(custom-set-variables
- ;; custom-set-variables was added by Custom.
- ;; If you edit it by hand, you could mess it up, so be careful.
- ;; Your init file should contain only one such instance.
- ;; If there is more than one, they won't work right.
+ ;; custom-set-variables was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
'(bibtex-user-optional-fields (quote (("annote" "Personal annotation (ignored)") ("abstract" "") ("pmid" "") ("doi" ""))))
'(calendar-latitude [33 57 north])
'(calendar-longitude [117 24 west])
'(case-fold-search t)
'(confirm-kill-emacs (quote y-or-n-p))
'(cperl-lazy-help-time nil)
- '(debian-changelog-mailing-address "don@debian.org")
+ '(debian-changelog-mailing-address "don@debian.org" t)
'(display-time t)
'(display-time-24hr-format t)
'(display-time-day-and-date t)
'(vc-delete-logbuf-window nil)
'(vc-follow-symlinks t))
+;; use git before SVN; use CVS earlier, because I have CVS
+;; repositories inside of git directories
+(setq vc-handled-backends (quote (CVS Git RCS SVN SCCS Bzr Hg Mtn Arch)))
;; switch back to the old primary selection method
(setq x-select-enable-clipboard nil)
"~/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 %17Effort(Estimated Effort){:} %CLOCKSUM")
+(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"
(add-hook 'org-clock-out-hook 'bh/remove-empty-drawer-on-clock-out 'append)
+; 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)
"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 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.
cperl-auto-newline nil
cperl-auto-newline-after-colon nil
cperl-continued-statement-offset 4
- cperl-brace-offset -4
+ cperl-brace-offset -1
+ cperl-continued-brace-offset 0
cperl-label-offset -4
cperl-highlight-variables-indiscriminately t
cperl-electric-lbrace-space nil
- )
-(add-hook 'cperl-mode-hook (lambda () (cperl-set-style "PerlStyle")))
+ cperl-indent-parens-as-block nil
+ cperl-close-paren-offset -1
+ cperl-tab-always-indent t)
+;(add-hook 'cperl-mode-hook (lambda () (cperl-set-style "PerlStyle")))
(add-hook 'LaTeX-mode-hook 'outline-minor-mode) ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'outline-minor-mode) ; with Emacs latex mode
+; use smart quotes by default instead of `` and ''
+; taken from http://kieranhealy.org/esk/kjhealy.html
+(setq TeX-open-quote "“")
+(setq TeX-close-quote "”")
+
;; (TeX-add-style-hook
;; "latex"
;; (lambda ()
;; )
(require 'font-latex)
-(add-to-list 'font-latex-match-reference-keywords "fref")
-(add-to-list 'font-latex-match-reference-keywords "Fref")
-(add-to-list 'font-latex-match-reference-keywords "citep")
-(add-to-list 'font-latex-match-reference-keywords "citet")
-(font-latex-match-reference-make)
-(add-to-list 'font-latex-match-function-keywords "DLA")
-(add-to-list 'font-latex-match-function-keywords "RZ")
-(add-to-list 'font-latex-match-function-keywords "OM")
-(add-to-list 'font-latex-match-function-keywords "DL")
-(add-to-list 'font-latex-match-function-keywords "fixme")
-(add-to-list 'font-latex-match-function-keywords "acs")
-(add-to-list 'font-latex-match-function-keywords "acsp")
-(add-to-list 'font-latex-match-function-keywords "ac")
-(add-to-list 'font-latex-match-function-keywords "acp")
-(add-to-list 'font-latex-match-function-keywords "acl")
-(add-to-list 'font-latex-match-function-keywords "aclp")
-(add-to-list 'font-latex-match-function-keywords "acsu")
-(add-to-list 'font-latex-match-function-keywords "aclu")
-(add-to-list 'font-latex-match-function-keywords "acused")
-(font-latex-match-function-make)
+(setq font-latex-match-reference-keywords
+ '(
+ ("fref" "{")
+ ("Fref" "{")
+ ("citep" "{")
+ ("citet" "{")
+ ("acs" "{")
+ ("acsp" "{")
+ ("ac" "{")
+ ("acp" "{")
+ ("acl" "{")
+ ("aclp" "{")
+ ("acsu" "{")
+ ("aclu" "{")
+ ("acused" "{")
+; ))
+; (setq font-latex-match-warning-keywords
+; '(
+ ("DLA" "{")
+ ("RZ" "{")
+ ("OM" "{")
+ ("DL" "{")
+ ("fixme" "{")))
+
(setq-default TeX-parse-self t)
(setq-default TeX-auto-save t)
(setq-default TeX-master nil)
+;; this doesn't seem to work; not currently sure why
+; (setq font-latex-user-keyword-classes
+; '(("my-warning-commands"
+; (("DLA" "{")
+; ("RZ" "{")
+; ("OM" "{")
+; ("DL" "{")
+; ("fixme" "{")
+; )
+; (:foreground "red" :weight bold :underline (:color foreground-color :style line)))
+; ))
+
+
(defun insert-date ()
"Insert date at point."
