Doom Emacs Configuration

;; These are used for a number of things, particularly for GPG configuration,
;; some email clients, file templates and snippets.
(setq user-full-name "Dehaeze Thomas"
      user-mail-address "dehaeze.thomas@gmail.com")

(setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 12 :weight 'semi-light)
      doom-variable-pitch-font (font-spec :family "Hack Nerd Font Mono")
      doom-unicode-font (font-spec :family "Hack Nerd Font Mono" :size 12)
      doom-big-font (font-spec :family "Hack Nerd Font Mono" :size 19))

(setq doom-theme 'doom-gruvbox)

(setq display-line-numbers-type t)

(after! evil
  (map! :m  "-"  #'dired-jump))

(define-key evil-normal-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-normal-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)

(setq-default evil-cross-lines t)

(after! which-key
  (setq which-key-idle-delay 0.5
        which-key-idle-secondary-delay 0.01
        which-key-sort-order 'which-key-key-order-alpha))

(global-visual-line-mode nil)

(auto-fill-mode -1)
(remove-hook 'text-mode-hook 'turn-on-auto-fill)
;; turn on auto-fill for text-mode
(add-hook 'text-mode-hook 'turn-on-auto-fill)
(after! org
  ;; turn off auto-fill for org-mode
  (add-hook 'org-mode-hook 'turn-off-auto-fill))

(setq alert-default-style 'libnotify)

(setq create-lockfiles nil)

(global-hl-line-mode -1)
(after! org
  (add-hook 'org-mode-hook
      (lambda()
          (hl-line-mode -1)
          (global-hl-line-mode -1))
      't
  ))

(with-eval-after-load 'better-jumper
  (map!
  :desc "Jump Forward"
  "C-i" #'better-jumper-jump-forward))

(setenv "GIT_ASKPASS" "git-gui--askpass")

(setq magit-diff-refine-hunk 'all)

(use-package! dired-narrow
  :config
  (map! :map dired-mode-map
        :n "f"
        'dired-narrow-fuzzy))

(use-package! pdf-tools
  :config
  (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
  )

(push "~/.config/doom/snippets" yas-snippet-dirs)
(yas-global-mode 1)

(defun tdh-export-everything-to-hugo ()
  "Export all the .org files in the specified directory to markdown using Hugo"
  (interactive)
  (setq org-files (directory-files (read-directory-name "Directory:" "/home/thomas/Cloud/brain/") t "org$" t))

  (while org-files
    (setq current-org-file (car org-files))
    (message "Exporting %s" current-org-file)
    (find-file current-org-file)
    (org-hugo-export-to-md)
    (setq org-files (cdr org-files))))

(setq org-directory "~/Cloud/org/")
(after! org
  (setq org-directory "~/Cloud/org/")

  ;; Replace the content marker, “⋯”, with a nice unicode arrow.
  (setq org-ellipsis " ⤵")

  (setq org-default-notes-file "~/Cloud/org/refile.org")

  ;; Avoid accidentally editing folded regions, say by adding text after an Org “⋯”.
  (setq org-catch-invisible-edits 'show)

  ;; The following setting hides blank lines between headings which keeps folded view nice and compact.
  (setq org-cycle-separator-lines 0)

  ;; Indent according to the outline structure
  (setq org-startup-indented t)
  (setq org-startup-folded t)

  ;; Record the information of when the task was marked as DONE
  (setq org-log-done 'time)

  ;; begining of line on heading behavior
  (setq org-special-ctrl-a/e nil)
)

(after! evil-org
  (remove-hook 'org-tab-first-hook #'+org-cycle-only-current-subtree-h))

(after! org
  (setq org-image-actual-width t))

(after! org
  (setq org-link-abbrev-alist
    '(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
      ("notes" . "~/Cloud/brain/%s.org")
      ("papers" . "~/Cloud/pdfs/%s.pdf")))
  )

(after! org
  ;; Align Tags and flush right
  (setq org-tags-column -78)
  ;; Tags with fast selection keys
  (setq org-tag-alist (quote (("@home" . ?h)
                              ("@work" . ?w)
                              ("@christophe" . ?c)
                              ("@veijo" . ?v))))
  )

(after! org
  (setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
  )

(after! org
  ;; Tags with fast selection keys
  (setq org-todo-keywords '(
                            (sequence "TODO(t)" "NEXT(n)" "MAIL(m)" "|" "DONE(d)")
                            (sequence "READ(r)" "BKMK(b)" "EXER(x)" "|" "DONE(d)")
                            (sequence "WAIT(w@/!)" "SDAY(s)" "|" "CANC(c@/!)")
                            (sequence "QUES(q)" "|" "ANSW(a)")
                            (sequence "EXAM(e)" "IDEA(i)" "|")
                            ))

  ;; Display of the keywords
  (setq org-todo-keyword-faces
        '(("TODO" . (:foreground "#cc241d" :weight bold)) ;; red
          ("EXER" . (:foreground "#cc241d" :weight bold)) ;; red
          ("NEXT" . (:foreground "#cc241d" :weight bold)) ;; red
          ("MAIL" . (:foreground "#cc241d" :weight bold)) ;; red
          ("READ" . (:foreground "#cc241d" :weight bold)) ;; red
          ("ANSW" . (:foreground "#689d6a" :weight bold)) ;; aqua
          ("DONE" . (:foreground "#689d6a" :weight bold)) ;; aqua
          ("WAIT" . (:foreground "#d65d0e" :weight bold)) ;; orange
          ("QUES" . (:foreground "#d79921" :weight bold)) ;; yellow
          ("CANC" . (:foreground "#a89984" :weight bold)) ;; grey
          ("SDAY" . (:foreground "#98971a" :weight bold)) ;; green
          ("BKMK" . (:foreground "#98971a" :weight bold)) ;; green
          ("IDEA" . (:foreground "#98971a" :weight bold)) ;; green
          ("EXAM" . (:foreground "#98971a" :weight bold)))) ;; green
  )

