-(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.
- '(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" t)
- '(display-time t)
- '(display-time-24hr-format t)
- '(display-time-day-and-date t)
- '(display-time-mode t)
- '(font-latex-fontify-script nil)
- '(font-latex-fontify-sectioning (quote color))
- '(font-latex-script-display (quote (nil)))
- '(global-auto-revert-mode t)
- '(global-font-lock-mode t nil (font-lock))
- '(global-set-key "\347" t)
- '(iswitchb-mode t)
- '(iswitchb-prompt-newbuffer nil)
- '(log-edit-keep-buffer t)
- '(mail-user-agent (quote sendmail-user-agent))
- '(markdown-enable-math t)
- '(markdown-follow-wiki-link-on-enter nil)
- '(mutt-alias-file-list (quote ("~/.mutt/aliases" "~/.mail_aliases")))
- '(post-email-address "don@donarmstrong.com")
- '(post-kill-quoted-sig nil)
- '(post-mail-message "mutt\\(ng\\|\\)-[a-z0-9]+-[0-9]+-.*")
- '(post-uses-fill-mode nil)
- '(ps-footer-font-size (quote (8 . 10)))
- '(ps-header-font-size (quote (8 . 10)))
- '(ps-header-title-font-size (quote (10 . 10)))
- '(ps-line-number-color "blue")
- '(ps-print-footer t)
- '(ps-print-footer-frame nil)
- '(ps-print-only-one-header t)
- '(safe-local-variable-values (quote ((auto-save-default) (make-backup-files))))
- '(sentence-end "[.?!][]\"')]*\\($\\| \\| \\)[
-]*")
- '(sentence-end-double-space nil)
- '(show-paren-mode t)
- '(tool-bar-mode nil nil (tool-bar))
- '(user-mail-address "don@donarmstrong.com")
- '(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)
-(setq x-select-enable-primary t)
-; (setq mouse-drag-copy-region t)
-
-(fset 'perl-mode 'cperl-mode)
-;;(load-file "cperl-mode.el")
-(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/tiny-tools/lisp/other")
-;;(add-to-list 'Tex-style-path '"~/lib/emacs_el/auctex/")
-
-(setq tinyprocmail--procmail-version "v3.22")
-(add-hook 'tinyprocmail--load-hook 'tinyprocmail-install)
-(require 'tinyprocmail)
-
-(require 'vcl-mode)
-
-(require 'tex-site)
-;;(require 'psvn)
-(require 'cperl-mode)
-;;(require 'ecasound)
-;;(require 'emacs-wiki)
-(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")
-
-; 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/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$" .
- (lambda () (html-mode) (auto-fill-mode)))
- auto-mode-alist))
-
-;; Use c-mode for perl .xs files
-(add-to-list 'auto-mode-alist '("\\.xs\\'" . c-mode))
-(add-to-list 'auto-mode-alist '("\\.\\([pP][Llm]\\|al\\)\\'" . cperl-mode))
-(add-to-list 'interpreter-mode-alist '("perl" . cperl-mode))
-(add-to-list 'interpreter-mode-alist '("perl5" . cperl-mode))
-(add-to-list 'interpreter-mode-alist '("miniperl" . cperl-mode))
-
-; use markdown mode for mdwn files
-(add-to-list 'auto-mode-alist '("\\.mdwn$" . 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]+-" . 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)
-
-(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)
-
-;;(autoload 'perl-mode "cperl-mode"
-;; "alternate mode for editing Perl programs" t)
-
-;; self-insert-command hack.
-;; Without this, "if<SP>" expands to
-;; if ( -!-) {
-;; }
-;; which really should be,
-;; if (-!-) {
-;; }
-(setq cperl-hairy t
- cperl-indent-level 4
- cperl-auto-newline nil
- cperl-auto-newline-after-colon nil
- cperl-continued-statement-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
- 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")))
-
-
-
-;(load-library "php-mode")
-
-(setq-default c-indent-level 4)
-(setq-default c-brace-imaginary-offset 0)
-(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 4)
-
-
-;; (autoload 'php-mode "php-mode" "PHP editing mode" t)
-;; (add-to-list 'auto-mode-alist '("\\.php3?\\'" . php-mode))
-;; (add-to-list 'auto-mode-alist '("\\.phtml?\\'" . php-mode))
-;; (add-to-list 'auto-mode-alist '("\\.php?\\'" . php-mode))
-;; (add-to-list 'auto-mode-alist '("\\.php4?\\'" . php-mode))
-
-;; REFTEX (much enhanced management of cross-ref, labels, etc)
-;; http://www.strw.leidenuniv.nl/~dominik/Tools/reftex/
-(autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t)
-(autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
-(autoload 'reftex-citation "reftex-cite" "Make citation" nil)
-(autoload 'reftex-index-phrase-mode "reftex-index" "Phrase mode" t)
-(add-hook 'LaTeX-mode-hook 'turn-on-reftex) ; with AUCTeX LaTeX mode
-(add-hook 'latex-mode-hook 'turn-on-reftex) ; with Emacs latex mode
-(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 ()
-;; (TeX-add-symbols
-;; '("DLA" 1))))
-;; (custom-set-variables
-;; '(font-latex-user-keyword-classes
-;; '(("fixme"
-;; ("DLA" "RZ")
-;; font-lock-function-name-face 2 (command 1 t))))
-;; )
-
-(require 'font-latex)
-(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)
- (insert (format-time-string "%A, %B %e, %Y %k:%M:%S %Z")))
-(global-set-key "\C-[d" 'insert-date)
-
-(defun unfill-paragraph (arg)
- "Pull this whole paragraph up onto one line."
