path: root/.emacs

;; (setq debug-on-error t)

(require 'package)
(setq package-enable-at-startup nil)
(add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/"))
(package-initialize)

;; Bootstrap `use-package'
(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

(eval-when-compile
  (require 'use-package))

;;; General emacs configuration
(use-package emacs
  :init   ; executed before package is loaded
  (fset 'yes-or-no-p 'y-or-n-p)
  (put 'narrow-to-region 'disabled nil)
  :hook   ; add functions onto hook; only basename needed
  ((text-mode   . turn-on-auto-fill)
   (before-save . whitespace-cleanup))
  :bind   ; key bindings
  (("C-x a r" . align-regexp))
  :custom ; options set by customize-variable
  (inhibit-startup-screen t)
  (default-input-method "TeX")
  :config ; executed after package is loaded
  (defadvice  ; align-regexp should use spaces.
      align-regexp
      (around align-regexp-with-spaces activate)
    (let ((indent-tabs-mode nil)) ad-do-it))
  :custom-face
  (default ((t (:family "Input Mono" :foundry "FBI " :slant normal :weight normal :height 89 :width normal)))))

;; (use-package auctex
;;   :config
;;   ;; From
;;   ;; https://github.com/jwiegley/dot-emacs/commit/6dffc2511c60e1e15c79080bf37a36f380d9567b
;;   (defun latex-help-get-cmd-alist ()    ;corrected version:
;;     "Scoop up the commands in the index of the latex info manual.
;;    The values are saved in `latex-help-cmd-alist' for speed."
;;     ;; mm, does it contain any cached entries
;;     (if (not (assoc "\\begin" latex-help-cmd-alist))
;;	(save-window-excursion
;;	  (setq latex-help-cmd-alist nil)
;;	  (Info-goto-node (concat latex-help-file "Command Index"))
;;	  (goto-char (point-max))
;;	  (while (re-search-backward "^\\* \\(.+\\): *\\(.+\\)\\." nil t)
;;	    (let ((key (buffer-substring (match-beginning 1) (match-end 1)))
;;		  (value (buffer-substring (match-beginning 2)
;;					   (match-end 2))))
;;	      (add-to-list 'latex-help-cmd-alist (cons key value))))))
;;     latex-help-cmd-alist))

(use-package ace-window
  :ensure t
  :custom
  ;; home row keys
  (aw-keys '(?h ?t ?n ?s ?a ?o ?e ?u ?i ?d))
  :bind (("M-o" . ace-window))
  :config
  ;; need to redefine a few of these because the defaults
  ;; overlap with customized aw-keys
  (setq aw-dispatch-alist
    '((?x aw-delete-window "Delete Window")
      (?m aw-swap-window "Swap Windows")
      (?M aw-move-window "Move Window")
      (?c aw-copy-window "Copy Window")
      (?j aw-switch-buffer-in-window "Select Buffer")
      (?f aw-flip-window)
      (?p aw-switch-buffer-other-window "Switch Buffer Other Window")
      (?c aw-split-window-fair "Split Fair Window")
      (?v aw-split-window-vert "Split Vert Window")
      (?b aw-split-window-horz "Split Horz Window")
      (?1 delete-other-windows "Delete Other Windows")
      (?? aw-show-dispatch-help))))

(use-package auto-complete
  :ensure t
  :config
  (ac-config-default)
  (ac-set-trigger-key "TAB")
  (add-to-list 'ac-dictionary-directories "~/.emacs.d/auto-complete/ac-dict")
  :hook
  ((Coq-mode LaTeX-mode sml-mode) . auto-complete-mode))

(use-package auto-indent-mode
  :ensure t
  :config
  (auto-indent-global-mode)
  :custom
  (auto-indent-next-pair-timer-interval
   (quote ((css-mode 1.5)
	   (haskell-mode 1.5)
	   (python-mode 1.5)
	   (latex-mode 1.5)
	   (coq-mode 1.5)
	   (default 0.0005)))))