(after! org
  (defadvice org-archive-subtree (around fix-hierarchy activate)
    (let* ((fix-archive-p (and (not current-prefix-arg)
                               (not (use-region-p))))
           (location (org-archive--compute-location org-archive-location))
           (afile (car location))
           (offset (if (= 0 (length (cdr location)))
                       1
                     (1+ (string-match "[^*]" (cdr location)))))
           (buffer (or (find-buffer-visiting afile) (find-file-noselect afile))))
      ad-do-it
      (when fix-archive-p
        (with-current-buffer buffer
          (goto-char (point-max))
          (while (> (org-current-level) offset) (org-up-heading-safe))
          (let* ((olpath (org-entry-get (point) "ARCHIVE_OLPATH"))
                 (path (and olpath (split-string olpath "/")))
                 (level offset)
                 tree-text)
            (when olpath
              (org-mark-subtree)
              (setq tree-text (buffer-substring (region-beginning) (region-end)))
              (let (this-command) (org-cut-subtree))
              (goto-char (point-min))
              (save-restriction
                (widen)
                (-each path
                  (lambda (heading)
                    (if (re-search-forward
                         (rx-to-string
                          `(: bol (repeat ,level "*") (1+ " ") ,heading)) nil t)
                        (org-narrow-to-subtree)
                      (goto-char (point-max))
                      (unless (looking-at "^")
                        (insert "\n"))
                      (insert (make-string level ?*)
                              " "
                              heading
                              "\n"))
                    (cl-incf level)))
                (widen)
                (org-end-of-subtree t t)
                (org-paste-subtree level tree-text))))))))
  )

(after! org
  ;; File to save todo items
  (setq org-agenda-files (list "~/Cloud/org/"))

  ;; Include archived files
  (setq org-agenda-archives-mode t)

  ;; Set priority range from A to C with default A
  (setq org-highest-priority ?A)
  (setq org-lowest-priority ?C)
  (setq org-default-priority ?C)

  ;; Set colours for priorities
  (setq org-priority-faces '((?A . (:foreground "#FB4934"))
                             (?B . (:foreground "#FABD2F"))
                             (?C . (:foreground "#98971A"))))

  ;; Open agenda in current window
  (setq org-agenda-window-setup 'current-window)

  (setq org-agenda-prefix-format
        '((agenda  . " %-12:c %?-12t% s")
          (todo  . "") ;; Don't show the filename for reading agenda
          (tags  . " %-12:c")
          (search . " %-12:c"))
        )
  )

(after! org-agenda
  (defun tdh-org-agenda-skip-scheduled ()
    (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))

  (setq org-agenda-custom-commands
        '(("w" "Work"
           ((org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "A"))
                          ((org-ql-block-header "Important TODOs")))
            (org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "B"))
                          ((org-ql-block-header "TODOs")))
            (org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "C"))
                          ((org-ql-block-header "Not important TODOs")))))
          ("h" "Home"
           ((org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "A"))
                          ((org-ql-block-header "Things to do")))
            (org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "B"))
                          ((org-ql-block-header "Things to do")))
            (org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "C"))
                          ((org-ql-block-header "Things to do")))))
          ("q" "Questions to ask"
           ((org-ql-block '(and (todo "QUES")
                                (tags "@christophe"))
                          ((org-ql-block-header "Questions to Christophe")))
            (org-ql-block '(and (todo "QUES")
                                (tags "@veijo"))
                          ((org-ql-block-header "Questions to Veijo")))
            (org-ql-block '(and (todo "QUES")
                                (not (tags "@veijo" "@christophe")))
                          ((org-ql-block-header "Other Questions")))))
          ("R" "Already read Articles and Books"
           ((org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "article" "inproceedings" "techreport" "inbook"))
                          ((org-ql-block-header "Articles")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "book"))
                          ((org-ql-block-header "Books")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "phdthesis"))
                          ((org-ql-block-header "Phd Thesis")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                          ((org-ql-block-header "Other Things"))))
           ((org-agenda-files '("~/Cloud/brain/"))))
          ("r" "Articles and Books to read"
           ((org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "article" "inproceedings" "techreport" "inbook"))
                          ((org-ql-block-header "Article to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "book"))
                          ((org-ql-block-header "Books to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "phdthesis"))
                          ((org-ql-block-header "Phd Thesis to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                          ((org-ql-block-header "Other Things to Read"))))
           ((org-agenda-files '("~/Cloud/brain/")))))
        )
  )

(use-package! org-fancy-priorities ; priority icons
  :hook (org-mode . org-fancy-priorities-mode)
  :config (setq org-fancy-priorities-list '("■" "■" "■")))

(after! org-agenda
  (setq appt-message-warning-time 5)
  (defun tdh-org-agenda-to-appt ()
    (interactive)
    (setq appt-time-msg-list nil)
    (org-agenda-to-appt))

  (tdh-org-agenda-to-appt)
                                        ; Display appointments as a window manager notification
  (setq appt-disp-window-function 'tdh-appt-display)
  (setq appt-delete-window-function (lambda () t))

  (setq tdh-appt-notification-app (concat (getenv "HOME") "/bin/appt-notification"))
  (defun tdh-appt-display (min-to-app new-time msg)
    (if (atom min-to-app)
        (start-process "tdh-appt-notification-app" nil tdh-appt-notification-app min-to-app msg)
      (dolist (i (number-sequence 0 (1- (length min-to-app))))
        (start-process "tdh-appt-notification-app" nil tdh-appt-notification-app (nth i min-to-app) (nth i msg)))))
  )

(after! org
  (setq org-structure-template-alist
    '(("c" . "center")
      ("C" . "comment")
      ("m" . "src matlab\n")
      ("l" . "src emacs-lisp\n")
      ("i" . "important")
      ("e" . "example")
      ("q" . "quote")
      ("s" . "src")))
)

