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) %6Effort{:} %CLOCKSUM %PRIORITY %TODO %13SCHEDULED %13DEADLINE %TAGS")
 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 (defadvice org-insert-todo-heading (after dla/create-id activate)
 328   (org-id-get-create)
 329   )
 330
 331 ;; org modules
 332 (add-to-list 'org-modules 'org-habit)
 333
 334 ; this comes from http://upsilon.cc/~zack/blog/posts/2010/02/integrating_Mutt_with_Org-mode/
 335 (defun open-mail-in-mutt (message)
 336   "Open a mail message in Mutt, using an external terminal.
 337
 338 Message can be specified either by a path pointing inside a
 339 Maildir, or by Message-ID."
 340   (interactive "MPath or Message-ID: ")
 341   (shell-command
 342    (format "faf xterm -e \"%s %s\""
 343        (substitute-in-file-name "$HOME/bin/mutt_open") message)))
 344
 345 ;; add support for "mutt:ID" links
 346 (org-add-link-type "mutt" 'open-mail-in-mutt)
 347
 348 (defun my-org-mode-setup ()
 349   (load-library "reftex")
 350   (and (buffer-file-name)
 351        (file-exists-p (buffer-file-name))
 352        (progn
 353          (reftex-parse-all)
 354          (reftex-set-cite-format
 355           '((?b . "[[bib:%l][%l-bib]]")
 356             (?n . "[[notes:%l][%l-notes]]")
 357             (?c . "\\cite{%l}")
 358             (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l paper]]")))
 359          ))
 360   (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
 361   (define-key org-mode-map (kbd "C-c [") 'reftex-citation)
 362   (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search)
 363   (define-key org-mode-map (kbd "C-c 0") 'reftex-view-crossref)
 364   )
 365 (add-hook 'org-mode-hook 'my-org-mode-setup)
 366
 367 (defun org-mode-reftex-search ()
 368   (interactive)
 369   (org-open-link-from-string (format "[[notes:%s]]" (first (reftex-citation t)))))
 370
 371 (defun open-research-paper (bibtexkey)
 372   "Open a paper by bibtex key"
 373   (interactive "bibtex key: ")
 374   (shell-command
 375    (format "%s %s"
 376        (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
 377 (org-add-link-type "papers" 'open-research-paper)
 378
 379 (add-to-list 'org-link-abbrev-alist
 380              '("notes" .
 381                "~/projects/research/paper_notes.org::#%s"))
 382
 383 ; I pretty much always want hiearchical checkboxes
 384 (setq org-hierachical-checkbox-statistics nil)
 385
 386 ;; stolen from
 387 ;; http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
 388 (defun my-rtcite-export-handler (path desc format)
 389   (message "my-rtcite-export-handler is called : path = %s, desc = %s, format = %s" path desc format)
 390   (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
 391                    (match-string 1 path)))
 392          (path (substring path 0 (match-beginning 0))))
 393     (cond ((eq format 'latex)
 394            (if (or (not desc)
 395                    (equal 0 (search "rtcite:" desc)))
 396                (format "\\cite{%s}" search)
 397              (format "\\cite[%s]{%s}" desc search))))))
 398
 399 (org-add-link-type "rtcite"
 400                    'org-bibtex-open
 401                    'my-rtcite-export-handler)
 402
 403
 404 (setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
 405 (setq-default org-directory "/home/don/org-mode/")
 406 (setq-default org-mobile-inbox-for-pull "/home/don/org-mode/from-mobile.org")
 407
 408 ;; org mode ical export
 409 (setq org-icalendar-timezone "America/Los_Angeles")
 410 (setq org-icalendar-use-scheduled '(todo-start event-if-todo))
 411 ;; we already add the id manually
 412 ;; (setq org-icalendar-store-UID t)
 413
 414 ;; org babel support
 415 (org-babel-do-load-languages
 416  'org-babel-load-languages
 417  '((emacs-lisp . t )
 418    (R . t)
 419    (latex . t)))
 420 ;; org-babel-by-backend
 421 (defmacro org-babel-by-backend (&rest body)
 422    `(case (if (boundp 'backend)
 423               (org-export-backend-name backend)
 424             nil) ,@body))
 425
 426
 427
 428 ;; org latex
 429 ;; stolen from http://kieranhealy.org/esk/kjhealy.html
 430 (require 'org-latex)
 431 ;; Choose either listings or minted for exporting source code blocks.