(use-package bibtex
  :mode ("\\.bib\'" . bibtex-mode)
  :custom
  (bibtex-dialect 'biblatex)
  (bibtex-maintain-sorted-entries 'crossref)
  ;; Use only the first author name if there are more than 2 authors
  (bibtex-autokey-names 1)
  ;; Otherwise use both names
  (bibtex-autokey-names-stretch 1)
  (bibtex-autokey-name-separator "_")
  (bibtex-autokey-name-year-separator "_")
  (bibtex-autokey-year-length 4)
  (bibtex-autokey-year-title-separator ":_")
  (bibtex-autokey-titleword-length 5)
  (bibtex-autokey-titlewords 3)
  ;; Make all title words lowercase
  (bibtex-autokey-preserve-case 1)
  :config
  ;; Until https://debbugs.gnu.org/cgi/bugreport.cgi?bug=36252 gets fixed
  (defun bibtex-autokey-get-year ()
    "Return year field contents as a string obeying `bibtex-autokey-year-length'.
If the year field is absent, extract the year from a valid ISO8601-2
Extended Format date in the date field and return it as a string obeing
`bibtex-autokey-year-length'."
    (let ((yearfield (bibtex-autokey-get-field "year"))
	  (datefield (bibtex-autokey-get-field "date"))
	  (shortener (lambda (year)
		       (substring year (max 0 (- (length year)
						 bibtex-autokey-year-length))))))
      (if (string= "" yearfield)
	  (cond ((string-match "[./]*\\(-?[[:digit:]]+X*\\)\\([-/.[:digit:]:T~?%X]*\\)"
			       datefield)
		 ;; Matches ISO8601-2 Extended Format specification level 1
		 ;; examples listed in tables 3, 4, and 5 on pp. 38-40 of the
		 ;; biblatex package manual, version 3.12
		 (funcall shortener (match-string 1 datefield)))
		(t (error "Date field `%s' is incorrectly formed" datefield)))
	(funcall shortener yearfield))))
  ;; Don't have accented characters in keys
  (let ((charMap '(;; This list based on Xah Lee's http://ergoemacs.org/emacs/emacs_zap_gremlins.html
		   ("ß" . "ss")
		   ("á\\|à\\|â\\|ä\\|ā\\|ǎ\\|ã\\|å\\|ą\\|ă\\|ạ\\|ả\\|ả\\|ấ\\|ầ\\|ẩ\\|ẫ\\|ậ\\|ắ\\|ằ\\|ẳ\\|ặ" . "a")
		   ("æ" . "ae")
		   ("ç\\|č\\|ć" . "c")
		   ("é\\|è\\|ê\\|ë\\|ē\\|ě\\|ę\\|ẹ\\|ẻ\\|ẽ\\|ế\\|ề\\|ể\\|ễ\\|ệ" . "e")
		   ("í\\|ì\\|î\\|ï\\|ī\\|ǐ\\|ỉ\\|ị" . "i")
		   ("ñ\\|ň\\|ń" . "n")
		   ("ó\\|ò\\|ô\\|ö\\|õ\\|ǒ\\|ø\\|ō\\|ồ\\|ơ\\|ọ\\|ỏ\\|ố\\|ổ\\|ỗ\\|ộ\\|ớ\\|ờ\\|ở\\|ợ" . "o")
		   ("ú\\|ù\\|û\\|ü\\|ū\\|ũ\\|ư\\|ụ\\|ủ\\|ứ\\|ừ\\|ử\\|ữ\\|ự" . "u")
		   ("ý\\|ÿ\\|ỳ\\|ỷ\\|ỹ" . "y")
		   ("þ" . "th")
		   ("ď\\|ð\\|đ" . "d")
		   ("ĩ" . "i")
		   ("ľ\\|ĺ\\|ł" . "l")
		   ("ř\\|ŕ" . "r")
		   ("š\\|ś" . "s")
		   ("ť" . "t")
		   ("ž\\|ź\\|ż" . "z")
		   ("œ" . "oe")
		   (" " . " ") ; thin space etc
		   ("–" . "-")
		   ("—\\|一" . "--"))))
    ;; For some reason, *-name-* and *-titleword-* get clobbered, even
    ;; though the original value in decribe-variable clearly shows
    ;; them having been based on the extended
    ;; bibtex-autokey-transcriptions. Force them to be the right
    ;; thing.
    (progn (seq-do (lambda (pair) (add-to-list 'bibtex-autokey-transcriptions pair)) charMap)
	   (seq-do (lambda (pair) (add-to-list 'bibtex-autokey-name-change-strings pair)) charMap)
	   (seq-do (lambda (pair) (add-to-list 'bibtex-autokey-titleword-change-strings pair)) charMap))))

