#+TITLE: Spacemacs configuration
#+PROPERTY: header-args:emacs-lisp :comments link :results silent

* User Init
  :PROPERTIES:
  :header-args:emacs-lisp+: :tangle ~/.spacemacs.d/user-init.el
  :END:

** Melpa
#+BEGIN_SRC emacs-lisp :tangle no
  (add-to-list 'package-archives '("melpa" . "http://www.mirrorservice.org/sites/melpa.org/packages/"))
#+END_SRC

** Ispell
#+BEGIN_SRC emacs-lisp
  (setq ispell-program-name "/usr/bin/aspell")
#+END_SRC

** Org latex fragment
#+BEGIN_SRC emacs-lisp
  (defvar kk/org-latex-fragment-last nil
    "Holds last fragment/environment you were on.")

  (defun kk/org-in-latex-fragment-p ()
    "Return the point where the latex fragment begins, if inside
  a latex fragment. Else return false"
    (let* ((el (org-element-context))
           (el-type (car el)))
      (and (or (eq 'latex-fragment el-type) (eq 'latex-environment el-type))
          (org-element-property :begin el))))

  (defun kk/org-latex-fragment-toggle ()
    "Toggle a latex fragment image "
    (and (eq 'org-mode major-mode)
   (let ((begin (kk/org-in-latex-fragment-p)))
           (cond
            ;; were on a fragment and now on a new fragment
            ((and
              ;; fragment we were on
              kk/org-latex-fragment-last
              ;; and are on a fragment now
              begin

              ;; but not on the last one this is a little tricky. as you edit the
              ;; fragment, it is not equal to the last one. We use the begin
              ;; property which is less likely to change for the comparison.
              (not (and kk/org-latex-fragment-last
      (= begin
         kk/org-latex-fragment-last))))
             ;; go back to last one and put image back, provided there is still a fragment there
             (save-excursion
               (goto-char kk/org-latex-fragment-last)
               (when (kk/org-in-latex-fragment-p) (org-preview-latex-fragment))

               ;; now remove current image
               (goto-char begin)
               (let ((ov (loop for ov in (org--list-latex-overlays)
                               if
                               (and
        (<= (overlay-start ov) (point))
        (>= (overlay-end ov) (point)))
                               return ov)))
     (when ov
                   (delete-overlay ov)))
               ;; and save new fragment
               (setq kk/org-latex-fragment-last begin)))

            ;; were on a fragment and now are not on a fragment
            ((and
              ;; not on a fragment now
              (not begin)
              ;; but we were on one
              kk/org-latex-fragment-last)
             ;; put image back on, provided that there is still a fragment here.
             (save-excursion
               (goto-char kk/org-latex-fragment-last)
               (when (kk/org-in-latex-fragment-p) (org-preview-latex-fragment)))

             ;; unset last fragment
             (setq kk/org-latex-fragment-last nil))

            ;; were not on a fragment, and now are
            ((and
              ;; we were not one one
              (not kk/org-latex-fragment-last)
              ;; but now we are
              begin)
             ;; remove image
             (save-excursion
               (goto-char begin)
               (let ((ov (loop for ov in (org--list-latex-overlays)
                               if
                               (and
        (<= (overlay-start ov) (point))
        (>= (overlay-end ov) (point)))
                               return ov)))
     (when ov
                   (delete-overlay ov))))
             (setq kk/org-latex-fragment-last begin))))))
#+END_SRC

** Default Browser
#+BEGIN_SRC emacs-lisp
  (setq browse-url-browser-function 'browse-url-generic
        browse-url-generic-program "qutebrowser")
#+END_SRC

* User-Config
  :PROPERTIES:
  :header-args:emacs-lisp+: :tangle ~/.spacemacs.d/user-config.el
  :END:
** Others
#+BEGIN_SRC emacs-lisp
  ;; Line Wrapping
  (spacemacs/toggle-truncate-lines-on)

  ;; Visual line navigation for textual modes
  (add-hook 'text-mode-hook 'spacemacs/toggle-visual-line-navigation-on)

  ;; leader-q-q just kill the frame without killink the server
  (evil-leader/set-key
    "q q" 'spacemacs/frame-killer)

  ;; Remove current light highlight
  (spacemacs/toggle-highlight-current-line-globally-off)
#+END_SRC

** Windows Management
#+BEGIN_SRC emacs-lisp
  (global-set-key (kbd "<C-up>") 'shrink-window)
  (global-set-key (kbd "<C-down>") 'enlarge-window)
  (global-set-key (kbd "<C-left>") 'shrink-window-horizontally)
  (global-set-key (kbd "<C-right>") 'enlarge-window-horizontally)
#+END_SRC

** Lockfiles
#+BEGIN_SRC emacs-lisp
  (setq create-lockfiles nil)
#+end_src

** Autosave
#+BEGIN_SRC emacs-lisp
  (setq backup-directory-alist `(("." . "~/.saves")))
  (setq backup-by-copying t)
#+END_SRC

** Path
#+BEGIN_SRC emacs-lisp
  (setq thesis-base-path (expand-file-name "~/MEGA/These"))
  (setq dropbox-base-path (expand-file-name "~/Dropbox"))
#+END_SRC

** Magit
#+BEGIN_SRC emacs-lisp
  (setenv "GIT_ASKPASS" "git-gui--askpass")

  (setq magit-diff-refine-hunk 'all)
#+END_SRC

** User informations
#+BEGIN_SRC emacs-lisp
  ;; Used to the \author for LaTeX export
  (setq user-full-name "Thomas Dehaeze")

  ;; Used to set \email for LaTeX export
  (setq user-mail-address "dehaeze.thomas@gmail.com")
#+END_SRC

** Change default alert backend
#+BEGIN_SRC emacs-lisp
  (setq alert-default-style 'libnotify)
#+END_SRC

** LaTeX
- https://tex.stackexchange.com/questions/52179/what-is-your-favorite-emacs-and-or-auctex-command-trick
- https://tex.stackexchange.com/questions/20843/useful-shortcuts-or-key-bindings-or-predefined-commands-for-emacsauctex

