X-Git-Url: https://git.donarmstrong.com/?p=lib.git;a=blobdiff_plain;f=emacs_el%2Fconfiguration%2Forg-mode-configuration.el;h=6b942a8fdf31dd104ca2377f500214884c409745;hp=63fe923126177d056874c226a7369229ed29e26c;hb=0e30697e213aabd31948d7576934c54324162432;hpb=ed46f8ecae183631ee2eeda49b696de283b32bb0 diff --git a/emacs_el/configuration/org-mode-configuration.el b/emacs_el/configuration/org-mode-configuration.el index 63fe923..6b942a8 100644 --- a/emacs_el/configuration/org-mode-configuration.el +++ b/emacs_el/configuration/org-mode-configuration.el @@ -2,9 +2,13 @@ (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) @@ -91,44 +95,62 @@ ; 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") +(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") ) ) @@ -137,7 +159,7 @@ (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) @@ -165,6 +187,12 @@ (global-set-key (kbd " n") 'bh/toggle-next-task-display) (global-set-key (kbd " 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 " I") 'bh/punch-in) (global-set-key (kbd " O") 'bh/punch-out) @@ -243,7 +271,7 @@ -(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 @@ -280,16 +308,16 @@ do not already have one." ; 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 @@ -304,7 +332,7 @@ do not already have one." ;; 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" @@ -357,7 +385,7 @@ Maildir, or by Message-ID." '((?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) @@ -377,6 +405,13 @@ Maildir, or by Message-ID." (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 %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" . @@ -384,8 +419,12 @@ Maildir, or by Message-ID." ; 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) @@ -404,50 +443,63 @@ Maildir, or by Message-ID." (setq-default org-mobile-directory "/rzlab.ucr.edu:/sites/dav.donarmstrong.com/root/org/") +(when (string= system-name "rzlab.ucr.edu") + (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 @@ -459,6 +511,20 @@ Maildir, or by Message-ID." ("\\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" @@ -485,7 +551,7 @@ Maildir, or by Message-ID." ;; 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) @@ -496,6 +562,9 @@ Maildir, or by Message-ID." ("" "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 @@ -520,6 +589,9 @@ Maildir, or by Message-ID." (setq ad-return-value contents) ad-do-it)) +;; keep latex logfiles + +(setq org-latex-remove-logfiles nil) ;; helper functions (defun bh/is-project-p () @@ -773,6 +845,7 @@ Skip project and sub-project tasks, habits, and loose non-project tasks." (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 @@ -791,6 +864,8 @@ Skip project and sub-project tasks, habits, and loose non-project tasks." ;; 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) @@ -884,7 +959,7 @@ as the default task." (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) @@ -910,3 +985,70 @@ A prefix arg forces clock in of the default task." (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)