(after! org
  (setq org-capture-templates
        (quote (("t"    ; key
                 "todo" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
                 "** TODO %?\n%U\n" ; template
                 )
                ("M"    ; key
                 "Meeting" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Meetings") ; target
                 "** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
                 )
                ("m"    ; key
                 "mail" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Mails") ; target
                 "** TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%a\n" ; template
                 )
                ("pm"
                 "Org-Protocol Mail"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Mails")
                 "* MAIL %:description [[message:%:link][link]]\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n\n"
                 :immediate-finish t
                 )
                ("pu"
                 "Org-Protocol Url"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
                 "* [[%:link][%:description]]\nCaptured On: %U\n\n"
                 :immediate-finish t
                 )
                ("pt"
                 "Org-Protocol text"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
                 "* %:description\nSource: %:link\nCaptured On: %U\n\n#+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n"
                 :immediate-finish t
                 )
                )))
  )

(after! org
  ;; How many levels of headline to export
  (setq org-export-headline-levels 4)

  ;; Authorize BIND to set local variables
  (setq org-export-allow-bind-keywords t)

  ;; Use doc instead of odt
  (setq org-odt-preferred-output-format "doc")
  )

(after! org
  (setq org-export-with-author t)
  (setq org-export-with-creator nil)
  (setq org-export-with-date t)
  (setq org-export-with-toc t)
  (setq org-export-with-drawers nil)
  (setq org-export-with-sub-superscripts nil)
  (setq org-export-with-todo-keywords nil)
  )

;; Used to not export headings with :ignore: tag
(after! org
  (require 'ox-extra)
  (ox-extras-activate '(ignore-headlines)))

(after! org
  (add-to-list 'org-src-lang-modes '("latex-macros" . latex))

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

  (defun prefix-all-lines (pre body)
    (with-temp-buffer
      (insert body)
      (string-insert-rectangle (point-min) (point-max) pre)
      (buffer-string)))

  (defun org-babel-execute:latex-macros (body _params)
    (concat
     "\n#+begin_export html\n<div style=\"display: none\"> \\(\n"
     body
     "\n\\)</div>\n#+end_export\n"))
  )

(setq org-publish-project-alist
      '(("config"
         :base-directory "~/.config/literate-dotfiles/dotfiles/"
         :publishing-directory "~/.config/literate-dotfiles/docs/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-sitemap nil
         :section-numbers nil
         :table-of-contents nil)
        ("stewart-simscape"
         :base-directory "~/Cloud/thesis/matlab/stewart-simscape/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/thesis/matlab/stewart-simscape/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)
        ("nass-simscape"
         :base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/thesis/matlab/nass-simscape/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)
        ("tikz-maker"
         :base-directory "~/Cloud/tikz/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/tikz/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)))

(setq org-publish-project-alist
      '(("website"
         :components ("nass-simscape" "nass-simscape-images"))
        ("nass-simscape"
         :base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/website/nass-simscape/"
         :publishing-function org-html-publish-to-html

         :html-link-up "./index.html"
         :html-link-home "~/Cloud/website/index.html"

         :html-footnotes-section "<div id='footnotes'><!--%s-->%s</div>"

         :recursive nil
         :auto-sitemap nil
         :language en)
        ("nass-simscape-images"
         :base-directory "~/Cloud/thesis/matlab/nass-simscape/docs/figs/"
         :base-extension "png"
         :publishing-directory "~/Cloud/website/nass-simscape/figs/"
         :publishing-function org-publish-attachment)
        ))

(after! org
  (defun tdh-eval-startblock ()
    (if (member "startblock" (org-babel-src-block-names))
        (save-excursion
          (org-babel-goto-named-src-block "startblock")
          (org-babel-execute-src-block))
      nil
      )
    )

  (add-hook 'org-mode-hook 'tdh-eval-startblock)
  )

;; required libraries
(require 'dash)
;; (require 'swiper)
(require 's)

;; start directory
(defvar tdh-image-dir (expand-file-name "/home/thomas/Pictures"))

(defun tdh-insert-conference-image ()
  "Insert image from conference directory, rename and add link in current file.

The file is taken from a start directory set by `tdh-image-dir' and moved to the current directory, renamed and embedded at the point as an org-mode link. The user is presented with a list of files in the start directory, from which to select the file to move, sorted by most recent first."
  (interactive)
  (let (file-list target-dir file-list-sorted start-file start-file-full file-ext end-file end-file-base end-file-full file-number)
    ;; Clean directories from list but keep times
    (setq file-list
          (-remove (lambda (x) (nth 1 x))
                   (directory-files-and-attributes tdh-image-dir)))

    ;; Get target directory
    (setq target-dir (file-name-directory (buffer-file-name)))

    ;; Sort list by most recent
    (setq file-list-sorted
          (mapcar #'car
                  (sort file-list
                        #'(lambda (x y) (time-less-p (nth 6 y) (nth 6 x))))))

    ;; Use ivy to select start-file
    (setq start-file (ivy-read
                      (concat "Move selected file to " target-dir ":")
                      file-list-sorted
                      :re-builder #'ivy--regex
                      :sort nil
                      :initial-input nil))

    ;; add full path to start file and end-file
    (setq start-file-full
          (expand-file-name start-file tdh-image-dir))

    ;; final file name including path
    (setq end-file-full
          (expand-file-name start-file target-dir))

    ;; rename file
    (rename-file start-file-full end-file-full)
    (message "moved %s to %s" start-file-full start-file)

    ;; insert link
    (insert (org-make-link-string (format "file:%s" start-file)))

    ;; display image
    (org-display-inline-images t t)))

(after! org
  (defun tdh-render-org-table-at-point ()
    (interactive)
    (save-excursion
      (beginning-of-line)
      ;; removes the overlay is already there
      (if (overlays-at (point))
          (delete-overlay (car (overlays-at (point))))

        (let* ((element-type (org-element-type (org-element-at-point))))
          (if (and (not (eq element-type 'table))
                   (not (eq element-type 'table-row)))
              (error "not at an org table")

            (while (not (eq 'table (org-element-type (org-element-at-point))))
              (forward-line -1))
            (tdh-render-org-table (org-element-at-point))
            )))))


