emacs_el/configuration/org-mode-configuration.el

   1 (require 'org-id)
   2 (require 'reftex)
   3 (require 'gnus)
   4
   5 ;; The following lines are always needed. Choose your own keys.
   6 (add-to-list 'auto-mode-alist '("\\.\\(org\\|org_archive\\|txt\\)$" . org-mode))
   7 (require 'org)
   8 (global-set-key "\C-cl" 'org-store-link)
   9 (global-set-key "\C-ca" 'org-agenda)
  10 (global-set-key "\C-cb" 'org-iswitchb)
  11 (setq-default org-log-done 'time)
  12 (setq-default org-agenda-ndays 5)
  13
  14 ;; agenda configuration
  15 ;; Do not dim blocked tasks
  16 (setq org-agenda-dim-blocked-tasks nil)
  17
  18 ;; Compact the block agenda view
  19 (setq org-agenda-compact-blocks t)
  20
  21 ;; Custom agenda command definitions
  22 (setq org-agenda-custom-commands
  23       (quote (("N" "Notes" tags "NOTE"
  24                ((org-agenda-overriding-header "Notes")
  25                 (org-tags-match-list-sublevels t)))
  26               ("h" "Habits" tags-todo "STYLE=\"habit\""
  27                ((org-agenda-overriding-header "Habits")
  28                 (org-agenda-sorting-strategy
  29                  '(todo-state-down effort-up category-keep))))
  30               (" " "Agenda"
  31                ((agenda "" nil)
  32                 (tags "REFILE"
  33                       ((org-agenda-overriding-header "Tasks to Refile")
  34                        (org-tags-match-list-sublevels nil)))
  35                 (tags-todo "-CANCELLED/!"
  36                            ((org-agenda-overriding-header "Stuck Projects")
  37                             (org-agenda-skip-function 'bh/skip-non-stuck-projects)
  38                             (org-agenda-sorting-strategy
  39                              '(category-keep))))
  40                 (tags-todo "-HOLD-CANCELLED/!"
  41                            ((org-agenda-overriding-header "Projects")
  42                             (org-agenda-skip-function 'bh/skip-non-projects)
  43                             (org-tags-match-list-sublevels 'indented)
  44                             (org-agenda-sorting-strategy
  45                              '(category-keep))))
  46                 (tags-todo "-CANCELLED/!NEXT"
  47                            ((org-agenda-overriding-header (concat "Project Next Tasks"
  48                                                                   (if bh/hide-scheduled-and-waiting-next-tasks
  49                                                                       ""
  50                                                                     " (including WAITING and SCHEDULED tasks)")))
  51                             (org-agenda-skip-function 'bh/skip-projects-and-habits-and-single-tasks)
  52                             (org-tags-match-list-sublevels t)
  53                             (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
  54                             (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
  55                             (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
  56                             (org-agenda-sorting-strategy
  57                              '(todo-state-down effort-up category-keep))))
  58                 (tags-todo "-REFILE-CANCELLED-WAITING-HOLD/!"
  59                            ((org-agenda-overriding-header (concat "Project Subtasks"
  60                                                                   (if bh/hide-scheduled-and-waiting-next-tasks
  61                                                                       ""
  62                                                                     " (including WAITING and SCHEDULED tasks)")))
  63                             (org-agenda-skip-function 'bh/skip-non-project-tasks)
  64                             (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
  65                             (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
  66                             (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
  67                             (org-agenda-sorting-strategy
  68                              '(category-keep))))
  69                 (tags-todo "-REFILE-CANCELLED-WAITING-HOLD/!"
  70                            ((org-agenda-overriding-header (concat "Standalone Tasks"
  71                                                                   (if bh/hide-scheduled-and-waiting-next-tasks
  72                                                                       ""
  73                                                                     " (including WAITING and SCHEDULED tasks)")))
  74                             (org-agenda-skip-function 'bh/skip-project-tasks)
  75                             (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
  76                             (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
  77                             (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
  78                             (org-agenda-sorting-strategy
  79                              '(category-keep))))
  80                 (tags-todo "-CANCELLED+WAITING|HOLD/!"
