(require 'reftex)
(require 'gnus)
+(require 'org)
+(require 'org-agenda)
+(require 'org-habit)
;; The following lines are always needed. Choose your own keys.
(add-to-list 'auto-mode-alist '("\\.\\(org\\|org_archive\\|txt\\)$" . org-mode))
-(require 'org)
+(eval-when-compile
+ (require 'cl))
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)
; org mode agenda files
(setq org-agenda-files
- (quote ("~/projects/debbugs/debbugs.org"
- "~/projects/notes/notes.org"
- "~/projects/notes/refile.org"
- "~/projects/notes/diary.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")))
+ (quote ("~/projects/org-notes/debbugs.org"
+ "~/projects/org-notes/notes.org"
+ "~/projects/org-notes/refile.org"
+ "~/projects/org-notes/diary.org"
+ "~/projects/org-notes/ool.org"
+ "~/projects/org-notes/sndservers.org"
+ "~/projects/org-notes/chaim.org"
+ "~/projects/org-notes/wildman.org"
+ "~/projects/org-notes/uddin.org"
+ "~/projects/org-notes/reviews.org"
+ "~/projects/org-notes/hpcbio.org"
+ "~/org-mode/from-mobile.org"
+ "~/projects/org-notes/fh.org")))
+
+(set-register ?n (cons 'file "~/projects/org-notes/notes.org"))
+(set-register ?r (cons 'file "~/projects/org-notes/refile.org"))
+(set-register ?o (cons 'file "~/projects/org-notes/ool.org"))
+(set-register ?s (cons 'file "~/projects/org-notes/sndservers.org"))
+(set-register ?c (cons 'file "~/projects/org-notes/chaim.org"))
+(set-register ?w (cons 'file "~/projects/org-notes/wildman.org"))
+(set-register ?u (cons 'file "~/projects/org-notes/uddin.org"))
+(set-register ?R (cons 'file "~/projects/reviews/reviews.org"))
+(set-register ?d (cons 'file "~/projects/org-notes/diary.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-columns-default-format "%40ITEM(Task) %6Effort{:} %CLOCKSUM %PRIORITY %TODO %13SCHEDULED %13DEADLINE %TAGS")
-(setq org-default-notes-file "~/projects/notes/notes.org")
+;; add automatic reminders for appointments
+(defadvice org-agenda-redo (after org-agenda-redo-add-appts)
+ "Pressing `r' on the agenda will also add appointments."
+ (progn
+ (setq appt-time-msg-list nil)
+ (org-agenda-to-appt)))
+
+(setq org-default-notes-file "~/projects/org-notes/notes.org")
+(setq org-id-link-to-org-use-id t)
(setq org-capture-templates ;; mail-specific note template, identified by "m"
- '(("m" "Mail" entry (file+headline "~/projects/notes/refile.org" "Mail")
+ '(("m" "Mail" entry (file+headline "~/projects/org-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")
+ ("t" "todo" entry (file "~/projects/org-notes/refile.org")
+ "* TODO %?\n :PROPERTIES:\n :END:\n :LOGBOOK:\n :END:\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("r" "respond" entry (file "~/projects/org-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")
+ ("n" "note" entry (file "~/projects/org-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")
+ ("s" "schedule" entry (file "~/projects/org-notes/refile.org")
+ "* %? :cal:\n%^{scheduled:}t\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("j" "Journal" entry (file+datetree "~/projects/org-notes/diary.org")
"* %?\n%U\n" :clock-in t :clock-resume t)
- ("w" "org-protocol" entry (file "~/projects/notes/refile.org")
+ ("w" "org-protocol" entry (file "~/projects/org-notes/refile.org")
"* TODO Review %c\n%U\n" :immediate-finish t)
- ("m" "Meeting" entry (file "~/projects/notes/refile.org")
+ ("M" "Meeting" entry (file "~/projects/org-notes/refile.org")
"* MEETING with %? :MEETING:\n%U" :clock-in t :clock-resume t)
- ("p" "Phone call" entry (file "~/projects/notes/refile.org")
+ ("S" "Seminar" entry (file "~/projects/org-notes/refile.org")
+ "* SEMINAR notes %? :SEMINAR:\n%U" :clock-in t :clock-resume t)
+ ("P" "Paper to read" entry (file+headline "~/projects/research/papers_to_read.org" "Refile")
+ "* TODO Get/Read %? \n%U" :clock-in t :clock-resume t)
+ ("p" "Phone call" entry (file "~/projects/org-notes/refile.org")
