--- /dev/null
+;; The following lines are always needed. Choose your own keys.
+(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
+(add-hook 'org-mode-hook 'turn-on-font-lock) ; not needed when global-font-lock-mode is on
+(global-set-key "\C-cl" 'org-store-link)
+(global-set-key "\C-ca" 'org-agenda)
+(global-set-key "\C-cb" 'org-iswitchb)
+(setq-default org-log-done 'time)
+(setq-default org-agenda-ndays 5)
+
+;; agenda configuration
+;; Do not dim blocked tasks
+(setq org-agenda-dim-blocked-tasks nil)
+
+;; Compact the block agenda view
+(setq org-agenda-compact-blocks t)
+
+;; Custom agenda command definitions
+(setq org-agenda-custom-commands
+ (quote (("N" "Notes" tags "NOTE"
+ ((org-agenda-overriding-header "Notes")
+ (org-tags-match-list-sublevels t)))
+ ("h" "Habits" tags-todo "STYLE=\"habit\""
+ ((org-agenda-overriding-header "Habits")
+ (org-agenda-sorting-strategy
+ '(todo-state-down effort-up category-keep))))
+ (" " "Agenda"
+ ((agenda "" nil)
+ (tags "REFILE"
+ ((org-agenda-overriding-header "Tasks to Refile")
+ (org-tags-match-list-sublevels nil)))
+ (tags-todo "-CANCELLED/!"
+ ((org-agenda-overriding-header "Stuck Projects")
+ (org-agenda-skip-function 'bh/skip-non-stuck-projects)
+ (org-agenda-sorting-strategy
+ '(category-keep))))
+ (tags-todo "-HOLD-CANCELLED/!"
+ ((org-agenda-overriding-header "Projects")
+ (org-agenda-skip-function 'bh/skip-non-projects)
+ (org-tags-match-list-sublevels 'indented)
+ (org-agenda-sorting-strategy
+ '(category-keep))))
+ (tags-todo "-CANCELLED/!NEXT"
+ ((org-agenda-overriding-header (concat "Project Next Tasks"
+ (if bh/hide-scheduled-and-waiting-next-tasks
+ ""
+ " (including WAITING and SCHEDULED tasks)")))
+ (org-agenda-skip-function 'bh/skip-projects-and-habits-and-single-tasks)
+ (org-tags-match-list-sublevels t)
+ (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-sorting-strategy
+ '(todo-state-down effort-up category-keep))))
+ (tags-todo "-REFILE-CANCELLED-WAITING-HOLD/!"
+ ((org-agenda-overriding-header (concat "Project Subtasks"
+ (if bh/hide-scheduled-and-waiting-next-tasks
+ ""
+ " (including WAITING and SCHEDULED tasks)")))
+ (org-agenda-skip-function 'bh/skip-non-project-tasks)
+ (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-sorting-strategy
+ '(category-keep))))
+ (tags-todo "-REFILE-CANCELLED-WAITING-HOLD/!"
+ ((org-agenda-overriding-header (concat "Standalone Tasks"
+ (if bh/hide-scheduled-and-waiting-next-tasks
+ ""
+ " (including WAITING and SCHEDULED tasks)")))
+ (org-agenda-skip-function 'bh/skip-project-tasks)
+ (org-agenda-todo-ignore-scheduled bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-deadlines bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-todo-ignore-with-date bh/hide-scheduled-and-waiting-next-tasks)
+ (org-agenda-sorting-strategy
+ '(category-keep))))
+ (tags-todo "-CANCELLED+WAITING|HOLD/!"