  81                            ((org-agenda-overriding-header "Waiting and Postponed Tasks")
  82                             (org-agenda-skip-function 'bh/skip-stuck-projects)
  83                             (org-tags-match-list-sublevels nil)
  84                             (org-agenda-todo-ignore-scheduled t)
  85                             (org-agenda-todo-ignore-deadlines t)))
  86                 (tags "-REFILE/"
  87                       ((org-agenda-overriding-header "Tasks to Archive")
  88                        (org-agenda-skip-function 'bh/skip-non-archivable-tasks)
  89                        (org-tags-match-list-sublevels nil))))
  90                nil))))
  91
  92 ; org mode agenda files
  93 (setq org-agenda-files
  94       (quote ("~/projects/debbugs/debbugs.org"
  95               "~/projects/notes/notes.org"
  96               "~/projects/notes/refile.org"
  97               "~/projects/notes/diary.org"
  98               "~/projects/origins_of_life/ool.org"
  99               "~/projects/sysadmin/sndservers/sndservers.org"
 100               "~/projects/chaim/chaim.org"
 101               "~/projects/chaim/papers/gwas_paper_2012/gwas_paper.org"
 102           "~/projects/reviews/reviews.org"
 103               "~/projects/fh/fh.org")))
 104
 105 (setq org-global-properties '(("Effort_ALL 0 0:10 0:30 1:00 2:00 3:00 4:00 5:00 6:00 7:00")))
 106 (setq org-columns-default-format "%40ITEM(Task) %TAGS %PRIORITY %TODO %13SCHEDULED %13DEADLINE %6Effort{:}  %CLOCKSUM")
 107
 108 (setq org-default-notes-file "~/projects/notes/notes.org")
 109 (setq org-capture-templates  ;; mail-specific note template, identified by "m"
 110       '(("m" "Mail" entry (file+headline "~/projects/notes/refile.org" "Mail")
 111          "* %?\n\n  Source: %u, %c\n  %i")
 112         ("t" "todo" entry (file "~/projects/notes/refile.org")
 113          "* TODO %?\n%U\n%a\n" :clock-in t :clock-resume t)
 114         ("r" "respond" entry (file "~/projects/notes/refile.org")
 115          "* NEXT Respond to %:from on %:subject\nSCHEDULED: %t\n%U\n%a\n" :clock-in t :clock-resume t :immediate-finish t)
 116         ("n" "note" entry (file "~/projects/notes/refile.org")
 117          "* %? :NOTE:\n%U\n%a\n" :clock-in t :clock-resume t)
 118         ("s" "schedule" entry (file "~/projects/notes/refile.org")
 119          "* %? \n%^{scheduled:}t\n%U\n%a\n" :clock-in t :clock-resume t)
 120         ("j" "Journal" entry (file+datetree "~/projects/notes/diary.org")
 121          "* %?\n%U\n" :clock-in t :clock-resume t)
 122         ("w" "org-protocol" entry (file "~/projects/notes/refile.org")
 123          "* TODO Review %c\n%U\n" :immediate-finish t)
 124         ("m" "Meeting" entry (file "~/projects/notes/refile.org")
 125          "* MEETING with %? :MEETING:\n%U" :clock-in t :clock-resume t)
 126         ("p" "Phone call" entry (file "~/projects/notes/refile.org")
 127          "* PHONE %? :PHONE:\n%U" :clock-in t :clock-resume t)
 128         ("h" "Habit" entry (file "~/projects/notes/refile.org")
 129          "* NEXT %?\n%U\n%a\nSCHEDULED: %(format-time-string \"<%Y-%m-%d %a .+1d/3d>\")\n:PROPERTIES:\n:STYLE: habit\n:REPEAT_TO_STATE: NEXT\n:END:\n")
 130         )
 131       )
 132
 133 ;; Remove empty LOGBOOK drawers on clock out
 134 (defun bh/remove-empty-drawer-on-clock-out ()
 135   (interactive)
 136   (save-excursion
 137     (beginning-of-line 0)
 138     (org-remove-empty-drawer-at "LOGBOOK" (point))))
 139
 140 (defun my/org-add-id ()
 141   (interactive)
 142   (save-excursion
 143     (if (org-current-level)
 144         ()
 145       (forward-char 1)
 146       )
 147     (org-id-get-create)
 148     )
 149 )
 150
 151 ; org mode configuration from http://doc.norang.ca/org-mode.html
 152 ;; Custom Key Bindings
 153 (global-set-key (kbd "<f12>") 'org-agenda)
 154 (global-set-key (kbd "<f5>") 'bh/org-todo)
 155 (global-set-key (kbd "<S-f5>") 'bh/widen)
 156 (global-set-key (kbd "<f7>") 'bh/set-truncate-lines)
 157 (global-set-key (kbd "<f8>") 'org-cycle-agenda-files)
 158 (global-set-key (kbd "<f9> <f9>") 'bh/show-org-agenda)
 159 (global-set-key (kbd "<f9> b") 'bbdb)
 160 (global-set-key (kbd "<f9> c") 'calendar)
 161 (global-set-key (kbd "<f9> f") 'boxquote-insert-file)
 162 (global-set-key (kbd "<f9> h") 'bh/hide-other)
 163 (global-set-key (kbd "<f9> n") 'bh/toggle-next-task-display)
 164 (global-set-key (kbd "<f9> w") 'widen)
 165
 166 (global-set-key (kbd "<f9> I") 'bh/punch-in)
 167 (global-set-key (kbd "<f9> O") 'bh/punch-out)
 168
 169 (global-set-key (kbd "<f9> o") 'bh/make-org-scratch)
 170
 171 (global-set-key (kbd "<f9> r") 'boxquote-region)
 172 (global-set-key (kbd "<f9> s") 'bh/switch-to-scratch)
 173
 174 (global-set-key (kbd "<f9> t") 'bh/insert-inactive-timestamp)
 175 (global-set-key (kbd "<f9> T") 'bh/toggle-insert-inactive-timestamp)
 176
 177 (global-set-key (kbd "<f9> v") 'visible-mode)
 178 (global-set-key (kbd "<f9> l") 'org-toggle-link-display)
 179 (global-set-key (kbd "<f9> SPC") 'bh/clock-in-last-task)
 180 (global-set-key (kbd "C-<f9>") 'previous-buffer)
 181 (global-set-key (kbd "M-<f9>") 'org-toggle-inline-images)
 182 (global-set-key (kbd "C-x n r") 'narrow-to-region)
 183 (global-set-key (kbd "C-<f10>") 'next-buffer)
 184 (global-set-key (kbd "<f11>") 'org-clock-goto)
 185 (global-set-key (kbd "C-<f11>") 'org-clock-in)
 186 (global-set-key (kbd "C-s-<f12>") 'bh/save-then-publish)
 187 (global-set-key (kbd "C-c c") 'org-capture)
 188
 189 (defun bh/hide-other ()
 190   (interactive)
 191   (save-excursion
 192     (org-back-to-heading 'invisible-ok)
 193     (hide-other)
 194     (org-cycle)
 195     (org-cycle)
 196     (org-cycle)))
 197
 198 (defun bh/set-truncate-lines ()
 199   "Toggle value of truncate-lines and refresh window display."