(use-package bibtex-completion
  :ensure helm-bibtex
  :custom
  (bibtex-completion-bibliography "~/Documents/papers/library.bib")
  (bibtex-completion-library-path "~/Documents/papers/pdfs/")
  (bibtex-completion-notes-path   "~/Documents/papers/notes/")
  (bibtex-completion-notes-extension ".org")
  :bind (("C-c b" . helm-bibtex)))

(use-package cc-mode
  :custom
  (c-default-style "bsd"))

(use-package cus-edit
  :custom
  (custom-file null-device "Don't store customizations"))

(use-package diary
  :ensure diary-lib
  :custom
  (diary-display-function 'diary-fancy-display)
  :hook ((diary-list-entries . diary-include-other-diary-files)
	 (diary-list-entries . diary-sort-entries)))

(use-package dictem
  :load-path "~/.emacs.d/dictem/")

(use-package doi-utils
  ;; provided by org-ref
  :ensure org-ref)

(use-package dtrt-indent
  :ensure t)

(use-package elpher
  :ensure t)

(use-package elpy
  :ensure t
  :after python
  :config (elpy-enable)
  :custom
  (elpy-rpc-python-command "python3"))

(use-package ess
  :ensure t)

(use-package fill-column-indicator
  :ensure t)

(use-package gnus
  :custom
  (gnus-select-method
   '(nntp "news.club.cc.cmu.edu"
	  (nntp-address "news.club.cc.cmu.edu")
	  (nntp-via-address "linux.gp.cs.cmu.edu")
	  (nntp-via-rlogin-command "ssh")
	  (nntp-via-rlogin-command-switches ("-C"))
	  (nntp-open-connection-function nntp-open-via-rlogin-and-netcat)))
  (gnus-home-score-file "gnus.SCORE")
  (gnus-secondary-select-methods
   '((nntp "news.gmane.io")
     (nntp "news.eternal-september.org")
     ; (nntp "nntp.olduse.net")
     (nntp "tilde.team"
	   (nntp-address "localhost")
	   (nntp-via-address "tilde.team")
	   (nntp-via-rlogin-command "ssh")
	   (nntp-via-rlogin-command-switches ("-C"))
	   (nntp-open-connection-function nntp-open-via-rlogin-and-netcat))))
  (message-citation-line-function 'message-insert-formatted-citation-line)
  (gnus-update-message-archive-method t)
  (gnus-message-archive-method
	'(nnfolder "archive" ; this gets included in the server buffer
	       (nnfolder-inhibit-expiry t)
	       (nnfolder-get-new-mail nil)
	       (nnfolder-active-file "~/News/sent/active")
	       (nnfolder-directory   "~/News/sent")))
  (gnus-check-new-newsgroups nil)
  :hook
  (message-send . gnus-score-followup-article))

(use-package haskell-mode
  :ensure t
  :hook ((haskell-mode . turn-on-haskell-doc-mode)
	 (haskell-mode . turn-on-haskell-indentation)))