  (defun tdh-render-org-table (table)
    (interactive)
    (let* ((begin (org-element-property :begin table))
           (end (let ((pos (org-element-property :end table)))
                  (goto-char pos)
                  (beginning-of-line)
                  ;; skip possible space after table
                  (while (not (looking-at " *[|#]"))
                    (setq pos (point))
                    (forward-line -1))
                  pos))
           (tabletxt (buffer-substring-no-properties begin end))
           (img (with-temp-buffer
                  (insert tabletxt)
                  (mark-whole-buffer)
                  (org-latex-convert-region-to-latex)
                  (org-latex-preview)
                  (goto-char (point-min))
                  (overlay-get  (car (overlays-at (point))) 'display)))
           (overlay (make-overlay begin end)))
      (overlay-put overlay 'display img)
      (forward-line -1))
    )


  (defun tdh-render-org-tables-in-buffer ()
    (save-excursion
      (org-element-map (org-element-parse-buffer) 'table 'tdh-render-org-table)))

  ;; Use F9 to globally generate tables
  (map! :map org-mode-map :n "<f8>" (lambda () (interactive) (tdh-render-org-table-at-point)))
  )

(use-package! org-gcal
  :after org
  :init
  :config
  (setq org-gcal-client-id "396102378658-dcmbcmrnthbe925519otsjbd921otq0v.apps.googleusercontent.com"
        org-gcal-client-secret "4M5PWrbhQjwYEMXGK85lDYX9"
        org-gcal-file-alist '(("dehaeze.thomas@gmail.com" . "~/Cloud/org/gcal.org")
                              ("8kjmhe2ar0abnm054ill1fb0gc@group.calendar.google.com" . "~/Cloud/org/gcal_phd.org")))
  ;; Automatic fetch of the new events
  ;; (add-hook 'org-agenda-mode-hook (lambda () (org-gcal-fetch) ))
)

(after! org
  (map! :map org-mode-map
   (:desc "Org Agenda"
     :ni "C-c a" 'org-agenda)
   (:desc "Archive"
     :n "C-c A" 'org-archive-subtree)
   (:desc "Org Capture"
     :ni "C-c c" 'org-capture)
   (:desc "Store Link"
     :ni "C-c l" 'org-store-link)
   (:desc "Narrow Subtree"
     :ni "C-c n" 'org-toggle-narrow-to-subtree)
   (:desc "Org Noter"
     :ni "C-c N" 'org-noter)
   (:desc "Align Block"
     :ni "C-c =" 'tdh-align-src-block)
   (:desc "Insert Reference"
     :ni "C-c r" 'org-ref-insert-ref-link)
   (:desc "Insert Image"
     :ni "C-c i" 'tdh-insert-image-org-link)
   (:desc "Insert Image SXIV"
     :ni "C-c I" 'tdh-insert-image-org-link-sxiv)
   (:desc "Link to next Figure"
     :ni "C-c f" 'tdh-insert-link-to-next-figure)
   (:desc "Link to previous Figure"
     :ni "C-c F" 'tdh-insert-link-to-previous-figure)
   (:desc "Insert Screenshot"
     :ni "C-c s" 'tdh-insert-screenshot-org-link)
   (:desc "Find Roam"
     :ni "C-c r" 'orb-find-non-ref-file)
   (:desc "Insert Roam"
     :ni "C-c R" 'orb-insert-non-ref)
   ))

(defun tdh-org-confirm-babel-evaluate (lang body)
  (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python"))))

(after! org
  (setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))

(after! org
  (setq org-babel-default-header-args '((:eval . "no-export"))))

(after! org
  (setq org-src-window-setup 'current-window))

(defun tdh-org-prettify-symbols ()
  (mapc (apply-partially 'add-to-list 'prettify-symbols-alist)
        (cl-reduce 'append
                   (mapcar (lambda (x) (list x (cons (upcase (car x)) (cdr x))))
                           `(("#+begin_src" . ?✎)
                             ("#+end_src"   . ?□)
                             ("#+begin_quote" . ?«)
                             ("#+end_quote" . ?»)))))
  (turn-on-prettify-symbols-mode))
(add-hook 'org-mode-hook #'tdh-org-prettify-symbols)

(after! org
  (setq org-edit-src-content-indentation 2
        org-src-tab-acts-natively nil
        org-src-preserve-indentation nil)
  )

(after! org
  (org-babel-lob-ingest "~/.config/literate-dotfiles/dotfiles/emacs-library-babel.org"))

(after! org
  (setq org-babel-matlab-shell-command "/home/thomas/.local/bin/matlab -softwareopengl -nodesktop -nosplash")

  (setq org-babel-matlab-emacs-link-wrapper-method
        "%s
      if ischar(ans);
      echo('test');
      fid = fopen('%s', 'w');
      fprintf(fid, '%s', ans);
      fclose(fid);
      else;
      save -ascii %s ans;
      end
      delete('%s');
      ")
  )

(after! org
  (setq org-babel-default-header-args:matlab
        '((:results . "none")
          (:session . "*MATLAB*")
          (:comments . "org")
          (:exports . "both")
          (:cache .   "no")
          (:noweb . "no")
          (:hlines . "no")
          (:tangle . "yes")
          (:mkdir . "yes")
          (:eval . "no-export")))
  )

(defun tdh-matlab-whos (&optional start end)
"Get what is in the Matlab workspace"
  (interactive)
  (if (use-region-p)
    (let ((regionp (buffer-substring (region-beginning) (region-end))))
      (process-send-string "*MATLAB*" (concat "whosEmacs " regionp "\n")))
    (process-send-string "*MATLAB*" (concat "whosEmacs" "\n"))))

(defun tdh-matlab-help (&optional start end)
  "Get help on the selected function"
  (interactive)
  (if (use-region-p)
    (let ((regionp (buffer-substring (region-beginning) (region-end))))
        (process-send-string "*MATLAB*" (concat "help " regionp "\n")))
    (process-send-string "*MATLAB*" (concat "help " (read-string "Matlab help:") "\n")))
  )

