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         ("J" "job" entry (file "~/projects/notes/refile.org")
 129          "* TODO Apply for %a%? :job:\n%U\n" :clock-in t :clock-resume t)
 130         ("h" "Habit" entry (file "~/projects/notes/refile.org")
 131          "* 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")
 132         )
 133       )
 134
 135 ;; Remove empty LOGBOOK drawers on clock out
 136 (defun bh/remove-empty-drawer-on-clock-out ()
 137   (interactive)
 138   (save-excursion
 139     (beginning-of-line 0)
 140     (org-remove-empty-drawer-at "LOGBOOK" (point))))
 141
 142 (defun my/org-add-id ()
 143   (interactive)
 144   (save-excursion
 145     (if (org-current-level)
 146         ()
 147       (forward-char 1)
 148       )
 149     (org-id-get-create)
 150     )
 151 )
 152
 153 ; org mode configuration from http://doc.norang.ca/org-mode.html
 154 ;; Custom Key Bindings
 155 (global-set-key (kbd "<f12>") 'org-agenda)
 156 (global-set-key (kbd "<f5>") 'bh/org-todo)
 157 (global-set-key (kbd "<S-f5>") 'bh/widen)
 158 (global-set-key (kbd "<f7>") 'bh/set-truncate-lines)
 159 (global-set-key (kbd "<f8>") 'org-cycle-agenda-files)
 160 (global-set-key (kbd "<f9> <f9>") 'bh/show-org-agenda)
 161 (global-set-key (kbd "<f9> b") 'bbdb)
 162 (global-set-key (kbd "<f9> c") 'calendar)
 163 (global-set-key (kbd "<f9> f") 'boxquote-insert-file)
 164 (global-set-key (kbd "<f9> h") 'bh/hide-other)
 165 (global-set-key (kbd "<f9> n") 'bh/toggle-next-task-display)
 166 (global-set-key (kbd "<f9> w") 'widen)
 167
 168 (global-set-key (kbd "<f9> I") 'bh/punch-in)
 169 (global-set-key (kbd "<f9> O") 'bh/punch-out)
 170
 171 (global-set-key (kbd "<f9> o") 'bh/make-org-scratch)
 172
 173 (global-set-key (kbd "<f9> r") 'boxquote-region)
 174 (global-set-key (kbd "<f9> s") 'bh/switch-to-scratch)
 175
 176 (global-set-key (kbd "<f9> t") 'bh/insert-inactive-timestamp)
 177 (global-set-key (kbd "<f9> T") 'bh/toggle-insert-inactive-timestamp)
 178
 179 (global-set-key (kbd "<f9> v") 'visible-mode)
 180 (global-set-key (kbd "<f9> l") 'org-toggle-link-display)
 181 (global-set-key (kbd "<f9> SPC") 'bh/clock-in-last-task)
 182 (global-set-key (kbd "C-<f9>") 'previous-buffer)
 183 (global-set-key (kbd "M-<f9>") 'org-toggle-inline-images)
 184 (global-set-key (kbd "C-x n r") 'narrow-to-region)
 185 (global-set-key (kbd "C-<f10>") 'next-buffer)
 186 (global-set-key (kbd "<f11>") 'org-clock-goto)
 187 (global-set-key (kbd "C-<f11>") 'org-clock-in)
 188 (global-set-key (kbd "C-s-<f12>") 'bh/save-then-publish)
 189 (global-set-key (kbd "C-c c") 'org-capture)
 190
 191 (defun bh/hide-other ()
 192   (interactive)
 193   (save-excursion
 194     (org-back-to-heading 'invisible-ok)
 195     (hide-other)
 196     (org-cycle)
 197     (org-cycle)
 198     (org-cycle)))
 199
 200 (defun bh/set-truncate-lines ()
 201   "Toggle value of truncate-lines and refresh window display."