*** Basic LaTeX configuration
#+BEGIN_SRC emacs-lisp
  (defun latex/clean ()
    "Clean LaTeX output using latexmk"
    (interactive)
    (async-shell-command
     ;; command and parameters
     "latexmk -c "
     (shell-quote-argument buffer-file-name)
     " &"
    ))

  (evil-define-key 'normal LaTeX-mode-map (kbd ", C") 'latex/clean)

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

*** Master file
#+BEGIN_SRC emacs-lisp
  (setq-default TeX-master nil)
#+END_SRC

*** Pdf Viewer
#+BEGIN_SRC emacs-lisp
  (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)))
#+END_SRC

** Helm-Bibtex
*** General Config
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'helm-bibtex
    ;; Use "tags" field when looking for bib entries
    (setq helm-bibtex-additional-search-fields '(keywords))
    ;; Special Tags:
    ;; - favorite

    ;; Reverse the order of display
    ;; (advice-add 'bibtex-completion-candidates
    ;;             :filter-return 'reverse)

    ;; 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 "✎")

    ;; Use file field to find the PDF
    ;; (setq bibtex-completion-pdf-field "file")

    ;; Bibliography file
    (setq bibtex-completion-bibliography "~/MEGA/These/Ressources/references.bib")

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

    ;; Directory with notes files
    (setq bibtex-completion-notes-path "~/MEGA/These/Ressources/notes")

    ;; Template used when creating new Note file
    (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
                                                                  ":DRAWER:\n"
                                                                  "#+LATEX_CLASS: biblioreport\n"
                                                                  "\n"
                                                                  "#+OPTIONS: toc:nil title:nil\n"
                                                                  "\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refType}{${=type=}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refKey}{${=key=}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refTitle}{${title}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refAuthor}{${author-or-editor}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refJournal}{${journal}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refYear}{${year}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refDoi}{${DOI}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refUrl}{${url}}\n"
                                                                  "#+LATEX_HEADER: \\newcommand{\\refKeywords}{${keywords}}\n"
                                                                  "#+LATEX_HEADER: \\input{config.tex}\n"
                                                                  "#+LATEX_HEADER: \\graphicspath{{./figs/${=key=}/}}\n"
                                                                  ":END:\n"
                                                                  "\n"
                                                                  "#+BEGIN_abstract\n"
                                                                  "\n"
                                                                  "#+END_abstract\n"
                                                                  "\n"
                                                                  "* ${title} :ignore:\n"
                                                                  "  :PROPERTIES:\n"
                                                                  "  :CUSTOM_ID: ${=key=}\n"
                                                                  "  :AUTHOR:    ${author}\n"
                                                                  "  :TYPE:      ${=type=}\n"
                                                                  "  :JOURNAL:   ${journal}\n"
                                                                  "  :YEAR:      ${year}\n"
                                                                  "  :VOLUME:    ${volume}\n"
                                                                  "  :PAGES:     ${pages}\n"
                                                                  "  :DOI:       ${DOI}\n"
                                                                  "  :URL:       ${url}\n"
                                                                  "  :NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
                                                                  "  :END:\n"
                                                                  "\n"))

    ;; 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)
    )
#+END_SRC

*** Open pdf externally
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'helm-bibtex
    (defun tdehaeze/open-pdf-externally (key)
      (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))

    ;; Action to open the pdf with Zathura
    (helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
    (helm-add-action-to-source "Open PDF Externally" 'tdehaeze/open-pdf-externally helm-source-bibtex 1)
    )
#+END_SRC

*** Special Commands
#+BEGIN_SRC emacs-lisp
  (defun helm-bibtex-favorites (&optional arg)
    "Search Favorite BibTeX entries"
    (interactive "P")
    (helm-bibtex arg nil "favorite "))
#+END_SRC
** Auto Complete
#+BEGIN_SRC emacs-lisp
  (global-company-mode)
#+END_SRC

** Yas Snippets
#+BEGIN_SRC emacs-lisp
  (setq yas-indent-line "fixed")
#+END_SRC

** Org-Mode
- http://cachestocaches.com/2016/9/my-workflow-org-agenda/
- http://doc.norang.ca/org-mode.html#TodoKeywords
- https://emacs.cafe/emacs/orgmode/gtd/2017/06/30/orgmode-gtd.html

*** Org Tagging
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    ;; Tags with fast selection keys
    (setq org-tag-alist (quote (("@christophe" . ?c)
                                ("@muriel" . ?m))))
    )
#+END_SRC
*** Org Gcal
- https://cestlaz.github.io/posts/using-emacs-26-gcal/#.WIqBud9vGAk

#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-gcal-client-id "396102378658-dcmbcmrnthbe925519otsjbd921otq0v.apps.googleusercontent.com"
        org-gcal-client-secret "4M5PWrbhQjwYEMXGK85lDYX9"
        org-gcal-file-alist '(("dehaeze.thomas@gmail.com" . "~/Dropbox/org/gcal.org")
                              ("udqehfhfqkecm984313pgat5192sm1cl@import.calendar.google.com" . "~/Dropbox/org/wunderlist.org")
                              ("8kjmhe2ar0abnm054ill1fb0gc@group.calendar.google.com" . "~/Dropbox/org/gcal_phd.org")))
    ;; Automatic fetch of the new events
    ;; (add-hook 'org-agenda-mode-hook (lambda () (org-gcal-sync) ))
    )
#+END_SRC

*** Org Refile
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
  )
#+END_SRC
*** Org Todos
http://sachachua.com/blog/2014/04/thinking-todo-keywords/
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load '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
    )
#+END_SRC
*** Org Agenda
**** General configuration
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    ;; File to save todo items
    (setq org-agenda-files (list (format "%s/%s" thesis-base-path "TODOs/")
                                 (format "%s/%s" dropbox-base-path "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 "#CC241D"))
                               (?B . (:foreground "#D65D0E"))
                               (?C . (:foreground "#D79921"))))

    ;; Open agenda in current window
    (setq org-agenda-window-setup (quote 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"))
    )
  )
#+END_SRC
**** Org Agenda Custom Views
https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (defun tdehaeze/org-agenda-skip-scheduled ()
      (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))