 200   (interactive)
 201   (setq truncate-lines (not truncate-lines))
 202   ;; now refresh window display (an idiom from simple.el):
 203   (save-excursion
 204     (set-window-start (selected-window)
 205                       (window-start (selected-window)))))
 206
 207 (defun bh/make-org-scratch ()
 208   (interactive)
 209   (find-file "/tmp/publish/scratch.org")
 210   (gnus-make-directory "/tmp/publish"))
 211
 212 (defun bh/switch-to-scratch ()
 213   (interactive)
 214   (switch-to-buffer "*scratch*"))
 215
 216 (setq org-use-fast-todo-selection t)
 217 (setq org-treat-S-cursor-todo-selection-as-state-change nil)
 218
 219 (setq org-todo-keywords
 220       (quote ((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d)")
 221               (sequence "WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c@/!)" "PHONE" "MEETING"))))
 222
 223 (setq org-todo-keyword-faces
 224       (quote (("TODO" :foreground "red" :weight bold)
 225               ("NEXT" :foreground "blue" :weight bold)
 226               ("DONE" :foreground "forest green" :weight bold)
 227               ("WAITING" :foreground "orange" :weight bold)
 228               ("HOLD" :foreground "magenta" :weight bold)
 229               ("CANCELLED" :foreground "forest green" :weight bold)
 230               ("MEETING" :foreground "forest green" :weight bold)
 231               ("PHONE" :foreground "forest green" :weight bold))))
 232
 233 (setq org-todo-state-tags-triggers
 234       (quote (("CANCELLED" ("CANCELLED" . t))
 235               ("WAITING" ("WAITING" . t))
 236               ("HOLD" ("WAITING") ("HOLD" . t))
 237               (done ("WAITING") ("HOLD"))
 238               ("TODO" ("WAITING") ("CANCELLED") ("HOLD"))
 239               ("NEXT" ("WAITING") ("CANCELLED") ("HOLD"))
 240               ("DONE" ("WAITING") ("CANCELLED") ("HOLD")))))
 241
 242
 243
 244 (add-hook 'org-clock-out-hook 'bh/remove-empty-drawer-on-clock-out 'append)
 245 ; add ids on creation of nodes
 246 (add-hook 'org-capture-prepare-finalize-hook 'my/org-add-id)
 247 ; create function to create headlines in file. This comes from
 248 ; http://stackoverflow.com/questions/13340616/assign-ids-to-every-entry-in-org-mode
 249 (defun my/org-add-ids-to-headlines-in-file ()
 250   "Add ID properties to all headlines in the current file which
 251 do not already have one."
