;; -*- emacs-lisp -*-
;; (setq debug-on-error t)

(require 'package)
(setq package-enable-at-startup nil)
(add-to-list 'package-archives '("melpa" . "http://melpa.org/packages/"))
(let ((default-directory  "~/.emacs.d/lisp/"))
  (normal-top-level-add-subdirs-to-load-path))
(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)
   (text-mode   . flyspell-mode)
   (before-save . whitespace-cleanup))
  :bind   ; key bindings
  (("C-x a r" . align-regexp))
  :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
  (inhibit-startup-screen t)
  (default-input-method "TeX")
  (user-full-name "Ryan Kavanagh")
  (user-mail-address "rak@rak.ac")
  (face-font-family-alternatives
   (append '(("Spleen 16x32" "Ubuntu Mono" "FreeMono" "Liberation Mono"))
	   face-font-family-alternatives))
  :custom-face
  (default ((t (:family {{ if (eq .chezmoi.os "openbsd") -}}
			"Spleen 12x24" :height 80 ; unit is 1/10 pt
			{{- else -}}
			"Spleen 16x32" :height 130 ; unit is 1/10 pt
			{{- end }}
			)))))

(if (string= (system-name) "demeter.rak.ac")
    (use-package leuven-theme ; nice theme for lecturing / projectors
      :ensure t
      :config
      (load-theme 'leuven t))
  (use-package moe-theme
    :ensure t
    :after powerline ; must be loaded after for powerline-moe-theme to work
    :config
    (moe-dark)
    (moe-theme-powerline)))

(defun single-lines-only ()
  "Replace multiple blank lines with a single one"
  (interactive)
  (goto-char (point-min))
  (while (re-search-forward "\\(^\\s-*$\\)\n" nil t)
    (replace-match "\n")
    (forward-char 1)))

(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 aggressive-indent
  :ensure t
  :config
  (global-aggressive-indent-mode 1))

(use-package autorevert
  :diminish auto-revert-mode)

(use-package avy
  :ensure t
  :config
  (avy-setup-default)
  :bind
  (("C-c C-j" . avy-resume)
   ("C-;" . avy-goto-char-2)))

(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)
  :bind (:map bibtex-mode-map
	      ("C-c C-c" . org-ref-clean-bibtex-entry)
	      ("C-c s" . bibtex-sort-buffer))
  :config
  (defun my/bibtex-generate-autokey (autogenerated)
    (let ((key (bibtex-autokey-get-field "_key")))
      (if (string= "" key) autogenerated key)))
  (advice-add 'bibtex-generate-autokey :filter-return #'my/bibtex-generate-autokey)
  ;; stolen from bibtex.el and modified to handle "Mac Lane"
  (defun my/bibtex-autokey-demangle-name (fullname)
    "Get the last part from a well-formed FULLNAME and perform abbreviations."
    (let* (case-fold-search
	   (name (cond ((string-match "\\(\\(Ma?c\\|De\\) +[[:upper:]][^, ]*\\)[^,]*," fullname)
			;; Name is of the form "Mac Last, First" or
			;; "Mac Last, Jr, First" or "Mc Last, First" or
			;; "Mc Last, Jr, First"
			;; --> Take Mac Last or Mc Last, as appropriate
			;;     and replace spaces by concatenation
			(let ((mclast (match-string 1 fullname)))
			  (when (string-match split-string-default-separators mclast)
			    (replace-match "" nil nil mclast))))
		       ((string-match "\\([[:upper:]][^, ]*\\)[^,]*," fullname)
			;; Name is of the form "von Last, First" or
			;; "von Last, Jr, First"
			;; --> Take the first capital part before the comma
			(match-string 1 fullname))
		       ((string-match "\\([^, ]*\\)," fullname)
			;; Strange name: we have a comma, but nothing capital
			;; So we accept even lowercase names
			(match-string 1 fullname))
		       ((string-match "\\(\\<[[:lower:]][^ ]* +\\)+\\([[:upper:]][^ ]*\\)"
				      fullname)
			;; name is of the form "First von Last", "von Last",
			;; "First von von Last", or "d'Last"
			;; --> take the first capital part after the "von" parts
			(match-string 2 fullname))
		       ((string-match "\\([^ ]+\\) *\\'" fullname)
			;; name is of the form "First Middle Last" or "Last"
			;; --> take the last token
			(match-string 1 fullname))
		       (t (error "Name `%s' is incorrectly formed" fullname)))))
      (funcall bibtex-autokey-name-case-convert-function
	       (bibtex-autokey-abbrev name bibtex-autokey-name-length))))
  (advice-add 'bibtex-autokey-demangle-name :override 'my/bibtex-autokey-demangle-name)
  ;; 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
		   ;; Case-sensitivity (see bibtex-autokey-name-change-strings) requires us to
		   ;; duplicate everything
		   ("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 ivy-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")
  (bibtex-completion-pdf-extension '(".pdf" ".djvu" ".txt")))