+ ((org-agenda-overriding-header "Waiting and Postponed Tasks")
+ (org-agenda-skip-function 'bh/skip-stuck-projects)
+ (org-tags-match-list-sublevels nil)
+ (org-agenda-todo-ignore-scheduled t)
+ (org-agenda-todo-ignore-deadlines t)))
+ (tags "-REFILE/"
+ ((org-agenda-overriding-header "Tasks to Archive")
+ (org-agenda-skip-function 'bh/skip-non-archivable-tasks)
+ (org-tags-match-list-sublevels nil))))
+ nil))))
+
+; org mode agenda files
+(setq org-agenda-files
+ (quote ("~/projects/debbugs/debbugs.org"
+ "~/projects/notes/notes.org"
+ "~/projects/origins_of_life/ool.org"
+ "~/projects/sysadmin/sndservers/sndservers.org"
+ "~/projects/chaim/chaim.org"
+ "~/projects/chaim/papers/gwas_paper_2012/gwas_paper.org"
+ "~/projects/reviews/reviews.org"
+ "~/projects/fh/fh.org")))
+
+(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")))
+(setq org-columns-default-format "%40ITEM(Task) %TAGS %PRIORITY %TODO %13SCHEDULED %13DEADLINE %6Effort{:} %CLOCKSUM")
+
+(setq org-default-notes-file "~/projects/notes/notes.org")
+(setq org-capture-templates ;; mail-specific note template, identified by "m"
+ '(("m" "Mail" entry (file+headline "~/projects/notes/refile.org" "Mail")
+ "* %?\n\n Source: %u, %c\n %i")
+ ("t" "todo" entry (file "~/projects/notes/refile.org")
+ "* TODO %?\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("r" "respond" entry (file "~/projects/notes/refile.org")
+ "* NEXT Respond to %:from on %:subject\nSCHEDULED: %t\n%U\n%a\n" :clock-in t :clock-resume t :immediate-finish t)
+ ("n" "note" entry (file "~/projects/notes/refile.org")
+ "* %? :NOTE:\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("s" "schedule" entry (file "~/projects/notes/refile.org")
+ "* %? \n%^{scheduled:}t\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("j" "Journal" entry (file+datetree "~/projects/notes/diary.org")
+ "* %?\n%U\n" :clock-in t :clock-resume t)
+ ("w" "org-protocol" entry (file "~/projects/notes/refile.org")
+ "* TODO Review %c\n%U\n" :immediate-finish t)
+ ("m" "Meeting" entry (file "~/projects/notes/refile.org")
+ "* MEETING with %? :MEETING:\n%U" :clock-in t :clock-resume t)
+ ("p" "Phone call" entry (file "~/projects/notes/refile.org")
+ "* PHONE %? :PHONE:\n%U" :clock-in t :clock-resume t)
+ ("h" "Habit" entry (file "~/projects/notes/refile.org")
+ "* 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")
+ )
+ )
+
+;; Remove empty LOGBOOK drawers on clock out
+(defun bh/remove-empty-drawer-on-clock-out ()
+ (interactive)
+ (save-excursion
+ (beginning-of-line 0)
+ (org-remove-empty-drawer-at "LOGBOOK" (point))))
+
+(defun my/org-add-id ()
+ (interactive)
+ (save-excursion
+ (if (org-current-level)
+ ()
+ (forward-char 1)
+ )
+ (org-id-get-create)
+ )
+)
+
+; org mode configuration from http://doc.norang.ca/org-mode.html
+;; Custom Key Bindings
+(global-set-key (kbd "<f12>") 'org-agenda)
+(global-set-key (kbd "<f5>") 'bh/org-todo)
+(global-set-key (kbd "<S-f5>") 'bh/widen)
+(global-set-key (kbd "<f7>") 'bh/set-truncate-lines)
+(global-set-key (kbd "<f8>") 'org-cycle-agenda-files)
+(global-set-key (kbd "<f9> <f9>") 'bh/show-org-agenda)
+(global-set-key (kbd "<f9> b") 'bbdb)
+(global-set-key (kbd "<f9> c") 'calendar)
+(global-set-key (kbd "<f9> f") 'boxquote-insert-file)
+(global-set-key (kbd "<f9> h") 'bh/hide-other)
+(global-set-key (kbd "<f9> n") 'bh/toggle-next-task-display)
+(global-set-key (kbd "<f9> w") 'widen)
+
+(global-set-key (kbd "<f9> I") 'bh/punch-in)
+(global-set-key (kbd "<f9> O") 'bh/punch-out)
+
+(global-set-key (kbd "<f9> o") 'bh/make-org-scratch)
+
+(global-set-key (kbd "<f9> r") 'boxquote-region)
+(global-set-key (kbd "<f9> s") 'bh/switch-to-scratch)
+
+(global-set-key (kbd "<f9> t") 'bh/insert-inactive-timestamp)
+(global-set-key (kbd "<f9> T") 'bh/toggle-insert-inactive-timestamp)
+
+(global-set-key (kbd "<f9> v") 'visible-mode)
+(global-set-key (kbd "<f9> l") 'org-toggle-link-display)
+(global-set-key (kbd "<f9> SPC") 'bh/clock-in-last-task)
+(global-set-key (kbd "C-<f9>") 'previous-buffer)
+(global-set-key (kbd "M-<f9>") 'org-toggle-inline-images)
+(global-set-key (kbd "C-x n r") 'narrow-to-region)
+(global-set-key (kbd "C-<f10>") 'next-buffer)
+(global-set-key (kbd "<f11>") 'org-clock-goto)
+(global-set-key (kbd "C-<f11>") 'org-clock-in)
+(global-set-key (kbd "C-s-<f12>") 'bh/save-then-publish)
+(global-set-key (kbd "C-c c") 'org-capture)
+
+(defun bh/hide-other ()
+ (interactive)
+ (save-excursion
+ (org-back-to-heading 'invisible-ok)
+ (hide-other)
+ (org-cycle)
+ (org-cycle)
+ (org-cycle)))
+
+(defun bh/set-truncate-lines ()
+ "Toggle value of truncate-lines and refresh window display."