    (setq org-agenda-custom-commands
          '(("q" . "Questions to ask")
            ("qc" "Questions to Cristophe" tags "@christophe/QUES" ((org-agenda-overriding-header "Questions to Christophe")))
            ("qm" "Questions to Muriel"    tags "@muriel/QUES"     ((org-agenda-overriding-header "Questions to Muriel")))
            ("qo" "Questions to Olivier"   tags "@olivier/QUES"    ((org-agenda-overriding-header "Questions to Olivier")))
            ("qq" "All questions"          tags "/QUES" ((org-agenda-overriding-header "Other questions")))
            ("n" "Next things to do"
             ((tags "+PRIORITY+\"A\""
                    ((org-agenda-skip-function '(org-agenda-skip-entry-if 'todo 'done))
                     (org-agenda-overriding-header "High-priority unfinished tasks:")))
              (agenda "")
              (todo "NEXT" ((org-agenda-skip-function 'tdehaeze/org-agenda-skip-scheduled)(org-agenda-overriding-header "Next thing to do that are not scheduled")))
              (todo "MAIL" ((org-agenda-overriding-header "Email to write/reply")))
              (todo "WAIT" ((org-agenda-overriding-header "Things Waiting")))))
            ("u" "Unscheduled tasks" todo "TODO"
             ((org-agenda-skip-function 'tdehaeze/org-agenda-skip-scheduled)
              (org-agenda-overriding-header "Unscheduled TODO entries: ")))
            ("r" "Things to read"
             ((todo "READ"   ((org-agenda-overriding-header "Things to read"))))
             ((org-agenda-files '("~/MEGA/These/Ressources/notes/")))))
          )
    )
#+END_SRC
**** TODO Add Custom Views for the bibliography
- Things reading (BOOKMARS)
- Things to read
- etc...

*** Org Notification based on calendar event
https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarms-audio-visual-triggered-by-org-mode-events
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq appt-message-warning-time 5)
    (defun my-org-agenda-to-appt ()
      (interactive)
      (setq appt-time-msg-list nil)
      (org-agenda-to-appt))

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

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

**** appt-notification script
  :PROPERTIES:
  :header-args:  :tangle ~/bin/appt-notification
  :header-args+: :comments none :mkdirp yes
  :header-args+: :shebang "#!/usr/bin/env bash"
  :END:
#+begin_src bash
  TIME="$1"
  MSG="$2"

  dunstify --replace=85401 "Event in $TIME minutes" "$MSG"
#+end_src

*** Org Structure Template
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-structure-template-alist
          '(("a" . "export ascii")
            ("c" . "center")
            ("C" . "comment")
            ("e" . "example")
            ("E" . "export")
            ("h" . "export html")
            ("l" . "export latex")
            ("q" . "quote")
            ("s" . "src")
            ("v" . "verse"))
          )
    )
#+END_SRC

*** Org Capture
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-directory "~/MEGA/These/TODOs/")
    (setq org-default-notes-file "~/MEGA/These/TODOs/refile.org")

    ;; Capture templates for: Tasks, Notes, appointments, phone calls, meetings, and org-protocol
    (setq org-capture-templates
          (quote (("t"    ; key
                   "todo" ; name
                   entry  ; type
                   (file (lambda () (concat (file-name-as-directory thesis-base-path) "TODOs/refile.org"))) ; target
                   "* TODO %?\n%U\n" ; template
                   )
                  ("m"    ; key
                   "mail" ; name
                   entry  ; type
                   (file (lambda () (format "%s/%s" thesis-base-path "TODOs/mails.org"))) ; target
                   "* TODO %a %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
                   )
                  ("Q" ; key
                   "quote org capture" ; name
                   entry ; type
                   (file+headline (lambda () (format "%s/%s" dropbox-base-path "org/refile.org")) "Unsorted") ; target
                   "* %?%:description Added %U\n#+BEGIN_QUOTE\n%x\n#+END_QUOTE" ; Template
                   :immediate-finish t ; properties
                   )
                  ("c"
                   "Contacts"
                   entry
                   (file (lambda () (format "%s/%s" dropbox-base-path "org/contacts.org")))
                   "* %(org-contacts-template-name)\n  :PROPERTIES:\n  :EMAIL: %(org-contacts-template-email)\n  :PHONE:\n  :ALIAS:\n  :NICKNAME:\n  :IGNORE:\n  :ICON:\n  :NOTE:\n  :ADDRESS:\n  :BIRTHDAY:\n  :END:")
                  ("a"               ; key
                   "Article"         ; name
                   entry             ; type
                   (file+headline (lambda () (format "%s/%s" thesis-base-path "Ressources/bibliography.org") "Article"))  ; target
                   "* %^{Title} %(org-set-tags)  :article: \n:PROPERTIES:\n:Created: %U\n:Linked: %A\n:END:\n%i\nBrief description:\n%?"  ; template
                   :prepend t        ; properties
                   :empty-lines 1    ; properties
                   :created t        ; properties
                   )
                  )))
    )
#+END_SRC

*** TODO Org Publish
https://orgmode.org/worg/org-tutorials/org-publish-html-tutorial.html

#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-publish-project-alist
          '(
            ("tikz-maker"
             :base-directory "~/MEGA/These/LaTeX/ressources/"
             :base-extension "org"
             :publishing-directory "~/MEGA/These/LaTeX/ressources/docs/"
             :recursive t
             :publishing-function org-html-publish-to-html
             :headline-levels 4             ; Just the default for this project.
             :auto-preamble t
             )
            ("tikz-maker-static"
             :base-directory "~/MEGA/These/LaTeX/ressources/Figures/"
             :base-extension "css\\|js\\|png\\|jpg\\|svg\\|gif\\|pdf\\|mp3\\|ogg\\|swf"
             :publishing-directory "~/MEGA/These/LaTeX/ressources/docs/Figures/"
             :recursive t
             :publishing-function org-publish-attachment
             )
            ("org" :components ("tikz-maker" "tikz-maker-static"))
            ))
    )
#+END_SRC