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

(use-package company
  :ensure t
  :bind
  ("<tab>" . company-indent-or-complete-common)
  :hook
  (after-init . global-company-mode))

(use-package company-auctex
  :ensure t
  :after latex
  :config
  (company-auctex-init))

(use-package company-bibtex
  :ensure t
  :hook
  (bibtex-mode . (lambda () (add-to-list 'company-backends 'company-bibtex))))

(use-package company-box
  :ensure t
  :diminish
  :hook (company-mode . company-box-mode))

(use-package company-coq
  :ensure t
  :hook (coq-mode . company-coq-mode))

(use-package company-math
  :ensure t
  :config
  (add-to-list 'company-backends 'company-math-symbols-unicode)
  (add-to-list 'company-backends 'company-latex-commands))

(use-package company-org-block
  :ensure t
  :hook ((org-mode . (lambda ()
		       (setq-local company-backends '(company-org-block))
		       (company-mode +1)))))

(use-package counsel
  :ensure t
  :bind (("C-x C-b" . counsel-ibuffer)
	 ("C-x C-f" . counsel-find-file)
	 ("M-x" . counsel-M-x)
	 ("M-y" . counsel-yank-pop)))

(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)

(use-package diminish
  :ensure t)

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

(use-package dtrt-indent
  :ensure t)

(use-package dune
  :ensure t)

(use-package dune-format
  :ensure t)

(use-package eldoc
  :diminish)

(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
  :ensure t
  :defer t
  :bind
  ;; (:map gnus-summary-buffer-map
  ;;	("SPC" . (gnus-summary-goto-next-page)
  :custom
  (gnus-select-method
   '(nntp "news.club.cc.cmu.edu"
	  (nntp-address "news.club.cc.cmu.edu")
	  (nntp-via-address "news-cclub")
	  (nntp-via-rlogin-command "ssh")
	  (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")
     (nnimap "imap.rak.ac")
     (nnimap "mail.cs.mcgill.ca")
     (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))))
  (gnus-parameters
   '(("^nntp+.*" (address . "rak@rak.ac"))
     ("^nnimap+imap\\.rak\\.ac:.*"
      (posting-style
       (address . "rak@rak.ac")
       (gcc "nnimap+imap.rak.ac:Sent")))
     ("^nnimap+mail\\.cs\\.mcgill\\.ca:.*"
      (posting-style
       (address . "rkavanagh@cs.mcgill.ca")
       (gcc "nnimap+mail.cs.mcgill.ca:INBOX.Sent")))))
  (gnus-cloud-method "imap.rak.ac")
  (gnus-cloud-storage-method 'base64)
  (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)
  (gnus-group-line-format "%M%S%p%P%5y:%B%(%G%) %z\n")
  (gnus-topic-display-empty-topics nil)
  :hook
  (message-send . gnus-score-followup-article)
  (gnus-group-mode . gnus-topic-mode))

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

(use-package info-look
  :ensure t)

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

(use-package ivy
  :ensure t
  :diminish
  :custom
  (ivy-use-virtual-buffers t)
  (ivy-count-format "(%d/%d) ")
  :config
  (ivy-mode 1))

(use-package ivy-bibtex
  :ensure t
  :bind (("C-c b" . ivy-bibtex)))

(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 () (set (make-local-variable 'TeX-electric-math)
			     (cons "\\(" "\\)"))))
   (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)
		    '("figure" 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:"))
		   (add-to-list 'LaTeX-label-alist '("figure" . "fig:")))))
  :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)
  :custom
  (magit-diff-refine-hunk 'all))

