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 . "[[notes:%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]]" (first (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 (add-to-list 'org-link-abbrev-alist
 377              '("notes" .
 378                "~/projects/research/paper_notes.org::#%s"))
 379
 380 ; I pretty much always want hiearchical checkboxes
 381 (setq org-hierachical-checkbox-statistics nil)
 382
 383 ;; stolen from
 384 ;; http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
 385 (defun my-rtcite-export-handler (path desc format)
 386   (message "my-rtcite-export-handler is called : path = %s, desc = %s, format = %s" path desc format)
 387   (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
 388                    (match-string 1 path)))
 389          (path (substring path 0 (match-beginning 0))))
 390     (cond ((eq format 'latex)
 391            (if (or (not desc)
 392                    (equal 0 (search "rtcite:" desc)))
 393                (format "\\cite{%s}" search)
 394              (format "\\cite[%s]{%s}" desc search))))))
 395
 396 (org-add-link-type "rtcite"
 397                    'org-bibtex-open
 398                    'my-rtcite-export-handler)
 399
 400
 401 (setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
 402 (setq-default org-directory "/home/don/org-mode/")
 403 (setq-default org-mobile-inbox-for-pull "/home/don/org-mode/from-mobile.org")
 404
 405 ;; org mode ical export
 406 (setq org-icalendar-timezone "America/Los_Angeles")
 407 (setq org-icalendar-use-scheduled '(todo-start event-if-todo))
 408 (setq org-icalendar-store-UID t)
 409
 410 ;; org babel support
 411 (org-babel-do-load-languages
 412  'org-babel-load-languages
 413  '((emacs-lisp . t )
 414    (R . t)
 415    (latex . t)))
 416 ;; org-babel-by-backend
 417 (defmacro org-babel-by-backend (&rest body)
 418    `(case (if (boundp 'backend)
 419               (org-export-backend-name backend)
 420             nil) ,@body))
 421
 422
 423
 424 ;; org latex
 425 ;; stolen from http://kieranhealy.org/esk/kjhealy.html
 426 (require 'org-latex)
 427 ;; Choose either listings or minted for exporting source code blocks.
 428 ;; Using minted (as here) requires pygments be installed. To use the
 429 ;; default listings package instead, use
 430 ;; (setq org-latex-listings t)
 431 ;; and change references to "minted" below to "listings"
 432 ; (setq org-latex-listings 'minted)
 433
 434 ;; default settings for minted code blocks
 435 (setq org-latex-minted-options
 436       '(;("frame" "single")
 437         ("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.
 438         ("fontsize" "\\small")
 439         ))
 440 ;; turn off the default toc behavior; deal with it properly in headers to files.
 441 (defun org-latex-no-toc (depth)
 442   (when depth
 443     (format "%% Org-mode is exporting headings to %s levels.\n"
 444             depth)))
 445 (setq org-latex-format-toc-function 'org-latex-no-toc)
 446
 447 (require 'ox-latex)
 448 (add-to-list 'org-latex-classes
 449              '("memarticle"
 450                "\\documentclass[11pt,oneside,article]{memoir}\n"
 451                ("\\section{%s}" . "\\section*{%s}")
 452                ("\\subsection{%s}" . "\\subsection*{%s}")
 453                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 454                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 455                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 456
 457 (add-to-list 'org-latex-classes
 458              '("membook"
 459                "\\documentclass[11pt,oneside]{memoir}\n"
 460                ("\\chapter{%s}" . "\\chapter*{%s}")
 461                ("\\section{%s}" . "\\section*{%s}")
 462                ("\\subsection{%s}" . "\\subsection*{%s}")
 463                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
 464
 465 (add-to-list 'org-latex-classes
 466              '("letter"
 467                "\\documentclass[11pt]{letter}
 468 [NO-DEFAULT-PACKAGES]
 469 [PACKAGES]
 470 [EXTRA]"
 471        ("\\section{%s}" . "\\section*{%s}")
 472                ("\\subsection{%s}" . "\\subsection*{%s}")
 473                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 474                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 475                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 476
 477 ;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432
 478 ;; but adapted to use latexmk 4.22 or higher.
