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