(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 message
  :config
  (defun whitespace-cleanup-mail ()
    "Kill the whitespace in a buffer while preserving the last instance of '-- '."
    (interactive)
    (save-excursion
      (save-restriction
	(widen)
	(let ((signature-delimiter
	       (progn
		 ;; Find the last occurence of "-- " in the buffer
		 ;; and set signature-delimiter to the position of the first -
		 ;; This means we must subtract 2, because re-search-backward
		 ;; returns the end of the occurence found
		 (goto-char (point-max))
		 (- (re-search-backward "^-- $" nil t) 2))))
	  (when signature-delimiter
	    (progn
	      ;; Run whitespace-cleanup on the region
	      ;; [start, signature-delimiter]. Include the first dash
	      ;; to avoid deleting any empty lines leading up to the
	      ;; delimiter.
	      (narrow-to-region (point-min) signature-delimiter)
	      (whitespace-cleanup)
	      (widen)
	      ;; Run it on the region [signature-delimiter, end).
	      ;; We include the signature delimiter so that we do not
	      ;; delete any empty lines immediately following it.
	      ;; A side-effect is that the first line might become "^--$".
	      ;; This means that we must re-add the space at the end of
	      ;; the first line. Easiest just replace the first line of the
	      ;; buffer by "^-- $".
	      (narrow-to-region signature-delimiter (point-max))
	      (whitespace-cleanup)
	      (goto-char (point-min))
	      (kill-whole-line 0)
	      (insert "-- ")))))))
  :hook
  ((message-mode . (lambda () (remove-hook 'before-save-hook 'whitespace-cleanup t)))
   (message-mode . (lambda () (add-hook 'before-save-hook 'whitespace-cleanup-mail nil t))))
  :custom
  (message-citation-line-function 'message-insert-formatted-citation-line)
  (message-send-mail-function 'message-send-mail-with-sendmail))

(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 ocp-indent
  :ensure t)

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

(use-package org
  :bind (:map org-mode-map
	      ("<tab>" . org-cycle))
  :hook
  (org-mode . visual-line-mode)
  :custom
  (org-link-file-path-type 'relative))

(use-package org-chef
  :ensure t)

(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
  :after ivy-bibtex)

(use-package org-ref-arxiv
  :ensure org-ref
  :custom
  (arxiv-entry-format-string "@Misc{%s,
title = {%s},
author = {%s},
eprinttype = {arxiv},
date = {%s},
eprint = {%s},
eprintclass = {%s},
abstract = {%s},
pagetotal = {MISSING},
_checked = {NOT CHECKED},
_source = {ev},
}")
  ;; redefine it to use a sensible date and stuff.
  ;; my version of arxiv-get-bibtex-entry-via-arxiv-api
  :config
  (defun my/arxiv-get-bibtex-entry-via-arxiv-api (arxiv-number)
    "Retrieve meta data for ARXIV-NUMBER.
Returns a formatted BibTeX entry."
    (with-current-buffer
	(url-retrieve-synchronously (format "http://export.arxiv.org/api/query?id_list=%s" arxiv-number) t)
      (let* ((parse-tree (libxml-parse-xml-region
			  (progn (goto-char 0)
				 (search-forward "<?xml ")
				 (match-beginning 0))
			  (point-max)))
	     (entry (assq 'entry parse-tree))
	     (authors (--map (nth 2 (nth 2 it))
			     (--filter (and (listp it) (eq (car it) 'author)) entry)))
	     (date (nth 2 (assq 'published entry)))
	     (title (nth 2 (assq 'title entry)))
	     (names (arxiv-bibtexify-authors authors))
	     (category (cdar (nth 1 (assq 'primary_category entry))))
	     (abstract (s-trim (nth 2 (assq 'summary entry))))
	     (url (nth 2 (assq 'id entry)))
	     (temp-bibtex (format arxiv-entry-format-string "" title names date arxiv-number category abstract url))
	     (key (with-temp-buffer
		    (insert temp-bibtex)
		    (bibtex-mode)
		    (bibtex-set-dialect (parsebib-find-bibtex-dialect) t)
		    (org-ref-replace-nonascii)
		    (bibtex-generate-autokey))))
	(format arxiv-entry-format-string key title names date arxiv-number category abstract url))))
  (advice-add 'arxiv-get-bibtex-entry-via-arxiv-api :override 'my/arxiv-get-bibtex-entry-via-arxiv-api))

