dotfiles/emacs

;; Platform-specific stuff!!!!
(setq document-view "setsid -w xdg-open %s"
      pdf-viewer "Evince" ; for C-c C-v LaTeX forward search
      keepass-folder "~/Syncthing/keepass/"
      bibliography-folder "~/Documents/bibliography/"
      biblio-key (kbd "<f12>") ; use <apps> for the menu button in
                               ; other OS's, or for example <f12> for
                               ; Termux and see its wiki for showing
                               ; this button on its interface. Also
                               ; <X86Launch1> works in Mate desktop,
                               ; but not terminals.
      windmove-key 'shift ; for 'shift, see
                          ; https://emacs.stackexchange.com/a/54002
;;       browse-url-browser-function 'browse-url-xdg-open ; in termux
      org-replace-disputed-keys t ; for windmove when using 'shift
      want-to-use-xclip nil ; termux clipboard, install termux-api too
)
;; Computed stuff:
(setq own-calendar-file (concat keepass-folder "calendar.org")
      own-bookmark-file (concat keepass-folder "bookmarks.org")
      gtd-folder (concat keepass-folder "gtd/")
      gtd-inbox (concat gtd-folder "inbox.org")
      gtd-gtd (concat gtd-folder "gtd.org")
      gtd-someday (concat gtd-folder "someday.org")
      gtd-archive (concat gtd-folder "archive.org")
      gtd-tickler (concat gtd-folder "tickler.org")
      bibliography-file (concat bibliography-folder "references.bib")
      bibliography-pdf-folder (concat bibliography-folder "bibtex-pdfs/")
      bibliography-notes (concat bibliography-folder "bibtex-notes/"))


;; Defer loading packages unless daemon
(setq use-package-always-demand (daemonp))

;; Always revert files, i.e. reload them to buffers if emacs notices
;; them changing by e.g. an external program.
(global-auto-revert-mode 1)

;; Load the MELPA package library
(require 'package)
(add-to-list 'package-archives '("melpa"
             . "https://melpa.org/packages/") t)
(package-initialize)

;; Download and load use-package
(unless (package-installed-p 'use-package)
  (package-install 'use-package))




;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; General text file handling ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Coding system
(modify-coding-system-alist 'file "" 'utf-8)
(setq-default buffer-file-coding-system 'utf-8)
(add-to-list 'safe-local-variable-values '(buffer-file-coding-system . utf-8))
;; Backups into ~/.emacs-saves
(unless (file-exists-p "~/.saves-emacs")
  (make-directory "~/.saves-emacs"))
(setq backup-directory-alist '(("." . "~/.saves-emacs"))
      backup-by-copying t
      delete-old-versions t
      kept-new-versions 6
      kept-old-versions 2
      version-control t)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;


;;;;;;;;;;;;;;;;;;;;;;;
;;;; Email related ;;;;
;;;;;;;;;;;;;;;;;;;;;;;
(setq mail-user-agent 'gnus-user-agent
      epg-pinentry-mode 'loopback) ; Avoids GPG password input entry
                                   ; issue in emacs termux. Might need
                                   ; to edit .gnupeg/gpg-agent.conf
                                   ; and add "allow-emacs-pinentry"
;; BBDB settings
(use-package bbdb
  :ensure t
  :custom
  (bbdb-file (concat keepass-folder "bbdb"))
  (bbdb-mua-pop-up t) ; Display BBDB in popup window
  (bbdb-mua-pop-up-window-size 3)
  (bbdb-mua-update-interactive-p
   '(query . create)) ; Look for existing contact, interactively
                      ; prompt to create
  :config
  (bbdb-initialize 'gnus 'message)
  (bbdb-mua-auto-update-init 'gnus 'message))
;;;;;;;;;;;;;;;;;;;;;;;


