(use-package keychain-environment 	; Store ssh passphrase
  :init
  (keychain-refresh-environment))
(use-package pass) 			; Manage passwords
;; (use-package tmdb
;;    :straight (tmdb :type git :host github :repo "StoffePro/tmdb"))
;; ;; Manage music (with dired)
;; (use-package emms
;;   :config
;;   (require 'emms-setup)
;;   ;; (emms-minimalistic)
;;   (emms-all)
;;   (emms-default-players)
;;   (setq emms-source-file-default-directory "/data/music/")
;;   ;; Disable irrating cover popup
;;   (setq emms-player-mplayer-parameters '("-novideo")))
;; ;; IRC
;; (use-package auth-source-pass
;;   :ensure t
;;   :config
;;   (auth-source-pass-enable))
;; (use-package erc
;;   :straight nil
;;   :commands (erc)
;;   :init
;;   (require 'erc-join)
;;   (setq erc-autojoin-channels-alist '(("irc.libera.chat" "#haskell" ))
;; 	erc-hide-list '("JOIN" "PART" "QUIT")
;; 	)
;;   (defun irc-connect ()
;;     (interactive)
;;     (erc
;;      :server "irc.libera.chat" :port 6667
;;      :nick (auth-source-pass-get "login" "irc/libera.chat")
;;      :password (auth-source-pass-get 'secret "irc/libera.chat"))))

;; Cleanup
(setq inhibit-startup-message t)
(scroll-bar-mode -1)        ; Disable visible scrollbar
(tool-bar-mode -1)          ; Disable the toolbar
(tooltip-mode -1)           ; Disable tooltips
(set-fringe-mode 10)        ; Give some breathing room
(menu-bar-mode -1)            ; Disable the menu bar
(load-theme 'modus-operandi) 		; Light theme, built-in emacs 28
;; Doome-one theme
;; (use-package doom-themes
;;   :ensure t
;;   :config
;;   (setq doom-one-brighter-comments t 	; Our ideal config: readable comments
;; 	doom-one-comment-bg nil) 	; without colored background !
;;   (load-theme 'doom-one t))

;; Built-in equivalent of snippets
;; Skeletons for template and abbrev for shortcuts
;; Complete abbreviation with <C-x '>
(define-skeleton red-ops-skeleton
  "Org TOODs for both red and ops"
  ""
  "**** TODO Red\n**** TODO Ops")
(define-abbrev org-mode-abbrev-table "ros" "" 'red-ops-skeleton)

;; --------------- Package manager ---------------
;; Use straight.el as our package manager
(defvar bootstrap-version)
(let ((bootstrap-file
       (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
      (bootstrap-version 5))
  (unless (file-exists-p bootstrap-file)
    (with-current-buffer
        (url-retrieve-synchronously
         "https://raw.githubusercontent.com/raxod502/straight.el/develop/install.el"
         'silent 'inhibit-cookies)
      (goto-char (point-max))
      (eval-print-last-sexp)))
  (load bootstrap-file nil 'nomessage))
;; Emacs >= 27
(setq package-enable-at-startup nil)
;; Use straight by default
(setq straight-use-package-by-default t)
;; use-package to manage them (download them with ":straight t")
(straight-use-package 'use-package)