 202   (interactive)
 203   (setq truncate-lines (not truncate-lines))
 204   ;; now refresh window display (an idiom from simple.el):
 205   (save-excursion
 206     (set-window-start (selected-window)
 207                       (window-start (selected-window)))))
 208
 209 (defun bh/make-org-scratch ()
 210   (interactive)
 211   (find-file "/tmp/publish/scratch.org")
 212   (gnus-make-directory "/tmp/publish"))
 213
 214 (defun bh/switch-to-scratch ()
 215   (interactive)
 216   (switch-to-buffer "*scratch*"))
 217
 218 (setq org-use-fast-todo-selection t)
 219 (setq org-treat-S-cursor-todo-selection-as-state-change nil)
 220
 221 (setq org-todo-keywords
 222       (quote ((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d)")
 223               (sequence "WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c@/!)" "PHONE" "MEETING"))))
 224
 225 (setq org-todo-keyword-faces
 226       (quote (("TODO" :foreground "red" :weight bold)
 227               ("NEXT" :foreground "blue" :weight bold)
 228               ("DONE" :foreground "forest green" :weight bold)
 229               ("WAITING" :foreground "orange" :weight bold)
 230               ("HOLD" :foreground "magenta" :weight bold)
 231               ("CANCELLED" :foreground "forest green" :weight bold)
 232               ("MEETING" :foreground "forest green" :weight bold)
 233               ("PHONE" :foreground "forest green" :weight bold))))
 234
 235 (setq org-todo-state-tags-triggers
 236       (quote (("CANCELLED" ("CANCELLED" . t))
 237               ("WAITING" ("WAITING" . t))
 238               ("HOLD" ("WAITING") ("HOLD" . t))
 239               (done ("WAITING") ("HOLD"))
 240               ("TODO" ("WAITING") ("CANCELLED") ("HOLD"))
 241               ("NEXT" ("WAITING") ("CANCELLED") ("HOLD"))
 242               ("DONE" ("WAITING") ("CANCELLED") ("HOLD")))))
 243
 244
 245
 246 (add-hook 'org-clock-out-hook 'bh/remove-empty-drawer-on-clock-out 'append)
 247 ; add ids on creation of nodes
 248 (add-hook 'org-capture-prepare-finalize-hook 'my/org-add-id)
 249 ; create function to create headlines in file. This comes from
 250 ; http://stackoverflow.com/questions/13340616/assign-ids-to-every-entry-in-org-mode
 251 (defun my/org-add-ids-to-headlines-in-file ()
 252   "Add ID properties to all headlines in the current file which
 253 do not already have one."
 254   (interactive)
 255   (org-map-entries 'org-id-get-create))
 256 ; if we wanted to do this to every buffer, do the following:
 257 ; (add-hook 'org-mode-hook
 258 ;           (lambda ()
 259 ;             (add-hook 'before-save-hook 'my/org-add-ids-to-headlines-in-file nil 'local)))
 260
 261
 262 ; resolve clocks after 10 minutes of idle; use xprintidle
 263 ; (setq org-clock-idle-time 10)
 264 ; (setq org-clock-x11idle-program-name "xprintidle")
 265
 266 ; this is from http://doc.norang.ca/org-mode.html#Capture
 267 ; use C-M-r for org mode capture
 268 (global-set-key (kbd "C-M-r") 'org-capture)
 269
 270 ; Targets include this file and any file contributing to the agenda - up to 9 levels deep
 271 (setq org-refile-targets (quote ((nil :maxlevel . 9)
 272                                  (org-agenda-files :maxlevel . 9))))
 273
 274 ; Use full outline paths for refile targets - we file directly with IDO
 275 (setq org-refile-use-outline-path t)
 276
 277 ; Targets complete directly with IDO
 278 (setq org-outline-path-complete-in-steps nil)
 279
 280 ; Allow refile to create parent tasks with confirmation
 281 (setq org-refile-allow-creating-parent-nodes (quote confirm))
 282
 283 ; Use IDO for both buffer and file completion and ido-everywhere to t
 284 (setq org-completion-use-ido t)
 285 (setq ido-everywhere t)
 286 (setq ido-max-directory-size 100000)
 287 (ido-mode (quote both))
 288 ; Use the current window when visiting files and buffers with ido
 289 (setq ido-default-file-method 'selected-window)
 290 (setq ido-default-buffer-method 'selected-window)
 291 ; Use the current window for indirect buffer display
 292 (setq org-indirect-buffer-display 'current-window)
 293
 294
 295 ;;;; Refile settings
 296 ; Exclude DONE state tasks from refile targets
 297 (defun bh/verify-refile-target ()
 298   "Exclude todo keywords with a done state from refile targets"
 299   (not (member (nth 2 (org-heading-components)) org-done-keywords)))
 300
 301 (setq org-refile-target-verify-function 'bh/verify-refile-target)
 302
 303 ;; ensure that emacsclient will show just the note to be edited when invoked
 304 ;; from Mutt, and that it will shut down emacsclient once finished;
 305 ;; fallback to legacy behavior when not invoked via org-protocol.