"* PHONE %? :PHONE:\n%U" :clock-in t :clock-resume t)
- ("J" "job" entry (file "~/projects/notes/refile.org")
- "* TODO Apply for %a%? :job:\n%U\n" :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")
+ ("J" "job" entry (file "~/projects/org-notes/refile.org")
+ "* TODO Apply for %a%? :job:\nSCHEDULED: %(format-time-string \"<%Y-%m-%d 17:00-17:30>\")\n%U\n%a\n" :clock-in t :clock-resume t)
+ ("h" "Habit" entry (file "~/projects/org-notes/refile.org")
+ "* NEXT %?\n%U\n%a\nSCHEDULED: %(format-time-string \"<%Y-%m-%d .+1d/3d>\")\n:PROPERTIES:\n:STYLE: habit\n:REPEAT_TO_STATE: NEXT\n:END:\n%a\n")
)
)
(interactive)
(save-excursion
(beginning-of-line 0)
- (org-remove-empty-drawer-at "LOGBOOK" (point))))
+ (org-remove-empty-drawer-at (point))))
(defun my/org-add-id ()
(interactive)
(global-set-key (kbd "<f9> n") 'bh/toggle-next-task-display)
(global-set-key (kbd "<f9> w") 'widen)
+; change the outline mode prefix from C-c @ to C-c C-2
+(setq outline-minor-mode-prefix "C-c C-2")
+;(add-hook 'outline-minor-mode-hook
+; (lambda () (local-set-key (kbd "C-c C-2")
+; outline-mode-prefix-map)))
+
(global-set-key (kbd "<f9> I") 'bh/punch-in)
(global-set-key (kbd "<f9> O") 'bh/punch-out)
-(add-hook 'org-clock-out-hook 'bh/remove-empty-drawer-on-clock-out 'append)
+; (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
; 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)
+; ; 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
;; 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)
+; (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"
'((?b . "[[bib:%l][%l-bib]]")
(?n . "[[notes:%l][%l-notes]]")
(?c . "\\cite{%l}")
- (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l paper]]")))
+ (?h . "*** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l xoj]] [[papers-pdf:%l][pdf]]")))
))
(define-key org-mode-map (kbd "C-c )") 'reftex-citation)
(define-key org-mode-map (kbd "C-c [") 'reftex-citation)
(format "%s %s"
(substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
(org-add-link-type "papers" 'open-research-paper)
+(defun open-research-paper-pdf (bibtexkey)
+ "Open a paper pdf by bibtex key"
+ (interactive "bibtex key: ")
+ (shell-command
+ (format "%s -p evince_annot %s"
+ (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
+(org-add-link-type "papers-pdf" 'open-research-paper-pdf)
(add-to-list 'org-link-abbrev-alist
'("notes" .
; I pretty much always want hiearchical checkboxes
(setq org-hierachical-checkbox-statistics nil)
-
-;; stolen from
+
+;; Add \begin{equation}\end{equation} templates to the org mode easy templates
+(add-to-list 'org-structure-template-alist
+ '("E" "\\begin{equation}\n?\n\\end{equation}"))
+
+ ;; 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)
'my-rtcite-export-handler)
-(setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/")
+(setq-default org-mobile-directory "/linnode.donarmstrong.com:/sites/dav.donarmstrong.com/root/org/")
+(when (string= system-name "linnode.donarmstrong.com")
+ (setq-default org-mobile-directory "/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)
+;; we already add the id manually
+;; (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)))
+ (latex . t)
+ (ditaa . t)
+ (dot . t)
+ ))
+;; use graphviz-dot for dot things
+(add-to-list 'org-src-lang-modes '("dot" . graphviz-dot))
;; 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)
+(defun my/fix-inline-images ()
+ (when org-inline-image-overlays
+ (org-redisplay-inline-images)))
+
+(add-hook 'org-babel-after-execute-hook
+ 'my/fix-inline-images)
+
+;; ;; 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
("\\paragraph{%s}" . "\\paragraph*{%s}")
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
+(setq org-beamer-outline-frame-options "")
+(require 'ox-beamer)
+(add-to-list 'org-latex-classes
+ '("beamer"
+ "\\documentclass[ignorenonframetext]{beamer}