 252   (interactive)
 253   (org-map-entries 'org-id-get-create))
 254 ; if we wanted to do this to every buffer, do the following:
 255 ; (add-hook 'org-mode-hook
 256 ;           (lambda ()
 257 ;             (add-hook 'before-save-hook 'my/org-add-ids-to-headlines-in-file nil 'local)))
 258
 259
 260 ; resolve clocks after 10 minutes of idle; use xprintidle
 261 ; (setq org-clock-idle-time 10)
 262 ; (setq org-clock-x11idle-program-name "xprintidle")
 263
 264 ; this is from http://doc.norang.ca/org-mode.html#Capture
 265 ; use C-M-r for org mode capture
 266 (global-set-key (kbd "C-M-r") 'org-capture)
 267
 268 ; Targets include this file and any file contributing to the agenda - up to 9 levels deep
 269 (setq org-refile-targets (quote ((nil :maxlevel . 9)
 270                                  (org-agenda-files :maxlevel . 9))))
 271
 272 ; Use full outline paths for refile targets - we file directly with IDO
 273 (setq org-refile-use-outline-path t)
 274
 275 ; Targets complete directly with IDO
 276 (setq org-outline-path-complete-in-steps nil)
 277
 278 ; Allow refile to create parent tasks with confirmation
 279 (setq org-refile-allow-creating-parent-nodes (quote confirm))
 280
 281 ; Use IDO for both buffer and file completion and ido-everywhere to t
 282 (setq org-completion-use-ido t)
 283 (setq ido-everywhere t)
 284 (setq ido-max-directory-size 100000)
 285 (ido-mode (quote both))
 286 ; Use the current window when visiting files and buffers with ido
 287 (setq ido-default-file-method 'selected-window)
 288 (setq ido-default-buffer-method 'selected-window)
 289 ; Use the current window for indirect buffer display
 290 (setq org-indirect-buffer-display 'current-window)
 291
 292
 293 ;;;; Refile settings
 294 ; Exclude DONE state tasks from refile targets
 295 (defun bh/verify-refile-target ()
 296   "Exclude todo keywords with a done state from refile targets"
 297   (not (member (nth 2 (org-heading-components)) org-done-keywords)))
 298
 299 (setq org-refile-target-verify-function 'bh/verify-refile-target)
 300
 301 ;; ensure that emacsclient will show just the note to be edited when invoked
 302 ;; from Mutt, and that it will shut down emacsclient once finished;
 303 ;; fallback to legacy behavior when not invoked via org-protocol.
 304 (require 'org-protocol)
 305 (add-hook 'org-capture-mode-hook 'delete-other-windows)
 306 (setq my-org-protocol-flag nil)
 307 (defadvice org-capture-finalize (after delete-frame-at-end activate)
 308   "Delete frame at remember finalization"
 309   (progn (if my-org-protocol-flag (delete-frame))
 310          (setq my-org-protocol-flag nil)))
 311 (defadvice org-capture-refile (around delete-frame-after-refile activate)
 312   "Delete frame at remember refile"
 313   (if my-org-protocol-flag
 314       (progn
 315         (setq my-org-protocol-flag nil)
 316         ad-do-it
 317         (delete-frame))
 318     ad-do-it)
 319   )
 320 (defadvice org-capture-kill (after delete-frame-at-end activate)
 321   "Delete frame at remember abort"
 322   (progn (if my-org-protocol-flag (delete-frame))
 323          (setq my-org-protocol-flag nil)))
 324 (defadvice org-protocol-capture (before set-org-protocol-flag activate)
 325   (setq my-org-protocol-flag t))
 326
 327
 328 ;; org modules
 329 (add-to-list 'org-modules 'org-habit)
 330
 331 ; this comes from http://upsilon.cc/~zack/blog/posts/2010/02/integrating_Mutt_with_Org-mode/
 332 (defun open-mail-in-mutt (message)
 333   "Open a mail message in Mutt, using an external terminal.
 334
 335 Message can be specified either by a path pointing inside a
 336 Maildir, or by Message-ID."
 337   (interactive "MPath or Message-ID: ")
 338   (shell-command
 339    (format "faf xterm -e \"%s %s\""
 340        (substitute-in-file-name "$HOME/bin/mutt_open") message)))
 341
 342 ;; add support for "mutt:ID" links
 343 (org-add-link-type "mutt" 'open-mail-in-mutt)
 344
 345 (defun my-org-mode-setup ()
 346   (load-library "reftex")
 347   (and (buffer-file-name)
 348        (file-exists-p (buffer-file-name))
 349        (progn
 350          (reftex-parse-all)
 351          (reftex-set-cite-format
 352           '((?b . "[[bib::%l][%l-bib]]")
 353             (?n . "[[note::%l][%l-notes]]")
 354             (?c . "\\cite{%l}")
 355             (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l paper]]")))
 356          ))
 357   (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
 358   (define-key org-mode-map (kbd "C-c [") 'reftex-citation)
 359   (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search)
 360   (define-key org-mode-map (kbd "C-c 0") 'reftex-view-crossref)
 361   )
 362 (add-hook 'org-mode-hook 'my-org-mode-setup)
 363
 364 (defun org-mode-reftex-search ()
 365   (interactive)
 366   (org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t))))
 367
 368 (defun open-research-paper (bibtexkey)
 369   "Open a paper by bibtex key"
 370   (interactive "bibtex key: ")
 371   (shell-command
 372    (format "%s %s"
 373        (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
 374 (org-add-link-type "papers" 'open-research-paper)
 375
 376 ; I pretty much always want hiearchical checkboxes
 377 (setq org-hierachical-checkbox-statistics nil)
 378
 379 ;; stolen from
 380 ;; http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
 381 (defun my-rtcite-export-handler (path desc format)
 382   (message "my-rtcite-export-handler is called : path = %s, desc = %s, format = %s" path desc format)
 383   (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
 384                    (match-string 1 path)))
 385          (path (substring path 0 (match-beginning 0))))
 386     (cond ((eq format 'latex)
 387            (if (or (not desc)
 388                    (equal 0 (search "rtcite:" desc)))
 389                (format "\\cite{%s}" search)
 390              (format "\\cite[%s]{%s}" desc search))))))
 391
 392 (org-add-link-type "rtcite"
 393                    'org-bibtex-open
 394                    'my-rtcite-export-handler)
 395
 396
 397 (setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
 398 (setq-default org-directory "/home/don/org-mode/")
 399 (setq-default org-mobile-inbox-for-pull "/home/don/org-mode/from-mobile.org")
 400
 401 ;; org mode ical export
 402 (setq org-icalendar-timezone "America/Los_Angeles")
 403 (setq org-icalendar-use-scheduled '(todo-start event-if-todo))
 404 (setq org-icalendar-store-UID t)
 405
 406 ;; org babel support
 407 (org-babel-do-load-languages
 408  'org-babel-load-languages
 409  '((emacs-lisp . t )
 410    (R . t)
 411    (latex . t)))
 412 ;; org-babel-by-backend
 413 (defmacro org-babel-by-backend (&rest body)
 414    `(case (if (boundp 'backend)
 415               (org-export-backend-name backend)
 416             nil) ,@body))
 417
 418
 419
 420 ;; org latex
 421 ;; stolen from http://kieranhealy.org/esk/kjhealy.html
 422 (require 'org-latex)
 423 ;; Choose either listings or minted for exporting source code blocks.
