(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)
(add-hook 'tinyprocmail--load-hook 'tinyprocmail-install)
(require 'tinyprocmail)
+(require 'vcl-mode)
+
(require 'tex-site)
;;(require 'psvn)
(require 'cperl-mode)
(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
+(require 'rainbow-mode)
+; add ess to the x major mode
+(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/notes.org"
+ (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/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-global-columns-default-format "%40ITEM(Task) %TAGS %PRIORITY %TODO %17Effort(Estimated Effort){:} %CLOCKSUM")
+(setq org-columns-default-format "%40ITEM(Task) %TAGS %PRIORITY %TODO %13SCHEDULED %17Effort(Estimated Effort){:} %CLOCKSUM")
(setq org-default-notes-file "~/projects/notes/notes.org")
(setq org-capture-templates ;; mail-specific note template, identified by "m"
(defadvice org-protocol-capture (before set-org-protocol-flag activate)
(setq my-org-protocol-flag t))
+
+; 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 "xterm -e \"%s %s\""
+ (substitute-in-file-name "$HOME/bin/mutt_open") message)))
+
+;; add support for "mutt:ID" links
+(org-add-link-type "mutt" 'open-mail-in-mutt)
+
+
(global-set-key "\C-xp" 'server-edit)
(setq-default auto-mode-alist (cons '("\.wml$" .
(add-to-list 'interpreter-mode-alist '("perl5" . cperl-mode))
(add-to-list 'interpreter-mode-alist '("miniperl" . cperl-mode))
-(add-to-list 'auto-mode-alist '("muttng-[a-z0-9]+-[0-9]+-" . post-mode))
+; use markdown mode for mdwn files
+(add-to-list 'auto-mode-alist '("\\.mdwn$" . markdown-mode))
+
+
+
+
+; mail configuration
+(add-to-list 'auto-mode-alist '("muttng-[a-z0-9]+-[0-9]+-" . message-mode))
(add-to-list 'auto-mode-alist '("muttngrc" . muttrc-mode))
-(add-to-list 'auto-mode-alist '("mutt-[a-z0-9]+-[0-9]+-" . post-mode))
+(add-to-list 'auto-mode-alist '("mutt-[a-z0-9]+-[0-9]+-" . message-mode))
(add-to-list 'auto-mode-alist '("muttrc" . muttrc-mode))
+(defun my-message-mode-settings ()
+ (font-lock-add-keywords nil
+ '(("^[ \t]*>[ \t]*>[ \t]*>.*$"
+ (0 'message-multiply-quoted-text-face))
+ ("^[ \t]*>[ \t]*>.*$"
+ (0 'message-double-quoted-text-face))))
+ (local-set-key (kbd "C-c C-a") 'my-post-attach-file)
+ )
+(add-hook 'message-mode-hook 'my-message-mode-settings)
-(add-to-list 'auto-mode-alist '("\\.mdwn$" . markdown-mode))
+(defun my-post-attach-file ()
+ "Prompt for an attachment."
+ (interactive)
+ (let ((file (read-file-name "Attach file: " nil nil t nil))
+ (description (string-read "Description: ")))
+ (my-header-attach-file file description)))
+(symbol-function 'my-post-attach-file)
+(defun my-header-attach-file (file description)
+ "Attach a FILE to the current message (works with Mutt).
+Argument DESCRIPTION MIME description."
+ (interactive "fAttach file: \nsDescription: ")
+ (when (> (length file) 0)
+ (save-excursion
+ (save-match-data
+ (save-restriction
+ (widen)
+ (goto-char (point-min))
+ (search-forward-regexp "^$")
+ (insert (concat "Attach: " (replace-regexp-in-string "\\([[:space:]\\]\\)" "\\\\\\1" (file-truename file)) " "
+ description "\n"))
+ (message (concat "Attached '" file "'."))