+ (interactive)
+ (setq truncate-lines (not truncate-lines))
+ ;; now refresh window display (an idiom from simple.el):
+ (save-excursion
+ (set-window-start (selected-window)
+ (window-start (selected-window)))))
+
+(defun bh/make-org-scratch ()
+ (interactive)
+ (find-file "/tmp/publish/scratch.org")
+ (gnus-make-directory "/tmp/publish"))
+
+(defun bh/switch-to-scratch ()
+ (interactive)
+ (switch-to-buffer "*scratch*"))
+
+(setq org-use-fast-todo-selection t)
+(setq org-treat-S-cursor-todo-selection-as-state-change nil)
+
+(setq org-todo-keywords
+ (quote ((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d)")
+ (sequence "WAITING(w@/!)" "HOLD(h@/!)" "|" "CANCELLED(c@/!)" "PHONE" "MEETING"))))
+
+(setq org-todo-keyword-faces
+ (quote (("TODO" :foreground "red" :weight bold)
+ ("NEXT" :foreground "blue" :weight bold)
+ ("DONE" :foreground "forest green" :weight bold)
+ ("WAITING" :foreground "orange" :weight bold)
+ ("HOLD" :foreground "magenta" :weight bold)
+ ("CANCELLED" :foreground "forest green" :weight bold)
+ ("MEETING" :foreground "forest green" :weight bold)
+ ("PHONE" :foreground "forest green" :weight bold))))
+
+(setq org-todo-state-tags-triggers
+ (quote (("CANCELLED" ("CANCELLED" . t))
+ ("WAITING" ("WAITING" . t))
+ ("HOLD" ("WAITING") ("HOLD" . t))
+ (done ("WAITING") ("HOLD"))
+ ("TODO" ("WAITING") ("CANCELLED") ("HOLD"))
+ ("NEXT" ("WAITING") ("CANCELLED") ("HOLD"))
+ ("DONE" ("WAITING") ("CANCELLED") ("HOLD")))))
+
+
+
+(add-hook 'org-clock-out-hook 'bh/remove-empty-drawer-on-clock-out 'append)
+; add ids on creation of nodes
+(add-hook 'org-capture-prepare-finalize-hook 'my/org-add-id)
+; create function to create headlines in file. This comes from
+; http://stackoverflow.com/questions/13340616/assign-ids-to-every-entry-in-org-mode
+(defun my/org-add-ids-to-headlines-in-file ()
+ "Add ID properties to all headlines in the current file which
+do not already have one."
+ (interactive)
+ (org-map-entries 'org-id-get-create))
+; if we wanted to do this to every buffer, do the following:
+; (add-hook 'org-mode-hook
+; (lambda ()
+; (add-hook 'before-save-hook 'my/org-add-ids-to-headlines-in-file nil 'local)))
+
+
+; resolve clocks after 10 minutes of idle; use xprintidle
+(setq org-clock-idle-time 10)
+(setq org-clock-x11idle-program-name "xprintidle")
+
+; this is from http://doc.norang.ca/org-mode.html#Capture
+; use C-M-r for org mode capture
+(global-set-key (kbd "C-M-r") 'org-capture)
+
+; Targets include this file and any file contributing to the agenda - up to 9 levels deep
+(setq org-refile-targets (quote ((nil :maxlevel . 9)
+ (org-agenda-files :maxlevel . 9))))
+
+; Use full outline paths for refile targets - we file directly with IDO
+(setq org-refile-use-outline-path t)
+
+; Targets complete directly with IDO
+(setq org-outline-path-complete-in-steps nil)
+
+; Allow refile to create parent tasks with confirmation
+(setq org-refile-allow-creating-parent-nodes (quote confirm))
+
+; Use IDO for both buffer and file completion and ido-everywhere to t
+(setq org-completion-use-ido t)
+(setq ido-everywhere t)
+(setq ido-max-directory-size 100000)
+(ido-mode (quote both))
+; Use the current window when visiting files and buffers with ido
+(setq ido-default-file-method 'selected-window)
+(setq ido-default-buffer-method 'selected-window)
+; Use the current window for indirect buffer display
+(setq org-indirect-buffer-display 'current-window)
+
+
+;;;; Refile settings
+; Exclude DONE state tasks from refile targets
+(defun bh/verify-refile-target ()
+ "Exclude todo keywords with a done state from refile targets"
+ (not (member (nth 2 (org-heading-components)) org-done-keywords)))
+
+(setq org-refile-target-verify-function 'bh/verify-refile-target)
+
+;; ensure that emacsclient will show just the note to be edited when invoked
+;; from Mutt, and that it will shut down emacsclient once finished;
+;; fallback to legacy behavior when not invoked via org-protocol.