 479 (setq org-latex-pdf-process '("latexmk -pdflatex=xelatex -bibtex -use-make -pdf %f"))
 480
 481 ;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
 482 (setq org-latex-default-packages-alist
 483       '())
 484 (setq org-latex-packages-alist
 485       '(("" "graphicx" t)
 486         ("" "fontspec" t)
 487         ("" "xunicode" t)
 488         ("" "hyperref" t)
 489         ("" "url" t)
 490         ("" "rotating" t)
 491         ("" "longtable" nil)
 492         ("" "float" )))
 493
 494 (defun org-create-formula--latex-header ()
 495   "Return LaTeX header appropriate for previewing a LaTeX snippet."
 496   (let ((info (org-combine-plists (org-export--get-global-options
 497                                    (org-export-get-backend 'latex))
 498                                   (org-export--get-inbuffer-options
 499                                    (org-export-get-backend 'latex)))))
 500     (org-latex-guess-babel-language
 501      (org-latex-guess-inputenc
 502       (org-splice-latex-header
 503        org-format-latex-header
 504        org-latex-default-packages-alist
 505        nil t
 506        (plist-get info :latex-header)))
 507      info)))
 508
 509
 510 ; support ignoring headers in org mode export to latex
 511 ; from http://article.gmane.org/gmane.emacs.orgmode/67692
 512 (defadvice org-latex-headline (around my-latex-skip-headlines
 513                                       (headline contents info) activate)
 514   (if (member "ignoreheading" (org-element-property :tags headline))
 515       (setq ad-return-value contents)
 516     ad-do-it))
 517
 518
 519 ;; helper functions
 520 (defun bh/is-project-p ()
 521   "Any task with a todo keyword subtask"
 522   (save-restriction
 523     (widen)
 524     (let ((has-subtask)
 525           (subtree-end (save-excursion (org-end-of-subtree t)))
 526           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 527       (save-excursion
 528         (forward-line 1)
 529         (while (and (not has-subtask)
 530                     (< (point) subtree-end)
 531                     (re-search-forward "^\*+ " subtree-end t))
 532           (when (member (org-get-todo-state) org-todo-keywords-1)
 533             (setq has-subtask t))))
 534       (and is-a-task has-subtask))))
 535
 536 (defun bh/is-project-subtree-p ()
 537   "Any task with a todo keyword that is in a project subtree.
 538 Callers of this function already widen the buffer view."
 539   (let ((task (save-excursion (org-back-to-heading 'invisible-ok)
 540                               (point))))
 541     (save-excursion
 542       (bh/find-project-task)
 543       (if (equal (point) task)
 544           nil
 545         t))))
 546
 547 (defun bh/is-task-p ()
 548   "Any task with a todo keyword and no subtask"
 549   (save-restriction
 550     (widen)
 551     (let ((has-subtask)
 552           (subtree-end (save-excursion (org-end-of-subtree t)))
 553           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 554       (save-excursion
 555         (forward-line 1)
 556         (while (and (not has-subtask)
 557                     (< (point) subtree-end)
 558                     (re-search-forward "^\*+ " subtree-end t))
 559           (when (member (org-get-todo-state) org-todo-keywords-1)
 560             (setq has-subtask t))))
 561       (and is-a-task (not has-subtask)))))
 562
 563 (defun bh/is-subproject-p ()
 564   "Any task which is a subtask of another project"
 565   (let ((is-subproject)
 566         (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 567     (save-excursion
 568       (while (and (not is-subproject) (org-up-heading-safe))
 569         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 570           (setq is-subproject t))))
 571     (and is-a-task is-subproject)))
 572
 573 (defun bh/list-sublevels-for-projects-indented ()
 574   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 575   This is normally used by skipping functions where this variable is already local to the agenda."
 576   (if (marker-buffer org-agenda-restrict-begin)
 577       (setq org-tags-match-list-sublevels 'indented)
 578     (setq org-tags-match-list-sublevels nil))
 579   nil)
 580
 581 (defun bh/list-sublevels-for-projects ()
 582   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 583   This is normally used by skipping functions where this variable is already local to the agenda."