 306 (require 'org-protocol)
 307 (add-hook 'org-capture-mode-hook 'delete-other-windows)
 308 (setq my-org-protocol-flag nil)
 309 (defadvice org-capture-finalize (after delete-frame-at-end activate)
 310   "Delete frame at remember finalization"
 311   (progn (if my-org-protocol-flag (delete-frame))
 312          (setq my-org-protocol-flag nil)))
 313 (defadvice org-capture-refile (around delete-frame-after-refile activate)
 314   "Delete frame at remember refile"
 315   (if my-org-protocol-flag
 316       (progn
 317         (setq my-org-protocol-flag nil)
 318         ad-do-it
 319         (delete-frame))
 320     ad-do-it)
 321   )
 322 (defadvice org-capture-kill (after delete-frame-at-end activate)
 323   "Delete frame at remember abort"
 324   (progn (if my-org-protocol-flag (delete-frame))
 325          (setq my-org-protocol-flag nil)))
 326 (defadvice org-protocol-capture (before set-org-protocol-flag activate)
 327   (setq my-org-protocol-flag t))
 328
 329 (defadvice org-insert-todo-heading (after dla/create-id activate)
 330   (org-id-get-create)
 331   )
 332
 333 ;; org modules
 334 (add-to-list 'org-modules 'org-habit)
 335
 336 ; this comes from http://upsilon.cc/~zack/blog/posts/2010/02/integrating_Mutt_with_Org-mode/
 337 (defun open-mail-in-mutt (message)
 338   "Open a mail message in Mutt, using an external terminal.
 339
 340 Message can be specified either by a path pointing inside a
 341 Maildir, or by Message-ID."
 342   (interactive "MPath or Message-ID: ")
 343   (shell-command
 344    (format "faf xterm -e \"%s %s\""
 345        (substitute-in-file-name "$HOME/bin/mutt_open") message)))
 346
 347 ;; add support for "mutt:ID" links
 348 (org-add-link-type "mutt" 'open-mail-in-mutt)
 349
 350 (defun my-org-mode-setup ()
 351   (load-library "reftex")
 352   (and (buffer-file-name)
 353        (file-exists-p (buffer-file-name))
 354        (progn
 355          (reftex-parse-all)
 356          (reftex-set-cite-format
 357           '((?b . "[[bib:%l][%l-bib]]")
 358             (?n . "[[notes:%l][%l-notes]]")
 359             (?c . "\\cite{%l}")
 360             (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l paper]]")))
 361          ))
 362   (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
 363   (define-key org-mode-map (kbd "C-c [") 'reftex-citation)
 364   (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search)
 365   (define-key org-mode-map (kbd "C-c 0") 'reftex-view-crossref)
 366   )
 367 (add-hook 'org-mode-hook 'my-org-mode-setup)
 368
 369 (defun org-mode-reftex-search ()
 370   (interactive)
 371   (org-open-link-from-string (format "[[notes:%s]]" (first (reftex-citation t)))))
 372
 373 (defun open-research-paper (bibtexkey)
 374   "Open a paper by bibtex key"
 375   (interactive "bibtex key: ")
 376   (shell-command
 377    (format "%s %s"
 378        (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
 379 (org-add-link-type "papers" 'open-research-paper)
 380
 381 (add-to-list 'org-link-abbrev-alist
 382              '("notes" .