+(require 'org-protocol)
+(add-hook 'org-capture-mode-hook 'delete-other-windows)
+(setq my-org-protocol-flag nil)
+(defadvice org-capture-finalize (after delete-frame-at-end activate)
+ "Delete frame at remember finalization"
+ (progn (if my-org-protocol-flag (delete-frame))
+ (setq my-org-protocol-flag nil)))
+(defadvice org-capture-refile (around delete-frame-after-refile activate)
+ "Delete frame at remember refile"
+ (if my-org-protocol-flag
+ (progn
+ (setq my-org-protocol-flag nil)
+ ad-do-it
+ (delete-frame))
+ ad-do-it)
+ )
+(defadvice org-capture-kill (after delete-frame-at-end activate)
+ "Delete frame at remember abort"
+ (progn (if my-org-protocol-flag (delete-frame))
+ (setq my-org-protocol-flag nil)))
+(defadvice org-protocol-capture (before set-org-protocol-flag activate)
+ (setq my-org-protocol-flag t))
+
+
+;; org modules
+(add-to-list 'org-modules 'org-habit)
+
+; this comes from http://upsilon.cc/~zack/blog/posts/2010/02/integrating_Mutt_with_Org-mode/
+(defun open-mail-in-mutt (message)
+ "Open a mail message in Mutt, using an external terminal.
+
+Message can be specified either by a path pointing inside a
+Maildir, or by Message-ID."
+ (interactive "MPath or Message-ID: ")
+ (shell-command
+ (format "faf xterm -e \"%s %s\""
+ (substitute-in-file-name "$HOME/bin/mutt_open") message)))
+
+;; add support for "mutt:ID" links
+(org-add-link-type "mutt" 'open-mail-in-mutt)
+
+(defun my-org-mode-setup ()
+ (load-library "reftex")
+ (and (buffer-file-name)
+ (file-exists-p (buffer-file-name))
+ (progn
+ (reftex-parse-all)
+ (reftex-set-cite-format
+ '((?b . "[[bib::%l][%l-bib]]")
+ (?n . "[[note::%l][%l-notes]]")
+ (?c . "\\cite{%l}")
+ (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l paper]]")))
+ ))
+ (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
+ (define-key org-mode-map (kbd "C-c [") 'reftex-citation)
+ (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search)
+ (define-key org-mode-map (kbd "C-c 0") 'reftex-view-crossref)
+ )
+(add-hook 'org-mode-hook 'my-org-mode-setup)
+
+(defun org-mode-reftex-search ()
+ (interactive)
+ (org-open-link-from-string (format "[[notes:%s]]" (reftex-citation t))))
+
+(defun open-research-paper (bibtexkey)
+ "Open a paper by bibtex key"
+ (interactive "bibtex key: ")
+ (shell-command
+ (format "%s %s"
+ (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
+(org-add-link-type "papers" 'open-research-paper)
+
+; I pretty much always want hiearchical checkboxes
+(setq org-hierachical-checkbox-statistics nil)
+
+;; stolen from
+;; http://www-public.it-sudparis.eu/~berger_o/weblog/2012/03/23/how-to-manage-and-export-bibliographic-notesrefs-in-org-mode/
+(defun my-rtcite-export-handler (path desc format)
+ (message "my-rtcite-export-handler is called : path = %s, desc = %s, format = %s" path desc format)
+ (let* ((search (when (string-match "::#?\\(.+\\)\\'" path)
+ (match-string 1 path)))
+ (path (substring path 0 (match-beginning 0))))
+ (cond ((eq format 'latex)
+ (if (or (not desc)
+ (equal 0 (search "rtcite:" desc)))
+ (format "\\cite{%s}" search)
+ (format "\\cite[%s]{%s}" desc search))))))
+
+(org-add-link-type "rtcite"
+ 'org-bibtex-open
+ 'my-rtcite-export-handler)
+
+
+(setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
+(setq-default org-directory "/home/don/org-mode/")
+(setq-default org-mobile-inbox-for-pull "/home/don/org-mode/from-mobile.org")
+
+;; org mode ical export
+(setq org-icalendar-timezone "America/Los_Angeles")
+(setq org-icalendar-use-scheduled '(todo-start event-if-todo))
+(setq org-icalendar-store-UID t)
+
+;; org babel support
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . t )
+ (R . t)
+ (latex . t)))
+;; org-babel-by-backend
+(defmacro org-babel-by-backend (&rest body)
+ `(case (if (boundp 'backend)
+ (org-export-backend-name backend)
+ nil) ,@body))
+
+
+
+;; org latex
+;; stolen from http://kieranhealy.org/esk/kjhealy.html
+(require 'org-latex)
+;; Choose either listings or minted for exporting source code blocks.