(use-package org-ref-bibtex
  :ensure org-ref
  :after bibtex-completion ; needs bibtex-completion-library-path
  :custom
  (org-ref-title-case-types '(("article" "title")
			      ("book" "booktitle" "title")
			      ("collection" "booktitle" "title")
			      ("incollection" "booktitle" "title")
			      ("inproceedings" "booktitle" "title")
			      ("misc" "title")
			      ("proceedings" "title")
			      ("report" "title")
			      ("thesis" "title")))
  (org-ref-bibtex-journal-abbreviations
   '(("CACM" "Communications of the ACM" "Comm. ACM")
     ("Discourse \\& Society")
     ("ENTCS" "Electronic Notes in Theoretical Computer Science")
     ("Information and Computation")
     ("International Journal of Foundations of Computer Science" "Int. J. Found. Comput. Sci.")
     ("JSL" "The Journal of Symbolic Logic")
     ("Journal of Computer Security")
     ("Journal of Logic and Computation" "J. Logic Computat.")
     ("LCNS" "Lecture Notes in Computer Science" "Lect. Notes Comput. Sc.")
     ("LMCS" "Logical Methods in Computer Science")
     ("Le Devoir")
     ("MSCS" "Mathematical Structures in Computer Science" "Math. Struct. Comp. Sci.")
     ("Nordic Journal of Philosophical Logic")
     ("PACMPL" "Proceedings of the ACM on Programming Languages" "Proc. ACM Program. Lang.")
     ("Philosophy Compass")
     ("Piping Today")
     ("Proceedings of the Aristotelian Society")
     ("Publications of the Research Institute for Mathematical Sciences" "Publ. RIMS")
     ("Reason Papers")
     ("Reprints in Theory and Applications of Categories")
     ("Rice University Studies")
     ("Rice University Studies")
     ("SICOMP" "SIAM Journal on Computing")
     ("Science")
     ("TAC" "Theory and Applications of Categories")
     ("TCS" "Theoretical Computer Science")
     ("TUGboat")
     ("The American Mathematical Monthly")
     ("The Review of Symbolic Logic")
     ("The Voice")
     ("Topoi")
     ("Transactions of the American Mathematical Society")
     ("{ACM} {SIGACT} News" "ACM SIGACT News"))))

(use-package reftex-cite
  :ensure t)

(use-package org-ref-core
  :ensure org-ref
  :after org-ref-bibtex
  :after reftex-cite
  :after ivy-bibtex
  :bind (:map bibtex-mode-map
	      ("C-c C-c" . org-ref-clean-bibtex-entry)
	      ("C-c e"   . my/set-source-ev)
	      ("C-c d"   . my/set-checked-date))
  :config
  (defun my/org-ref-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))))
  (defun my/set-checked-date ()
    "Set the _checked field of a bibtex entry to the current date."
    (interactive)
    (save-excursion
      (bibtex-beginning-of-entry)
      (bibtex-set-field "_checked" (format-time-string "%Y-%m-%d"))))
  (defun my/set-source-ev ()
    "Set the _source field of a bibtex entry to ev."
    (interactive)
    (save-excursion
      (bibtex-beginning-of-entry)
      (bibtex-set-field "_source" "ev")))
  ;; taken from org-ref-bibtex.el and extended
  (setq org-ref-nonascii-latex-replacements
	(append '(("fi" . "fi")
		  ("ı́" . "{\\\\'i}")
		  ("ω" . "$\\\\omega$")
		  ("‘" . "`") ; LEFT SINGLE QUOTATION MARK
		  ("’" . "'") ; RIGHT SINGLE QUOTATION MARK
		  ("“" . "``")
		  ("′" . "'") ; PRIME
		  ("∇" . "$\\\\nabla$")
		  ("ι" . "$\\\\iota$")
		  ("”" . "''"))
		org-ref-nonascii-latex-replacements))
  (defun my/org-ref-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 (string-empty-p doi)
	  (when (string-match-p (regexp-quote (org-ref-bibtex-entry-doi))
				(bibtex-autokey-get-field "url"))
	    (bibtex-set-field "url" ""))))))
  (defun my/org-ref-biblatex-journaltitle ()
    "Rename journal to journaltitle"
    (interactive)
    (save-excursion
      (bibtex-beginning-of-entry)
      (let ((journal (bibtex-autokey-get-field "journal"))
	    (journaltitle (bibtex-autokey-get-field "journaltitle")))
	(when (and (string-empty-p journaltitle)
		   (not (string-empty-p journal)))
	  (bibtex-beginning-of-entry)
	  (bibtex-set-field "journal" "")
	  (bibtex-set-field "journaltitle" journal)))))
  (defun my/biblatex-date ()
    "Convert 'year' + 'month' fields to 'date' field"
    (interactive)
    (save-excursion
      (bibtex-beginning-of-entry)
      (let* ((year (bibtex-autokey-get-field "year"))
	     (month (downcase (bibtex-autokey-get-field "month")))
	     (nummonth (cond ((string= month "jan") "01")
			     ((string= month "feb") "02")
			     ((string= month "mar") "03")
			     ((string= month "apr") "04")
			     ((string= month "may") "05")
			     ((string= month "jun") "06")
			     ((string= month "jul") "07")
			     ((string= month "aug") "08")
			     ((string= month "sep") "09")
			     ((string= month "oct") "10")
			     ((string= month "nov") "11")
			     ((string= month "dec") "12")
			     (t "")))
	     (olddate (bibtex-autokey-get-field "date"))
	     (newdate (cond ((string-empty-p year) nil)
			    ((string-empty-p nummonth) year)
			    (t (concat year "-" nummonth)))))
	(when (and (string-empty-p olddate)
		   (not (string-empty-p newdate)))
	  (bibtex-beginning-of-entry)
	  (bibtex-set-field "date" newdate)
	  (bibtex-set-field "year" "")
	  (bibtex-set-field "month" "")))))
  (defun my/orcb-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-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
   '(my/org-ref-biblatex-journaltitle
     bibtex-clean-entry
     my/org-ref-format-url-if-doi
     orcb-key-comma
     org-ref-replace-nonascii
     orcb-&
     orcb-%
     my/org-ref-title-case-english ;; all entries, -article does only articles
     my/org-ref-biblatex-journaltitle
     my/biblatex-date
     orcb-key
     orcb-clean-doi
     my/orcb-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 ox-md
  ;; org-mode to markdown exporter
  :ensure org
  :after (org))

