factor out org configuration

diff --git a/.emacs b/.emacs
index 910d8bf02e7b8f088ebe31e0ff0b546941cee7ac..672e569c2058286d6fd12a8a2ada2c170a3fabb8 100644 (file)
--- a/.emacs
+++ b/.emacs
@@ -59,6 +59,7 @@
 
 (fset 'perl-mode 'cperl-mode)
 ;;(load-file "cperl-mode.el")
 
 (fset 'perl-mode 'cperl-mode)
 ;;(load-file "cperl-mode.el")

+(add-to-list 'load-path '"~/lib/emacs_el/configuration/")

 (add-to-list 'load-path '"~/lib/emacs_el/")
 ;; this is the tiny-tools module from https://github.com/jaalto/project--emacs-tiny-tools.git
 (add-to-list 'load-path '"~/lib/emacs_el/tiny-tools/lisp/tiny")
 (add-to-list 'load-path '"~/lib/emacs_el/")
 ;; this is the tiny-tools module from https://github.com/jaalto/project--emacs-tiny-tools.git
 (add-to-list 'load-path '"~/lib/emacs_el/tiny-tools/lisp/tiny")


@@ -79,9 +80,9 @@
 (require 'bibtex)
 (require 'post)
 ;;(require 'fixme)
 (require 'bibtex)
 (require 'post)
 ;;(require 'fixme)

-(require 'google-weather)
-(require 'org-google-weather)
-(setq-default org-google-weather-format "%i %c, [%l,%h] %s %C")
+; (require 'google-weather)
+; (require 'org-google-weather)
+; (setq-default org-google-weather-format "%i %c, [%l,%h] %s %C")

 
 ; http://julien.danjou.info/projects/emacs-packages#rainbow-mode
 ; this colorizes color strings
 
 ; http://julien.danjou.info/projects/emacs-packages#rainbow-mode
 ; this colorizes color strings


@@ -90,146 +91,6 @@
 (add-to-list 'rainbow-x-colors-major-mode-list 'ESS[S])
 (add-to-list 'rainbow-x-colors-major-mode-list 'ESS[R])
 
 (add-to-list 'rainbow-x-colors-major-mode-list 'ESS[S])
 (add-to-list 'rainbow-x-colors-major-mode-list 'ESS[R])
 

-; 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)
-        ("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))))
-
-(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 'org-id-get-create)
-; 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))
-
-;;;; 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)
-
-

 (global-set-key "\C-xp" 'server-edit)
 
 (setq-default auto-mode-alist (cons '("\.wml$" . 
 (global-set-key "\C-xp" 'server-edit)
 
 (setq-default auto-mode-alist (cons '("\.wml$" . 


@@ -508,15 +369,6 @@ Argument DESCRIPTION MIME description."
 (put 'downcase-region 'disabled nil)
 (put 'narrow-to-region 'disabled nil)
 
 (put 'downcase-region 'disabled nil)
 (put 'narrow-to-region 'disabled nil)
 

-;; 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)
-

 
 (autoload 'flyspell-mode "flyspell" "On-the-fly spelling checker." t)
 (add-hook 'message-mode-hook 'turn-on-flyspell)
 
 (autoload 'flyspell-mode "flyspell" "On-the-fly spelling checker." t)
 (add-hook 'message-mode-hook 'turn-on-flyspell)


@@ -565,174 +417,6 @@ Argument DESCRIPTION MIME description."
  (define-key cm-map "b" 'outline-backward-same-level)       ; Backward - same level
  (global-set-key "\M-o" cm-map)
 
  (define-key cm-map "b" 'outline-backward-same-level)       ; Backward - same level
  (global-set-key "\M-o" cm-map)
 

-(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))

 
 ; debian stuff
 (setq-default debian-changelog-mailing-address "don@debian.org")
 
 ; debian stuff
 (setq-default debian-changelog-mailing-address "don@debian.org")


@@ -762,46 +446,6 @@ Argument DESCRIPTION MIME description."
 (setq mweb-filename-extensions '("php" "htm" "html" "ctp" "phtml" "php4" "php5"))
 (multi-web-global-mode 1)
 
 (setq mweb-filename-extensions '("php" "htm" "html" "ctp" "phtml" "php4" "php5"))
 (multi-web-global-mode 1)
 

-; clean-mode-line from http://www.masteringemacs.org/articles/2012/09/10/hiding-replacing-modeline-strings/
-(defvar mode-line-cleaner-alist
-  `((auto-complete-mode . " α")
-    (yas/minor-mode . " υ")
-    (paredit-mode . " π")
-    (eldoc-mode . "")
-    (abbrev-mode . "")
-    (my-keys-minor-mode . "")
-    ;; Major modes
-    (lisp-interaction-mode . "λ")
-    (hi-lock-mode . "")
-    (python-mode . "Py")
-    (cperl-mode . "ρ")
-    (auctex-mode . "Lχ")
-    (org-agenda-mode . "øα")
-    (org-mode . "ø")
-    (emacs-lisp-mode . "EL")
-    (nxhtml-mode . "nx"))
-  "Alist for `clean-mode-line'.
- 
-When you add a new element to the alist, keep in mind that you
-must pass the correct minor/major mode symbol and a string you
-want to use in the modeline *in lieu of* the original.")
- 
- 
-(defun clean-mode-line ()
-  (interactive)
-  (loop for cleaner in mode-line-cleaner-alist
-        do (let* ((mode (car cleaner))
-                 (mode-str (cdr cleaner))
-                 (old-mode-str (cdr (assq mode minor-mode-alist))))
-             (when old-mode-str
-                 (setcar old-mode-str mode-str))
-               ;; major mode
-             (when (eq mode major-mode)
-               (setq mode-name mode-str)))))
- 
- 
-(add-hook 'after-change-major-mode-hook 'clean-mode-line)
- 

 ;;; alias the new `flymake-report-status-slim' to
 ;;; `flymake-report-status'
 (defalias 'flymake-report-status 'flymake-report-status-slim)
 ;;; alias the new `flymake-report-status-slim' to
 ;;; `flymake-report-status'
 (defalias 'flymake-report-status 'flymake-report-status-slim)


@@ -913,6 +557,9 @@ want to use in the modeline *in lieu of* the original.")
       )
   )
 
       )
   )
 

+; require org mode
+(load "org-mode-configuration")
+

 ; apparently things like to step on C-;, so we'll use a hack from
 ; http://stackoverflow.com/questions/683425/globally-override-key-binding-in-emacs/5340797#5340797 to fix this
 
 ; apparently things like to step on C-;, so we'll use a hack from
 ; http://stackoverflow.com/questions/683425/globally-override-key-binding-in-emacs/5340797#5340797 to fix this