(defun tdh-matlab-run-command ()
  "Prompt user to enter a matlab command"
  (interactive)
  (process-send-string "*MATLAB*" (concat (read-string "Matlab Command: ") "\n")))

(defun tdh-matlab-run-command-show-output ()
  "Prompt user to enter a matlab command"
  (interactive)
  (process-send-string "*MATLAB*" (concat "evalEmacs('" (read-string "Matlab Command: ") "')\n")))

(defun tdh-matlab-tangle-and-execute ()
  "Jump to tangle file for the source block at point."
  (interactive)
  (let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
    (cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
                         (setq file filename)))
          ((symbol-function 'delete-file) #'ignore))
      (org-babel-tangle '(4)))
    (when file
      (setq file (expand-file-name file))
      (if (file-readable-p file)
      (process-send-string "*MATLAB*" (concat "run " file "\n"))
    (error "Cannot open tangle file %S" file)))))

(after! org
  (map! :map org-mode-map
        (:prefix (",m" . "Matlab")
        :n  "e" 'tdh-matlab-run-command
        :n  "E" 'tdh-matlab-run-command-show-output
        :n  "T" 'tdh-matlab-tangle-and-execute
        :nv "h" 'tdh-matlab-help
        :nv "w" 'tdh-matlab-whos)))

(defun tdh-ctrl-ret ()
  (interactive)
  (defun tdh-in-src-block-p ()
    "Returns t when the point is inside a source code block"
    (string= "src" (org-in-block-p '("src"))))

  (if (tdh-in-src-block-p)
      (progn
        (org-babel-execute-src-block)
        (org-babel-next-src-block))
    (+org--insert-item 'below)))

(map! :after evil-org
      :map evil-org-mode-map
      :n "<C-return>" #'tdh-ctrl-ret)

(defun tdh-align-src-block ()
  (interactive)
  (defun tdh-in-src-block-p ()
    "Returns t when the point is inside a source code block"
    (string= "src" (org-in-block-p '("src"))))

  (if (tdh-in-src-block-p)
      (progn
        (org-edit-special)
        (evil-indent (point-min) (point-max))
        (org-edit-src-exit))
    (org-table-eval-formula)))

(defun tdh-org-babel-tangle-subtree ()
  "Tangle the current subtree"
  (interactive)
  (progn
    (org-narrow-to-subtree)
    (org-babel-tangle)
    (widen))
  )

(defun tdh-org-babel-jump-to-tangle-file ()
  "Jump to tangle file for the source block at point."
  (interactive)
  (let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
    (cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
                                                 (setq file filename)))
              ((symbol-function 'delete-file) #'ignore))
      (org-babel-tangle '(4)))
    (when file
      (setq file (expand-file-name file))
      (if (file-readable-p file)
          (find-file file)
        (error "Cannot open tangle file %S" file)))))

(after! org
  (map! :map org-mode-map
        (:prefix (",b" . "Tangle")
        :n  "F" 'tdh-org-babel-jump-to-tangle-file
        :n  "T" 'tdh-org-babel-tangle-subtree)))

(use-package! org-ref
  :after org
  :init
  :config
  ;; Folder where the notes files are located (or file if just one Note file)
  (setq org-ref-notes-directory "~/Cloud/brain")
  (setq org-ref-bibliography-notes "~/Cloud/brain")

  ;; Bibliography File
  (setq reftex-default-bibliography  '("~/Cloud/brain/biblio/references.bib"))
  (setq org-ref-default-bibliography '("~/Cloud/brain/biblio/references.bib"))

  ;; Folder where all the pdf are located
  (setq org-ref-pdf-directory "~/Cloud/pdfs")

  ;; Tell org-ref to let helm-bibtex find notes for it
  (setq org-ref-notes-function
        (lambda (thekey)
          (let ((bibtex-completion-bibliography (org-ref-find-bibliography)))
            (bibtex-completion-edit-notes
             (list (car (org-ref-get-bibtex-key-and-file thekey)))))))

  ;; Problem with speed: don't display broken links
  (setq org-ref-show-broken-links t)
  ;; Display information on the citation
  (setq org-ref-show-citation-on-enter t)

  (add-to-list 'org-ref-helm-user-candidates
               '("Open pdf in Zathura" . (lambda () (call-process "zathura" nil 0 nil  (concat
                                                                                        (file-name-as-directory org-ref-pdf-directory)
                                                                                        (car (org-ref-get-bibtex-key-and-file))
                                                                                        ".pdf"))))
               t)

  (add-to-list 'org-ref-helm-user-candidates
               '("Drag and Drop" . (lambda () (call-process "/bin/bash" nil 0 nil "-c" (concat
                                                                                        "dragon-drag-and-drop "
                                                                                        (file-name-as-directory org-ref-pdf-directory)
                                                                                        (car (org-ref-get-bibtex-key-and-file))
                                                                                        ".pdf"))))
               t)

  ;; Let Mathjax deals with equation reference
  (defun org-ref-eqref-export (keyword desc format)
    (cond
     ((eq format 'latex) (format "\\eqref{%s}" keyword))
     ((eq format 'html) (format "\\eqref{%s}" keyword))
     ((eq format 'md) (format "\\eqref{%s}" keyword))))
  )

(defun tdh-org-ref-open-pdf-at-point ()
  "Open the pdf in external program for bibtex key under point if it exists."
  (interactive)
  (let* ((results (org-ref-get-bibtex-key-and-file))
         (key (car results))
         (pdf-file (funcall org-ref-get-pdf-filename-function key)))
    (if (file-exists-p pdf-file)
        (call-process "zathura" nil 0 nil pdf-file)
      (message "no pdf found for %s" key))))

(use-package! org-noter
  :defer t
  :after (:any org pdf-view)
  :config
  (setq org-noter-always-create-frame nil)

  (setq org-noter-kill-frame-at-session-end nil)