(use-package helm
  :ensure t
  :bind (("M-x"     . helm-M-x)
	 ("C-x C-f" . helm-find-files)
	 ("C-x C-b" . helm-mini))
  :config
  (helm-mode 1))

(use-package info-look
  :ensure t)

(use-package ispell
  :ensure t
  :defer t
  :custom
  (ispell-dictionary "en_CA-w_accents"))

(use-package latex
  :ensure auctex
  :after info-look
  :mode ("\\.tex\\'" . TeX-latex-mode)
  :init
  ;; http://www.cs.au.dk/~abizjak/emacs/2016/03/06/latex-fill-paragraph.html
  (defun ales/fill-paragraph (&optional P)
    "When called with prefix argument call `fill-paragraph'.
Otherwise split the current paragraph into one sentence per line."
    (interactive "P")
    (if (not P)
	(save-excursion
	  (let ((fill-column 12345678)) ;; relies on dynamic binding
	    (fill-paragraph) ;; this will not work correctly if the paragraph is
	    ;; longer than 12345678 characters (in which case the
	    ;; file must be at least 12MB long. This is unlikely.)
	    (let ((end (save-excursion
			 (forward-paragraph 1)
			 (backward-sentence)
			 (point-marker))))  ;; remember where to stop
	      (beginning-of-line)
	      (while (progn (forward-sentence)
			    (<= (point) (marker-position end)))
		(just-one-space) ;; leaves only one space, point is after it
		(delete-char -1) ;; delete the space
		(newline)        ;; and insert a newline
		(LaTeX-indent-line) ;; I only use this in combination with late, so this makes sense
		))))
      ;; otherwise do ordinary fill paragraph
      (fill-paragraph P)))
  :hook
  ((LaTeX-mode . turn-on-reftex)
   (LaTeX-mode . turn-off-auto-fill)
   (LaTeX-mode . turn-on-flyspell)
   (LaTeX-mode . LaTeX-math-mode)
   (LaTeX-mode . (lambda ()
		   (LaTeX-add-environments
		    '("axiom" LaTeX-env-label)
		    '("theorem" LaTeX-env-label)
		    '("proposition" LaTeX-env-label)
		    '("definition" LaTeX-env-label)
		    '("corollary" LaTeX-env-label)
		    '("lemma" LaTeX-env-label)
		    '("example" LaTeX-env-label)
		    '("conjecture" LaTeX-env-label))))
   (LaTeX-mode . (lambda ()
		   ;; This must be a hook. Trying to set it in :config
		   ;; causes the variable to become buffer-local, so
		   ;; it never actually takes effect in all
		   ;; latex-moded buffers. So much time wasted debugging.
		   (add-to-list 'LaTeX-label-alist '("axiom" . "ax:"))
		   (add-to-list 'LaTeX-label-alist '("conjecture" . "conj:"))
		   (add-to-list 'LaTeX-label-alist '("corollary" . "cor:"))
		   (add-to-list 'LaTeX-label-alist '("definition" . "def:"))
		   (add-to-list 'LaTeX-label-alist '("proposition" . "prop:"))
		   (add-to-list 'LaTeX-label-alist '("theorem" . "theorem:"))
		   (add-to-list 'LaTeX-label-alist '("example" . "ex:"))
		   (add-to-list 'LaTeX-label-alist '("lemma" . "lemma:")))))
  :config
  (info-lookup-add-help :mode 'LaTeX-mode
			:regexp ".*"
			:parse-rule "\\\\?[a-zA-Z]+\\|\\\\[^a-zA-Z]"
			:doc-spec '(("(latex2e)Concept Index")
				    ("(latex2e)Command Index")))
  :bind
  (:map LaTeX-mode-map
	("M-q" . ales/fill-paragraph)))

(use-package magit
  :ensure t
  :config
  (put 'magit-clean 'disabled nil))

(use-package markdown-mode
  :ensure t
  :init
  (autoload 'markdown-mode "markdown-mode"
    "Major mode for editing Markdown files" t)
  :mode (("\\.markdown\\'" . markdown-mode)
	 ("\\.mdown\'" . markdown-mode)))

