(require 'ox-latex)
(add-to-list 'org-latex-classes
	     '("phd"
	       "\\documentclass[twoside]{iitbreport}"
	       ("\\chapter{%s}" . "\\chapter*{%s}")
	       ("\\section{%s}" . "\\section*{%s}")
	       ("\\subsection{%s}" . "\\subsection*{%s}")
	       ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
	       ("\\paragraph{%s}" . "\\paragraph*{%s}")
	       ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
(eval-after-load "org"
  '(progn
     ;; .txt files aren't in the list initially, but in case that changes
     ;; in a future version of org, use if to avoid errors
     (if (assoc "\\.txt\\'" org-file-apps)
	 (setcdr (assoc "\\.txt\\'" org-file-apps) "notepad.exe %s")
       (add-to-list 'org-file-apps '("\\.txt\\'" . "notepad.exe %s") t))
     ;; Change .pdf association directly within the alist
     (setcdr (assoc "\\.pdf\\'" org-file-apps) "evince %s")))

(use-package org-ref
  :ensure t
  :defer t)

(setq org-ref-completion-library 'org-ref-ivy-cite)
(use-package org-ref
  :after org
  :init
  (setq reftex-default-bibliography '("~/Dropbox/Research/references.bib"))
  (setq org-ref-bibliography-notes "~/Dropbox/Research/notes/notes.org"
        org-ref-default-bibliography '("~/Dropbox/Research/references.bib")
        org-ref-pdf-directory "~/Dropbox/papers/")

  (setq helm-bibtex-bibliography "~/Dropbox/Research/references.bib")
  (setq helm-bibtex-library-path "~/Dropbox/papers/")

  (setq helm-bibtex-pdf-open-function
        (lambda (fpath)
          (start-process "open" "*open*" "open" fpath)))

  (setq helm-bibtex-notes-path "~/Dropbox/Research/notes/notes.org")
  :config
  (key-chord-define-global "uu" 'org-ref-cite-hydra/body)
  ;; variables that control bibtex key format for auto-generation
  ;; I want firstauthor-year-title-words
  ;; this usually makes a legitimate filename to store pdfs under.
  (setq bibtex-autokey-year-length 4
        bibtex-autokey-name-year-separator "-"
        bibtex-autokey-year-title-separator "-"
        bibtex-autokey-titleword-separator "-"
        bibtex-autokey-titlewords 2
        bibtex-autokey-titlewords-stretch 1
        bibtex-autokey-titleword-length 5))

(use-package org-autolist
  :after org
  :config
  (org-autolist-mode +1))

(use-package doi-utils
  :after org)

(use-package org-ref-bibtex
  :after org
  :init
  (setq org-ref-bibtex-hydra-key-binding "\C-cj"))

(use-package org
  :defer t
  :bind (("C-c a" . org-agenda)
         ("C-c c" . org-capture)
         ("C-c l" . org-store-link))
  :config
  (require 'ox-md)
  (unbind-key "C-c ;" org-mode-map)

  ;;file to save todo items
  (setq org-agenda-files (quote ("~/Dropbox/Research/todo.org")))


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


  ;;set colours for priorities
  (setq org-priority-faces '((?A . (:foreground "OliveDrab" :weight bold))
                             (?B . (:foreground "LightSteelBlue"))
                             (?C . (:foreground "#F0DFAF"))))


  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
  ;; org-mode agenda options                                                ;;
  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
  ;;open agenda in current window
  (setq org-agenda-window-setup (quote current-window))
  ;;warn me of any deadlines in next 7 days
  (setq org-deadline-warning-days 7)

  ;;don't show tasks as scheduled if they are already shown as a deadline
  (setq org-agenda-skip-scheduled-if-deadline-is-shown t)
  ;;don't give awarning colour to tasks with impending deadlines
  ;;if they are scheduled to be done
  (setq org-agenda-skip-deadline-prewarning-if-scheduled (quote pre-scheduled))
  ;;don't show tasks that are scheduled or have deadlines in the
  ;;normal todo list
  (setq org-agenda-todo-ignore-deadlines (quote all))
  (setq org-agenda-todo-ignore-scheduled (quote all))