 383                "~/projects/research/paper_notes.org::#%s"))
 384
 385 ; I pretty much always want hiearchical checkboxes
 386 (setq org-hierachical-checkbox-statistics nil)
 387
 388 ;; stolen from
 389 ;; http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
 390 (defun my-rtcite-export-handler (path desc format)
 391   (message "my-rtcite-export-handler is called : path = %s, desc = %s, format = %s" path desc format)
 392   (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
 393                    (match-string 1 path)))
 394          (path (substring path 0 (match-beginning 0))))
 395     (cond ((eq format 'latex)
 396            (if (or (not desc)
 397                    (equal 0 (search "rtcite:" desc)))
 398                (format "\\cite{%s}" search)
 399              (format "\\cite[%s]{%s}" desc search))))))
 400
 401 (org-add-link-type "rtcite"
 402                    'org-bibtex-open
 403                    'my-rtcite-export-handler)
 404
 405
 406 (setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
 407 (setq-default org-directory "/home/don/org-mode/")
 408 (setq-default org-mobile-inbox-for-pull "/home/don/org-mode/from-mobile.org")
 409
 410 ;; org mode ical export
 411 (setq org-icalendar-timezone "America/Los_Angeles")
 412 (setq org-icalendar-use-scheduled '(todo-start event-if-todo))
 413 (setq org-icalendar-store-UID t)
 414
 415 ;; org babel support
 416 (org-babel-do-load-languages
 417  'org-babel-load-languages
 418  '((emacs-lisp . t )
 419    (R . t)
 420    (latex . t)))
 421 ;; org-babel-by-backend
 422 (defmacro org-babel-by-backend (&rest body)
 423    `(case (if (boundp 'backend)
 424               (org-export-backend-name backend)
 425             nil) ,@body))
 426
 427
 428
 429 ;; org latex
 430 ;; stolen from http://kieranhealy.org/esk/kjhealy.html
 431 (require 'org-latex)
 432 ;; Choose either listings or minted for exporting source code blocks.
 433 ;; Using minted (as here) requires pygments be installed. To use the
 434 ;; default listings package instead, use
 435 ;; (setq org-latex-listings t)
 436 ;; and change references to "minted" below to "listings"
 437 ; (setq org-latex-listings 'minted)
 438
 439 ;; default settings for minted code blocks
 440 (setq org-latex-minted-options
 441       '(;("frame" "single")
 442         ("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.
 443         ("fontsize" "\\small")
 444         ))
 445 ;; turn off the default toc behavior; deal with it properly in headers to files.
 446 (defun org-latex-no-toc (depth)
 447   (when depth
 448     (format "%% Org-mode is exporting headings to %s levels.\n"
 449             depth)))
 450 (setq org-latex-format-toc-function 'org-latex-no-toc)
 451
 452 (require 'ox-latex)
 453 (add-to-list 'org-latex-classes
 454              '("memarticle"
 455                "\\documentclass[11pt,oneside,article]{memoir}\n"
 456                ("\\section{%s}" . "\\section*{%s}")
 457                ("\\subsection{%s}" . "\\subsection*{%s}")
 458                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 459                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 460                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 461
 462 (add-to-list 'org-latex-classes
 463              '("membook"
 464                "\\documentclass[11pt,oneside]{memoir}\n"
 465                ("\\chapter{%s}" . "\\chapter*{%s}")
 466                ("\\section{%s}" . "\\section*{%s}")
 467                ("\\subsection{%s}" . "\\subsection*{%s}")
 468                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
 469
 470 (add-to-list 'org-latex-classes
 471              '("letter"
 472                "\\documentclass[11pt]{letter}
 473 [NO-DEFAULT-PACKAGES]
 474 [PACKAGES]
 475 [EXTRA]"
 476        ("\\section{%s}" . "\\section*{%s}")
 477                ("\\subsection{%s}" . "\\subsection*{%s}")
 478                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
 479                ("\\paragraph{%s}" . "\\paragraph*{%s}")
 480                ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
 481
 482 ;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432
 483 ;; but adapted to use latexmk 4.22 or higher.