 432 ;; Using minted (as here) requires pygments be installed. To use the
 433 ;; default listings package instead, use
 434 ;; (setq org-latex-listings t)
 435 ;; and change references to "minted" below to "listings"
 436 ; (setq org-latex-listings 'minted)
 437
 438 ;; default settings for minted code blocks
 439 (setq org-latex-minted-options
 440       '(;("frame" "single")
 441         ("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.
 442         ("fontsize" "\\small")
 443         ))
 444 ;; turn off the default toc behavior; deal with it properly in headers to files.
 445 (defun org-latex-no-toc (depth)
 446   (when depth
 447     (format "%% Org-mode is exporting headings to %s levels.\n"
 448             depth)))
 449 (setq org-latex-format-toc-function 'org-latex-no-toc)
 450
 451 (require 'ox-latex)
 452 (add-to-list 'org-latex-classes
 453              '("memarticle"
 454                "\\documentclass[11pt,oneside,article]{memoir}\n"
 455                ("\\section{%s}" . "\\section*{%s}")
 456                ("\\subsection{%s}" . "\\subsection*{%s}")
 457                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 458                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 459                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 460
 461 (add-to-list 'org-latex-classes
 462              '("membook"
 463                "\\documentclass[11pt,oneside]{memoir}\n"
 464                ("\\chapter{%s}" . "\\chapter*{%s}")
 465                ("\\section{%s}" . "\\section*{%s}")
 466                ("\\subsection{%s}" . "\\subsection*{%s}")
 467                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
 468
 469 (add-to-list 'org-latex-classes
 470              '("letter"
 471                "\\documentclass[11pt]{letter}
 472 [NO-DEFAULT-PACKAGES]
 473 [PACKAGES]
 474 [EXTRA]"
 475        ("\\section{%s}" . "\\section*{%s}")
 476                ("\\subsection{%s}" . "\\subsection*{%s}")
 477                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 478                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 479                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 480
 481 ;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432
 482 ;; but adapted to use latexmk 4.22 or higher.
 483 (setq org-latex-pdf-process '("latexmk -pdflatex=xelatex -bibtex -use-make -pdf %f"))
 484
 485 ;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
 486 (setq org-latex-default-packages-alist
 487       '())
 488 (setq org-latex-packages-alist
 489       '(("" "graphicx" t)
 490         ("" "fontspec" t)
 491         ("" "xunicode" t)
 492         ("" "hyperref" t)
 493         ("" "url" t)
 494         ("" "rotating" t)
 495         ("" "longtable" nil)
 496         ("" "float" )))
 497
 498 (defun org-create-formula--latex-header ()
 499   "Return LaTeX header appropriate for previewing a LaTeX snippet."
 500   (let ((info (org-combine-plists (org-export--get-global-options
 501                                    (org-export-get-backend 'latex))
 502                                   (org-export--get-inbuffer-options
 503                                    (org-export-get-backend 'latex)))))
 504     (org-latex-guess-babel-language
 505      (org-latex-guess-inputenc
 506       (org-splice-latex-header
 507        org-format-latex-header
 508        org-latex-default-packages-alist
 509        nil t
 510        (plist-get info :latex-header)))
 511      info)))
 512
 513
 514 ; support ignoring headers in org mode export to latex
 515 ; from http://article.gmane.org/gmane.emacs.orgmode/67692
 516 (defadvice org-latex-headline (around my-latex-skip-headlines
 517                                       (headline contents info) activate)
 518   (if (member "ignoreheading" (org-element-property :tags headline))
 519       (setq ad-return-value contents)
 520     ad-do-it))
 521
 522
 523 ;; helper functions
 524 (defun bh/is-project-p ()
 525   "Any task with a todo keyword subtask"
 526   (save-restriction
 527     (widen)
 528     (let ((has-subtask)
 529           (subtree-end (save-excursion (org-end-of-subtree t)))
 530           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 531       (save-excursion
 532         (forward-line 1)
 533         (while (and (not has-subtask)
 534                     (< (point) subtree-end)
 535                     (re-search-forward "^\*+ " subtree-end t))
 536           (when (member (org-get-todo-state) org-todo-keywords-1)
 537             (setq has-subtask t))))
 538       (and is-a-task has-subtask))))
 539
 540 (defun bh/is-project-subtree-p ()
 541   "Any task with a todo keyword that is in a project subtree.