  ;; Fraction of the frame that the document window will occupy when split
  (setq org-noter-doc-split-fraction '(0.6 . 0.6))

  ;; Save the last visited location automatically; when starting a new session, go to that location
  (setq org-noter-auto-save-last-location nil)

  ;; Add an empty line between each note's heading and content
  (setq org-noter-separate-notes-from-heading t)

  ;; List of paths to check (non recursively) when searching for a notes file
  (setq org-noter-notes-search-path "~/Cloud/brain")

  (defun org-noter-init-pdf-view ()
    (pdf-view-fit-page-to-window)
    (pdf-view-auto-slice-minor-mode)
    (run-at-time "0.5 sec" nil #'org-noter))
  (add-hook 'pdf-view-mode-hook 'org-noter-init-pdf-view)

  (map!
   :map pdf-view-mode-map
   (:desc "Insert Note"
     :n "i" #'org-noter-insert-note))
  )

(use-package! org-roam
  :custom-face
  (org-roam-link ((t (:inherit org-link :foreground "#cc241d"))))
  :config
  (setq org-roam-directory "~/Cloud/brain/")
  (setq org-roam-completion-system 'helm)
  (setq org-roam-capture-templates
        `(("d" "default" plain (function org-roam--capture-get-point)
           "%?"
           :file-name "${slug}"
           :head ,(concat "#+TITLE: ${title}\n"
                          "#+SETUPFILE: ./setup/org-setup-file.org\n"
                          "#+HUGO_SECTION: zettels\n"
                          "\n"
                          "- Tags ::\n"
                          "\n"
                          "* Bibliography                                                        :ignore:\n"
                          "bibliography:./biblio/references.bib"
                          )
           :unnarrowed t)))
  (setq org-roam-capture-ref-templates
        `(("r" "ref" plain (function org-roam--capture-get-point)
           "%?"
           :file-name "${slug}"
           :head ,(concat "#+TITLE: ${title}\n"
                          "#+SETUPFILE: ./setup/org-setup-file.org\n"
                          "#+HUGO_SECTION: websites\n"
                          "#+ROAM_KEY: ${ref}\n"
                          "\n"
                          "- Tags ::\n"
                          )
           :unnarrowed t)))
  )

(defun tdh-org-roam--backlinks-list (file)
  (if (org-roam--org-roam-file-p file)
      (--reduce-from
       (concat acc (format "- [[file:%s][%s]]\n"
                           (file-relative-name (car it) org-roam-directory)
                           (org-roam--get-title-or-slug (car it))))
       "" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
    ""))

(defun tdh-org-export-preprocessor (backend)
  (let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
    (unless (string= links "")
      (save-excursion
        (goto-char (point-max))
        (insert (concat "\n* Backlinks\n") links)))))

(add-hook 'org-export-before-processing-hook 'tdh-org-export-preprocessor)

(use-package! helm-bibtex
  :after-call helm-bibtex
  :init
  :config
  ;; Bibliography file
  (setq bibtex-completion-bibliography "~/Cloud/brain/biblio/references.bib")

  ;; Directory with all the pdfs
  (setq bibtex-completion-library-path "~/Cloud/pdfs")

  ;; Directory with notes files
  (setq bibtex-completion-notes-path "~/Cloud/brain/")

  (setq bibtex-completion-notes-extension ".org")

  (setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))

  ;; Use "tags" field when looking for bib entries
  (setq helm-bibtex-additional-search-fields '(tags))

  (setq helm-bibtex-full-frame nil)

  ;; Display of bibtex entries with helm
  (setq bibtex-completion-display-formats
        '((t . "${author:36} ${title:*} ${year:4} ${=type=:7} ${=has-note=:1}")))

  ;; Special symbols for notes and pdf
  (setq bibtex-completion-pdf-symbol "⌘")
  (setq bibtex-completion-notes-symbol "✎")

  ;; Template used when creating new Note file
  (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
                                                                "#+SETUPFILE: ./setup/org-setup-file.org\n"
                                                                "#+HUGO_SECTION: ${=type=}\n"
                                                                "#+ROAM_KEY: ${=key=}\n"
                                                                "\n"
                                                                "- Tags ::\n"
                                                                "- Reference :: cite:${=key=}\n"
                                                                "- Author(s) :: ${author}\n"
                                                                "- Year :: ${year}\n"
                                                                "\n"
                                                                "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
                                                                ":PROPERTIES:\n"
                                                                ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
                                                                ":END:\n"
                                                                "\n"
                                                                "* Bibliography                                                        :ignore:\n"
                                                                "bibliography:./biblio/references.bib"
                                                                ))

  ;; Make "Edit notes" the default action
  (helm-delete-action-from-source "Edit notes" helm-source-bibtex)
  (helm-add-action-to-source "Edit notes" 'helm-bibtex-edit-notes helm-source-bibtex 0)

  (helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
  (helm-add-action-to-source "Open PDF Externally" 'tdh-open-pdf-externally helm-source-bibtex 1)

  (helm-add-action-to-source "Insert Link to Note" 'tdh-insert-link-to-note helm-source-bibtex 2)
  )

(defun tdh-insert-link-to-note (key)
  "Insert a link to a note associated with the bibtex entry."
  (if (and bibtex-completion-notes-path
           (f-directory? bibtex-completion-notes-path))
      (let* ((path (f-join bibtex-completion-notes-path
                           (s-concat key bibtex-completion-notes-extension))))
        (if (file-exists-p path)
            (insert (concat "[[" (file-relative-name path) "][Notes]]"))
          (message "No note file associated"))
        )))

(defun tdh-open-pdf-externally (key)
  (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))

(defun tdh-helm-bibtex-favorites (&optional arg)
  "Search Favorite BibTeX entries"
  (interactive "P")
  (helm-bibtex arg nil "favorite "))

(defun tdh-list-bib-without-pdf-associated ()
  (interactive)
  (bibtex-completion-init)
  (setq candidates (bibtex-completion-candidates))