(use-package menu-bar
  :config
  (menu-bar-mode -1)
  :bind
  ([S-f10] . menu-bar-mode))

(use-package merlin
  ;; ocaml assistant
  :ensure t)

(use-package mingus
  ;; mpd client
  :ensure t)

(use-package minibuffer
  :config
  (add-to-list 'completion-styles 'substring)
  :custom
  ;; Cycle  through tab-completions with tab if there are less than 5
  (setq completion-cycle-threshold 5))

(use-package moe-theme
  :ensure t
  :after powerline ; must be loaded after for powerline-moe-theme to work
  :config
  (moe-dark)
  (moe-theme-set-color 'blue)
  (powerline-moe-theme))

(use-package ocp-indent
  :ensure t)

(use-package octave
  :mode ("\\.m\'" . octave-mode))

(use-package org
  :ensure t
  :bind
  (("C-c l" . 'org-store-link)
   ("C-c a" . 'org-agenda)
   ("C-c c" . 'org-capture))
  :custom
  (org-agenda-files '("~/org/"))
  (org-default-notes-file "~/org/notes.org")
  (org-agenda-include-diary t)
  ;; Define the custum capture templates
  ;; Courtesy of Gregory J. Stein,
  ;; http://cachestocaches.com/2016/9/my-workflow-org-agenda/
  (org-capture-templates
   '(("t" "todo" entry (file "~/org/todo.org")
      "* TODO %?\n%u\n%a\n" :clock-in t :clock-resume t)
     ("m" "Meeting" entry (file org-default-notes-file)
      "* MEETING with %? :MEETING:\n%t" :clock-in t :clock-resume t)
     ("d" "Diary" entry (file+olp+datetree "~/org/diary.org")
      "* %?\n%U\n" :clock-in t :clock-resume t)
     ("i" "Idea" entry (file org-default-notes-file)
      "* %? :IDEA: \n%t" :clock-in t :clock-resume t)
     ("n" "Next Task" entry (file+headline org-default-notes-file "Tasks")
      "** NEXT %? \nDEADLINE: %t")))
  ;; Include org-agenda-files in the list of refile targets
  (org-refile-targets (quote ((nil :maxlevel . 9)
			      (org-agenda-files :maxlevel . 9))))
  (org-columns-default-format "%25ITEM %TODO %3PRIORITY %10CLOCKSUM %16TIMESTAMP_IA %TAGS")
  ;; Tags with fast selection keys
  (org-tag-alist (quote ((:startgroup)
			 ("@errand" . ?e)
			 ("@cmu" . ?c)
			 ("@home" . ?h)
			 (:endgroup)
			 ("WAITING" . ?W)
			 ("HOLD" . ?H)
			 ("WORK" . ?w)
			 ("PERSONAL" . ?p)
			 ("CANCELLED" . ?c)
			 ("NOTE" . ?n)
			 ("IDEA" . ?i)
			 ("FLAGGED" . ??))))
  ;;;; TODO states and shortcuts
  (org-todo-keywords
   (quote ((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d)")
	   ;; c   : shortcut for org-use-fast-todo-selection
	   ;; @   : add a note (with time)
	   ;; !   : record only the time of the state change
	   ;; x/y : use x when entering & y when leaving iff target does not define x
	   (sequence "WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c@/!)" "PHONE" "MEETING"))))
  (org-todo-keyword-faces
   (quote (("TODO" :foreground "red" :weight bold)
	   ("NEXT" :foreground "blue" :weight bold)
	   ("DONE" :foreground "forest green" :weight bold)
	   ("WAITING" :foreground "orange" :weight bold)
	   ("HOLD" :foreground "magenta" :weight bold)
	   ("CANCELLED" :foreground "forest green" :weight bold)
	   ("MEETING" :foreground "forest green" :weight bold)
	   ("PHONE" :foreground "forest green" :weight bold))))
  ;; add/remove the following tags
  (setq org-todo-state-tags-triggers
	(quote (("CANCELLED" ("CANCELLED" . t))
		("WAITING" ("WAITING" . t))
		("HOLD" ("WAITING") ("HOLD" . t))
		(done ("WAITING") ("HOLD"))
		("TODO" ("WAITING") ("CANCELLED") ("HOLD"))
		("NEXT" ("WAITING") ("CANCELLED") ("HOLD"))
		("DONE" ("WAITING") ("CANCELLED") ("HOLD")))))
  (org-use-fast-todo-selection t)
  ;; Don't update timestamps/notes when going S-left/S-right
  (org-treat-S-cursor-todo-selection-as-state-change nil)
  ;;;; customize the agenda view
  ;; Compact view
  (org-agenda-compact-blocks t)
  ;; Custom ordering
  (org-agenda-custom-commands
   ;; each entry is of the form (key desc type match settings files)
   ;; this is based off of http://doc.norang.ca/org-mode.html#CustomAgendaViews
   ;; and should be finished at some point.
   (quote ((" " "Agenda"
	    ((agenda "")
	     (tags-todo "REFILE"
			((org-agenda-overriding-header "Tasks to Refile")
			 (org-tags-match-list-sublevels nil)))
	     (tags-todo "-CANCELLED/!NEXT"
			((org-agenda-overriding-header "Next Tasks")
			 (org-agenda-sorting-strategy
			  '(todo-state-down effort-up category-keep))))
	     (tags-todo "-CANCELLED+WAITING|HOLD/!"
			((org-agenda-overriding-header "Waiting & Postponed Tasks")))
	     (tags-todo "-REFILE-CANCELLED-WAITING-HOLD/!"
			((org-agenda-overriding-header "Standalone tasks")
			 (org-agenda-sorting-strategy '(category-keep))))
	     (tags "-REFILE/"
		   ((org-agenda-overriding-header "Tasks to Archive")))))
	   ("e" "Everything" ((agenda "") (alltodo ""))))))
  :config
  (add-to-list 'org-modules 'org-habit))