 584   (if (marker-buffer org-agenda-restrict-begin)
 585       (setq org-tags-match-list-sublevels t)
 586     (setq org-tags-match-list-sublevels nil))
 587   nil)
 588
 589 (defvar bh/hide-scheduled-and-waiting-next-tasks t)
 590
 591 (defun bh/toggle-next-task-display ()
 592   (interactive)
 593   (setq bh/hide-scheduled-and-waiting-next-tasks (not bh/hide-scheduled-and-waiting-next-tasks))
 594   (when  (equal major-mode 'org-agenda-mode)
 595     (org-agenda-redo))
 596   (message "%s WAITING and SCHEDULED NEXT Tasks" (if bh/hide-scheduled-and-waiting-next-tasks "Hide" "Show")))
 597
 598 (defun bh/skip-stuck-projects ()
 599   "Skip trees that are not stuck projects"
 600   (save-restriction
 601     (widen)
 602     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 603       (if (bh/is-project-p)
 604           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 605                  (has-next ))
 606             (save-excursion
 607               (forward-line 1)
 608               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 609                 (unless (member "WAITING" (org-get-tags-at))
 610                   (setq has-next t))))
 611             (if has-next
 612                 nil
 613               next-headline)) ; a stuck project, has subtasks but no next task
 614         nil))))
 615
 616 (defun bh/skip-non-stuck-projects ()
 617   "Skip trees that are not stuck projects"
 618   ;; (bh/list-sublevels-for-projects-indented)
 619   (save-restriction
 620     (widen)
 621     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 622       (if (bh/is-project-p)
 623           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 624                  (has-next ))
 625             (save-excursion
 626               (forward-line 1)
 627               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 628                 (unless (member "WAITING" (org-get-tags-at))
 629                   (setq has-next t))))
 630             (if has-next
 631                 next-headline
 632               nil)) ; a stuck project, has subtasks but no next task
 633         next-headline))))
 634
 635 (defun bh/skip-non-projects ()
 636   "Skip trees that are not projects"
 637   ;; (bh/list-sublevels-for-projects-indented)
 638   (if (save-excursion (bh/skip-non-stuck-projects))
 639       (save-restriction
 640         (widen)
 641         (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 642           (cond
 643            ((bh/is-project-p)
 644             nil)
 645            ((and (bh/is-project-subtree-p) (not (bh/is-task-p)))
 646             nil)
 647            (t
 648             subtree-end))))
 649     (save-excursion (org-end-of-subtree t))))
 650
 651 (defun bh/skip-project-trees-and-habits ()
 652   "Skip trees that are projects"
 653   (save-restriction
 654     (widen)
 655     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 656       (cond
 657        ((bh/is-project-p)
 658         subtree-end)
 659        ((org-is-habit-p)
 660         subtree-end)
 661        (t
 662         nil)))))
 663
 664 (defun bh/skip-projects-and-habits-and-single-tasks ()
 665   "Skip trees that are projects, tasks that are habits, single non-project tasks"
 666   (save-restriction
 667     (widen)
 668     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 669       (cond
 670        ((org-is-habit-p)
 671         next-headline)
 672        ((and bh/hide-scheduled-and-waiting-next-tasks
 673              (member "WAITING" (org-get-tags-at)))
 674         next-headline)
 675        ((bh/is-project-p)
 676         next-headline)
 677        ((and (bh/is-task-p) (not (bh/is-project-subtree-p)))
 678         next-headline)
 679        (t
 680         nil)))))
 681
 682 (defun bh/skip-project-tasks-maybe ()
 683   "Show tasks related to the current restriction.
 684 When restricted to a project, skip project and sub project tasks, habits, NEXT tasks, and loose tasks.
 685 When not restricted, skip project and sub-project tasks, habits, and project related tasks."
 686   (save-restriction
 687     (widen)
 688     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 689            (next-headline (save-excursion (or (outline-next-heading) (point-max))))
 690            (limit-to-project (marker-buffer org-agenda-restrict-begin)))
 691       (cond
 692        ((bh/is-project-p)
 693         next-headline)
 694        ((org-is-habit-p)
 695         subtree-end)
 696        ((and (not limit-to-project)
 697              (bh/is-project-subtree-p))
 698         subtree-end)
 699        ((and limit-to-project
 700              (bh/is-project-subtree-p)
 701              (member (org-get-todo-state) (list "NEXT")))
 702         subtree-end)
 703        (t
 704         nil)))))
 705
 706 (defun bh/skip-project-tasks ()
 707   "Show non-project tasks.