  (defun canditate-is-pdf-present (candidate)
    (bibtex-completion-find-pdf-in-library (cdr (assoc "=key=" candidate)))
    )

  (setq candidates-without-pdf (remove-if #'canditate-is-pdf-present candidates))

  (setq candidate-without-pdf-names (mapcar
                                     (lambda (x) (cdr (assoc "title" x)))
                                     candidates-without-pdf))

  (with-output-to-temp-buffer "*bib-without-pdf*" (princ (string-join candidate-without-pdf-names "\n")))
  (switch-to-buffer-other-window "*bib-without-pdf*")
  )

(use-package! deft
  :custom
  (deft-directory "~/Cloud/brain/"))

(use-package! org-roam-bibtex
  :hook (org-roam-mode . org-roam-bibtex-mode)
  :config
  (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))

  (setq org-roam-bibtex-templates
        `(("r" "ref" plain (function org-roam-capture--get-point) ""
           :file-name "${=key=}"
           :head ,(concat "#+TITLE: ${title}\n"
                          "#+SETUPFILE: ./setup/org-setup-file.org\n"
                          "#+HUGO_SECTION: ${=type=}\n"
                          "#+ROAM_KEY: ${ref}\n"
                          "\n"
                          "- Tags ::\n"
                          "- Reference :: ${ref}\n"
                          "- Author(s) :: ${author}\n"
                          "- Year :: ${year}\n"
                          "\n"
                          "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
                          ":PROPERTIES:\n"
                          ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
                          ":END:\n"
                          "\n"
                          "* Bibliography                                                        :ignore:\n"
                          "bibliography:./biblio/references.bib"
                          )
           :unnarrowed t)))

  (setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
  )

(defun tdh-open-bib-with-zathura (key)
  "Open the pdf corresponding to the reference KEY with Zathura"
  (if (listp key)
      (setq key (car key)))
  (call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))

(use-package! org-ref-ox-hugo
  :load-path "~/.config/doom/packages/org-ref-ox-hugo/"
  :config
  (add-to-list 'org-ref-formatted-citation-formats
               '("md"
                 ("article" . "${author}, *${title}*, ${journal}, *${volume}(${number})*, ${pages} (${year}). ${doi}")
                 ("inproceedings" . "${author}, *${title}*, In ${editor}, ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
                 ("book" . "${author}, *${title}* (${year}), ${address}: ${publisher}.")
                 ("phdthesis" . "${author}, *${title}* (${year}). ${school}.")
                 ("inbook" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
                 ("incollection" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
                 ("proceedings" . "${editor} (Eds.), _${booktitle}_ (${year}). ${address}: ${publisher}.")
                 ("unpublished" . "${author}, *${title}* (${year}). Unpublished manuscript.")
                 ("misc" . "${author} (${year}). *${title}*. Retrieved from [${howpublished}](${howpublished}). ${note}.")
                 (nil . "${author}, *${title}* (${year}).")))

  (setq reference-link-class "reference-link")
  (setq bibtex-entry-class "bibtex-entry")
  )

(setq-default TeX-master nil)

(defun tdh-latex-clean ()
  "Clean LaTeX output using latexmk"
  (interactive)
  (async-shell-command
   ;; command and parameters
   "latexmk -c "
   (shell-quote-argument buffer-file-name)
   " &"
   ))

(map! :map LaTeX-mode-map
      :n ",C" 'tdh-latex-clean)

(add-hook 'TeX-mode-hook #'TeX-fold-mode)

(setq TeX-view-program-selection '((output-pdf "Zathura")))
(setq TeX-source-correlate-mode t)
(setq TeX-source-correlate-start-server t)
(setq TeX-source-correlate-method 'synctex)
(setq TeX-view-program-list
      '(("PDF Tools" TeX-pdf-tools-sync-view)))

(use-package! bibtex
  :config
  (bibtex-set-dialect 'BibTeX))

(setq matlab-shell-command "/home/thomas/.local/bin/matlab")
(setq matlab-shell-command-switches (list "-nodesktop -nosplash"))
(setq mlint-programs '("mlint" "/home/thomas/.local/bin/mlint"))

(defvar mlint-executable "/home/thomas/.local/bin/mlint")

(flycheck-define-command-checker 'matlab-mlint
  "A Matlab checker based on mlint."
  :command `(,mlint-executable source)
  :error-patterns
  '((warning line-start "L " line " (C " (1+ digit)  "): " (message) line-end))
  :modes '(matlab-mode))

(add-to-list 'flycheck-checkers 'matlab-mlint)

;; Automatic startup of flycheck for matlab
(add-hook 'matlab-mode-hook 'flycheck-mode)

(map! :map matlab-shell-mode-map
      :i "<tab>" 'matlab-shell-tab)

(defun tdh-matlab-beautify-buffer ()
  "Beautify Current Matlab Buffer"
  (interactive)
  ;; First verifies is the current file is a Matlab file
  (if (string= (file-name-extension (buffer-file-name)) "m")
      (progn
        (save-buffer)
        (matlab-shell-run-command (concat "MBeautify.formatFileNoEditor(\"" (buffer-file-name) "\", \"" (buffer-file-name) "\")"))
        (revert-buffer :ignore-auto :noconfirm))
    (message "Current buffer is not a matlab file")
    )
  )

(defun tdh-matlab-add-breakpoint ()
  (interactive)
  (matlab-shell-run-command (concat "dbstop in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))

(defun tdh-matlab-remove-breakpoint ()
  (interactive)
  (matlab-shell-run-command (concat "dbclear in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))

(defun tdh-matlab-list-breakpoints ()
  (interactive)
  (matlab-shell-run-command (concat "dbstatus " (buffer-name))))

(defun tdh-matlab-clear-breakpoints ()
  (interactive)
  (matlab-shell-run-command (concat "dbclear in " (buffer-name))))

(defun tdh-matlab-go-to-file-directory ()
  (interactive)
  (matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))