 542 Callers of this function already widen the buffer view."
 543   (let ((task (save-excursion (org-back-to-heading 'invisible-ok)
 544                               (point))))
 545     (save-excursion
 546       (bh/find-project-task)
 547       (if (equal (point) task)
 548           nil
 549         t))))
 550
 551 (defun bh/is-task-p ()
 552   "Any task with a todo keyword and no subtask"
 553   (save-restriction
 554     (widen)
 555     (let ((has-subtask)
 556           (subtree-end (save-excursion (org-end-of-subtree t)))
 557           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 558       (save-excursion
 559         (forward-line 1)
 560         (while (and (not has-subtask)
 561                     (< (point) subtree-end)
 562                     (re-search-forward "^\*+ " subtree-end t))
 563           (when (member (org-get-todo-state) org-todo-keywords-1)
 564             (setq has-subtask t))))
 565       (and is-a-task (not has-subtask)))))
 566
 567 (defun bh/is-subproject-p ()
 568   "Any task which is a subtask of another project"
 569   (let ((is-subproject)
 570         (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 571     (save-excursion
 572       (while (and (not is-subproject) (org-up-heading-safe))
 573         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 574           (setq is-subproject t))))
 575     (and is-a-task is-subproject)))
 576
 577 (defun bh/list-sublevels-for-projects-indented ()
 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 'indented)
 582     (setq org-tags-match-list-sublevels nil))
 583   nil)
 584
 585 (defun bh/list-sublevels-for-projects ()
 586   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 587   This is normally used by skipping functions where this variable is already local to the agenda."
 588   (if (marker-buffer org-agenda-restrict-begin)
 589       (setq org-tags-match-list-sublevels t)
 590     (setq org-tags-match-list-sublevels nil))
 591   nil)
 592
 593 (defvar bh/hide-scheduled-and-waiting-next-tasks t)
 594
 595 (defun bh/toggle-next-task-display ()
 596   (interactive)
 597   (setq bh/hide-scheduled-and-waiting-next-tasks (not bh/hide-scheduled-and-waiting-next-tasks))
 598   (when  (equal major-mode 'org-agenda-mode)
 599     (org-agenda-redo))
 600   (message "%s WAITING and SCHEDULED NEXT Tasks" (if bh/hide-scheduled-and-waiting-next-tasks "Hide" "Show")))
 601
 602 (defun bh/skip-stuck-projects ()
 603   "Skip trees that are not stuck projects"
 604   (save-restriction
 605     (widen)
 606     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 607       (if (bh/is-project-p)
 608           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 609                  (has-next ))
 610             (save-excursion
 611               (forward-line 1)
 612               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 613                 (unless (member "WAITING" (org-get-tags-at))
 614                   (setq has-next t))))
 615             (if has-next
 616                 nil
 617               next-headline)) ; a stuck project, has subtasks but no next task
 618         nil))))
 619
 620 (defun bh/skip-non-stuck-projects ()
 621   "Skip trees that are not stuck projects"
 622   ;; (bh/list-sublevels-for-projects-indented)
 623   (save-restriction
 624     (widen)
 625     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 626       (if (bh/is-project-p)
 627           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 628                  (has-next ))
 629             (save-excursion
 630               (forward-line 1)
 631               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 632                 (unless (member "WAITING" (org-get-tags-at))
 633                   (setq has-next t))))
 634             (if has-next
 635                 next-headline
 636               nil)) ; a stuck project, has subtasks but no next task
 637         next-headline))))
 638
 639 (defun bh/skip-non-projects ()
 640   "Skip trees that are not projects"
 641   ;; (bh/list-sublevels-for-projects-indented)
 642   (if (save-excursion (bh/skip-non-stuck-projects))
 643       (save-restriction
 644         (widen)
 645         (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 646           (cond
 647            ((bh/is-project-p)
 648             nil)
 649            ((and (bh/is-project-subtree-p) (not (bh/is-task-p)))
 650             nil)
 651            (t
 652             subtree-end))))
 653     (save-excursion (org-end-of-subtree t))))
 654
 655 (defun bh/skip-project-trees-and-habits ()
 656   "Skip trees that are projects"
 657   (save-restriction
 658     (widen)
 659     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 660       (cond
 661        ((bh/is-project-p)
 662         subtree-end)
 663        ((org-is-habit-p)
 664         subtree-end)
 665        (t
 666         nil)))))
 667
 668 (defun bh/skip-projects-and-habits-and-single-tasks ()
 669   "Skip trees that are projects, tasks that are habits, single non-project tasks"
 670   (save-restriction
 671     (widen)
 672     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 673       (cond
 674        ((org-is-habit-p)
 675         next-headline)
 676        ((and bh/hide-scheduled-and-waiting-next-tasks
 677              (member "WAITING" (org-get-tags-at)))
 678         next-headline)
 679        ((bh/is-project-p)
 680         next-headline)
 681        ((and (bh/is-task-p) (not (bh/is-project-subtree-p)))
 682         next-headline)
 683        (t
 684         nil)))))
 685
 686 (defun bh/skip-project-tasks-maybe ()
 687   "Show tasks related to the current restriction.