 484 (setq org-latex-pdf-process '("latexmk -pdflatex=xelatex -bibtex -use-make -pdf %f"))
 485
 486 ;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
 487 (setq org-latex-default-packages-alist
 488       '())
 489 (setq org-latex-packages-alist
 490       '(("" "graphicx" t)
 491         ("" "fontspec" t)
 492         ("" "xunicode" t)
 493         ("" "hyperref" t)
 494         ("" "url" t)
 495         ("" "rotating" t)
 496         ("" "longtable" nil)
 497         ("" "float" )))
 498
 499 (defun org-create-formula--latex-header ()
 500   "Return LaTeX header appropriate for previewing a LaTeX snippet."
 501   (let ((info (org-combine-plists (org-export--get-global-options
 502                                    (org-export-get-backend 'latex))
 503                                   (org-export--get-inbuffer-options
 504                                    (org-export-get-backend 'latex)))))
 505     (org-latex-guess-babel-language
 506      (org-latex-guess-inputenc
 507       (org-splice-latex-header
 508        org-format-latex-header
 509        org-latex-default-packages-alist
 510        nil t
 511        (plist-get info :latex-header)))
 512      info)))
 513
 514
 515 ; support ignoring headers in org mode export to latex
 516 ; from http://article.gmane.org/gmane.emacs.orgmode/67692
 517 (defadvice org-latex-headline (around my-latex-skip-headlines
 518                                       (headline contents info) activate)
 519   (if (member "ignoreheading" (org-element-property :tags headline))
 520       (setq ad-return-value contents)
 521     ad-do-it))
 522
 523
 524 ;; helper functions
 525 (defun bh/is-project-p ()
 526   "Any task with a todo keyword subtask"
 527   (save-restriction
 528     (widen)
 529     (let ((has-subtask)
 530           (subtree-end (save-excursion (org-end-of-subtree t)))
 531           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 532       (save-excursion
 533         (forward-line 1)
 534         (while (and (not has-subtask)
 535                     (< (point) subtree-end)
 536                     (re-search-forward "^\*+ " subtree-end t))
 537           (when (member (org-get-todo-state) org-todo-keywords-1)
 538             (setq has-subtask t))))
 539       (and is-a-task has-subtask))))
 540
 541 (defun bh/is-project-subtree-p ()
 542   "Any task with a todo keyword that is in a project subtree.
 543 Callers of this function already widen the buffer view."
 544   (let ((task (save-excursion (org-back-to-heading 'invisible-ok)
 545                               (point))))
 546     (save-excursion
 547       (bh/find-project-task)
 548       (if (equal (point) task)
 549           nil
 550         t))))
 551
 552 (defun bh/is-task-p ()
 553   "Any task with a todo keyword and no subtask"
 554   (save-restriction
 555     (widen)
 556     (let ((has-subtask)
 557           (subtree-end (save-excursion (org-end-of-subtree t)))
 558           (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 559       (save-excursion
 560         (forward-line 1)
 561         (while (and (not has-subtask)
 562                     (< (point) subtree-end)
 563                     (re-search-forward "^\*+ " subtree-end t))
 564           (when (member (org-get-todo-state) org-todo-keywords-1)
 565             (setq has-subtask t))))
 566       (and is-a-task (not has-subtask)))))
 567
 568 (defun bh/is-subproject-p ()
 569   "Any task which is a subtask of another project"
 570   (let ((is-subproject)
 571         (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
 572     (save-excursion
 573       (while (and (not is-subproject) (org-up-heading-safe))
 574         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 575           (setq is-subproject t))))
 576     (and is-a-task is-subproject)))
 577
 578 (defun bh/list-sublevels-for-projects-indented ()
 579   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 580   This is normally used by skipping functions where this variable is already local to the agenda."
 581   (if (marker-buffer org-agenda-restrict-begin)
 582       (setq org-tags-match-list-sublevels 'indented)
 583     (setq org-tags-match-list-sublevels nil))
 584   nil)
 585
 586 (defun bh/list-sublevels-for-projects ()
 587   "Set org-tags-match-list-sublevels so when restricted to a subtree we list all subtasks.