*** Org Babel
**** Main configuration
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    ;; Don't ask for confirmation when evalutating latex blocs
    (defun my-org-confirm-babel-evaluate (lang body)
      (not (member lang '("emacs-lisp" "latex" "matlab" "sh"))))
    (setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)

    ;; Enable Babel evalutation
    (org-babel-do-load-languages 'org-babel-load-languages '((latex . t)
                                                             (shell . t)
                                                             (matlab . t)
                                                             (python . t)
                                                             (emacs-lisp . t)))
    )
#+END_SRC

**** Library of Babel
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (org-babel-lob-ingest "~/MEGA/These/org-mode/org-babel-tutorial/org-babel-library.org")
  )
#+END_SRC

**** Matlab
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-babel-matlab-shell-command "/usr/local/bin/matlab -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');
      ")

    (setq org-babel-octave-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');
      ")
    )
#+end_src

**** Asynchronous execution
https://github.com/astahlman/ob-async
#+BEGIN_SRC emacs-lisp
  (require 'ob-async)
#+end_src

**** Theme
#+BEGIN_SRC emacs-lisp
  (require 'color)
  (set-face-attribute 'org-block nil :background (color-darken-name (face-attribute 'default :background) 3))
#+end_src

*** Org Export
**** Basic
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load '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)

    (setq org-odt-preferred-output-format "doc")

    ;; Used to not export headings with :ignore: tag
    (require 'ox-extra)
    (ox-extras-activate '(ignore-headlines))
  )
#+END_SRC
**** Ox Latex Subfigure package
#+BEGIN_SRC emacs-lisp
  (use-package ox-latex-subfigure
    :init
    (setq org-latex-prefer-user-labels t)
    :config (require 'ox-latex-subfigure))
#+END_SRC

**** Clear page before heading
https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-heading/30892

#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-latex
      (defun org/get-headline-string-element  (headline backend info)
        (let ((prop-point (next-property-change 0 headline)))
          (if prop-point (plist-get (text-properties-at prop-point headline) :parent))))

      (defun org/ensure-latex-clearpage (headline backend info)
        (when (org-export-derived-backend-p backend 'latex)
          (let ((elmnt (org/get-headline-string-element headline backend info)))
            (when (and elmnt (org-element-property :CLEARPAGE elmnt))
              (concat "\\clearpage\n" headline)))))

      (add-to-list 'org-export-filter-headline-functions
                   'org/ensure-latex-clearpage)
      ))
#+END_SRC
**** TODO HTML Export
***** Export with css class instead of inline css
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-html-htmlize-output-type 'css)
    )
#+END_SRC

***** TODO MP4 movies
#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (setq org-html-html5-fancy t)
    (setq org-html-doctype "xhtml-strict")
    )
#+END_SRC

***** TODO MathJax with SIunix
#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (setq org-html-mathjax-template
          "<script type=\"text/x-mathjax-config\">
        MathJax.Hub.Config({
            extensions: [\"tex2jax.js\", \"[siunitx]/siunitx.js\"],
            jax: [\"input/TeX\",\"output/HTML-CSS\"],
            tex2jax: {inlineMath: [[\"$\",\"$\"],[\"\\(\",\"\\)\"]]},
            displayAlign: \"%ALIGN\",
            displayIndent: \"%INDENT\",

            \"HTML-CSS\": { scale: %SCALE,
                            linebreaks: { automatic: \"%LINEBREAKS\" },
                            webFont: \"%FONT\"
                           },
            SVG: {scale: %SCALE,
                  linebreaks: { automatic: \"%LINEBREAKS\" },
                  font: \"%FONT\"},
            NativeMML: {scale: %SCALE},
            TeX: { equationNumbers: {autoNumber: \"%AUTONUMBER\"},
                   extensions: [\"AMSmath.js\",\"AMSsymbols.js\", \"sinuitx.js\"],
                   MultLineWidth: \"%MULTLINEWIDTH\",
                   TagSide: \"%TAGSIDE\",
                   TagIndent: \"%TAGINDENT\"
                 }
    });
    MathJax.Ajax.config.path['siunitx']  = '../js';
    </script>
    <script type=\"text/javascript\"
            src=\"%PATH\"></script>"
          )
    )
#+END_SRC

*** Org LaTeX
**** LaTeX Classes
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-latex
      ;; Custom classes to use when exporting to latex
      '(add-to-list 'org-latex-classes
                `("beamer"
                  ,(concat "\\documentclass[presentation]{beamer}\n"
                           "[DEFAULT-PACKAGES]"
                           "[PACKAGES]"
                           "[EXTRA]\n")
                  ("\\section{%s}" . "\\section*{%s}")
                  ("\\subsection{%s}" . "\\subsection*{%s}")
                  ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
      (add-to-list 'org-latex-classes
                   '("clean-cheatsheet"
                     "\\documentclass{clean-cheatsheet}"
                     ("\\section{%s}" . "\\section*{%s}")
                     ("\\subsection{%s}" . "\\subsection*{%s}")
                     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                     ("\\paragraph{%s}" . "\\paragraph*{%s}")
                     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                   )
      (add-to-list 'org-latex-classes
                   '("clean-beamer"
                     "\\documentclass{clean-beamer}"
                     ("\\section{%s}" . "\\section*{%s}")
                     ("\\subsection{%s}" . "\\subsection*{%s}")
                     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                     ("\\paragraph{%s}" . "\\paragraph*{%s}")
                     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                   )
      (add-to-list 'org-latex-classes
                   '("cleanreport"
                     "\\documentclass{cleanreport}"
                     ("\\section{%s}" . "\\section*{%s}")
                     ("\\subsection{%s}" . "\\subsection*{%s}")
                     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                     ("\\paragraph{%s}" . "\\paragraph*{%s}")
                     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                   )
      (add-to-list 'org-latex-classes
                   '("biblioreport"
                     "\\documentclass{biblioreport}"
                     ("\\section{%s}" . "\\section*{%s}")
                     ("\\subsection{%s}" . "\\subsection*{%s}")
                     ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                     ("\\paragraph{%s}" . "\\paragraph*{%s}")
                     ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                   )
      )
    )
#+END_SRC