;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; Appearance related ;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Nyan-mode.
(use-package nyan-mode
  :ensure t
  :config
  (nyan-mode 1)
  (nyan-start-animation)
  ;; Install sox in termux to play music and uncomment below.
  ;; (defun nyan-start-music ()
  ;;   (interactive)
  ;;   (unless nyan-music-process
  ;;     (setq nyan-music-process (start-process-shell-command "nyan-music" "nyan-music" (concat "play " +nyan-music+ " repeat 9001")))))
  )
;; Theme
(use-package nord-theme ; Good candidates: nord-theme, dracula-theme
  :ensure t)
(use-package theme-changer
  :ensure t
  :after nord-theme
  :config
  (setq calendar-location-name "Espoo")
  (setq calendar-latitude 60.18)
  (setq calendar-longitude 24.82)
  (change-theme nil 'nord))
;; Color issues
(setq shr-use-colors nil) ; Don't use text color when rendering html
                          ; using shr (links ok)
;; Olivetti mode for org-mode etc long texts.
;; Add
;; ((nil . ((fill-column . 80)
;;         (mode . olivetti))))
;; inside a folder's .dir-locals.el to use olivetti for all files there
(use-package olivetti
  :ensure t
  :config
  (setq visual-line-fringe-indicators '(left-curly-arrow right-curly-arrow))
  (setq gnus-treat-fill-long-lines nil)
  :hook
  ((latex-mode LaTeX-mode gnus-article-mode message-mode) . olivetti-mode))
(use-package adaptive-wrap
  :ensure t
  :hook
  (visual-line-mode . adaptive-wrap-prefix-mode))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; Emacs buffer etc. behaviour ;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Expand region
(use-package expand-region
  :ensure t
  :config
  (global-set-key (kbd "<f11>") 'er/expand-region)
  (delete-selection-mode t) ; typed text replaces the selection
  )
;; Smartparens
(use-package smartparens
  :ensure t
  :hook
  ((lisp-mode emacs-lisp-mode gfm-mode markdown-mode LaTeX-mode)
  . show-paren-mode)
  ((lisp-mode emacs-lisp-mode gfm-mode markdown-mode LaTeX-mode)
  . smartparens-mode)
  :config
  (sp-local-pair '(lisp-mode emacs-lisp-mode) "'" nil :actions nil)
  (sp-local-pair '(lisp-mode emacs-lisp-mode) "`" nil :actions nil)
  ;; Add \big( \big), etc. without having to use \bigl( \bigr).
  (sp-with-modes '(tex-mode plain-tex-mode latex-mode LaTeX-mode)
    (sp-local-pair "\\big(" "\\big)" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\bigg(" "\\bigg)" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Big(" "\\Big)" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Bigg(" "\\Bigg)" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\big[" "\\big]" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\bigg[" "\\bigg]" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Big[" "\\Big]" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Bigg[" "\\Bigg]" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\big\\{" "\\big\\}" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\bigg\\{" "\\bigg\\}" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Big\\{" "\\Big\\}" :post-handlers '(sp-latex-insert-spaces-inside-pair))
    (sp-local-pair "\\Bigg\\{" "\\Bigg\\}" :post-handlers '(sp-latex-insert-spaces-inside-pair)))
  (eval-after-load 'latex '(require 'smartparens-latex))
  )
;; Helm (completion framework)
(use-package helm
  :ensure t
  :bind (("M-x" . helm-M-x))
  :custom
  (helm-move-to-line-cycle-in-source nil)
  :config
  (helm-mode 1))
(winner-mode t) ; C-c ←/→ for going between used window configurations
(setq-default word-wrap nil)
(defun unfill-paragraph () ; for copy-pasting to external program
  "Takes a multi-line paragraph and makes it into a single line of text."
  (interactive)
  (let ((fill-column (point-max)))
    (fill-paragraph nil)))
(define-key global-map "\M-Q" 'unfill-paragraph) ; alt+shift+q
;; Sort words
;; https://www.emacswiki.org/emacs/SortWords
(defun sort-words (reverse beg end)
  "Sort words in region alphabetically, in REVERSE if negative.
    Prefixed with negative \\[universal-argument], sorts in reverse.
  
    The variable `sort-fold-case' determines whether alphabetic case
    affects the sort order.
  
    See `sort-regexp-fields'."
  (interactive "*P\nr")
  (sort-regexp-fields reverse "\\w+" "\\&" beg end))
(windmove-default-keybindings windmove-key)
(setq mouse-yank-at-point t) ; Use current cursor position for middle
                             ; mouse pasting instead of jumping to new
                             ; location then paste
;; F9 opens file where we save www-bookmarks
(global-set-key (kbd "<f9>") (lambda() (interactive)(find-file own-bookmark-file)))
;; Xclip
(when want-to-use-xclip
  (use-package xclip
    :ensure t
    :config
    (xclip-mode 1)
    ))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;