 588   This is normally used by skipping functions where this variable is already local to the agenda."
 589   (if (marker-buffer org-agenda-restrict-begin)
 590       (setq org-tags-match-list-sublevels t)
 591     (setq org-tags-match-list-sublevels nil))
 592   nil)
 593
 594 (defvar bh/hide-scheduled-and-waiting-next-tasks t)
 595
 596 (defun bh/toggle-next-task-display ()
 597   (interactive)
 598   (setq bh/hide-scheduled-and-waiting-next-tasks (not bh/hide-scheduled-and-waiting-next-tasks))
 599   (when  (equal major-mode 'org-agenda-mode)
 600     (org-agenda-redo))
 601   (message "%s WAITING and SCHEDULED NEXT Tasks" (if bh/hide-scheduled-and-waiting-next-tasks "Hide" "Show")))
 602
 603 (defun bh/skip-stuck-projects ()
 604   "Skip trees that are not stuck projects"
 605   (save-restriction
 606     (widen)
 607     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 608       (if (bh/is-project-p)
 609           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 610                  (has-next ))
 611             (save-excursion
 612               (forward-line 1)
 613               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 614                 (unless (member "WAITING" (org-get-tags-at))
 615                   (setq has-next t))))
 616             (if has-next
 617                 nil
 618               next-headline)) ; a stuck project, has subtasks but no next task
 619         nil))))
 620
 621 (defun bh/skip-non-stuck-projects ()
 622   "Skip trees that are not stuck projects"
 623   ;; (bh/list-sublevels-for-projects-indented)
 624   (save-restriction
 625     (widen)
 626     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 627       (if (bh/is-project-p)
 628           (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 629                  (has-next ))
 630             (save-excursion
 631               (forward-line 1)
 632               (while (and (not has-next) (< (point) subtree-end) (re-search-forward "^\\*+ NEXT " subtree-end t))
 633                 (unless (member "WAITING" (org-get-tags-at))
 634                   (setq has-next t))))
 635             (if has-next
 636                 next-headline
 637               nil)) ; a stuck project, has subtasks but no next task
 638         next-headline))))
 639
 640 (defun bh/skip-non-projects ()
 641   "Skip trees that are not projects"
 642   ;; (bh/list-sublevels-for-projects-indented)
 643   (if (save-excursion (bh/skip-non-stuck-projects))
 644       (save-restriction
 645         (widen)
 646         (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 647           (cond
 648            ((bh/is-project-p)
 649             nil)
 650            ((and (bh/is-project-subtree-p) (not (bh/is-task-p)))
 651             nil)
 652            (t
 653             subtree-end))))
 654     (save-excursion (org-end-of-subtree t))))
 655
 656 (defun bh/skip-project-trees-and-habits ()
 657   "Skip trees that are projects"
 658   (save-restriction
 659     (widen)
 660     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 661       (cond
 662        ((bh/is-project-p)
 663         subtree-end)
 664        ((org-is-habit-p)
 665         subtree-end)
 666        (t
 667         nil)))))
 668
 669 (defun bh/skip-projects-and-habits-and-single-tasks ()
 670   "Skip trees that are projects, tasks that are habits, single non-project tasks"
 671   (save-restriction
 672     (widen)
 673     (let ((next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 674       (cond
 675        ((org-is-habit-p)
 676         next-headline)
 677        ((and bh/hide-scheduled-and-waiting-next-tasks
 678              (member "WAITING" (org-get-tags-at)))
 679         next-headline)
 680        ((bh/is-project-p)
 681         next-headline)
 682        ((and (bh/is-task-p) (not (bh/is-project-subtree-p)))
 683         next-headline)
 684        (t
 685         nil)))))
 686
 687 (defun bh/skip-project-tasks-maybe ()
 688   "Show tasks related to the current restriction.
 689 When restricted to a project, skip project and sub project tasks, habits, NEXT tasks, and loose tasks.
 690 When not restricted, skip project and sub-project tasks, habits, and project related tasks."
 691   (save-restriction
 692     (widen)
 693     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 694            (next-headline (save-excursion (or (outline-next-heading) (point-max))))
 695            (limit-to-project (marker-buffer org-agenda-restrict-begin)))
 696       (cond
 697        ((bh/is-project-p)
 698         next-headline)
 699        ((org-is-habit-p)
 700         subtree-end)
 701        ((and (not limit-to-project)
 702              (bh/is-project-subtree-p))
 703         subtree-end)
 704        ((and limit-to-project
 705              (bh/is-project-subtree-p)
 706              (member (org-get-todo-state) (list "NEXT")))
 707         subtree-end)
 708        (t
 709         nil)))))
 710
 711 (defun bh/skip-project-tasks ()
 712   "Show non-project tasks.