(map! :map matlab-mode-map
      :n ",g" 'tdh-matlab-go-to-file-directory
      :n ",da" 'tdh-matlab-add-breakpoint
      :n ",dr" 'tdh-matlab-remove-breakpoint
      :n ",dL" 'tdh-matlab-list-breakpoints
      :n ",dc" 'tdh-matlab-clear-breakpoints
      :n ",dl" 'gud-cont
      :n ",ds" 'gud-step
      :n ",dn" 'gud-next
      :n ",dq" 'gud-finish)

(defun mu4e-message-maildir-matches (msg rx)
  (when rx
    (if (listp rx)
        ;; If rx is a list, try each one for a match
        (or (mu4e-message-maildir-matches msg (car rx))
            (mu4e-message-maildir-matches msg (cdr rx)))
      ;; Not a list, check rx
      (string-match rx (mu4e-message-field msg :maildir)))))

(defun choose-msmtp-account ()
  (if (message-mail-p)
      (save-excursion
        (let*
            ((from (save-restriction
                     (message-narrow-to-headers)
                     (message-fetch-field "from")))
             (account
              (cond
               ((string-match "dehaeze.thomas@gmail.com" from) "gmail")
               ((string-match "thomas.dehaeze@esrf.fr" from) "esrf"))))
          (setq message-sendmail-extra-arguments (list '"-a" account))))))

(use-package! mu4e
  :config
  (setq mail-user-agent 'mu4e-user-agent
        mu4e-mu-binary "/usr/bin/mu"
        mu4e-maildir "~/.mail"
        mu4e-compose-format-flowed t
        mu4e-compose-in-new-frame nil
        mu4e-view-show-images t
        mu4e-html2text-command "w3m -dump -T text/html"
        mu4e-use-fancy-chars t
        mu4e-headers-include-related t
        mu4e-attachment-dir  "~/Downloads"
        message-kill-buffer-on-exit t
        mu4e-compose-signature-auto-include t
        mu4e-view-show-images t
        mu4e-view-show-addresses t)
  )

(use-package! mu4e
  :config
  ;; Use imagemagick, if available.
  (when (fboundp 'imagemagick-register-types)
    (imagemagick-register-types))

  ;; Sometimes html email is just not readable in a text based client, this lets me open the
  ;; email in my browser.
  (add-to-list 'mu4e-view-actions '("View in browser" . mu4e-action-view-in-browser) t)

  ;; Spell checking ftw.
  (add-hook 'mu4e-compose-mode-hook 'flyspell-mode)

  ;; Use Helm to select mailboxes
  (setq mu4e-completing-read-function 'completing-read)
  ;; Don't ask for a 'context' upon opening mu4e
  (setq mu4e-context-policy 'pick-first)
  ;; Don't ask to quit... why is this the default?
  (setq mu4e-confirm-quit nil)
  )

(use-package! mu4e
  :config
  (setq mu4e-user-mail-address-list '("dehaeze.thomas@gmail.com" "thomas.dehaeze@esrf.fr")
        mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")
  ;; Default Folders
  (setq mu4e-sent-folder "/gmail/Sent"
        mu4e-drafts-folder "/gmail/Drafts"
        mu4e-trash-folder "/gmail/Trash"
        mu4e-refile-folder "/gmail/Archive")
  )

(use-package! mu4e
  :config
  (setq mu4e-get-mail-command "checkmail"
        mu4e-update-interval nil
        mu4e-change-filenames-when-moving t) ;; Fix for mbsync
  )

(use-package! mu4e
  :config
  (setq mu4e-contexts
        `( ,(make-mu4e-context
             :name "gmail"
             :enter-func (lambda () (mu4e-message "Switch to the gmail context"))
             :match-func (lambda (msg) (when msg
                                         (string-prefix-p "/gmail" (mu4e-message-field msg :maildir))))
             :leave-func (lambda () (mu4e-clear-caches))
             :vars '(
                     (user-mail-address . "dehaeze.thomas@gmail.com")
                     (user-full-name        . "Thomas Dehaeze")
                     (mu4e-sent-folder . "/gmail/Sent")
                     (mu4e-trash-folder . "/gmail/Trash")
                     (mu4e-drafts-folder . "/gmail/Drafts")
                     (mu4e-refile-folder . "/gmail/Archive")
                     (mu4e-compose-signature  . "Thomas Dehaeze\n")
                     ))
           ,(make-mu4e-context
             :name "esrf"
             :enter-func (lambda () (mu4e-message "Switch to the esrf context"))
             :match-func (lambda (msg) (when msg
                                         (string-prefix-p "/esrf" (mu4e-message-field msg :maildir))))
             :leave-func (lambda () (mu4e-clear-caches))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@esrf.fr")
                     (user-full-name        . "Thomas Dehaeze")
                     (mu4e-sent-folder . "/esrf/Sent")
                     (mu4e-trash-folder . "/esrf/Trash")
                     (mu4e-drafts-folder . "/esrf/Drafts")
                     (mu4e-refile-folder . "/esrf/Archive")
                     (mu4e-compose-signature  . "Thomas Dehaeze\n")
                     ))
           ))
  )

(use-package! mu4e
  :config
  (setq message-send-mail-function 'message-send-mail-with-sendmail
        sendmail-program "/usr/bin/msmtp"
        user-full-name "Thomas Dehaeze")

  ;; This prevents saving the email to the Sent folder since gmail will do this for us on their end.
  (setq mu4e-sent-messages-behavior 'delete)

  ;; Use the correct account context when sending mail based on the from header.
  (setq message-sendmail-envelope-from 'header)
  (add-hook 'message-send-mail-hook 'choose-msmtp-account)
  )

(use-package! mu4e
  :config
  (setq mu4e-bookmarks `(,(make-mu4e-bookmark
                          :name "All Inboxes"
                          :query "maildir:/gmail/Inbox OR maildir:/esrf/Inbox"
                          :key ?i)
                         ("flag:unread" "Unread messages" ?u)
                         ("date:today..now" "Today's messages" ?t)
                         ("date:7d..now" "Last 7 days" ?w)))
  )