(use-package org-noter
  :ensure t
  :custom
  ;; Surely there's an easier way of setting this?
  (org-noter-notes-search-path '("~/Documents/papers/notes/")))

(use-package org-ref
  :ensure t
  :requires helm-bibtex)

(use-package org-ref-arxiv
  :ensure org-ref)

(use-package org-ref-bibtex
  :ensure org-ref
  :config
  (defun org-ref-rak-bibtex-format-url-if-doi ()
    "Override built-in function. Originally, this reformatted
the url to point to DOI. I would rather kill the URL field
entirely if it contains the DOI. bibtex-clean-entry will then
delete the field."
    (interactive)
    (save-excursion
      (bibtex-beginning-of-entry)
      (let ((doi (bibtex-autokey-get-field "doi")))
	(unless (null doi)
	  (when (string-match-p (regexp-quote (org-ref-bibtex-entry-doi))
				(bibtex-autokey-get-field "url"))
	    (bibtex-set-field "url" ""))))))
  (defun orcb-rak-check-journal ()
    "Check entry at point to see if journal exists in `org-ref-bibtex-journal-abbreviations'.
If not, issue a warning."
    (interactive)
    (when
	(string= "article"
		 (downcase
		  (cdr (assoc "=type=" (bibtex-parse-entry)))))
      (save-excursion
	(bibtex-beginning-of-entry)
	(let* ((entry (bibtex-parse-entry t))
	       (journal (replace-regexp-in-string "[[:space:]\n]+" " " (reftex-get-bib-field "journaltitle" entry))))
	  (when (null journal)
	    (error "Unable to get journal for this entry."))
	  (unless (member journal (-flatten org-ref-bibtex-journal-abbreviations))
	    (message "Journal \"%s\" not found in org-ref-bibtex-journal-abbreviations." journal))))))
  :custom
  (org-ref-title-case-types '("article" "book" "inproceedings" "proceedings" "report"))
  (org-ref-bibtex-journal-abbreviations
   '(("Journal of Computer Security")
     ("International Journal of Foundations of Computer Science" "Int. J. Found. Comput. Sci.")
     ("LCNS" "Lecture Notes in Computer Science" "Lect. Notes Comput. Sc.")
     ("LMCS" "Logical Methods in Computer Science")
     ("MSCS" "Mathematical Structures in Computer Science" "Math. Struct. Comp. Sci.")
     ("PACMPL" "Proceedings of the ACM on Programming Languages" "Proc. ACM Program. Lang.")
     ("Journal of Logic and Computation" "J. Logic Computat.")
     ("Publications of the Research Institute for Mathematical Sciences" "Publ. RIMS"))))