 424 ;; Using minted (as here) requires pygments be installed. To use the
 425 ;; default listings package instead, use
 426 ;; (setq org-latex-listings t)
 427 ;; and change references to "minted" below to "listings"
 428 ; (setq org-latex-listings 'minted)
 429
 430 ;; default settings for minted code blocks
 431 (setq org-latex-minted-options
 432       '(;("frame" "single")
 433         ("bgcolor" "bg") ; bg will need to be defined in the preamble of your document. It's defined in org-preamble-pdflatex.sty and org-preamble-xelatex.sty below.
 434         ("fontsize" "\\small")
 435         ))
 436 ;; turn off the default toc behavior; deal with it properly in headers to files.
 437 (defun org-latex-no-toc (depth)
 438   (when depth
 439     (format "%% Org-mode is exporting headings to %s levels.\n"
 440             depth)))
 441 (setq org-latex-format-toc-function 'org-latex-no-toc)
 442
 443 (require 'ox-latex)
 444 (add-to-list 'org-latex-classes
 445              '("memarticle"
 446                "\\documentclass[11pt,oneside,article]{memoir}\n"
 447                ("\\section{%s}" . "\\section*{%s}")
 448                ("\\subsection{%s}" . "\\subsection*{%s}")
 449                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 450                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 451                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 452
 453 (add-to-list 'org-latex-classes
 454              '("membook"
 455                "\\documentclass[11pt,oneside]{memoir}\n"
 456                ("\\chapter{%s}" . "\\chapter*{%s}")
 457                ("\\section{%s}" . "\\section*{%s}")
 458                ("\\subsection{%s}" . "\\subsection*{%s}")
 459                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
 460
 461 (add-to-list 'org-latex-classes
 462              '("letter"
 463                "\\documentclass[11pt]{letter}
 464 [NO-DEFAULT-PACKAGES]
 465 [PACKAGES]
 466 [EXTRA]"
 467        ("\\section{%s}" . "\\section*{%s}")
 468                ("\\subsection{%s}" . "\\subsection*{%s}")
 469                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 470                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 471                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 472
 473 ;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432
 474 ;; but adapted to use latexmk 4.22 or higher.
 475 (setq org-latex-pdf-process '("latexmk -pdflatex=xelatex -bibtex -use-make -pdf %f"))
 476
 477 ;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
 478 (setq org-latex-default-packages-alist
 479       '())
 480 (setq org-latex-packages-alist
 481       '(("" "graphicx" t)
 482         ("" "fontspec" t)
 483         ("" "xunicode" t)
 484         ("" "hyperref" t)
 485         ("" "url" t)
 486         ("" "rotating" t)
 487         ("" "longtable" nil)
 488         ("" "float" )))
 489
 490 (defun org-create-formula--latex-header ()
 491   "Return LaTeX header appropriate for previewing a LaTeX snippet."