;;---------------------- Agenda
(require 'org-habit)
(remap-global "C-à" 'org-agenda)
(remap-global "C-ç" 'org-capture)
;; My agenda files
(setq org-agenda-files (list "~/projects/blog/todo.org"))
;; Common variables for org-agenda
;; Important : agenda view does not show notes with imcomplete parents in Doom
(setq org-agenda-dim-blocked-notes nil
      org-agenda-start-day "today"
      org-agenda-skip-deadline-if-done t
      org-deadline-warning-days 0)
;; But it's easier to use org-super-agenda !
;;Warning : org-agenda-tag-filter-preset is set for all the view !! Cannot be used in blocks
(setq org-agenda-custom-commands
      '(("d" "daily"
	 ((agenda "" ((org-agenda-span 1))))
	 ((org-agenda-filter-preset '("+daily"))))
	("t" "today"
	 ((agenda "" ((org-agenda-span 1)
		      (org-super-agenda-groups
		       '((:name "Studying"
				;; :deadline today
				:tag "revisions")
			 (:name "Daily"
				:tag "daily")
			 (:name "Others"
				:todo "WAIT"
				:not (:tag ("revisions" "daily"))
				)
			 )))))
	 )))
;; ----------- Org + latex
;; (use-package org-ref
;;   :config
;;   (setq org-ref-completion-library 'org-ref-ivy-cite
;;         reftex-default-bibliography '("~/projects/sir/manuscript/references.bib")
;;         org-ref-bibliography-notes '("~/projects/blog/notes/books.org")
;;         org-ref-default-bibliography '("~/projects/sir/manuscript/references.bib")
;;         org-ref-pdf-directory "~/projects/blog/notes/pdfs/")
;;   ;; Customization : we want to insert the title of an entry in a reading list
;;   (push '("justtitle" . ((nil . "${title}"))) org-ref-formatted-citation-formats)
;;   ;; Helm bibtex configuration must be set
;;   (setq bibtex-completion-library-path '("~/projects/blog/notes/pdfs")
;;         bibtex-completion-bibliography '("~/projects/sir/manuscript/references.bib")
;;         bibtex-completion-library-path "~/projects/blog/notes/pdfs"
;;         bibtex-completion-notes-path "~/projects/blog/notes/books.org"
;;         ;; Do not open on default
;;         ivy-bibtex-default-action 'ivy-bibtex-insert-citation))
(setq org-latex-pdf-process '("latexmk -pdflatex='lualatex --shell-escape -interaction nonstopmode' -pdf -bibtex -f %f"))
;; Fast export: F5 is for users
(define-key org-mode-map (kbd "<f5>") #'(lambda() (interactive) (org-latex-export-to-pdf t)))
(setq revert-without-query '(".pdf")) ; Avoid confirmation with pdf
(require 'ox-beamer) ; Beamer presentations
;; Mimosis class for thesis
(add-to-list 'org-latex-classes
             '("mimosis"
               "\\documentclass{mimosis}
  [NO-DEFAULT-PACKAGES]
  [PACKAGES]
  [EXTRA]"
               ("\\chapter{%s}" . "\\addchap{%s}")
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
;;------------------------------- Workout template
(setq org-capture-templates
      '(
        ;; Workout
        ("h" "Handstand" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Handstand
 StW %^{StW}
 BtW %^{BtW}" )
	("j" "Jump ro»pe" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
	 "* Jump rope
%^{today}")
        ("l" "L-sit" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* L-sit
 %^{GtG}" )
        ("p" "Parkour")
        ("pm" "Parkour (passe-muraille)" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Parkour
Passe-muraille :
- cat hang (each side) : %^{Cat hang shimmy}
- top out (each side) : %^{Top out}
- cat hang leg press (each side) : %^{Cat hang leg press}
- cat hang pull-up (each side) : %^{Cat hang pull-up}
- knee raises (each side) : %^{Knee raises}
- passe-muraille: %^{passe-muraille}")
        ("po" "Parkour (autre)" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Parkour
%^{Parkour}")
        ("s" "Splits" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Splits
Standing splits (2-5s + rest) : %^{Standing splits}
Wall calf : %^{Wall calf}
Low lunge : %^{Low lunge}
Frog pose (dynamic) : %^{Frog pose}
Horse stance : %^{Horse stance}
Standing pancake : %^{Standing pancake}
Front split : %^{Front split}")
        ("r" "Running")
        ("rs" "Sprint" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Running
:PROPERTIES:
:type: sprint
:END:
%^{reps}p
%^{sprint}p
%^{rest}p
")
        ("ro" "Other" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Running
%^{type}p
%^{distance}p
%^{duration}p
%^{speed}p
")
        ("t" "Tricks" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
	 "* Tricks
Kip up : %^{kip-up}
Back flip : %^{backflip}
Front flip : %^{frontflip}
Front handspring : : %^{front handspring}")
        ("w" "Workout" entry (file+olp+datetree "~/projects/blog/notes/workout.org")
         "* Workout
RTO : %^{RTO}
Skin-the-cat : %^{Skin the cat}
L-sit : %^{L-sit}
Muscle-up L-sit : %^{Muscle-up}
Pistols (assisted) : %^{Pistols}
Extension (lower-back) : %^{Extension}
Front-lever row (tuck) : %^{Rows}
Planche on rings (tuck): %^{Planche tucked}
Norwegian curls: %^{Curls}
Compression : %^{Compression}"
         )
        ("c" "Cookbook" entry (file "~/projects/blog/notes/cooking.org") ;; Needs org-chef
         "%(org-chef-get-recipe-from-url)")
        ("m" "Manual Cookbook" entry (file "~/projects/blog/notes/cooking.org")
         "* %^{Recipe title: }\n  :PROPERTIES:\n  :source-url:\n  :servings:\n  :prep-time:\n  :cook-time:\n  :ready-in:\n  :END:\n** Ingredients\n   %?\n** Directions\n\n")
        ))
;; ------------------- Other
(add-to-list 'org-modules 'ol-gnus) ; Manage link to mail in gnus
(require 'ob-shell)