 688 When restricted to a project, skip project and sub project tasks, habits, NEXT tasks, and loose tasks.
 689 When not restricted, skip project and sub-project tasks, habits, and project related tasks."
 690   (save-restriction
 691     (widen)
 692     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 693            (next-headline (save-excursion (or (outline-next-heading) (point-max))))
 694            (limit-to-project (marker-buffer org-agenda-restrict-begin)))
 695       (cond
 696        ((bh/is-project-p)
 697         next-headline)
 698        ((org-is-habit-p)
 699         subtree-end)
 700        ((and (not limit-to-project)
 701              (bh/is-project-subtree-p))
 702         subtree-end)
 703        ((and limit-to-project
 704              (bh/is-project-subtree-p)
 705              (member (org-get-todo-state) (list "NEXT")))
 706         subtree-end)
 707        (t
 708         nil)))))
 709
 710 (defun bh/skip-project-tasks ()
 711   "Show non-project tasks.
 712 Skip project and sub-project tasks, habits, and project related tasks."
 713   (save-restriction
 714     (widen)
 715     (let* ((subtree-end (save-excursion (org-end-of-subtree t))))
 716       (cond
 717        ((bh/is-project-p)
 718         subtree-end)
 719        ((org-is-habit-p)
 720         subtree-end)
 721        ((bh/is-project-subtree-p)
 722         subtree-end)
 723        (t
 724         nil)))))
 725
 726 (defun bh/skip-non-project-tasks ()
 727   "Show project tasks.
 728 Skip project and sub-project tasks, habits, and loose non-project tasks."
 729   (save-restriction
 730     (widen)
 731     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 732            (next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 733       (cond
 734        ((bh/is-project-p)
 735         next-headline)
 736        ((org-is-habit-p)
 737         subtree-end)
 738        ((and (bh/is-project-subtree-p)
 739              (member (org-get-todo-state) (list "NEXT")))
 740         subtree-end)
 741        ((not (bh/is-project-subtree-p))
 742         subtree-end)
 743        (t
 744         nil)))))
 745
 746 (defun bh/skip-projects-and-habits ()
 747   "Skip trees that are projects and tasks that are habits"
 748   (save-restriction
 749     (widen)
 750     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 751       (cond
 752        ((bh/is-project-p)
 753         subtree-end)
 754        ((org-is-habit-p)
 755         subtree-end)
 756        (t
 757         nil)))))
 758
 759 (defun bh/skip-non-subprojects ()
 760   "Skip trees that are not projects"
 761   (let ((next-headline (save-excursion (outline-next-heading))))
 762     (if (bh/is-subproject-p)
 763         nil
 764       next-headline)))
 765 ;
 766 ;; Resume clocking task when emacs is restarted
 767 (org-clock-persistence-insinuate)
 768 ;;
 769 ;; Show lot of clocking history so it's easy to pick items off the C-F11 list
 770 (setq org-clock-history-length 23)
 771 ;; Resume clocking task on clock-in if the clock is open
 772 (setq org-clock-in-resume t)
 773 ;; Change tasks to NEXT when clocking in
 774 (setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
 775 ;; Separate drawers for clocking and logs
 776 (setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
 777 ;; Save clock data and state changes and notes in the LOGBOOK drawer
 778 (setq org-clock-into-drawer t)
 779 (setq org-log-into-drawer t)
 780 ;; Sometimes I change tasks I'm clocking quickly - this removes clocked tasks with 0:00 duration
 781 (setq org-clock-out-remove-zero-time-clocks t)
 782 ;; Clock out when moving task to a done state
 783 (setq org-clock-out-when-done t)
 784 ;; Save the running clock and all clock history when exiting Emacs, load it on startup
 785 (setq org-clock-persist t)
 786 ;; Do not prompt to resume an active clock
 787 (setq org-clock-persist-query-resume nil)
 788 ;; Enable auto clock resolution for finding open clocks
 789 (setq org-clock-auto-clock-resolution (quote when-no-clock-is-running))
 790 ;; Include current clocking task in clock reports
 791 (setq org-clock-report-include-clocking-task t)
 792
 793
 794 (defvar bh/keep-clock-running nil)
 795
 796 (defun bh/clock-in-to-next (kw)
 797   "Switch a task from TODO to NEXT when clocking in.