+;; Using minted (as here) requires pygments be installed. To use the
+;; default listings package instead, use
+;; (setq org-latex-listings t)
+;; and change references to "minted" below to "listings"
+; (setq org-latex-listings 'minted)
+
+;; default settings for minted code blocks
+(setq org-latex-minted-options
+ '(;("frame" "single")
+ ("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.
+ ("fontsize" "\\small")
+ ))
+;; turn off the default toc behavior; deal with it properly in headers to files.
+(defun org-latex-no-toc (depth)
+ (when depth
+ (format "%% Org-mode is exporting headings to %s levels.\n"
+ depth)))
+(setq org-latex-format-toc-function 'org-latex-no-toc)
+
+(require 'ox-latex)
+(add-to-list 'org-latex-classes
+ '("memarticle"
+ "\\documentclass[11pt,oneside,article]{memoir}\n"
+ ("\\section{%s}" . "\\section*{%s}")
+ ("\\subsection{%s}" . "\\subsection*{%s}")
+ ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+ ("\\paragraph{%s}" . "\\paragraph*{%s}")
+ ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+(add-to-list 'org-latex-classes
+ '("membook"
+ "\\documentclass[11pt,oneside]{memoir}\n"
+ ("\\chapter{%s}" . "\\chapter*{%s}")
+ ("\\section{%s}" . "\\section*{%s}")
+ ("\\subsection{%s}" . "\\subsection*{%s}")
+ ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
+
+(add-to-list 'org-latex-classes
+ '("letter"
+ "\\documentclass[11pt]{letter}
+[NO-DEFAULT-PACKAGES]
+[PACKAGES]
+[EXTRA]"
+ ("\\section{%s}" . "\\section*{%s}")
+ ("\\subsection{%s}" . "\\subsection*{%s}")
+ ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+ ("\\paragraph{%s}" . "\\paragraph*{%s}")
+ ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+
+;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432
+;; but adapted to use latexmk 4.22 or higher.
+(setq org-latex-pdf-process '("latexmk -pdflatex=xelatex -bibtex -use-make -pdf %f"))
+
+;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
+(setq org-latex-default-packages-alist
+ '())
+(setq org-latex-packages-alist
+ '(("" "graphicx" t)
+ ("" "fontspec" t)
+ ("" "xunicode" t)
+ ("" "hyperref" t)
+ ("" "url" t)
+ ("" "rotating" t)
+ ("" "longtable" nil)
+ ("" "float" )))
+
+(defun org-create-formula--latex-header ()
+ "Return LaTeX header appropriate for previewing a LaTeX snippet."
+ (let ((info (org-combine-plists (org-export--get-global-options
+ (org-export-get-backend 'latex))
+ (org-export--get-inbuffer-options
+ (org-export-get-backend 'latex)))))
+ (org-latex-guess-babel-language
+ (org-latex-guess-inputenc
+ (org-splice-latex-header
+ org-format-latex-header
+ org-latex-default-packages-alist
+ nil t
+ (plist-get info :latex-header)))
+ info)))
+
+
+; support ignoring headers in org mode export to latex
+; from http://article.gmane.org/gmane.emacs.orgmode/67692
+(defadvice org-latex-headline (around my-latex-skip-headlines
+ (headline contents info) activate)
+ (if (member "ignoreheading" (org-element-property :tags headline))
+ (setq ad-return-value contents)
+ ad-do-it))
projects / lib.git / commitdiff