Jack Baty's Emacs Configuration

(load "~/.emacs.secrets" t)

(require 'ob-jira-rest)
(require 'org-protocol)

;; (setq spacemacs-theme-org-height nil)
;;(setq spacemacs-theme-org-agenda-height nil)

(setq backup-directory-alist '(("." . "~/.emacs.backups")))

(setq delete-old-versions -1)
(setq version-control t)
(setq vc-make-backup-files t)
;; (setq auto-save-file-name-transforms '((".*" "~/.emacs.d/auto-save-list/" t)))

(setq bookmark-default-file "~/Dropbox/Sync/dotfiles/emacs-bookmarks")

;; Reading a PDF while taking notes in another window (2 window setup)
;; Hit M-[/M-] to go up/down while keeping cursor in current window.
;; http://www.idryman.org/blog/2013/05/20/emacs-and-pdf/
(fset 'doc-prev "\C-xo\C-u\C-xo")
(fset 'doc-next "\C-xo\C-d\C-xo")
(global-set-key (kbd "M-[") 'doc-prev)
(global-set-key (kbd "M-]") 'doc-next)

;; refresh on change
(add-hook 'doc-view-mode-hook 'auto-revert-mode)

(add-hook 'text-mode-hook 'turn-on-auto-fill)

  (setq org-modules '(org-bbdb
                      org-info
                      org-habit
                      org-irc
                      org-mouse
                      org-protocol
                      org-annotate-file
                      org-eval
                      org-expiry
                      org-interactive-query
                      org-man
                      org-collector
                      org-panel
                      org-screen
                      org-toc))
(eval-after-load 'org
 '(org-load-modules-maybe t))
;; Prepare stuff for org-export-backends
(setq org-export-backends '(org latex icalendar html ascii))

  ;;
  ;; General org-mode configuration
  ;;

  (setq org-directory "~/Dropbox/org/")
  (setq org-agenda-files (quote ("~/Dropbox/org")))
  (setq org-default-notes-file (quote (concat org-directory "inbox.org")))
  (setq org-refile-targets (quote ((nil :maxlevel . 2)
                                  (org-agenda-files :maxlevel . 2))))

  (setq org-refile-use-outline-path t)
  (setq org-outline-path-complete-in-steps nil)
  (setq org-refile-allow-creating-parent-nodes (quote confirm))
  (setq org-todo-keywords
        '((sequence "TODO(t)" "PEND(p)" "NEXT(n)" "WAIT(w@)" "|" "DONE(d!)" "CANC(@c)")))

  (org-agenda-to-appt)
  (setq org-agenda-include-diary nil)
  (setq org-icalendar-timezone "America/Detroit")
  (setq org-cycle-separator-lines 0)
  ;; Throw error if you try to delete hidden/folded text
  (setq org-catch-invisible-edits 'error)
  ;; export settings
  (setq org-html-head-include-default-scripts nil)
  (setq org-html-head-include-default-style nil)
  (setq org-agenda-skip-deadline-prewarning-if-scheduled t)
  ;;don't show tasks that are scheduled or have deadlines in the
  ;;normal todo list
  (setq org-agenda-todo-ignore-deadlines (quote all))
  (setq org-agenda-todo-ignore-scheduled (quote all))

  ;; org-babel config
  (setq org-startup-folded "overview")
  (setq org-src-tab-acts-natively t)
  (setq org-confirm-babel-evaluate nil)
  (setq org-ditaa-jar-path "/usr/local/bin/ditaa")

  (setq org-contacts-files '("/Users/jbaty/Dropbox/People/"))

  (setq org-adapt-indentation t)
  (setq org-agenda-insert-diary-strategy (quote date-tree-last))
  (setq org-agenda-log-mode-items (quote (closed)))
  (setq org-agenda-skip-scheduled-if-deadline-is-shown (quote not-today))
  (setq org-agenda-skip-scheduled-if-done t)
  (setq org-agenda-span (quote day))
  (setq org-agenda-text-search-extra-files (quote (agenda-archives)))
  (setq org-agenda-window-setup (quote other-window))