;; Everything relation to navigation (file, buffers, windows .. is here
;; With fish, there are some troubles to run commands...
;; For example with projectile-find-file...
(setq shell-file-name "/bin/sh")
; remember recent files every 30 minutes
(recentf-mode 1)     
(run-at-time nil (* 30 60) 'recentf-save-list)
;; Show the end of a combination (useful for short memory....)
(use-package which-key
  :init
  (which-key-mode))
;; ------------------- Dired ---------------
;; No details by default, toggle back with (
;; No dotfiles either (activate back with C-x M-o
;; does not work
(use-package dired
  :straight nil			       ; Needed to avoid installing it
  :init
  (setq dired-use-ls-dired nil		; For freebsd
	dired-dwim-target t ; suggest a target for moving/copying intelligently
	dired-listing-switches "-alh" ; Human readable size
	)
  :bind (:map dired-mode-map
	      (("ê" . dired-do-async-shell-command)
	       ("è" . dired-up-directory)))
  ;; For wdired, use C-x C-q (builtin)
  )
:root-dir
(use-package dired-x  			; Dired-x is needed to omit 
   :straight nil 			; Needed to avoid installing it
   :config
   (setq dired-omit-files
	 (concat dired-omit-files "\\|^\\..+$"))
   :hook
   ((dired-mode . dired-hide-details-mode) ; No details
    (dired-mode . dired-omit-mode) ; No details
    ))
;; Open movies and ebooks in dired
(use-package openwith
  :config
  (openwith-mode 1)
  (add-hook 'dired-mode-hook 'openwith-mode 1)
  (setq openwith-associations
	(list
	 ;; (list (openwith-make-extension-regexp '("pdf" "epub"))
	 (list (openwith-make-extension-regexp '("epub"))
	       "zathura" '(file))
	 (list (openwith-make-extension-regexp '("mkv"))
	       "mpv" '(file))
	 )))
;; -------------- other ------------------
;; Workspaces support: use tab-bar-mode instead (built in)
;; Manage pdfs
(use-package pdf-tools
  :init
  (pdf-loader-install)
  (setq pdf-view-display-size 'fit-height)
  :bind
  (:map pdf-view-mode-map ("M-g g" . pdf-view-goto-page))
  )
;;  Nice modeline (support tab-mode too)
(use-package doom-modeline
  :ensure t
  :init (doom-modeline-mode 1))
(remap-global "C-c e" 'eshell)
;; ------------------- Windows ---------------
;; Use windmove (built-in). Ace-windows is not *that* useful
;; S-left for going left andl so on
(windmove-default-keybindings) 
;; With repeat mode (emacs 28), we can easily switch windows with C-x o then o o o...
(repeat-mode)
;;--------------------- Recentf -----------------
(recentf-mode 1)
(setq recentf-max-menu-items 25)
(setq recentf-max-saved-items 25)
(run-at-time nil (* 10 60) 'recentf-save-list) ;; Every 10min

;; Manage mails with notmuch
;; Use default mapping (emacs)
(defun +notmuch/search-delete ()
  (interactive)
  (notmuch-search-add-tag (list "+deleted" "-inbox" "-unread"))
  (notmuch-tree-next-message))
(use-package notmuch
  :config
  (setq-default notmuch-search-oldest-first nil) ;; setq does NOT work
  (setq sendmail-program  "/usr/local/bin/msmtp" ;; Freebsd
	notmuch-fcc-dirs nil
	notmuch-archive-tags '("-inbox" "-unread" "-new" "+archived")
	notmuch-saved-searches '(
				 (:name "inbox"   :query "tag:inbox "    :key "i" :search-type 'tree)
				 (:name "sent"    :query "tag:sent"      :key "s" :search-type 'tree)
				 (:name "archived":query "tag:archived"  :key "a" :search-type 'tree)
				 (:name "drafts"  :query "tag:draft"     :key "d" :search-type 'tree))
	send-mail-function 'sendmail-send-it ; Activate mail sending
	message-cite-reply-position 'above) ; mailing list reply style
  (add-to-list 'mm-inhibit-file-name-handlers 'openwith-file-handler)
  ;;  Jump to inbox
  (remap-global "C-c m" '(lambda () (interactive) (notmuch-search "tag:inbox")))
  (define-key notmuch-search-mode-map (kbd "d") '+notmuch/search-delete))