 492   (let ((info (org-combine-plists (org-export--get-global-options
 493                                    (org-export-get-backend 'latex))
 494                                   (org-export--get-inbuffer-options
 495                                    (org-export-get-backend 'latex)))))
 496     (org-latex-guess-babel-language
 497      (org-latex-guess-inputenc
 498       (org-splice-latex-header
 499        org-format-latex-header
 500        org-latex-default-packages-alist
 501        nil t
 502        (plist-get info :latex-header)))
 503      info)))
 504
 505
 506 ; support ignoring headers in org mode export to latex
 507 ; from http://article.gmane.org/gmane.emacs.orgmode/67692
 508 (defadvice org-latex-headline (around my-latex-skip-headlines
 509                                       (headline contents info) activate)
 510   (if (member "ignoreheading" (org-element-property :tags headline))
 511       (setq ad-return-value contents)
 512     ad-do-it))
 513
 514
 515 ;; helper functions
 516 (defun bh/is-project-p ()
 517   "Any task with a todo keyword subtask"
 518   (save-restriction
 519     (widen)
 520     (let ((has-subtask)
 521           (subtree-end (save-excursion (org-end-of-subtree t)))
 522           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 523       (save-excursion
 524         (forward-line 1)
 525         (while (and (not has-subtask)
 526                     (< (point) subtree-end)
 527                     (re-search-forward "^\*+ " subtree-end t))
 528           (when (member (org-get-todo-state) org-todo-keywords-1)
 529             (setq has-subtask t))))
 530       (and is-a-task has-subtask))))
 531
 532 (defun bh/is-project-subtree-p ()
 533   "Any task with a todo keyword that is in a project subtree.
 534 Callers of this function already widen the buffer view."
 535   (let ((task (save-excursion (org-back-to-heading 'invisible-ok)
 536                               (point))))
 537     (save-excursion
 538       (bh/find-project-task)
 539       (if (equal (point) task)
 540           nil
 541         t))))
 542
 543 (defun bh/is-task-p ()
 544   "Any task with a todo keyword and no subtask"
 545   (save-restriction
 546     (widen)
 547     (let ((has-subtask)
 548           (subtree-end (save-excursion (org-end-of-subtree t)))
 549           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 550       (save-excursion
 551         (forward-line 1)
 552         (while (and (not has-subtask)
 553                     (< (point) subtree-end)
 554                     (re-search-forward "^\*+ " subtree-end t))
 555           (when (member (org-get-todo-state) org-todo-keywords-1)
 556             (setq has-subtask t))))
 557       (and is-a-task (not has-subtask)))))
 558
 559 (defun bh/is-subproject-p ()
 560   "Any task which is a subtask of another project"
 561   (let ((is-subproject)
 562         (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 563     (save-excursion
 564       (while (and (not is-subproject) (org-up-heading-safe))
 565         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 566           (setq is-subproject t))))
 567     (and is-a-task is-subproject)))
 568
 569 (defun bh/list-sublevels-for-projects-indented ()
 570   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 571   This is normally used by skipping functions where this variable is already local to the agenda."
 572   (if (marker-buffer org-agenda-restrict-begin)
 573       (setq org-tags-match-list-sublevels 'indented)
 574     (setq org-tags-match-list-sublevels nil))
 575   nil)
 576
 577 (defun bh/list-sublevels-for-projects ()
 578   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 579   This is normally used by skipping functions where this variable is already local to the agenda."
 580   (if (marker-buffer org-agenda-restrict-begin)
 581       (setq org-tags-match-list-sublevels t)
 582     (setq org-tags-match-list-sublevels nil))
 583   nil)
 584
 585 (defvar bh/hide-scheduled-and-waiting-next-tasks t)
 586
 587 (defun bh/toggle-next-task-display ()
 588   (interactive)
 589   (setq bh/hide-scheduled-and-waiting-next-tasks (not bh/hide-scheduled-and-waiting-next-tasks))
 590   (when  (equal major-mode 'org-agenda-mode)
 591     (org-agenda-redo))
 592   (message "%s WAITING and SCHEDULED NEXT Tasks" (if bh/hide-scheduled-and-waiting-next-tasks "Hide" "Show")))
 593
 594 (defun bh/skip-stuck-projects ()
 595   "Skip trees that are not stuck projects"
 596   (save-restriction
 597     (widen)
 598     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 599       (if (bh/is-project-p)
 600           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 601                  (has-next ))
 602             (save-excursion
 603               (forward-line 1)
 604               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 605                 (unless (member "WAITING" (org-get-tags-at))
 606                   (setq has-next t))))
 607             (if has-next
 608                 nil
 609               next-headline)) ; a stuck project, has subtasks but no next task
 610         nil))))
 611
 612 (defun bh/skip-non-stuck-projects ()
 613   "Skip trees that are not stuck projects"
 614   ;; (bh/list-sublevels-for-projects-indented)
 615   (save-restriction
 616     (widen)
 617     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 618       (if (bh/is-project-p)
 619           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 620                  (has-next ))
 621             (save-excursion
 622               (forward-line 1)
 623               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 624                 (unless (member "WAITING" (org-get-tags-at))
 625                   (setq has-next t))))
 626             (if has-next
 627                 next-headline
 628               nil)) ; a stuck project, has subtasks but no next task
 629         next-headline))))
 630
 631 (defun bh/skip-non-projects ()
 632   "Skip trees that are not projects"
 633   ;; (bh/list-sublevels-for-projects-indented)
 634   (if (save-excursion (bh/skip-non-stuck-projects))
 635       (save-restriction
 636         (widen)
 637         (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 638           (cond
 639            ((bh/is-project-p)
 640             nil)
 641            ((and (bh/is-project-subtree-p) (not (bh/is-task-p)))
 642             nil)
 643            (t
 644             subtree-end))))
 645     (save-excursion (org-end-of-subtree t))))
 646
 647 (defun bh/skip-project-trees-and-habits ()
 648   "Skip trees that are projects"
 649   (save-restriction
 650     (widen)
 651     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 652       (cond
 653        ((bh/is-project-p)
 654         subtree-end)
 655        ((org-is-habit-p)
 656         subtree-end)
 657        (t
 658         nil)))))
 659
 660 (defun bh/skip-projects-and-habits-and-single-tasks ()
 661   "Skip trees that are projects, tasks that are habits, single non-project tasks"
 662   (save-restriction
 663     (widen)
 664     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 665       (cond
 666        ((org-is-habit-p)
 667         next-headline)
 668        ((and bh/hide-scheduled-and-waiting-next-tasks
 669              (member "WAITING" (org-get-tags-at)))
 670         next-headline)
 671        ((bh/is-project-p)
 672         next-headline)
 673        ((and (bh/is-task-p) (not (bh/is-project-subtree-p)))
 674         next-headline)
 675        (t
 676         nil)))))
 677
 678 (defun bh/skip-project-tasks-maybe ()
 679   "Show tasks related to the current restriction.