(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:%f:" "~\\ref{%s}" t ("axiom" "ax.") -3)
			("theorem" ?h "theorem:%F:" "~\\ref{%s}" t ("theorem" "th.") -3)
			("proposition" ?p "prop:%F:" "~\\ref{%s}" t ("proposition" "prop.") -3)
			("definition" ?d "def:%F:" "~\\ref{%s}" t ("definition" "def.") -3)
			("corollary" ?c "cor:%F:" "~\\ref{%s}" t ("corollary" "cor.") -3)
			("lemma" ?l "lemma:%F:" "~\\ref{%s}" t ("lemma" "lem.") -3)
			("conjecture" ?j "conj:%F:" "~\\ref{%s}" t ("conjecture" "conj.") -3)
			("example" ?X "ex:%F:" "~\\ref{%s}" t ("example" "ex.") -3)
			("figure" ?F "fig:%F:" "~\\ref{%s}" t ("figure" "fig.") -3)
			("ax" ?a "ax:%F:" "~\\ref{%s}" t ("axiom" "ax.") -3)
			("thm" ?h "theorem:%F:" "~\\ref{%s}" t ("theorem" "th.") -3)
			("prop" ?p "prop:%F:" "~\\ref{%s}" t ("proposition" "prop.") -3)
			("defi" ?d "def:%F:" "~\\ref{%s}" t ("definition" "def.") -3)
			("cor" ?c "cor:%F:" "~\\ref{%s}" t ("corollary" "cor.") -3)
			("lem" ?l "lemma:%F:" "~\\ref{%s}" t ("lemma" "lem.") -3)
			("conj" ?j "conj:%F:" "~\\ref{%s}" t ("conjecture" "conj.") -3)
			("enumerate" 105 "item:%F:" "~\\ref{%s}" item (regexp "items?" "Punkte?"))
			("equation" 101 "eq:%F:" "~\\eqref{%s}" t
			 (regexp "equations?" "eqs?\\." "eqn\\." "Gleichung\\(en\\)?" "Gl\\."))
			("eqnarray" 101 "eq:%F:" nil eqnarray-like))))

(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))

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

(use-package smerge-mode
  :commands smerge-mode
  :init ;; weirdly won't work if under custom
  (setq smerge-command-prefix (kbd "C-c v")))

(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
  (cond
   ((eq system-type 'darwin)
    (add-to-list 'TeX-view-program-list
		 '("Zathura"
		   ("zathura "
		    (mode-io-correlate " --synctex-forward %n:0:%b -x \"emacsclient +%{line} %{input}\" ")
		    " %o")
		   "zathura"))))
  (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)