 713 Skip project and sub-project tasks, habits, and project related tasks."
 714   (save-restriction
 715     (widen)
 716     (let* ((subtree-end (save-excursion (org-end-of-subtree t))))
 717       (cond
 718        ((bh/is-project-p)
 719         subtree-end)
 720        ((org-is-habit-p)
 721         subtree-end)
 722        ((bh/is-project-subtree-p)
 723         subtree-end)
 724        (t
 725         nil)))))
 726
 727 (defun bh/skip-non-project-tasks ()
 728   "Show project tasks.
 729 Skip project and sub-project tasks, habits, and loose non-project tasks."
 730   (save-restriction
 731     (widen)
 732     (let* ((subtree-end (save-excursion (org-end-of-subtree t)))
 733            (next-headline (save-excursion (or (outline-next-heading) (point-max)))))
 734       (cond
 735        ((bh/is-project-p)
 736         next-headline)
 737        ((org-is-habit-p)
 738         subtree-end)
 739        ((and (bh/is-project-subtree-p)
 740              (member (org-get-todo-state) (list "NEXT")))
 741         subtree-end)
 742        ((not (bh/is-project-subtree-p))
 743         subtree-end)
 744        (t
 745         nil)))))
 746
 747 (defun bh/skip-projects-and-habits ()
 748   "Skip trees that are projects and tasks that are habits"
 749   (save-restriction
 750     (widen)
 751     (let ((subtree-end (save-excursion (org-end-of-subtree t))))
 752       (cond
 753        ((bh/is-project-p)
 754         subtree-end)
 755        ((org-is-habit-p)
 756         subtree-end)
 757        (t
 758         nil)))))
 759
 760 (defun bh/skip-non-subprojects ()
 761   "Skip trees that are not projects"
 762   (let ((next-headline (save-excursion (outline-next-heading))))
 763     (if (bh/is-subproject-p)
 764         nil
 765       next-headline)))
 766 ;
 767 ;; Resume clocking task when emacs is restarted
 768 (org-clock-persistence-insinuate)
 769 ;;
 770 ;; Show lot of clocking history so it's easy to pick items off the C-F11 list
 771 (setq org-clock-history-length 23)
 772 ;; Resume clocking task on clock-in if the clock is open
 773 (setq org-clock-in-resume t)
 774 ;; Change tasks to NEXT when clocking in
 775 (setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
 776 ;; Separate drawers for clocking and logs
 777 (setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
 778 ;; Save clock data and state changes and notes in the LOGBOOK drawer
 779 (setq org-clock-into-drawer t)
 780 (setq org-log-into-drawer t)
 781 ;; Sometimes I change tasks I'm clocking quickly - this removes clocked tasks with 0:00 duration
 782 (setq org-clock-out-remove-zero-time-clocks t)
 783 ;; Clock out when moving task to a done state
 784 (setq org-clock-out-when-done t)
 785 ;; Save the running clock and all clock history when exiting Emacs, load it on startup
 786 (setq org-clock-persist t)
 787 ;; Do not prompt to resume an active clock
 788 (setq org-clock-persist-query-resume nil)
 789 ;; Enable auto clock resolution for finding open clocks
 790 (setq org-clock-auto-clock-resolution (quote when-no-clock-is-running))
 791 ;; Include current clocking task in clock reports
 792 (setq org-clock-report-include-clocking-task t)
 793
 794
 795 (defvar bh/keep-clock-running nil)
 796
 797 (defun bh/clock-in-to-next (kw)
 798   "Switch a task from TODO to NEXT when clocking in.