(interactive)
(add-hook 'post-mode-hook
(auto-fill-mode nil)
)
+; abbrev mode settings
+; load abbreviations from
+(setq abbrev-file-name
+ "~/.emacs_abbrev_def")
+
+; read the abbrev file if it exists
+(if (file-exists-p abbrev-file-name)
+ (quietly-read-abbrev-file))
+
+; for now, use abbrev mode everywhere
+(setq default-abbrev-mode t)
+
(defun insert-function-documentation ()
"Insert function documentation"
(desktop-read)
'(iswitchb-mode on)
(custom-set-faces
- ;; custom-set-faces was added by Custom.
- ;; If you edit it by hand, you could mess it up, so be careful.
- ;; Your init file should contain only one such instance.
- ;; If there is more than one, they won't work right.
+ ;; custom-set-faces was added by Custom.
+ ;; If you edit it by hand, you could mess it up, so be careful.
+ ;; Your init file should contain only one such instance.
+ ;; If there is more than one, they won't work right.
'(menu ((((type x-toolkit)) (:background "black" :foreground "grey90")))))
(defun ess-change-directory (path)
(global-set-key "\M-o" cm-map)
(defun my-org-mode-setup ()
- (when (and (buffer-file-name)
- (file-exists-p (buffer-file-name)))
(load-library "reftex")
(and (buffer-file-name)
- (file-exists-p (buffer-file-name))
- (reftex-parse-all))
- (reftex-set-cite-format
- '((?b . "[[bib::%l]]")
- (?n . "[[note::%l]]"))))
- (define-key org-mode-map "\C-c\C-g" 'reftex-citation)
-)
+ (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)
+
+
+;; 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}"
+ ("\\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
+ '(("" "fontspec" t)
+ ("" "xunicode" t)
+ ))
+(setq org-latex-packages-alist
+ '(("" "graphicx" t)
+ ("" "fontspec" t)
+ ("" "xunicode" t)
+ ("" "hyperref" t)
+ ("" "url" t)
+ ("" "rotating" t)
+ ("" "longtable" nil)
+ ("" "float" )))
+
+; 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")
(setq-default debian-changelog-full-name "Don Armstrong")
+; ediff configuration
+; don't use the multi-window configuration
+(setq ediff-window-setup-function 'ediff-setup-windows-plain)
+
; use iedit
(require 'iedit)
(define-key global-map (kbd "C-;") 'iedit-mode)
(setq flymake-mode-line mode-line)
(force-mode-line-update)))
+; load sql-indent when sql is loaded
+(eval-after-load "sql"
+ '(load-library "sql-indent"))
+
+; fix up tmux xterm keys
+; stolen from http://unix.stackexchange.com/questions/24414/shift-arrow-not-working-in-emacs-within-tmux
+(if (getenv "TMUX")
+ (progn
+ (let ((x 2) (tkey ""))
+ (while (<= x 8)
+ ;; shift
+ (if (= x 2)
+ (setq tkey "S-"))
+ ;; alt
+ (if (= x 3)
+ (setq tkey "M-"))
+ ;; alt + shift
+ (if (= x 4)
+ (setq tkey "M-S-"))
+ ;; ctrl
+ (if (= x 5)
+ (setq tkey "C-"))
+ ;; ctrl + shift
+ (if (= x 6)
+ (setq tkey "C-S-"))
+ ;; ctrl + alt
+ (if (= x 7)
+ (setq tkey "C-M-"))
+ ;; ctrl + alt + shift
+ (if (= x 8)
+ (setq tkey "C-M-S-"))
+
+ ;; arrows
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d A" x)) (kbd (format "%s<up>" tkey)))
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d B" x)) (kbd (format "%s<down>" tkey)))