**** Basic
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-latex
      ;; Add packages by default
      (add-to-list 'org-latex-packages-alist '("" "siunitx" t))
      (add-to-list 'org-latex-packages-alist '("most" "tcolorbox" t))

      ;; Setup default option for image size when exporting to LaTeX
      (setq org-latex-image-default-option "scale=1")
      (setq org-latex-image-default-width nil)

      ;; Use define labels instead of automatic generated ones
      (setq org-latex-prefer-user-labels t)

      ;; Captions above the table
      ;; (setq org-latex-caption-above (table))

      ;; Settings to export code with `minted' instead of `verbatim'.
      (setq org-latex-listings 'minted)

      ;; Command used when exporting to pdf
      (setq org-latex-pdf-process
            '("latexmk -cd -pdflatex=\"xelatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory %o\" -pdf -bibtex -f %f"))
      ;; (setq org-latex-pdf-process
      ;;   '("xelatex -interaction nonstopmode -output-directory %o %f"
      ;;     "xelatex -interaction nonstopmode -output-directory %o %f"
      ;;     "xelatex -interaction nonstopmode -output-directory %o %f"))
      )
    )
#+END_SRC

**** Beamer
***** TODO Make a custom environment for columns with title
#+beamer: \csubtitle{title}\vspace{1em}

***** Custom Environments
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-beamer
      (add-to-list 'org-beamer-environments-extra
                   '("cbox" ;; Name of environment
                     "m" ;; Selection key
                     "\\onslide%a{\\begin{cbox}[%h]%O"
                     "\\end{cbox}}\\vspace{0.5em}"))
      (add-to-list 'org-beamer-environments-extra
                   '("csubbox" ;; Name of environment
                     "M" ;; Selection key
                     "\\onslide%a{\\tcbsubtitle{%h}"
                     "}"))
      )
    )
#+END_SRC

***** Beamer export options
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-beamer
      (defun my-beamer-bold (contents backend info)
        (when (eq backend 'beamer)
          (replace-regexp-in-string "\\`\\\\[A-Za-z0-9]+" "\\\\textbf" contents)))

      (add-to-list 'org-export-filter-bold-functions 'my-beamer-bold)
      )
    )
#+END_SRC

**** Latex Fragments
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (with-eval-after-load 'ox-latex
      ;; Automatic toggle of latex fragments http://slumpy.org/blog/2017-02-01-automatic-latex-preview-in-org-mode/
      ;; Activate Automatic LaTeX fragment
      (spacemacs/set-leader-keys "ol" '(lambda () (interactive) (add-hook 'post-command-hook 'kk/org-latex-fragment-toggle t)))
      ;; Disable Automatic LaTeX fragment
      (spacemacs/set-leader-keys "oL" '(lambda () (interactive) (remove-hook 'post-command-hook 'kk/org-latex-fragment-toggle t)))

      ;; Use F9 to globally generate all the latex fragments
      (global-set-key (kbd "<f9>") (lambda () (interactive) (org-preview-latex-fragment 16)))

      ;; Put all the preview images in some directory
      (setq org-preview-latex-image-directory "~/.ltximg/")

      ;; Define backends to preview LaTeX fragments
      (setq org-preview-latex-process-alist '((imagemagick
                                               :programs ("latex" "convert")
                                               :description "pdf > png"
                                               :message "you need to install the programs: pdflatex and imagemagick."
                                               :use-xcolor t
                                               :image-input-type "pdf"
                                               :image-output-type "png"
                                               :image-size-adjust (1.0 . 1.0)
                                               :latex-compiler ("xelatex -interaction nonstopmode -output-directory %o %f")
                                               ;; :latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
                                               :image-converter ("convert -density %D -trim -antialias %f -quality 100 %O"))
                                              (pdf2svg
                                               :programs ("latex" "pdf2svg")
                                               :description "pdf > svg"
                                               :message "you need to install the programs: pdflatex and pdf2svg."
                                               :use-xcolor t
                                               :image-input-type "pdf"
                                               :image-output-type "svg"
                                               :image-size-adjust (1.0 . 1.0)
                                               :latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
                                               :image-converter ("pdfcrop %f ~/Downloads/test.pdf && pdf2svg %f %O"))
                                              (dvisvgm
                                               :programs ("latex" "dvisvgm")
                                               :description "dvi > svg"
                                               :message "you need to install the programs: latex and dvisvgm."
                                               :use-xcolor t
                                               :image-input-type "dvi"
                                               :image-output-type "svg"
                                               :image-size-adjust (1.0 . 1.0)
                                               :latex-compiler ("latex -interaction nonstopmode -output-directory %o %f")
                                               ;; :image-converter ("dvisvgm %f -e -n -b min -Z 1.2 -c %S -o %O"))
                                               :image-converter ("dvisvgm %f -n -b min -c %S -o %O"))
                                              ))

      ;; Use imagemagick/dvisvgm to generate png from pdf
      (setq org-preview-latex-default-process 'dvisvgm)
      ;; (setq org-preview-latex-default-process 'pdf2svg)
      ;; (setq org-preview-latex-default-process 'imagemagick)
      ))
#+END_SRC

**** TODO Custom Export - Add Page and Label for LaTeX export
https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbitrary-org-property-into-an-arbitrary-string-na?rq=1

#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (defcustom tdehaeze/org-property-mapping
      '((latex ("CUSTOM_PAGE" . tdehaeze/insert-org-page-latex)
               ("CUSTOM_LABEL" . tdehaeze/insert-org-label-latex)))
      "List of mappings from org property to arbitrary strings.
    Each element is a list:
      (BACKEND (PROPERTY1 . FUNCTION1) (PROPERTY2 . FUNCTION2) ...)
    FUNCTION are functions which get called with a single
    argument (the value of PROPERTY) and are responsible for doing
    whatever should be done."
      :type '(repeat (cons symbol (repeat (cons string string)))))
    )
#+END_SRC