  ;;sort tasks in order of when they are due and then by priority

  (setq org-agenda-sorting-strategy
        (quote
         ((agenda deadline-up priority-down)
          (todo priority-down category-keep)
          (tags priority-down category-keep)
          (search category-keep))))

  (setq org-capture-templates
        '(("t" "todo" entry (file+headline "~/Dropbox/Research/todo.org" "Tasks")
           "* TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n")))


  (defun my/org-mode-defaults ()
    (turn-on-org-cdlatex)
    ;; (diminish 'org-cdlatex-mode "")
    (turn-on-auto-fill)

    ;; make `company-backends' local is critcal
    ;; or else, you will have completion in every major mode, that's very annoying!
    (make-local-variable 'company-backends)
    ;; company-ispell is the plugin to complete words
    (add-to-list 'company-backends 'company-ispell))

  (add-hook 'org-mode-hook 'my/org-mode-defaults)

  ;; Fontify org-mode code blocks
  (setq org-src-fontify-natively t)

  (setq org-todo-keywords
        (quote ((sequence "TODO(t)" "|" "CANCELLED(c@/!)" "DONE(d)"))))

  (setq org-use-fast-todo-selection t)
  (setq org-treat-S-cursor-todo-selection-as-state-change nil)

  (setq org-todo-keyword-faces
        '(("TODO" . (:foreground "green" :weight bold))
          ("NEXT" :foreground "blue" :weight bold)
          ("WAITING" :foreground "orange" :weight bold)
          ("HOLD" :foreground "magenta" :weight bold)
          ("CANCELLED" :foreground "forest green" :weight bold)))

  (setq org-enforce-todo-dependencies t)
  (setq org-src-tab-acts-natively t)

  (setq org-latex-pdf-process
        (quote ("pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
                "bibtex $(basename %b)"
                "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
                "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f")))

  (setq org-latex-create-formula-image-program 'imagemagick)

  ;; Tell the latex export to use the minted package for source
  ;; code coloration.
  (add-to-list 'org-latex-packages-alist '("" "minted"))
  (require 'ox-latex)
  (setq org-latex-listings 'minted)

  ;; (setq org-latex-minted-options
  ;;       '(("frame" "lines") ("framesep" "6pt")
  ;;         ("mathescape" "true") ("fontsize" "\\small")))

  (setq org-confirm-babel-evaluate nil)

  ;; execute external programs.
  (org-babel-do-load-languages
   (quote org-babel-load-languages)
   (quote ((emacs-lisp . t)
           (dot . t)
           (ditaa . t)
           (python . t)
           (ruby . t)
           (gnuplot . t)
           (clojure . t)
           (sh . t)
           (haskell . t)
           (octave . t)
           (org . t)
           (plantuml . t)
           (scala . t)
           (sql . t)
           (latex . t))))

  (eval-after-load 'org-src
    '(define-key org-src-mode-map
       "\C-x\C-s" #'org-edit-src-exit)))

(setq org-src-fontify-natively t
      org-confirm-babel-evaluate nil
      org-src-preserve-indentation t)

(org-babel-do-load-languages
 'org-babel-load-languages '((python . t)))

(setq org-latex-pdf-process
      '("pdflatex -interaction nonstopmode -output-directory %o %f"
	"bibtex %b"
	"pdflatex -interaction nonstopmode -output-directory %o %f"
	"pdflatex -interaction nonstopmode -output-directory %o %f"))

(require 'org-ref)
(require 'org-ref-pdf)
(require 'org-ref-url-utils)
(require 'org-ref-latex)
(setq org-latex-prefer-user-labels t)
;; (setq org-latex-pdf-process '("latexmk -pdflatex='%latex -shell-escape -interaction nonstopmode' -pdf -output-directory=%o -f %f"))