 708 Skip project and sub-project tasks, habits, and project related tasks."
 709   (save-restriction
 710     (widen)
 711     (let* ((subtree-end (save-excursion (org-end-of-subtree t))))
 712       (cond
 713        ((bh/is-project-p)
 714         subtree-end)
 715        ((org-is-habit-p)
 716         subtree-end)
 717        ((bh/is-project-subtree-p)
 718         subtree-end)
 719        (t
 720         nil)))))
 721
 722 (defun bh/skip-non-project-tasks ()
 723   "Show project tasks.
 724 Skip project and sub-project tasks, habits, and loose non-project tasks."
 725   (save-restriction
 726     (widen)
 727     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 728            (next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 729       (cond
 730        ((bh/is-project-p)
 731         next-headline)
 732        ((org-is-habit-p)
 733         subtree-end)
 734        ((and (bh/is-project-subtree-p)
 735              (member (org-get-todo-state) (list "NEXT")))
 736         subtree-end)
 737        ((not (bh/is-project-subtree-p))
 738         subtree-end)
 739        (t
 740         nil)))))
 741
 742 (defun bh/skip-projects-and-habits ()
 743   "Skip trees that are projects and tasks that are habits"
 744   (save-restriction
 745     (widen)
 746     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 747       (cond
 748        ((bh/is-project-p)
 749         subtree-end)
 750        ((org-is-habit-p)
 751         subtree-end)
 752        (t
 753         nil)))))
 754
 755 (defun bh/skip-non-subprojects ()
 756   "Skip trees that are not projects"
 757   (let ((next-headline (save-excursion (outline-next-heading))))
 758     (if (bh/is-subproject-p)
 759         nil
 760       next-headline)))
 761 ;
 762 ;; Resume clocking task when emacs is restarted
 763 (org-clock-persistence-insinuate)
 764 ;;
 765 ;; Show lot of clocking history so it's easy to pick items off the C-F11 list
 766 (setq org-clock-history-length 23)
 767 ;; Resume clocking task on clock-in if the clock is open
 768 (setq org-clock-in-resume t)
 769 ;; Change tasks to NEXT when clocking in
 770 (setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
 771 ;; Separate drawers for clocking and logs
 772 (setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
 773 ;; Save clock data and state changes and notes in the LOGBOOK drawer
 774 (setq org-clock-into-drawer t)
 775 (setq org-log-into-drawer t)
 776 ;; Sometimes I change tasks I'm clocking quickly - this removes clocked tasks with 0:00 duration
 777 (setq org-clock-out-remove-zero-time-clocks t)
 778 ;; Clock out when moving task to a done state
 779 (setq org-clock-out-when-done t)
 780 ;; Save the running clock and all clock history when exiting Emacs, load it on startup
 781 (setq org-clock-persist t)
 782 ;; Do not prompt to resume an active clock
 783 (setq org-clock-persist-query-resume nil)
 784 ;; Enable auto clock resolution for finding open clocks
 785 (setq org-clock-auto-clock-resolution (quote when-no-clock-is-running))
 786 ;; Include current clocking task in clock reports
 787 (setq org-clock-report-include-clocking-task t)
 788
 789
 790 (defvar bh/keep-clock-running nil)
 791
 792 (defun bh/clock-in-to-next (kw)
 793   "Switch a task from TODO to NEXT when clocking in.