#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (defun tdehaeze/replace-org-property (backend)
      "Convert org properties using `tdehaeze/org-property-mapping'.
    Lookup BACKEND in `tdehaeze/org-property-mapping' for a list of
    (PROPERTY REPLACEMENT). For each healine being exported, if it has a
    PROPERTY listed insert a string immediately after the healine given by
        (format REPLACEMENT PROPERTY-VALUE)"
      (let ((map (cdr (assoc backend tdehaeze/org-property-mapping)))
            value replacement)
        (when map
          (org-map-entries
           (lambda ()
             (dolist (it map)
               (save-excursion
                 (when (setq value (org-entry-get (point) (car it)))
                   (funcall (cdr it) value)))))))))

    (add-hook 'org-export-before-processing-hook #'tdehaeze/replace-org-property)
    )
#+END_SRC

#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (defun tdehaeze/insert-org-label-latex (label)
      "Insert \"\\\\label{LABEL}\\n\" after the :PROPERTY: drawer."
      (search-forward-regexp org-property-end-re)
      (forward-char 1)
      (insert (format "\\label{%s}\n" label)))
    (defun tdehaeze/insert-org-page-latex (page)
      "Insert \"\\\\page{PAGE}\\n\" after the :PROPERTY: drawer."
      (search-forward-regexp org-property-end-re)
      (forward-char 1)
      (insert (format "\\page{%s}\n" page)))
    )
#+END_SRC

#+BEGIN_SRC emacs-lisp :tangle no
  (with-eval-after-load 'org
    (defun org-latex-format-headline-default-function (todo _todo-type priority text tags _info)
      "Default format function for a headline.
       See `org-latex-format-headline-function' for details."
      (concat
       (and todo (format "{\\bfseries\\sffamily %s} " todo))
       (and priority (format "\\framebox{\\#%c} " priority))
       text
       (and tags
            (format "\\hfill{}\\textsc{%s}"
                    (mapconcat #'org-latex--protect-text tags ":")))
       (and todo (format "{\n\\page{%s} " todo)))
    )
#+END_SRC

*** TODO Org-Bibtex
It seems it is uncompatble with org-ref (https://github.com/jkitchin/org-ref/issues/101)
#+BEGIN_SRC emacs-lisp
  ;; (require 'ox-bibtex)
  ;; (with-eval-after-load 'org
  ;;   )
#+END_SRC

*** TODO Org-pomodoro
*** Org Ref
Ressources:
- https://github.com/tmalsburg/helm-bibtex
- https://github.com/jkitchin/org-ref
- https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking/

#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    ;; Folder where the notes files are located (or file if just one Note file)
    (setq org-ref-notes-directory "~/MEGA/These/Ressources/notes")
    (setq org-ref-bibliography-notes "~/MEGA/These/Ressources/notes")
    ;; Bibliography File
    (setq reftex-default-bibliography '("~/MEGA/These/Ressources/references.bib"))
    ;; TODO - determine why it is not working with format or concat?
    (setq org-ref-default-bibliography '("~/MEGA/These/Ressources/references.bib"))
    ;; Folder where all the pdf are located
    (setq org-ref-pdf-directory "~/MEGA/These/Ressources/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 nil)
    ;; Display information on the citation
    (setq org-ref-show-citation-on-enter t)
    )
#+END_SRC

*** Org Noter
- https://github.com/weirdNox/org-noter

#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (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 t)
    ;; 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 (format "%s/%s" thesis-base-path "/Ressources/notes"))
  )
#+END_SRC

*** TODO Custom key bindings
#+BEGIN_SRC emacs-lisp
  ;; Export to LaTeX
  (evil-define-key 'normal org-mode-map (kbd ", l") 'org-latex-export-to-latex)
  ;; Open pdf externally with Zathura
  ;; (evil-define-key 'normal org-mode-map (kbd ", v") 'org-latex-export-to-latex)
  ;; (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))
#+END_SRC

*** Org-Contacts
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    (setq org-contacts-files (list (format "%s/%s" dropbox-base-path "org/contacts.org")))
  )
#+END_SRC

*** Org-Wunderlist
#+BEGIN_SRC emacs-lisp :tangle no
  (require 'org-wunderlist)
  (setq org-wunderlist-client-id "6799d9caeb2f5d8bd641"
        org-wunderlist-token "fd5965cde436c2587850a7c517d366561d8a1cbf7b6d96ab62f3fc8c9930"
        org-wunderlist-file "~/MEGA/These/TODOs/wunderlist.org"
        org-wunderlist-dir "~/.emacs.d/org-wunderlist/")
#+END_SRC

*** ox-hugo
#+begin_src emacs-lisp
  (use-package ox-hugo
      :ensure t          ;Auto-install the package from Melpa (optional)
      :after ox)
#+end_src

*** More Config
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'org
    ;; Highligh latex parts in org mode
    (setq org-highlight-latex-and-related '(latex))

    ;; Automatically change to DONE when all children are done
    (defun org-summary-todo (n-done n-not-done)
      "Switch entry to DONE when all subentries are done, to TODO otherwise."
      (let (org-log-done org-log-states)   ; turn off logging
        (org-todo (if (= n-not-done 0) "DONE" "TODO"))))
    (add-hook 'org-after-todo-statistics-hook 'org-summary-todo)
  )
#+END_SRC

Disable automatic highlight of TODO keywords in orgmode buffers
#+BEGIN_SRC emacs-lisp
  (add-hook 'org-mode-hook (lambda () (hl-todo-mode -1)))
#+END_SRC

** Projectile
#+BEGIN_SRC emacs-lisp
  (setq projectile-generic-command "fd -H --ignore-file .projectile -t f -0")
#+END_SRC

** TODO [#A] Matlab
- https://github.com/yuhonglin/matlab-mode
- https://github.com/pronobis/matlab-mode

*** Setup Matlab Mode
#+BEGIN_SRC emacs-lisp
  ;; (setq matlab-shell-command "/usr/local/bin/matlab")
  ;; (setq matlab-shell-command-switches (list "-nodesktop -nosplash"))
  ;; (setq mlint-programs '("mlint" "/usr/local/matlab/r2018a/bin/glnxa64/mlint"))
#+END_SRC