;;;;;;;;;;;;;;;;;;;;;;;;
;;;; Coding related ;;;;
;;;;;;;;;;;;;;;;;;;;;;;;
(global-set-key "\C-x\C-m" 'compile) ; C-x C-m compile
(setq compilation-read-command nil ; compile with "make -k"
      compilation-scroll-output t) ; autoscroll compilation buffer
(use-package magit
  :ensure t
  :bind
  ("C-x g" . magit-status)
  :custom
  (magit-diff-refine-hunk 'all))
(use-package abridge-diff
  :ensure t
  :after magit
  :init (abridge-diff-mode 1))
(use-package company ; Company (complete anything) mode
  :ensure t
  :hook
  (emacs-lisp-mode . company-mode)
  ((latex-mode LaTeX-mode) . (lambda ()
                               (set (make-local-variable 'company-backends)
                                    '((company-dabbrev)))))
  :custom
  (company-tooltip-align-annotations 1)
  (company-minimum-prefix-length 1)
  (company-idle-delay 0.0)
  (company-selection-wrap-around t)
  (company-dabbrev-ignore-case nil)
  (company-dabbrev-downcase nil)
  :config
  (company-tng-mode)
  (define-key company-active-map [up] nil)
  (define-key company-active-map [down] nil))
(use-package slime ; SLIME (Common LISP)
  :ensure t
  :custom
  (inferior-lisp-program "clisp")
  :config
  (slime-setup '(slime-fancy)))
(use-package slime-company
  :ensure t
  :after (slime company)
  :custom
  (slime-company-completion 'fuzzy)
  :config
  (slime-setup '(slime-company)))
(use-package geiser-chez ; For Chez Scheme, start M-x run-geiser
  :ensure t)
(use-package markdown-mode
  :ensure t
  :mode ("README\\.md\\'" . gfm-mode)
  :custom
  (markdown-command "pandoc"))
;; Indentation & behaviour
(setq-default indent-tabs-mode nil
              standard-indent 2)
;;;;;;;;;;;;;;;;;;;;;;;;




;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; LaTeX / math related ;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(add-to-list 'auto-mode-alist '("\\.m\\'" . octave-mode))
(setq bibtex-align-at-equal-sign t) ; align = in bibtex using C-c C-q
(if (display-graphic-p)
    (progn
      (use-package pdf-tools
        :ensure t
        :config
        (pdf-tools-install :no-query))
      (use-package org-noter
        :ensure t
        :after (pdf-tools)
        :custom
        (org-noter-notes-search-path (list bibliography-notes)))))
(use-package tex
  :ensure auctex
  :after cdlatex
  :custom
  (TeX-source-correlate-mode t) ; for forward search
  :config
  ;; Make sure that when tabbing in org-cdlatex-mode it will not
  ;; complain of missing "LaTeX-indent-line".
  (defun own-LaTeX-indent-line ()
    (when (or (eq major-mode 'LaTeX-mode)
              (eq major-mode 'latex-mode))
      (LaTeX-indent-line)))
  (add-hook 'cdlatex-tab-hook 'own-LaTeX-indent-line)
  (add-to-list 'TeX-view-program-selection
               `(output-pdf ,pdf-viewer)) ; ` is like quote but allows
                                          ; evaluation inside using ,
  :hook
  ; Make \ part of words in LaTeX-mode
  ((latex-mode LaTeX-mode) . (lambda () (modify-syntax-entry
                                         (string-to-char TeX-esc)
                                         "w"
                                         LaTeX-mode-syntax-table))))
(use-package cdlatex
  :ensure t
  :custom
  (cdlatex-takeover-parenthesis . nil)
  :hook
  ((latex-mode LaTeX-mode) . cdlatex-mode)
  (org-mode . turn-on-org-cdlatex)
  :config
  (setq cdlatex-env-alist
        '(("definition" "\\begin{definition} AUTOLABEL\n?\n\\end{definition}\n" nil)
          ("theorem" "\\begin{theorem} AUTOLABEL\n?\n\\end{theorem}\n" nil)
          ("lemma" "\\begin{lemma} AUTOLABEL\n?\n\\end{lemma}\n" nil)))
  (setq cdlatex-command-alist
        '(("def" "Insert definition env"   "" cdlatex-environment ("definition") t nil)
          ("thm" "Insert theorem env"   "" cdlatex-environment ("theorem") t nil)
          ("lem" "Insert lemma env"   "" cdlatex-environment ("lemma") t nil)
          ("wt" "Insert \\widetilde{}" "\\widetilde{?}" cdlatex-position-cursor nil nil t))))