 794 Skips capture tasks, projects, and subprojects.
 795 Switch projects and subprojects from NEXT back to TODO"
 796   (when (not (and (boundp 'org-capture-mode) org-capture-mode))
 797     (cond
 798      ((and (member (org-get-todo-state) (list "TODO"))
 799            (bh/is-task-p))
 800       "NEXT")
 801      ((and (member (org-get-todo-state) (list "NEXT"))
 802            (bh/is-project-p))
 803       "TODO"))))
 804
 805 (defun bh/find-project-task ()
 806   "Move point to the parent (project) task if any"
 807   (save-restriction
 808     (widen)
 809     (let ((parent-task (save-excursion (org-back-to-heading 'invisible-ok) (point))))
 810       (while (org-up-heading-safe)
 811         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 812           (setq parent-task (point))))
 813       (goto-char parent-task)
 814       parent-task)))
 815
 816 (defun bh/punch-in (arg)
 817   "Start continuous clocking and set the default task to the
 818 selected task.  If no task is selected set the Organization task
 819 as the default task."
 820   (interactive "p")
 821   (setq bh/keep-clock-running t)
 822   (if (equal major-mode 'org-agenda-mode)
 823       ;;
 824       ;; We're in the agenda
 825       ;;
 826       (let* ((marker (org-get-at-bol 'org-hd-marker))
 827              (tags (org-with-point-at marker (org-get-tags-at))))
 828         (if (and (eq arg 4) tags)
 829             (org-agenda-clock-in '(16))
 830           (bh/clock-in-organization-task-as-default)))
 831     ;;
 832     ;; We are not in the agenda
 833     ;;
 834     (save-restriction
 835       (widen)
 836       ; Find the tags on the current task
 837       (if (and (equal major-mode 'org-mode) (not (org-before-first-heading-p)) (eq arg 4))
 838           (org-clock-in '(16))
 839         (bh/clock-in-organization-task-as-default)))))
 840
 841 (defun bh/punch-out ()
 842   (interactive)
 843   (setq bh/keep-clock-running nil)
 844   (when (org-clock-is-active)
 845     (org-clock-out))
 846   (org-agenda-remove-restriction-lock))
 847
 848 (defun bh/clock-in-default-task ()
 849   (save-excursion
 850     (org-with-point-at org-clock-default-task
 851       (org-clock-in))))
 852
 853 (defun bh/clock-in-parent-task ()
 854   "Move point to the parent (project) task if any and clock in"
 855   (let ((parent-task))
 856     (save-excursion
 857       (save-restriction
 858         (widen)
 859         (while (and (not parent-task) (org-up-heading-safe))
 860           (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 861             (setq parent-task (point))))
 862         (if parent-task
 863             (org-with-point-at parent-task
 864               (org-clock-in))
 865           (when bh/keep-clock-running
 866             (bh/clock-in-default-task)))))))
 867
 868 (defvar bh/organization-task-id "e22cb8bf-07c7-408b-8f60-ff3aadac95e4")
 869
 870 (defun bh/clock-in-organization-task-as-default ()
 871   (interactive)
 872   (org-with-point-at (org-id-find bh/organization-task-id 'marker)
 873     (org-clock-in '(16))))
 874
 875 (defun bh/clock-out-maybe ()
 876   (when (and bh/keep-clock-running
 877              (not org-clock-clocking-in)
 878              (marker-buffer org-clock-default-task)
 879              (not org-clock-resolving-clocks-due-to-idleness))
 880     (bh/clock-in-parent-task)))
 881
 882 (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
 883
 884 (require 'org-id)
 885 (defun bh/clock-in-task-by-id (id)
 886   "Clock in a task by id"
 887   (org-with-point-at (org-id-find id 'marker)
 888     (org-clock-in nil)))
 889
 890 (defun bh/clock-in-last-task (arg)
 891   "Clock in the interrupted task if there is one
 892 Skip the default task and get the next one.
 893 A prefix arg forces clock in of the default task."
 894   (interactive "p")
 895   (let ((clock-in-to-task
 896          (cond
 897           ((eq arg 4) org-clock-default-task)
 898           ((and (org-clock-is-active)
 899                 (equal org-clock-default-task (cadr org-clock-history)))
 900            (caddr org-clock-history))
 901           ((org-clock-is-active) (cadr org-clock-history))
 902           ((equal org-clock-default-task (car org-clock-history)) (cadr org-clock-history))
 903           (t (car org-clock-history)))))
 904     (widen)
 905     (org-with-point-at clock-in-to-task
 906       (org-clock-in nil))))
 907