 799 Skips capture tasks, projects, and subprojects.
 800 Switch projects and subprojects from NEXT back to TODO"
 801   (when (not (and (boundp 'org-capture-mode) org-capture-mode))
 802     (cond
 803      ((and (member (org-get-todo-state) (list "TODO"))
 804            (bh/is-task-p))
 805       "NEXT")
 806      ((and (member (org-get-todo-state) (list "NEXT"))
 807            (bh/is-project-p))
 808       "TODO"))))
 809
 810 (defun bh/find-project-task ()
 811   "Move point to the parent (project) task if any"
 812   (save-restriction
 813     (widen)
 814     (let ((parent-task (save-excursion (org-back-to-heading 'invisible-ok) (point))))
 815       (while (org-up-heading-safe)
 816         (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 817           (setq parent-task (point))))
 818       (goto-char parent-task)
 819       parent-task)))
 820
 821 (defun bh/punch-in (arg)
 822   "Start continuous clocking and set the default task to the
 823 selected task.  If no task is selected set the Organization task
 824 as the default task."
 825   (interactive "p")
 826   (setq bh/keep-clock-running t)
 827   (if (equal major-mode 'org-agenda-mode)
 828       ;;
 829       ;; We're in the agenda
 830       ;;
 831       (let* ((marker (org-get-at-bol 'org-hd-marker))
 832              (tags (org-with-point-at marker (org-get-tags-at))))
 833         (if (and (eq arg 4) tags)
 834             (org-agenda-clock-in '(16))
 835           (bh/clock-in-organization-task-as-default)))
 836     ;;
 837     ;; We are not in the agenda
 838     ;;
 839     (save-restriction
 840       (widen)
 841       ; Find the tags on the current task
 842       (if (and (equal major-mode 'org-mode) (not (org-before-first-heading-p)) (eq arg 4))
 843           (org-clock-in '(16))
 844         (bh/clock-in-organization-task-as-default)))))
 845
 846 (defun bh/punch-out ()
 847   (interactive)
 848   (setq bh/keep-clock-running nil)
 849   (when (org-clock-is-active)
 850     (org-clock-out))
 851   (org-agenda-remove-restriction-lock))
 852
 853 (defun bh/clock-in-default-task ()
 854   (save-excursion
 855     (org-with-point-at org-clock-default-task
 856       (org-clock-in))))
 857
 858 (defun bh/clock-in-parent-task ()
 859   "Move point to the parent (project) task if any and clock in"
 860   (let ((parent-task))
 861     (save-excursion
 862       (save-restriction
 863         (widen)
 864         (while (and (not parent-task) (org-up-heading-safe))
 865           (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
 866             (setq parent-task (point))))
 867         (if parent-task
 868             (org-with-point-at parent-task
 869               (org-clock-in))
 870           (when bh/keep-clock-running
 871             (bh/clock-in-default-task)))))))
 872
 873 (defvar bh/organization-task-id "e22cb8bf-07c7-408b-8f60-ff3aadac95e4")
 874
 875 (defun bh/clock-in-organization-task-as-default ()
 876   (interactive)
 877   (org-with-point-at (org-id-find bh/organization-task-id 'marker)
 878     (org-clock-in '(16))))
 879
 880 (defun bh/clock-out-maybe ()
 881   (when (and bh/keep-clock-running
 882              (not org-clock-clocking-in)
 883              (marker-buffer org-clock-default-task)
 884              (not org-clock-resolving-clocks-due-to-idleness))
 885     (bh/clock-in-parent-task)))
 886
 887 (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
 888
 889 (require 'org-id)
 890 (defun bh/clock-in-task-by-id (id)
 891   "Clock in a task by id"
 892   (org-with-point-at (org-id-find id 'marker)
 893     (org-clock-in nil)))
 894
 895 (defun bh/clock-in-last-task (arg)
 896   "Clock in the interrupted task if there is one
 897 Skip the default task and get the next one.
 898 A prefix arg forces clock in of the default task."
 899   (interactive "p")
 900   (let ((clock-in-to-task
 901          (cond
 902           ((eq arg 4) org-clock-default-task)
 903           ((and (org-clock-is-active)
 904                 (equal org-clock-default-task (cadr org-clock-history)))
 905            (caddr org-clock-history))
 906           ((org-clock-is-active) (cadr org-clock-history))
 907           ((equal org-clock-default-task (car org-clock-history)) (cadr org-clock-history))
 908           (t (car org-clock-history)))))
 909     (widen)
 910     (org-with-point-at clock-in-to-task
 911       (org-clock-in nil))))
 912