(use-package reftex
  :ensure t
  :hook
  ((latex-mode LaTeX-mode) . turn-on-reftex))
(use-package bibtex
  :custom
  ;; Ignore only lower case title words instead of all non-uppercased
  ;; ones when generating keys for bibtex
  (bibtex-autokey-titleword-ignore
   '("A" "An" "On" "The" "Eine?" "Der" "Die" "Das" "[[:lower:]].*" ".*[^[:upper:][:lower:]0-9].*")))
;; Helm-bibtex
(use-package helm-bibtex
  :ensure t
  :demand t ; otherwise biblio-key will be bound to void
  :init ; can't have a form like biblio-key under :bind
  (bind-key biblio-key 'helm-command-prefix)
  :config
  (define-key helm-command-map biblio-key 'helm-resume)
  :bind
  (:map helm-command-map
        ("b" . helm-bibtex)
        ("B" . helm-bibtex-with-local-bibliography)
        ("n" . helm-bibtex-with-notes))
;;  (define-key helm-command-map (kbd "<f12>") 'helm-resume)
  :custom
  (bibtex-completion-bibliography
   (list ; needs (list ...)  for new org-ref to work
    bibliography-file))
  (bibtex-completion-library-path
   (list ; needs (list ...) for new org-ref to work
    bibliography-pdf-folder))
  (bibtex-completion-pdf-extension '(".pdf" ".djvu"))
  (bibtex-completion-pdf-open-function 'org-open-file)
  (bibtex-completion-notes-path bibliography-notes)
  (bibtex-completion-additional-search-fields '(keywords tags))
  (bibtex-completion-pdf-field "File")
  (bibtex-completion-pdf-symbol "⌘")
  (bibtex-completion-notes-symbol "✎")
  )
(use-package org-ref ; Includes doi-utils
  :ensure t
  :custom
  ;; Words which shouldn't be capitalized in titles
  (org-ref-lower-case-words '("a" "an" "at" "on" "and" "for" "the" "of" "in"))
  ;; Allow the following fields Into Title Case of the Following Items
  (org-ref-title-case-types '(("article" "title")
                              ("book" "booktitle")
                              ("misc" "title")))
  ;; Don't convert ä,ö,å, etc when org-ref-clean-bibtex-entry
  (org-ref-clean-bibtex-entry-hook
   '(org-ref-bibtex-format-url-if-doi orcb-key-comma orcb-& orcb-% org-ref-title-case orcb-clean-year orcb-key orcb-clean-doi orcb-clean-pages orcb-check-journal org-ref-sort-bibtex-entry orcb-fix-spacing)))
(use-package emacsql :ensure t)
(use-package org-roam
  :ensure t
  :after emacsql
  :init
  (setq org-roam-database-connector 'sqlite-builtin)
  :custom
  (org-roam-directory bibliography-notes)
  (org-roam-capture-templates
   `(("d" "default" plain "%?"
      :target (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: ${title}")
      :unnarrowed t)
     ("b" "bibliography notes" plain             ; Org-noter integration
      (file ,(concat bibliography-notes "notes-template.org"))
      :target (file+head "${citekey}.org" "#+title: ${title}\n")
      :unnarrowed t)))
  :config
  (org-roam-db-autosync-mode 1))
(use-package org-roam-bibtex
  :ensure t
  :custom
  (orb-preformat-keywords '("citekey" "title" "url" "author-or-editor" "keywords" "file")) ; customisation for notes, org-noter integration
  (orb-process-file-keyword t)
  (orb-attached-file-extensions '("pdf"))
  ;;(bibtex-completion-edit-notes-function 'bibtex-completion-edit-notes-default) ; default to org-ref for notes
  (bibtex-completion-edit-notes-function 'orb-bibtex-completion-edit-note) ; use org-roam-capture-templates for notes
  :config
  (require 'org-ref))
(use-package org-roam-ui
  :ensure t
  :after org-roam
  :custom
  (org-roam-ui-sync-theme t)
  (org-roam-ui-follow t)
  (org-roam-ui-update-on-save t)
  (org-roam-ui-open-on-start t))
(use-package scihub
  :ensure t
  :custom
  (scihub-download-directory (car bibtex-completion-library-path))
  (scihub-open-after-download nil)
  (scihub-fetch-domain 'scihub-fetch-domains-lovescihub))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;