;; WARNING:  This config is for a bepo keyboard 
;; Native comp: disable warnings
(setq native-comp-async-report-warnings-errors nil)
(setq package-native-compile t)
;; Slightly faster booting time. The default is 800 kilobytes.  Measured in bytes.
(setq gc-cons-threshold (* 50 1000 1000))
;; Default mappings are used, with minor adaptation to a bepo keyboard
;; See https://yiufung.net/post/emacs-key-binding-conventions-and-why-you-should-try-it/ for tips about emacs mapping
(load-file "~/.emacs.d/theme.el") 	; Show theme as quickly as possible
(load-file "~/.emacs.d/packages.el") 	; Package manager must be loaded first
(load-file "~/.emacs.d/emacs-bepo.el") 	; Remap vanilla emacs
(load-file "~/.emacs.d/code.el")
(load-file "~/.emacs.d/mail.el")
(load-file "~/.emacs.d/navigation.el")
(load-file "~/.emacs.d/org.el")
(load-file "~/.emacs.d/skeletons.el")
(load-file "~/.emacs.d/utilities.el")
(put 'downcase-region 'disabled nil)
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(custom-safe-themes
   '("d6da24347c813d1635a217d396cf1e3be26484fd4d05be153f3bd2b293d2a0b5" default)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )

;; Remap some default emacs keybindings to adapt to bepo
;; We try to minimize the number of remappings: only 0,1...9 keys
;; No need for general.el if we only use vanilla emacs
(defun remap-global (s f)
  (define-key global-map (kbd s) f))
;; Window : remap 0,1...9
(remap-global "C-x 0" nil)
(remap-global "C-x *" 'delete-window)
(remap-global "C-x 1" nil)
(remap-global "C-x \"" 'delete-other-windows)
(remap-global "C-x 2" nil)
(remap-global "C-x «" 'split-window-below)
(remap-global "C-x 3" nil)
(remap-global "C-x »" 'split-window-right)
;; Tab-bar: remap 0,1...
(remap-global "C-x t 0" nil)
(remap-global "C-x t *" 'tab-close)
(remap-global "C-x t 1" nil)
(remap-global "C-x t \"" 'tab-close-other)
(remap-global "C-x t 2" nil)
(remap-global "C-x t «" 'tab-new)
;; Navigation with bepo
(remap-global "M-«" 'backward-paragraph)
(remap-global "M-»" 'forward-paragraph)
;; ";" is harder to reach
(remap-global "M-;" nil)
(remap-global "M-ç" 'comment-dwim)
(remap-global "C-x C-ç" 'comment-line)
;; Swap : and , for evaluating lisp
(remap-global "M-:" 'xref-pop-marker-stack)
(remap-global "M-," 'eval-expression)
;; Not bepo specific
(remap-global "C-x x e" 'eval-buffer) ; Emacs 28
;; Avoid typing ^ twice by remapping it to è
(remap-global "M-è" 'delete-indentation) ; Same as join-line