(use-package org-ref-core
  :ensure org-ref
  :requires helm-bibtex
  :config
  (defun org-ref-rak-title-case-english ()
    "Call org-ref-title-case only if the language field is set
       to `english' or is missing. This will avoid having foreign-
       language titles re-cased."
    (interactive)
    (let ((langfield (bibtex-autokey-get-field "language")))
      (if (= (length langfield) 0)
	  (org-ref-title-case))))
  :custom
  (org-ref-default-bibliography '("~/Documents/papers/library.bib"))
  (org-ref-bibliography-notes "~/Documents/papers/notes.org")
  (org-ref-pdf-directory "~/Documents/papers/pdfs/")
  ;; don't fudge with the output of bibtex-generate-autokey
  (org-ref-clean-bibtex-key-function 'identity)
  ;; let helm-bibtex find the notes file for an entry
  (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)))))))
  (org-ref-clean-bibtex-entry-hook
   '(org-ref-rak-bibtex-format-url-if-doi
     orcb-key-comma
     org-ref-replace-nonascii
     orcb-&
     orcb-%
     org-ref-rak-title-case-english ;; all entries, -article does only articles
     orcb-clean-year
     orcb-key
     orcb-clean-doi
     orcb-clean-pages
     orcb-rak-check-journal
     org-ref-sort-bibtex-entry
     orcb-fix-spacing
     orcb-clean-nil-opinionated)))

(use-package org-ref-isbn
  :ensure org-ref)

(use-package org-ref-pdf
  :ensure org-ref)

(use-package outline
  :ensure t
  :hook (LaTeX-mode . outline-minor-mode))

(use-package outline-magic
  :ensure t
  :after outline
  :bind (:map outline-minor-mode-map ([f10] . outline-cycle)))

(use-package paren
  :ensure t
  :config
  (show-paren-mode t)
  :custom
  ;; highlight entire expression when on delimiters
  (show-paren-style 'expression))

(use-package pdf-tools
  :ensure t
  :config
  (pdf-tools-install))

(use-package powerline
  :ensure t)

(use-package proof-general
  :ensure t
  :custom
  (proof-disappearing-proofs t)
  (proof-electric-terminator-enable t)
  (proof-three-window-enable t)
  (proof-three-window-mode-policy 'hybrid)
  :custom-face
  (proof-locked-face ((t (:weight bold)))))

(use-package py-autopep8
  :ensure t
  :hook (python-mode . py-autopep8-enable-on-save)
  :custom
  (py-autopep8-options '("--max-line-length=80")))

(use-package python
  :ensure t
  :mode ("\\.py\\'" . python-mode)
  :custom (python-python-command "/usr/bin/python3")
  :interpreter ("python3" . python-mode)
  :custom
  (python-indent-guess-indent-offset nil)
  (python-indent-offset 4)
  (python-shell-interpreter "python3"))

(use-package rainbow-delimiters
  :ensure t
  :hook ((LaTeX-mode prog-mode) . rainbow-delimiters-mode))

(use-package rainbow-mode
  :ensure t)