;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;; Org-mode related ;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;
(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 (list own-calendar-file
                          gtd-inbox
                          gtd-gtd
                          gtd-tickler
                          gtd-someday))
  (org-agenda-start-on-weekday 1) ; nil means current day
  (org-agenda-span 7)
  (org-refile-targets '((org-agenda-files :maxlevel . 9)
                        (gtd-inbox :maxlevel . 3)
                        (gtd-someday :maxlevel . 2)
                        (gtd-tickler :maxlevel . 2)
                        (gtd-archive :level . 1)))
  (org-archive-reversed-order t) ; same for archiving with C-c C-x A
  (org-refile-use-outline-path t)
  (org-todo-keywords
   '((sequence "TODO(t)" "MEET(m)"
               "|" "DONE(d)" "WAIT(w@)" "CANCELLED(c@)")))
  (org-todo-repeat-to-state t)
  (org-log-done 'time)
  ;; See see http://cachestocaches.com/2016/9/my-workflow-org-agenda/
  (org-capture-templates
   `(("t" "Todo [gtd inbox]" entry (file+headline ,gtd-inbox "Tasks")
      "* TODO %i%? %A")
     ("T" "Tickler" entry (file+headline ,gtd-tickler "Tickler")
      "* %i%? \n%T")
     ("m" "Meeting" entry (file+headline ,gtd-inbox "Tasks")
      "* MEET %i%? %A")
     ("b" "Bookmark" entry (file+headline ,own-bookmark-file "Bookmarks")
      "* %x %?%^g\n:PROPERTIES:\n:CREATED: %U\n:END:\n\n" :empty-lines-before 1)
     ("n" "Pdf note from email" plain (file ,bibliography-file)
      "@misc{????,\nauthor = {%^{author}},\nday = %^{day},\nmonth = %^{month},\nyear = %^{year},\ntags = {%^{comma-separated tags}},\ntitle = {%\\4/%\\3/%\\2 Notes - %^{topic (remember to save the PDF from email!!)}},\nurl = %l\n}\n\n" :empty-lines 1 :before-finalize org-ref-clean-bibtex-entry :immediate-finish 1)))
  ;; Org & agendar look
  (org-todo-keyword-faces '(("MEET" .
                             (:foreground "#486f66"
                              :background "#f4bbce"
                              :weight ultra-bold))))
  (org-agenda-prefix-format
   '((agenda . " %i %?-12t% s") ; default: " %i %-12:c%?-12t% s"
     (todo . " %i %-12:c")
     (tags . " %i %-12:c")
     (search . " %i %-12:c")))
  (org-format-latex-options '(:foreground default
                              :background default
                              :scale 1.0
                              :html-foreground "Black"
                              :html-background "Transparent"
                              :html-scale 1.0
                              :matchers ("begin" "$1" "$" "$$" "\\(" "\\[")))
  (org-outline-path-complete-in-steps nil) ; for completions to work in Helm
  :config
  ;; Open pdf & djvu outside emacs
  (defun alist-set (KEY PROP ALIST)
    (set ALIST (assoc-delete-all KEY (symbol-value ALIST)))
    (add-to-list ALIST (cons KEY PROP)))
  (alist-set "\\.pdf\\'" document-view 'org-file-apps)
  (alist-set "\\.djvu\\'" document-view 'org-file-apps)
  ;; C-c C-s RET inserts block. See ":exports both" for results.
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((calc . t)
     (octave . t)
     (R . t)
     (python . t) ; see https://emacs.stackexchange.com/a/64539
     (shell . t)))
  (setq org-babel-python-command
        "python3") ; add ":python python" to block for python2
  ;; Automagically save org-buffers after org-refile moves stuff
  (defun my-org-refile (&optional goto default-buffer rfloc msg)
    (interactive "P")
    "Does an ~org-refile~ and then a ~org-save-all-org-buffers~."
    (org-refile goto default-buffer rfloc msg) (org-save-all-org-buffers))
  (define-key org-mode-map (kbd "C-c C-w") 'my-org-refile)
  ;; F8 opens GTD file
  (global-set-key (kbd "<f8>") (lambda() (interactive)(find-file gtd-gtd)))
  )
(use-package helm-org
  :ensure t
  :after (org helm)
  :config
  (add-to-list 'helm-completing-read-handlers-alist '(org-capture . helm-org-completing-read-tags))
  (add-to-list 'helm-completing-read-handlers-alist '(org-set-tags . helm-org-completing-read-tags)))
(use-package suomalainen-kalenteri
  :ensure t
  :config
  (set-face-attribute 'org-agenda-calendar-sexp nil
                      :inherit 'org-level-2)
  )
;;;;;;;;;;;;;;;;;;;;;;;;;;