;;------------ Languages -------------
;; 2 issues with project.el : straight.el use the local version 
;; - Symbol’s value as variable is void: project-switch-commands (magit)
;; - Symbol’s value as variable is void: project-root (eglot)
;; So we have to install it by hand with `package-install` -> `project`
(use-package eglot
  :config
  (add-hook 'haskell-mode-hook 'eglot-ensure))
;;---------- Haskell 
;; With egplot, we have haskell-server too
(use-package haskell-mode
  :bind ("C-c l" . haskell-process-load-file))
;; Project management with project.el (builtin)
;; ------------------- Completion ---------------
;; Selectrum replaces ivy (uses Emacs API)
;; Minimalist alternative to selectrum, fully compatible with Emacs api
;; We could use icomplete (vertical mode built-in in emacs 28) but it's less fluid
(use-package vertico
  :init
  (vertico-mode)
  )
;; Use orderless to improve filtering (faster that prescient it seems)
(use-package orderless
  :init
  (setq completion-styles '(orderless))
  ;; Persist history over Emacs restarts
  (savehist-mode)
  )
;; ---  Show more details in the minibuffer
(use-package marginalia
  :init
  ;; Enabled right away. Note that this forces loading the package.
  (marginalia-mode))
;; Counsel alternative (Super uselful). Default mapping suggested from the authors
(use-package consult
   :bind (;; C-c bindings (mode-specific-map)
         ("C-c h" . consult-history)
         ("C-c b" . consult-bookmark)
         ("C-c k" . consult-kmacro)
	 ("C-c r" . consult-recent-file)
         ;; C-x bindings (ctl-x-map)
         ("C-x M-:" . consult-complex-command) ;; orig. repeat-complex-command
         ("C-x b" . consult-buffer) ;; orig. switch-to-buffer
         ("C-x 4 b" . consult-buffer-other-window) ;; orig. switch-to-buffer-other-window
         ("C-x 5 b" . consult-buffer-other-frame) ;; orig. switch-to-buffer-other-frame
         ;; Custom M-# bindings for fast register access
         ("M-#" . consult-register-load)
         ("M-'" . consult-register-store) ;; orig. abbrev-prefix-mark (unrelated)
         ("C-M-#" . consult-register)
         ;; Other custom bindings
         ("M-y" . consult-yank-pop)	;; orig. yank-pop
         ("<help> a" . consult-apropos)	;; orig. apropos-command
         ;; M-g bindings (goto-map)
         ("M-g e" . consult-compile-error)
         ("M-g f" . consult-flymake) ;; Alternative: consult-flycheck
         ("M-g g" . consult-goto-line) ;; orig. goto-line
         ("M-g o" . consult-outline)
         ("M-g m" . consult-mark)
         ("M-g k" . consult-global-mark)
         ("M-g i" . consult-imenu)
         ("M-g I" . consult-project-imenu)
         ;; M-s bindings (search-map)
         ("M-s f" . consult-find)
         ("M-s g" . consult-grep)
         ("M-s G" . consult-git-grep)
         ("M-s r" . consult-ripgrep)
         ("M-s l" . consult-line)
         ("M-s m" . consult-multi-occur)
         ("M-s k" . consult-keep-lines)
         ("M-s u" . consult-focus-lines)
         ;; Isearch integration
         ("M-s e" . consult-isearch)
         :map isearch-mode-map
         ("M-e" . consult-isearch)   ;; orig. isearch-edit-string
         ("M-s e" . consult-isearch) ;; orig. isearch-edit-string
         ("M-s l" . consult-line)) ;; required by consult-line to detect isearch
  ;; Enable automatic preview at point in the *Completions* buffer.
  :hook (completion-list-mode consult-preview-at-point-mode)
  :config
  ;; Ripgrep-all (cannot jump to pdf page though)
  (defcustom consult-ripgrep-all-command
    "rga --null --line-buffered --color=ansi --max-columns=1000\
   --no-heading --line-number . -e ARG OPTS"
    "Command line string for ripgrep-all, see `consult-ripgrep-all'.
The command string must have a specific format, including ARG and OPTS
substrings. ARG is replaced by the filter string and OPTS by the auxillary
command options."
    :type 'string)
  (defun consult-ripgrep-all (&optional dir initial)
    (interactive "P")
    (consult--grep "Ripgrep-all" consult-ripgrep-all-command dir initial))
  )
;; Lighter alternative to company, without backend to programming languages
;; With eglot, we should be fine
(use-package corfu
  :init
  (corfu-global-mode) ; Enable globally (recommended)
  ;; Optionally use TAB for cycling, default is `corfu-complete'.
  :bind (:map corfu-map
	      ("TAB" . corfu-next)
	      ("S-TAB" . corfu-previous))
  )
(use-package emacs
  :init
  ;; TAB cycle if there are only few candidates
  (setq completion-cycle-threshold 3)
  ;; Enable indentation+completion using the TAB
  ;; Won't work properly with TAB without this !
  (setq tab-always-indent 'complete))
;; ------------- Others --------------
(use-package magit)
;; Do not use lispy, but built-in sexp
;; Do not use yasnippet but skeleton (builti)n
(use-package wgrep) ; Editable grep results <3
(show-paren-mode 1) ; Show matching parenthesis
;; Yank from mouse selection. By default, only available with mouse-2....
(defun my/yank-primary ()
  "Yank from primary selection."
  (interactive)
  (push-mark)
  (insert-for-yank (gui-get-primary-selection)))
(use-package fish-mode) ; Fish shell

My emacs configuration, from scratch, after trying Doom. The idea is use vanilla Emacs as much as possible, so that means:
- only a handful of packages
- avoid remapping default keybindings
This setup is adapted to the bepo keyboard layout.