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (emacs-lisp . nil)
   (emacs-lisp . t)
   (latex . t)
   (org . t)
   (ruby . t)
   (ledger . t)
   (awk . t)
   ))
  (setq org-clock-mode-line-total (quote current))
  (setq org-deadline-warning-days 4)
  (setq org-latex-pdf-process
   (quote
    ("xelatex -interaction nonstopmode -output-directory %o %f" "xelatex -interaction nonstopmode -output-directory %o %f")))
  (setq org-log-into-drawer t)
  (setq org-refile-targets (quote ((org-agenda-files :maxlevel . 3))))
  (setq org-refile-use-outline-path t)
  (setq org-reverse-note-order t)
  (setq org-startup-indented t)
  (setq org-stuck-projects (quote ("project/-DONE-CANC" ("TODO" "NEXT") nil "")))
  (setq org-use-tag-inheritance nil)

;; org-habit
(require 'org-habit)
(add-to-list 'org-modules "org-habit")
(setq org-habit-preceding-days 7
      org-habit-following-days 1
      org-habit-show-habits-only-for-today t
      org-habit-graph-column 50
      org-habit-show-all-today t)

;; Org clock config
;; Don't Resume clocking task when emacs is restarted (takes too long)
;;(org-clock-persistence-insinuate nil)
;; Resume clocking task on clock-in if the clock is open
(setq org-clock-in-resume t)
;; Separate drawers for clocking and logs
;;(setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
(setq org-clock-into-drawer t)
(setq org-clock-out-remove-zero-time-clocks t)
(setq org-clock-out-when-done t)
;; Save the running clock and all clock history when exiting Emacs, load it on startup
(setq org-clock-persist t)
(setq org-clock-report-include-clocking-task t)
;; Tidy up the clockreport
(setq org-agenda-clockreport-parameter-plist
    (quote (:link t :maxlevel 5 :fileskip0 t :compact t :narrow 60 :formula %)))

(setq org-agenda-custom-commands
      (append '(("c" "Waiting for Client" tags-todo "Client")
                ("w" "Waiting" todo "WAIT" nil)
                ("p" "Active Projects" tags "project/-DONE-CANC" nil)
                ("Q" tags "questions")
                ("b" tags "bought")
                ("l" tags "Links")
                ("v" tags-todo "Events"))))

;;
;; Capture
;;
(setq org-capture-templates
          '(("t" "Todo" entry
             (file+headline "~/org/todo.org" "Inbox")
             "* TODO %? \n %i\n")
            ("T" "Todo and clock in" entry
             (file+headline "~/org/todo.org" "Inbox")
             "* TODO %? \n %i\n"
             :clock-in t
             :clock-keep t)
            ("n" "Take a note")
            ("ns" "Scraps for processing later" entry
             (file+headline "~/org/scraps.org" "Scraps")
             "* %?\n%u")
            ("nt" "Log to Technotes" entry
             (file+headline "~/org/technotes.org" "Technotes")
             "* %?\n%u")
            ("nb" "Notes.baty.net" entry
             (file+headline "~/Dropbox/Sites/notes-emacs/content/index.org" "Latest Notes")
             "* %? %t\n "
             :prepend t)
            ("nk" "Sparkfile entry" item
             (file+headline "~/org/sparkfile.org" "2016")
             "- [ ] %? %u"
             :prepend t)
            ("nf" "Fusionary Notebook entry" entry
             (file+datetree "~/org/fusionary.org")
             "**** %? \n%U"
             :empty-lines 1)
            ("w" "Worklog" entry
             (file+datetree "~/org/worklog.org")
             "* %? %^g\n%T")
            ("W" "Worklog and clock in" entry
             (file+datetree "~/org/worklog.org")
             "* %? %^g\n%T"
             :clock-in t
             :clock-keep nil)
            ("c" "Client log entries")
            ("ch" "HealthcareSource" entry
             (file+datetree "~/org/HCS.org")
             "* %? %^g")
            ("ct" "Trademarx" entry
             (file+datetree "~/org/Trademarx.org")
             "* %? %^g")
            ("cs" "Steelcase" entry
             (file+datetree "~/org/Steelcase.org")
             "* %? %^g")
            ("f" "Food log entries")
            ("fb" "Breakfast entry" entry
             (file+olp "~/org/daybook.org" "Food Log" "December")
             "* %u %? :Breakfast:%^g"
             :prepend nil)
            ("fl" "Lunch entry" entry
             (file+olp "~/org/daybook.org" "Food Log" "December")
             "* %u %? :Lunch:%^g"
             :prepend nil)
            ("fd" "Dinner entry" entry
             (file+olp "~/org/daybook.org" "Food Log" "December")
             "* %u %? :Dinner:%^g"
             :prepend nil)
            ("d" "Daybook" entry
             (file+olp "~/org/daybook.org" "Daybook" "December")
             "* %u %? %^g")
            ("m" "TODO from Mail" entry
             (file+headline "~/org/todo.org" "Inbox")
             "* TODO Followup%? (%:fromname about %:subject)\n%U\n%a\n")
            ("b" "Bookmark links" entry
             (file+headline "~/org/links.org" "Bookmarks")
             "* %? %^g\nEntered on: %U\n%c")
            ))
(with-eval-after-load 'org-capture
    (add-hook 'org-capture-mode-hook 'evil-insert-state))

