many more renames

1 files changed, 923 insertions, 0 deletions

diff --git a/dot_emacs b/dot_emacs
new file mode 100644
index 0000000..3e0cd34
--- /dev/null
+++ b/dot_emacs
@@ -0,0 +1,923 @@
+;; (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)))))
+
+(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)
+    (powerline-moe-theme)))
+
+;; (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))
+
+(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 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)
+  :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 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")
+  (bibtex-completion-pdf-extension '(".pdf" ".djvu" ".txt"))
+  :bind (("C-c b" . helm-bibtex)))
+
+(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
+  :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
+  :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 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 dune
+  :ensure t)
+
+(use-package dune-format
+  :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
+  :ensure t
+  :defer t
+  :custom
+  (gnus-select-method
+   '(nntp "news.club.cc.cmu.edu"
+	  (nntp-address "news.club.cc.cmu.edu")
+	  (nntp-via-address "unix.club.cc.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)
+  (gnus-group-line-format "%M%S%p%P%5y:%B%(%G%) %z\n")
+  :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 helm
+  :ensure t
+  :bind (("M-x"     . helm-M-x)
+	 ("C-x C-f" . helm-find-files)
+	 ("C-x C-b" . helm-mini)
+	 :map helm-map
+	 ("<tab>"   . helm-select-action))
+  :config
+  (helm-mode 1))
+
+(use-package helm-org
+  :ensure t)
+
+(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 () (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))
+
+(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 ocp-indent
+  :ensure t)
+
+(use-package octave
+  :mode ("\\.m\'" . octave-mode))
+
+(use-package org
+  :custom
+  (org-link-file-path-type 'relative))
+
+(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 helm-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
+  :config
+  (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-title-case-types '(("article" "title")
+			      ("book" "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.")
+     ("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 org-ref-core
+  :ensure org-ref
+  :after helm-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
+		  ("”" . "''"))
+		org-ref-nonascii-latex-replacements))
+  :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 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)
+  (message-send-mail-function 'sendmail-send-it))
+
+(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)