 798 Skips capture tasks, projects, and subprojects.
 799 Switch projects and subprojects from NEXT back to TODO"
 800   (when (not (and (boundp 'org-capture-mode) org-capture-mode))
 801     (cond
 802      ((and (member (org-get-todo-state) (list "TODO"))
 803            (bh/is-task-p))
 804       "NEXT")
 805      ((and (member (org-get-todo-state) (list "NEXT"))
 806            (bh/is-project-p))
 807       "TODO"))))
 808
 809 (defun bh/find-project-task ()
 810   "Move point to the parent (project) task if any"
 811   (save-restriction
 812     (widen)
 813     (let ((parent-task (save-excursion (org-back-to-heading 'invisible-ok) (point))))
 814       (while (org-up-heading-safe)
 815         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 816           (setq parent-task (point))))
 817       (goto-char parent-task)
 818       parent-task)))
 819
 820 (defun bh/punch-in (arg)
 821   "Start continuous clocking and set the default task to the
 822 selected task.  If no task is selected set the Organization task
 823 as the default task."
 824   (interactive "p")
 825   (setq bh/keep-clock-running t)
 826   (if (equal major-mode 'org-agenda-mode)
 827       ;;
 828       ;; We're in the agenda
 829       ;;
 830       (let* ((marker (org-get-at-bol 'org-hd-marker))
 831              (tags (org-with-point-at marker (org-get-tags-at))))
 832         (if (and (eq arg 4) tags)
 833             (org-agenda-clock-in '(16))
 834           (bh/clock-in-organization-task-as-default)))
 835     ;;
 836     ;; We are not in the agenda
 837     ;;
 838     (save-restriction
 839       (widen)
 840       ; Find the tags on the current task
 841       (if (and (equal major-mode 'org-mode) (not (org-before-first-heading-p)) (eq arg 4))
 842           (org-clock-in '(16))
 843         (bh/clock-in-organization-task-as-default)))))
 844
 845 (defun bh/punch-out ()
 846   (interactive)
 847   (setq bh/keep-clock-running nil)
 848   (when (org-clock-is-active)
 849     (org-clock-out))
 850   (org-agenda-remove-restriction-lock))
 851
 852 (defun bh/clock-in-default-task ()
 853   (save-excursion
 854     (org-with-point-at org-clock-default-task
 855       (org-clock-in))))
 856
 857 (defun bh/clock-in-parent-task ()
 858   "Move point to the parent (project) task if any and clock in"
 859   (let ((parent-task))
 860     (save-excursion
 861       (save-restriction
 862         (widen)
 863         (while (and (not parent-task) (org-up-heading-safe))
 864           (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 865             (setq parent-task (point))))
 866         (if parent-task
 867             (org-with-point-at parent-task
 868               (org-clock-in))
 869           (when bh/keep-clock-running
 870             (bh/clock-in-default-task)))))))
 871
 872 (defvar bh/organization-task-id "e22cb8bf-07c7-408b-8f60-ff3aadac95e4")
 873
 874 (defun bh/clock-in-organization-task-as-default ()
 875   (interactive)
 876   (org-with-point-at (org-id-find bh/organization-task-id 'marker)
 877     (org-clock-in '(16))))
 878
 879 (defun bh/clock-out-maybe ()
 880   (when (and bh/keep-clock-running
 881              (not org-clock-clocking-in)
 882              (marker-buffer org-clock-default-task)
 883              (not org-clock-resolving-clocks-due-to-idleness))
 884     (bh/clock-in-parent-task)))
 885
 886 (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
 887
 888 (require 'org-id)
 889 (defun bh/clock-in-task-by-id (id)
 890   "Clock in a task by id"
 891   (org-with-point-at (org-id-find id 'marker)
 892     (org-clock-in nil)))
 893
 894 (defun bh/clock-in-last-task (arg)
 895   "Clock in the interrupted task if there is one
 896 Skip the default task and get the next one.
 897 A prefix arg forces clock in of the default task."
 898   (interactive "p")
 899   (let ((clock-in-to-task
 900          (cond
 901           ((eq arg 4) org-clock-default-task)
 902           ((and (org-clock-is-active)
 903                 (equal org-clock-default-task (cadr org-clock-history)))
 904            (caddr org-clock-history))
 905           ((org-clock-is-active) (cadr org-clock-history))
 906           ((equal org-clock-default-task (car org-clock-history)) (cadr org-clock-history))
 907           (t (car org-clock-history)))))
 908     (widen)
 909     (org-with-point-at clock-in-to-task
 910       (org-clock-in nil))))
 911