;; open fusionary.org  with Spc of
(defun my/open-fusionary-notebook ()
  "Open fusionary.org"
  (interactive)
  (find-file "~/Dropbox/org/fusionary.org"))

(evil-leader/set-key "of" 'my/open-fusionary-notebook)

;; Open todos with Spc ot
(defun my/open-todo ()
  "Open Todo file"
  (interactive)
  (find-file "~/Dropbox/org/todo.org"))

(evil-leader/set-key "ot" 'my/open-todo)

;; Open daybook with Spc od
(defun my/open-daybook ()
  "Open Daybook file"
  (interactive)
  (find-file "~/Dropbox/org/daybook.org"))

(evil-leader/set-key "od" 'my/open-daybook)

;; Open special url-handler links with macOS `open' command
;; This means you can open DevonThink and Papers links in org files
(defun jab-org/org-pass-link-to-system (link)
  (if (string-match "^[a-zA-Z0-9\-]+:" link)
      (shell-command (concat "open " (shell-quote-argument link)))
    nil)
  )

(add-hook 'org-open-link-functions 'jab-org/org-pass-link-to-system)

;; LaTeX

;; My default LaTeX class
(with-eval-after-load 'ox-latex
  (add-to-list 'org-latex-classes
             '("scrartcl"
               "\\documentclass{scrartcl}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))))

(setq org-latex-caption-above nil)

;; For counting tag frequency
;; http://emacs.stackexchange.com/questions/29127/make-statistics-of-the-tag-use-in-org-mode#29133

(defun org-freq-count (search targets &optional cmp)
  (let ((cmp (if (functionp cmp)
                 cmp
               (lambda (a b) nil))))

    (mapcar (lambda (x)
              (list x (length (org-map-entries t (format search x) nil))))
            (sort
             (delete-dups
              (-filter #'stringp targets))
             cmp)
            )
    ))

(defun org--tagblock-all-tags ()
  (-filter #'stringp (-map #'car (append
                                  (org-get-buffer-tags)
                                  org-tag-alist
                                  org-tag-persistent-alist))))

(defun org-write-freq-count (search targets name)
  (insert (s-concat
           (if name (insert (format "#+NAME: %s\n" name)))
           (mapconcat
            (lambda (x) (format "| %s | %s |" (nth 0 x) (nth 1 x)))
            (org-freq-count search targets)
            "\n")))
  (org-table-align)
  )

(defun org-dblock-write:tagblock (params)
  (let ((todo (plist-get params :todo))
        (tags (or (plist-get params :tags) (org--tagblock-all-tags)))
        (label (plist-get params :label))
        (caption (plist-get params :caption))
        )
    (when caption (insert (format "#+CAPTION: %s\n" caption)))
    (org-write-freq-count (cond ((equal todo t)
                                 (format "%%s/%s" (mapconcat 'identity
                                                             org-not-done-keywords
                                                             "|"
                                                             )))
                                ((listp todo)
                                 (format "%%s/%s" (mapconcat 'identity
                                                             todo
                                                        "|"
                                                        )))
                                (t "%s"))
                        tags
                        label
                        )))

;; from Sacha Chua
;; "Sometimes I want a region's HTML in my kill-ring/clipboard without any of the extra fluff:"
(defun my/org-copy-region-as-html (beg end &optional level)
  "Make it easier to copy code for Wordpress posts and other things."
  (interactive "r\np")
  (let ((org-export-html-preamble nil)
        (org-html-toplevel-hlevel (or level 3)))
    (kill-new
     (org-export-string-as (buffer-substring beg end) 'html t))))