*** Setup Flycheck
#+BEGIN_SRC emacs-lisp
  (defvar mlint-executable "/usr/local/MATLAB/R2018a/bin/glnxa64/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)
#+END_SRC

#+BEGIN_SRC emacs-lisp :tangle no
  (defadvice org-edit-src-code (around set-buffer-file-name activate compile)
    (let ((file-name (buffer-file-name))) ;; (1)
      ad-do-it                            ;; (2)
      (setq buffer-file-name file-name))) ;; (3)
#+END_SRC

*** Setup Company - not working
#+BEGIN_SRC emacs-lisp
  ;; (add-to-list 'company-backends 'company-matlab)
#+END_SRC

** TODO [#B] Mails With Mu4e
  :PROPERTIES:
  :header-args:emacs-lisp+: :tangle no
  :END:

- https://github.com/kzar/davemail
- http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
- http://spacemacs.org/layers/+email/mu4e/README.html
- http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
- https://notanumber.io/2016-10-03/better-email-with-mu4e/
- https://vxlabs.com/2017/02/07/mu4e-0-9-18-e-mailing-with-emacs-now-even-better/
- http://www.brool.com/post/using-mu4e/
- https://www.reddit.com/r/emacs/comments/8q84dl/tip_how_to_easily_manage_your_emails_with_mu4e/

*** Set default mail user agent to mu4e
   #+BEGIN_SRC emacs-lisp
     (setq mail-user-agent 'mu4e-user-agent)
   #+END_SRC

*** Default config
**** Default behavior
#+BEGIN_SRC emacs-lisp
  (setq mu4e-maildir "~/.mail"
        mu4e-update-interval nil
        mu4e-compose-signature-auto-include t
        mu4e-view-show-images t
        mu4e-view-show-addresses t)
#+END_SRC

**** Default folders
#+BEGIN_SRC emacs-lisp
  (setq mu4e-sent-folder "/gmail/Sent"
        mu4e-drafts-folder "/gmail/Drafts"
        mu4e-trash-folder "/gmail/Trash"
        mu4e-refile-folder "/gmail/Archive"
        mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")
#+END_SRC

**** Default signature and email address
#+BEGIN_SRC emacs-lisp
  (setq mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")
#+END_SRC

**** Saving the attachment to Downloads directory
#+BEGIN_SRC emacs-lisp
  (setq mu4e-attachment-dir "~/Downloads")
#+END_SRC

**** A list of user's e-mail addresses
#+BEGIN_SRC emacs-lisp
  (setq mu4e-user-mail-address-list '("dehaeze.thomas@gmail.com" "thomas.dehaeze@esrf.fr" "thomas.dehaeze@doct.ulg.ac.be"))
#+END_SRC

**** Mail directory shortcuts
#+BEGIN_SRC emacs-lisp
  (setq mu4e-maildir-shortcuts
        '(
          ("/gmail/Inbox" . ?g)
          ("/esrf/Inbox"  . ?e)
          ("/ulg/Inbox"   . ?u)
          ))
#+END_SRC

*** Contexts - Email accounts
#+BEGIN_SRC emacs-lisp :tangle no
  (setq mu4e-contexts
        `( ,(make-mu4e-context
             :name "gmail"
             :enter-func (lambda () (mu4e-message "Entering Gmail context"))
             :leave-func (lambda () (mu4e-message "Leaving Gmail context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/gmail" (mu4e-message-field msg :maildir))))
             :vars '(
                     (mu4e-sent-messages-behavior . (delete))
                     (user-mail-address . "dehaeze.thomas@gmail.com")
                     (mu4e-sent-folder . "/gmail/Sent")
                     (mu4e-trash-folder . "/gmail/Trash")
                     (mu4e-drafts-folder . "/gmail/Drafts")
                     (mu4e-refile-folder . "/gmail/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ,(make-mu4e-context
             :name "esrf"
             :enter-func (lambda () (mu4e-message "Entering ESRF context"))
             :leave-func (lambda () (mu4e-message "Leaving ESRF context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/esrf" (mu4e-message-field msg :maildir))))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@esrf.fr")
                     (mu4e-sent-folder . "/esrf/Sent")
                     (mu4e-trash-folder . "/esrf/Trash")
                     (mu4e-drafts-folder . "/esrf/Drafts")
                     (mu4e-refile-folder . "/esrf/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ,(make-mu4e-context
             :name "ulg"
             :enter-func (lambda () (mu4e-message "Entering ULG context"))
             :leave-func (lambda () (mu4e-message "Leaving ULG context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/ulg" (mu4e-message-field msg :maildir))))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@doct.ulg.ac.be")
                     (mu4e-sent-folder . "/ulg/Sent")
                     (mu4e-trash-folder . "/ulg/Trash")
                     (mu4e-drafts-folder . "/ulg/Drafts")
                     (mu4e-refile-folder . "/ulg/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ))
  (setq mu4e-context-policy 'pick-first)
#+END_SRC

*** Receiving emails - Mbsync
#+BEGIN_SRC emacs-lisp :tangle no
  (setq mu4e-get-mail-command "mbsync -a"
        smtpmail-default-smtp-server "smtp.gmail.com"
        smtpmail-smtp-server "smtp.gmail.com"
        smtpmail-smtp-service 587)
#+END_SRC

Let systemd get the mail, then pressing =U= will just run =mu= to reindex everything.
#+BEGIN_SRC emacs-lisp
  (setq mu4e-get-mail-command "true")
#+end_src

Fix for mbsync found [[http://pragmaticemacs.com/emacs/fixing-duplicate-uid-errors-when-using-mbsync-and-mu4e/][here]].
#+BEGIN_SRC emacs-lisp
  (setq mu4e-change-filenames-when-moving t)
#+end_src

*** Sending emails - Msmtp
#+BEGIN_SRC emacs-lisp
  (setq smtpmail-default-smtp-server "smtp.gmail.com"
        smtpmail-smtp-server "smtp.gmail.com"
        smtpmail-smtp-service 587)