+[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}")))
+
(add-to-list 'org-latex-classes
'("membook"
"\\documentclass[11pt,oneside]{memoir}\n"
;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
(setq org-latex-default-packages-alist
- '())
+ '(("" "amsmath" t)))
(setq org-latex-packages-alist
'(("" "graphicx" t)
("" "fontspec" t)
("" "longtable" nil)
("" "float" )))
+;; make equations larger
+(setq org-format-latex-options (plist-put org-format-latex-options :scale 2.0))
+
(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
(setq ad-return-value contents)
ad-do-it))
+;; keep latex logfiles
+
+(setq org-latex-remove-logfiles nil)
;; helper functions
(defun bh/is-project-p ()
(setq org-clock-in-resume t)
;; Change tasks to NEXT when clocking in
(setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
+;; (setq org-clock-in-switch-to-state "NEXT")
;; Separate drawers for clocking and logs
(setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
;; Save clock data and state changes and notes in the LOGBOOK drawer
;; Include current clocking task in clock reports
(setq org-clock-report-include-clocking-task t)
+;; the cache seems to be broken
+(setq org-element-use-cache nil)
(defvar bh/keep-clock-running nil)
(not org-clock-resolving-clocks-due-to-idleness))
(bh/clock-in-parent-task)))
-(add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
+; (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
(require 'org-id)
(defun bh/clock-in-task-by-id (id)
(org-with-point-at clock-in-to-task
(org-clock-in nil))))
+
+(defun org-export-to-ods ()
+ (interactive)
+ (let ((csv-file "data.csv"))
+ (org-table-export csv-file "orgtbl-to-csv")
+ (org-odt-convert csv-file "ods" 'open)))
+
+; allow for zero-width-space to be a break in regexp too
+; (setcar org-emphasis-regexp-components " [:space:] \t('\"{")
+; (setcar (nthcdr 1 org-emphasis-regexp-components) " [:space:]- \t.,:!?;'\")}\\")
+; (org-set-emph-re 'org-emphasis-regexp-components org-emphasis-regexp-components)
+
+;; support inserting screen shots
+(defun my/org-insert-screenshot ()
+ "Take a screenshot into a time stamped unique-named file in the
+same directory as the org-buffer and insert a link to this file."
+ (interactive)
+ (defvar my/org-insert-screenshot/filename)
+ (setq my/org-insert-screenshot/filename
+ (read-file-name
+ "Screenshot to insert: "
+ nil
+ (concat (buffer-file-name) "_" (format-time-string "%Y%m%d_%H%M%S") ".png")
+ )
+ )
+ (call-process "import" nil nil nil my/org-insert-screenshot/filename)
+ (insert (concat "[[" my/org-insert-screenshot/filename "]]"))
+ (org-display-inline-images))
+
+(defun my/fix-inline-images ()
+ (when org-inline-image-overlays
+ (org-redisplay-inline-images)))
+
+(add-hook 'org-babel-after-execute-hook 'my/fix-inline-images)
+
+; from http://orgmode.org/Changes.html
+(defun my/org-repair-property-drawers ()
+ "Fix properties drawers in current buffer.
+ Ignore non Org buffers."
+ (interactive)
+ (when (eq major-mode 'org-mode)
+ (org-with-wide-buffer
+ (goto-char (point-min))
+ (let ((case-fold-search t)
+ (inline-re (and (featurep 'org-inlinetask)
+ (concat (org-inlinetask-outline-regexp)
+ "END[ \t]*$"))))
+ (org-map-entries
+ (lambda ()
+ (unless (and inline-re (org-looking-at-p inline-re))
+ (save-excursion
+ (let ((end (save-excursion (outline-next-heading) (point))))
+ (forward-line)
+ (when (org-looking-at-p org-planning-line-re) (forward-line))
+ (when (and (< (point) end)
+ (not (org-looking-at-p org-property-drawer-re))
+ (save-excursion
+ (and (re-search-forward org-property-drawer-re end t)
+ (eq (org-element-type
+ (save-match-data (org-element-at-point)))
+ 'drawer))))
+ (insert (delete-and-extract-region
+ (match-beginning 0)
+ (min (1+ (match-end 0)) end)))
+ (unless (bolp) (insert "\n"))))))))))))
+
+(provide 'org-mode-configuration)
projects / lib.git / blobdiff