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d C" x)) (kbd (format "%s<right>" tkey)))
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d D" x)) (kbd (format "%s<left>" tkey)))
+ ;; home
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d H" x)) (kbd (format "%s<home>" tkey)))
+ ;; end
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d F" x)) (kbd (format "%s<end>" tkey)))
+ ;; page up
+ (define-key key-translation-map (kbd (format "M-[ 5 ; %d ~" x)) (kbd (format "%s<prior>" tkey)))
+ ;; page down
+ (define-key key-translation-map (kbd (format "M-[ 6 ; %d ~" x)) (kbd (format "%s<next>" tkey)))
+ ;; insert
+ (define-key key-translation-map (kbd (format "M-[ 2 ; %d ~" x)) (kbd (format "%s<delete>" tkey)))
+ ;; delete
+ (define-key key-translation-map (kbd (format "M-[ 3 ; %d ~" x)) (kbd (format "%s<delete>" tkey)))
+ ;; f1
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d P" x)) (kbd (format "%s<f1>" tkey)))
+ ;; f2
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d Q" x)) (kbd (format "%s<f2>" tkey)))
+ ;; f3
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d R" x)) (kbd (format "%s<f3>" tkey)))
+ ;; f4
+ (define-key key-translation-map (kbd (format "M-[ 1 ; %d S" x)) (kbd (format "%s<f4>" tkey)))
+ ;; f5
+ (define-key key-translation-map (kbd (format "M-[ 15 ; %d ~" x)) (kbd (format "%s<f5>" tkey)))
+ ;; f6
+ (define-key key-translation-map (kbd (format "M-[ 17 ; %d ~" x)) (kbd (format "%s<f6>" tkey)))
+ ;; f7
+ (define-key key-translation-map (kbd (format "M-[ 18 ; %d ~" x)) (kbd (format "%s<f7>" tkey)))
+ ;; f8
+ (define-key key-translation-map (kbd (format "M-[ 19 ; %d ~" x)) (kbd (format "%s<f8>" tkey)))
+ ;; f9
+ (define-key key-translation-map (kbd (format "M-[ 20 ; %d ~" x)) (kbd (format "%s<f9>" tkey)))
+ ;; f10
+ (define-key key-translation-map (kbd (format "M-[ 21 ; %d ~" x)) (kbd (format "%s<f10>" tkey)))
+ ;; f11
+ (define-key key-translation-map (kbd (format "M-[ 23 ; %d ~" x)) (kbd (format "%s<f11>" tkey)))
+ ;; f12
+ (define-key key-translation-map (kbd (format "M-[ 24 ; %d ~" x)) (kbd (format "%s<f12>" tkey)))
+ ;; f13
+ (define-key key-translation-map (kbd (format "M-[ 25 ; %d ~" x)) (kbd (format "%s<f13>" tkey)))
+ ;; f14
+ (define-key key-translation-map (kbd (format "M-[ 26 ; %d ~" x)) (kbd (format "%s<f14>" tkey)))
+ ;; f15
+ (define-key key-translation-map (kbd (format "M-[ 28 ; %d ~" x)) (kbd (format "%s<f15>" tkey)))
+ ;; f16
+ (define-key key-translation-map (kbd (format "M-[ 29 ; %d ~" x)) (kbd (format "%s<f16>" tkey)))
+ ;; f17
+ (define-key key-translation-map (kbd (format "M-[ 31 ; %d ~" x)) (kbd (format "%s<f17>" tkey)))
+ ;; f18
+ (define-key key-translation-map (kbd (format "M-[ 32 ; %d ~" x)) (kbd (format "%s<f18>" tkey)))
+ ;; f19
+ (define-key key-translation-map (kbd (format "M-[ 33 ; %d ~" x)) (kbd (format "%s<f19>" tkey)))
+ ;; f20
+ (define-key key-translation-map (kbd (format "M-[ 34 ; %d ~" x)) (kbd (format "%s<f20>" tkey)))
+
+ (setq x (+ x 1))
+ ))
+ )
+ )
+
; 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
projects / emacs.git / blobdiff