  (setq message-send-mail-function 'message-send-mail-with-sendmail
        sendmail-program "msmtp"
        user-full-name "Thomas Dehaeze")
#+END_SRC

*** Bookmarks
#+BEGIN_SRC emacs-lisp :tangle no
  (setq mu4e-bookmarks
        `(("flag:unread AND NOT flag:trashed" "Unread messages" ?u)
          ("date:today..now" "Today's messages" ?t)
          ("date:7d..now" "Last 7 days" ?w)
          ("mime:image/*" "Messages with images" ?p)
          (,(mapconcat 'identity
                       (mapcar
                        (lambda (maildir)
                          (concat "maildir:" (car maildir)))
                        mu4e-maildir-shortcuts) " OR ")
           "All inboxes" ?i)))
#+END_SRC

*** Notifications
#+BEGIN_SRC emacs-lisp
  (with-eval-after-load 'mu4e-alert
    (mu4e-alert-set-default-style 'libnotify))
  (mu4e-alert-enable-notifications)
#+END_SRC

**** TODO Mode-line notifications
#+BEGIN_SRC emacs-lisp
  (setq mu4e-enable-mode-line t)
#+END_SRC

*** TODO [#A] When putting something on the Trash, it will be in the archive folder on gmail
Even when totally deleting it. It will stage on gmail. How to fix that?

*** TODO Verify that sending mails with gmail account works and that there is no duplicate
   SCHEDULED: <2019-01-17 jeu.>
Should check this variable: mu4e-sent-messages-behavior
#+BEGIN_SRC emacs-lisp :tangle no
  (setq mu4e-sent-messages-behavior 'delete)
#+END_SRC
And [[https://www.djcbsoftware.nl/code/mu/mu4e/Gmail-configuration.html][here]].

If I put it to delete, it works for gmail but not for the other ones...

Check [[https://github.com/djcb/mu/issues/179][here]].

*** TODO Cheatsheet
| Command | Usage                 |
|---------+-----------------------|
| =C-j=   | Next mail             |
| =C-k=   | Previous mail         |
| =R/C/F= | Reply/Compose/Forward |
| =t=     | Move to Archive       |
| =d=     | Move to Trash         |

**** TODO Add keybindings to refresh mu

**** TODO Send email using org-mode

**** Store emails into org-mode
Use =mu4e-org-store-and-capture= when on an email to store it using a capture template.
Org simply =C-c l= to store the link to the email and then =C-c C-l= and paste the link.

** PDF-Tools
#+BEGIN_SRC emacs-lisp
  (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
#+END_SRC

** Custom command and leader keys
*** Watch LaTeX file using latexmk
#+BEGIN_SRC emacs-lisp
  (defun latex/watch ()
    "Watch LaTeX file using latexmk"
    (interactive)
    (start-process-shell-command "latexmk-watch" "*latexmk-watch-output*"
                                 "latexmk" (format "-pdflatex=\"xelatex -synctex=1 -shell-escape -interaction nonstopmode  -output-directory='%s'\" -pdf -pvc -bibtex -f %s.tex"
                                                   (file-name-directory buffer-file-name)
                                                   (file-name-base buffer-file-name))))
  (defun latex/watch/kill ()
    "Kill the currently running TeX job."
    (interactive)
    (delete-process "latexmk-watch")
    )

  (spacemacs/set-leader-keys "ow" 'latex/watch)
  (spacemacs/set-leader-keys "ok" 'latex/watch/kill)
#+END_SRC

*** Helm-Bibtex
#+BEGIN_SRC emacs-lisp
  (spacemacs/set-leader-keys "ob" 'helm-bibtex)
  (spacemacs/set-leader-keys "of" 'helm-bibtex-favorites)
  (spacemacs/set-leader-keys "or" 'helm-resume)
#+END_SRC

*** Eshell
#+BEGIN_SRC emacs-lisp
  (spacemacs/set-leader-keys "os" 'eshell)
#+END_SRC

** Path for Shell
#+BEGIN_SRC emacs-lisp
  (when (memq window-system '(mac ns x))
    (exec-path-from-shell-initialize))
#+END_SRC

** Proxy
#+BEGIN_SRC emacs-lisp :tangle no
  (setq url-proxy-services
     '(("http" . "proxy.esrf.fr:3128")
       ("https" . "proxy.esrf.fr:3128")
       ("no_proxy" . "^.*esrf.fr")))
#+END_SRC

** Remove the problem of recentf files
#+BEGIN_SRC emacs-lisp
  (cancel-timer recentf-auto-save-timer)
#+END_SRC

** TODO [#C] Neomutt connection
https://mentat.za.net/blog/2018/10/31/using-org-mode-with-neomutt/

#+BEGIN_SRC emacs-lisp
  (require 'org-protocol)
  ;; Call this function, which spawns neomutt, whenever org-mode
  ;; tries to open a link of the form mutt:message-id+goes_here@mail.gmail.com

  (defun tdehaeze/mutt-open-message (message-id)
    "In neomutt, open the email with the the given Message-ID"
    (let*
        ((message-id (replace-regexp-in-string "^/*" "" message-id))
        (mail-file
          (replace-regexp-in-string
          "\n$" "" (shell-command-to-string
                    (format "mu find -n 1 -f l i:%s" message-id))))
        (mail-dir (replace-regexp-in-string "/\\(cur\\|new\\|tmp\\)/$" ""
                                            (file-name-directory mail-file)))
        (message-id-escaped (regexp-quote message-id))
        (mutt-keystrokes
          (format "L~i %s\n\n" (shell-quote-argument message-id-escaped)))
        (mutt-command (list "neomutt" "-R" "-f" mail-dir
                            "-e" (format "push '%s'" mutt-keystrokes))))

      (message "Launching neomutt for message %s" message-id)
      (call-process "setsid" nil nil
                    "-f" "termite" "-e"
                    (concat "neomutt -R -f " mail-dir " -e \"" (format "push '%s a l'\"" mutt-keystrokes)))))

  ;; Hook up `message:...` style URLs
  (org-add-link-type "message" 'tdehaeze/mutt-open-message)
#+end_src