+ (setq post-has-attachment t))))))
+
+
+
+(setq mail-yank-prefix "> ")
(global-unset-key "\M-g")
(global-set-key "\M-g" 'goto-line)
;; which really should be,
;; if (-!-) {
;; }
-(setq-default cperl-hairy t
+(setq cperl-hairy t
cperl-indent-level 4
-;; cperl-auto-newline t
-;; cperl-auto-newline-after-colon t
+ cperl-auto-newline nil
+ cperl-auto-newline-after-colon nil
cperl-continued-statement-offset 4
cperl-brace-offset -4
cperl-label-offset -4
cperl-highlight-variables-indiscriminately t
cperl-electric-lbrace-space nil
- )
+ cperl-indent-parens-as-block t
+ cperl-tab-always-indent t)
(add-hook 'cperl-mode-hook (lambda () (cperl-set-style "PerlStyle")))
;(load-library "php-mode")
-(setq-default c-indent-level 8)
+(setq-default c-indent-level 4)
(setq-default c-brace-imaginary-offset 0)
-(setq-default c-brace-offset -8)
-(setq-default c-argdecl-indent 8)
-(setq-default c-label-offset -8)
-(setq-default c-continued-statement-offset 8)
+(setq-default c-brace-offset -4)
+(setq-default c-argdecl-indent 4)
+(setq-default c-label-offset -4)
+(setq-default c-continued-statement-offset 4)
; tabs are annoying
(setq-default indent-tabs-mode nil)
-(setq-default tab-width 8)
+(setq-default tab-width 4)
;; (autoload 'php-mode "php-mode" "PHP editing mode" t)
;; )
(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)
-(fset 'insert-function-documentation
- [?\C-x ?i home ?\C-k ?/ ?h ?o ?m ?e ?/ ?d ?o ?n ?/ ?l ?i ?b ?/ ?t ?e ?m ?p ?l ?a ?t ?e ?s ?/ ?p ?e ?r ?l ?_ ?f ?u ?n ?c ?t ?i ?o ?n ?_ ?d ?o ?c ?u ?m ?e ?n ?t ?a ?t ?i ?o ?n return])
+
+(defun insert-function-documentation ()
+ "Insert function documentation"
+ (interactive)
+ (insert-file-contents "/home/don/lib/templates/perl_function_documentation" nil))
(global-set-key "\M-f" 'insert-function-documentation)
(eval-after-load "lilypond-mode"
(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)
;;; outlining support for ess modes
(add-hook 'ess-mode-hook
- '(lambda ()
- (outline-minor-mode)
- (setq outline-regexp "\\(^#\\{4,5\\} \\)\\|\\(^[a-zA-Z0-9_\.]+ ?<- ?function(.*{\\)")
- (defun outline-level
- (lambda () (interactive) (cond ((looking-at "^##### ") 1)((looking-at "^#### ") 2)((looking-at "^[a-zA-Z0-9_\.]+ ?<- ?function(.*{") 3) (t 1000)))
- )))
+ '(lambda ()
+ (outline-minor-mode)
+ (setq outline-regexp "\\(^#\\{4,5\\} \\)\\|\\(^[a-zA-Z0-9_\.]+ ?<- ?function\\)")
+ (defun outline-level ()
+ (cond ((looking-at "^##### ") 1)
+ ((looking-at "^#### ") 2)
+ ((looking-at "^[a-zA-Z0-9_\.]+ ?<- ?function(.*{") 3)
+ (t 1000)))
+ ))
; Outline-minor-mode key map
(define-prefix-command 'cm-map nil "Outline-")
(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 (") '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)))
+
+;; 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")
(define-key global-map (kbd "C-;") 'iedit-mode)
(global-set-key (kbd "C-;") 'iedit-mode)
+; fix up css mode to not be silly
+; from http://www.stokebloke.com/wordpress/2008/03/21/css-mode-indent-buffer-fix/
+(setq cssm-indent-level 4)
+(setq cssm-newline-before-closing-bracket t)
+(setq cssm-indent-function #'cssm-c-style-indenter)
+(setq cssm-mirror-mode nil)
+
(require 'multi-web-mode)
(setq mweb-default-major-mode 'html-mode)
(setq mweb-tags '((php-mode "<\\?php\\|<\\? \\|<\\?=" "\\?>")