ispell-local-dictionary-alist
'(("en_US" "[[:alpha:]]" "[^[:alpha:]]" "[']" nil ("-d" "en_US") nil utf-8)
("fr_FR" "[[:alpha:]]" "[^[:alpha:]]" "[']" nil ("-d" "fr_FR") nil utf-8))
ispell-hunspell-dictionary-alist ispell-local-dictionary-alist
ispell-personal-dictionary "~/.emacs.d/.hunspell_en_US"
ispell-silently-savep t)
:bind
("C-M-$" . ispell-word))
(use-package flyspell-correct
:after flyspell
:bind (:map flyspell-mode-map
("M-$" . flyspell-correct-at-point))
)
(use-package flyspell-correct-ivy
:demand t
:after flyspell-correct)
(defun my-unfill-paragraph ()
"Unfill paragraph."
(interactive)
(let ((fill-column (point-max)))
(fill-paragraph nil)))
(defun my-unfill-region (start end)
"Unfill region."
(interactive "r")
(let ((fill-column (point-max)))
(fill-region start end nil)))
(setq-default fill-column 80)
(use-package adaptive-wrap)
(use-package visual-fill-column
:custom
(visual-fill-column-width 100)
:config
(defun my-visual-fill ()
"Toggle visual fill column, visual line mode, and adaptive wrap mode."
(interactive)
(visual-line-mode 'toggle)
(visual-fill-column-mode 'toggle)
;; org-indent does play nicely with adaptive-wrap-prefix-mode so we exclude the later in org
(unless (member major-mode '(org-mode))
(adaptive-wrap-prefix-mode 'toggle)))
(defun my-center-text ()
"Center text in visual fill column."
(interactive)
(setq-local visual-fill-column-center-text t))
(defun my-uncenter-text ()
"Uncenter text in visual fill column."
(interactive)
(setq-local visual-fill-column-center-text nil))
:bind ("C-c v" . my-visual-fill)
:hook
(bibtex-mode . my-visual-fill)
(text-mode . (lambda()
(unless (member major-mode '(csv-mode))
(my-visual-fill)))))
(use-package yaml-mode
:mode ("\\.yml$" "\\.dvc" "dvc.lock")