 680 When restricted to a project, skip project and sub project tasks, habits, NEXT tasks, and loose tasks.
 681 When not restricted, skip project and sub-project tasks, habits, and project related tasks."
 682   (save-restriction
 683     (widen)
 684     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 685            (next-headline (save-excursion (or (outline-next-heading) (point-max))))
 686            (limit-to-project (marker-buffer org-agenda-restrict-begin)))
 687       (cond
 688        ((bh/is-project-p)
 689         next-headline)
 690        ((org-is-habit-p)
 691         subtree-end)
 692        ((and (not limit-to-project)
 693              (bh/is-project-subtree-p))
 694         subtree-end)
 695        ((and limit-to-project
 696              (bh/is-project-subtree-p)
 697              (member (org-get-todo-state) (list "NEXT")))
 698         subtree-end)
 699        (t
 700         nil)))))
 701
 702 (defun bh/skip-project-tasks ()
 703   "Show non-project tasks.
 704 Skip project and sub-project tasks, habits, and project related tasks."
 705   (save-restriction
 706     (widen)
 707     (let* ((subtree-end (save-excursion (org-end-of-subtree t))))
 708       (cond
 709        ((bh/is-project-p)
 710         subtree-end)
 711        ((org-is-habit-p)
 712         subtree-end)
 713        ((bh/is-project-subtree-p)
 714         subtree-end)
 715        (t
 716         nil)))))
 717
 718 (defun bh/skip-non-project-tasks ()
 719   "Show project tasks.
 720 Skip project and sub-project tasks, habits, and loose non-project tasks."
 721   (save-restriction
 722     (widen)
 723     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 724            (next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 725       (cond
 726        ((bh/is-project-p)
 727         next-headline)
 728        ((org-is-habit-p)
 729         subtree-end)
 730        ((and (bh/is-project-subtree-p)
 731              (member (org-get-todo-state) (list "NEXT")))
 732         subtree-end)
 733        ((not (bh/is-project-subtree-p))
 734         subtree-end)
 735        (t
 736         nil)))))
 737
 738 (defun bh/skip-projects-and-habits ()
 739   "Skip trees that are projects and tasks that are habits"
 740   (save-restriction
 741     (widen)
 742     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 743       (cond
 744        ((bh/is-project-p)
 745         subtree-end)
 746        ((org-is-habit-p)
 747         subtree-end)
 748        (t
 749         nil)))))
 750
 751 (defun bh/skip-non-subprojects ()
 752   "Skip trees that are not projects"
 753   (let ((next-headline (save-excursion (outline-next-heading))))
 754     (if (bh/is-subproject-p)
 755         nil
 756       next-headline)))
 757 ;
 758 ;; Resume clocking task when emacs is restarted
 759 (org-clock-persistence-insinuate)
 760 ;;
 761 ;; Show lot of clocking history so it's easy to pick items off the C-F11 list
 762 (setq org-clock-history-length 23)
 763 ;; Resume clocking task on clock-in if the clock is open
 764 (setq org-clock-in-resume t)
 765 ;; Change tasks to NEXT when clocking in
 766 (setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
 767 ;; Separate drawers for clocking and logs
 768 (setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
 769 ;; Save clock data and state changes and notes in the LOGBOOK drawer
 770 (setq org-clock-into-drawer t)
 771 ;; Sometimes I change tasks I'm clocking quickly - this removes clocked tasks with 0:00 duration
 772 (setq org-clock-out-remove-zero-time-clocks t)
 773 ;; Clock out when moving task to a done state
 774 (setq org-clock-out-when-done t)
 775 ;; Save the running clock and all clock history when exiting Emacs, load it on startup
 776 (setq org-clock-persist t)
 777 ;; Do not prompt to resume an active clock
 778 (setq org-clock-persist-query-resume nil)
 779 ;; Enable auto clock resolution for finding open clocks
 780 (setq org-clock-auto-clock-resolution (quote when-no-clock-is-running))
 781 ;; Include current clocking task in clock reports
 782 (setq org-clock-report-include-clocking-task t)
 783
 784
 785 (defvar bh/keep-clock-running nil)
 786
 787 (defun bh/clock-in-to-next (kw)
 788   "Switch a task from TODO to NEXT when clocking in.