(use-package reftex
  :ensure t
  :after latex
  :hook (LaTeX-mode . reftex-mode)
  :custom
  (reftex-default-bibliography '("~/Documents/papers/library.bib"))
  (reftex-label-alist '(("axiom" ?a "ax:" "~\\ref{%s}" nil ("axiom" "ax.") -3)
			("theorem" ?h "theorem:" "~\\ref{%s}" t ("theorem" "th.") -3)
			("proposition" ?p "prop:" "~\\ref{%s}" t ("proposition" "prop.") -3)
			("definition" ?d "def:" "~\\ref{%s}" t ("definition" "def.") -3)
			("corollary" ?c "cor:" "~\\ref{%s}" t ("corollary" "cor.") -3)
			("lemma" ?l "lemma:" "~\\ref{%s}" t ("lemma" "lem.") -3)
			("conjecture" ?j "conj:" "~\\ref{%s}" t ("conjecture" "conj.") -3)
			("ax" ?a "ax:" "~\\ref{%s}" nil ("axiom" "ax.") -3)
			("thm" ?h "theorem:" "~\\ref{%s}" t ("theorem" "th.") -3)
			("prop" ?p "prop:" "~\\ref{%s}" t ("proposition" "prop.") -3)
			("defi" ?d "def:" "~\\ref{%s}" t ("definition" "def.") -3)
			("cor" ?c "cor:" "~\\ref{%s}" t ("corollary" "cor.") -3)
			("lem" ?l "lemma:" "~\\ref{%s}" t ("lemma" "lem.") -3)
			("conj" ?j "conj:" "~\\ref{%s}" t ("conjecture" "conj.") -3))))

(use-package sass-mode
  :ensure t)

(use-package scroll-bar
  :custom
  (scroll-bar-mode nil))

(use-package sendmail
  :custom
  (mail-specify-envelope-from t)
  (mail-envelope-from 'header)
  (message-send-mail-function 'sendmail-send-it))

(use-package simple
  :custom
  (column-mode-number t))

(use-package sml-mode
  :ensure t
  :mode ("\\.sml\\'" . sml-mode))

(use-package solar
  :custom
  ;; Use 24 hour time in diary, calendar, etc.
  (calendar-time-display-form
   '(24-hours ":" minutes (if time-zone " (") time-zone (if time-zone ")")))
  (calendar-latitude 40.4)
  (calendar-longitude -79.9)
  (calendar-location-name "Pittsburgh, PA"))

(use-package spaceline
  :ensure t
  :requires spaceline-config)

(use-package tex
  :ensure auctex
  :custom
  (reftex-plug-into-AUCTeX t)
  (TeX-parse-self t) ; Parse documents to provide completion for packages, etc.
  (TeX-auto-save t) ; Automatically save style information
  (TeX-clean-confirm nil) ; Don't ask for confirmation when cleaning
  (TeX-source-correlate-mode t) ; Provide forward and inverse search with SyncTeX
  (TeX-source-correlate-method 'synctex)
  (TeX-PDF-mode t) ; use pdftex by default
  :config
  (add-to-list 'TeX-view-program-selection '(output-pdf "Zathura")))

(use-package tool-bar
  :config
  (tool-bar-mode -1))

(use-package tramp
  :defer t
  :custom
  (tramp-default-method "ssh"))

(use-package tuareg
  :ensure t
  :config
  (add-hook 'tuareg-mode-hook 'merlin-mode t))

(use-package twittering-mode
  :ensure t
  :custom
  (twittering-icon-mode t)
  (twittering-icon-storage-file "~/.emacs.d/storage/twittering-mode-icons.gz")
  (twittering-use-icon-storage t))

(use-package vc-git
  :requires vc
  :config
  (add-to-list 'vc-handled-backends 'git))

(use-package windmove
  :config
  (windmove-default-keybindings)
  :custom
  (windmove-wrap-around t))

(use-package yaml-mode
  :ensure t)