 789 Skips capture tasks, projects, and subprojects.
 790 Switch projects and subprojects from NEXT back to TODO"
 791   (when (not (and (boundp 'org-capture-mode) org-capture-mode))
 792     (cond
 793      ((and (member (org-get-todo-state) (list "TODO"))
 794            (bh/is-task-p))
 795       "NEXT")
 796      ((and (member (org-get-todo-state) (list "NEXT"))
 797            (bh/is-project-p))
 798       "TODO"))))
 799
 800 (defun bh/find-project-task ()
 801   "Move point to the parent (project) task if any"
 802   (save-restriction
 803     (widen)
 804     (let ((parent-task (save-excursion (org-back-to-heading 'invisible-ok) (point))))
 805       (while (org-up-heading-safe)
 806         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 807           (setq parent-task (point))))
 808       (goto-char parent-task)
 809       parent-task)))
 810
 811 (defun bh/punch-in (arg)
 812   "Start continuous clocking and set the default task to the
 813 selected task.  If no task is selected set the Organization task
 814 as the default task."
 815   (interactive "p")
 816   (setq bh/keep-clock-running t)
 817   (if (equal major-mode 'org-agenda-mode)
 818       ;;
 819       ;; We're in the agenda
 820       ;;
 821       (let* ((marker (org-get-at-bol 'org-hd-marker))
 822              (tags (org-with-point-at marker (org-get-tags-at))))
 823         (if (and (eq arg 4) tags)
 824             (org-agenda-clock-in '(16))
 825           (bh/clock-in-organization-task-as-default)))
 826     ;;
 827     ;; We are not in the agenda
 828     ;;
 829     (save-restriction
 830       (widen)
 831       ; Find the tags on the current task
 832       (if (and (equal major-mode 'org-mode) (not (org-before-first-heading-p)) (eq arg 4))
 833           (org-clock-in '(16))
 834         (bh/clock-in-organization-task-as-default)))))
 835
 836 (defun bh/punch-out ()
 837   (interactive)
 838   (setq bh/keep-clock-running nil)
 839   (when (org-clock-is-active)
 840     (org-clock-out))
 841   (org-agenda-remove-restriction-lock))
 842
 843 (defun bh/clock-in-default-task ()
 844   (save-excursion
 845     (org-with-point-at org-clock-default-task
 846       (org-clock-in))))
 847
 848 (defun bh/clock-in-parent-task ()
 849   "Move point to the parent (project) task if any and clock in"
 850   (let ((parent-task))
 851     (save-excursion
 852       (save-restriction
 853         (widen)
 854         (while (and (not parent-task) (org-up-heading-safe))
 855           (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 856             (setq parent-task (point))))
 857         (if parent-task
 858             (org-with-point-at parent-task
 859               (org-clock-in))
 860           (when bh/keep-clock-running
 861             (bh/clock-in-default-task)))))))
 862
 863 (defvar bh/organization-task-id "e22cb8bf-07c7-408b-8f60-ff3aadac95e4")
 864
 865 (defun bh/clock-in-organization-task-as-default ()
 866   (interactive)
 867   (org-with-point-at (org-id-find bh/organization-task-id 'marker)
 868     (org-clock-in '(16))))
 869
 870 (defun bh/clock-out-maybe ()
 871   (when (and bh/keep-clock-running
 872              (not org-clock-clocking-in)
 873              (marker-buffer org-clock-default-task)
 874              (not org-clock-resolving-clocks-due-to-idleness))
 875     (bh/clock-in-parent-task)))
 876
 877 (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
 878
 879 (require 'org-id)
 880 (defun bh/clock-in-task-by-id (id)
 881   "Clock in a task by id"
 882   (org-with-point-at (org-id-find id 'marker)
 883     (org-clock-in nil)))
 884
 885 (defun bh/clock-in-last-task (arg)
 886   "Clock in the interrupted task if there is one
 887 Skip the default task and get the next one.
 888 A prefix arg forces clock in of the default task."
 889   (interactive "p")
 890   (let ((clock-in-to-task
 891          (cond
 892           ((eq arg 4) org-clock-default-task)
 893           ((and (org-clock-is-active)
 894                 (equal org-clock-default-task (cadr org-clock-history)))
 895            (caddr org-clock-history))
 896           ((org-clock-is-active) (cadr org-clock-history))
 897           ((equal org-clock-default-task (car org-clock-history)) (cadr org-clock-history))
 898           (t (car org-clock-history)))))
 899     (widen)
 900     (org-with-point-at clock-in-to-task
 901       (org-clock-in nil))))
 902