- (interactive "*p")
- (let ((fill-column 10000))
- (fill-paragraph arg))
- )
-
-;(iswitchb-default-keybindings)
-
-(column-number-mode t)
-(setq-default reftex-plug-into-AUCTeX t)
-
-(server-start)
-
-(require 'mode-compile)
-
-(setq-default reftex-default-bibliography
- '("~/projects/research/references.bib"))
-
-(defadvice server-process-filter (after post-mode-message first activate)
- "If the buffer is in post mode, overwrite the server-edit
- message with a post-save-current-buffer-and-exit message."
- (if (eq major-mode 'post-mode)
- (message
- (substitute-command-keys "Type \\[describe-mode] for help composing; \\[post-save-current-buffer-and-exit] when done."))))
- ; This is also needed to see the magic message. Set to a higher
- ; number if you have a faster computer or read slower than me.
-'(font-lock-verbose 1000)
-;(setq-default server-temp-file-regexp "mutt\(-\|ng-\)")
-; (add-hook 'server-switch-hook
-; (function (lambda()
-; (cond ((string-match "Post" mode-name)
-; (post-goto-body)))
-; set-buffer-file-coding-system 'utf-8
-; )))
-;
-
-(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"
- (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"
- '(progn
- (load-library "lyqi-mode")
- (define-key LilyPond-mode-map "\C-cq" 'lyqi-mode)))
-
-(autoload 'spamassassin-mode "spamassassin-mode" nil t)
-
-(desktop-load-default)
-(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.
- '(menu ((((type x-toolkit)) (:background "black" :foreground "grey90")))))
-
-(defun ess-change-directory (path)
- "Set the current working directory to PATH for both *R* and Emacs."
- (interactive "DDirectory to change to: ")
-
- (when (file-exists-p path)
- (ess-command (concat "setwd(\"" path "\")\n"))
- ;; use file-name-as-directory to ensure it has trailing /
- (setq default-directory (file-name-as-directory path))))
-
-(put 'upcase-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)
-(add-hook 'text-mode-hook 'turn-on-flyspell)
-(add-hook 'c-mode-common-hook 'flyspell-prog-mode)
-(add-hook 'cperl-mode-hook 'flyspell-prog-mode)
-(add-hook 'tcl-mode-hook 'flyspell-prog-mode)
-(add-hook 'ess-mode-hook 'flyspell-prog-mode)
-(defun turn-on-flyspell ()
- "Force flyspell-mode on using a positive arg. For use in hooks."
- (interactive)
- (flyspell-mode 1))
-
-;;; 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 ()
- (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-")
- ; HIDE
- (define-key cm-map "q" 'hide-sublevels) ; Hide everything but the top-level headings
- (define-key cm-map "t" 'hide-body) ; Hide everything but headings (all body lines)
- (define-key cm-map "o" 'hide-other) ; Hide other branches
- (define-key cm-map "c" 'hide-entry) ; Hide this entry's body
- (define-key cm-map "l" 'hide-leaves) ; Hide body lines in this entry and sub-entries
- (define-key cm-map "d" 'hide-subtree) ; Hide everything in this entry and sub-entries
- ; SHOW
- (define-key cm-map "a" 'show-all) ; Show (expand) everything
- (define-key cm-map "e" 'show-entry) ; Show this heading's body
- (define-key cm-map "i" 'show-children) ; Show this heading's immediate child sub-headings
- (define-key cm-map "k" 'show-branches) ; Show all sub-headings under this heading
- (define-key cm-map "s" 'show-subtree) ; Show (expand) everything in this heading & below
- ; MOVE
- (define-key cm-map "u" 'outline-up-heading) ; Up
- (define-key cm-map "n" 'outline-next-visible-heading) ; Next
- (define-key cm-map "p" 'outline-previous-visible-heading) ; Previous
- (define-key cm-map "f" 'outline-forward-same-level) ; Forward - same level
- (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")
-(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)
-(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\\|<\\? \\|<\\?=" "\\?>")
- (js-mode "<script +\\(type=\"text/javascript\"\\|language=\"javascript\"\\)[^>]*>" "</script>")
- (css-mode "<style +type=\"text/css\"[^>]*>" "</style>")))
-(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)
-(defun flymake-report-status-slim (e-w &optional status)
- "Show \"slim\" flymake status in mode line."
- (when e-w
- (setq flymake-mode-line-e-w e-w))
- (when status
- (setq flymake-mode-line-status status))
- (let* ((mode-line " Φ"))
- (when (> (length flymake-mode-line-e-w) 0)
- (setq mode-line (concat mode-line ":" flymake-mode-line-e-w)))
- (setq mode-line (concat mode-line flymake-mode-line-status))
- (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
-
-(defvar my-keys-minor-mode-map (make-keymap) "my-keys-minor-mode keymap.")
-
-; use iedit everywhere
-(define-key my-keys-minor-mode-map (kbd "C-;") 'iedit-mode)
-
-(define-minor-mode my-keys-minor-mode
- "A minor mode so that my key settings override annoying major modes."
- t " my-keys" 'my-keys-minor-mode-map)
-
-(my-keys-minor-mode 1)
-(defun my-minibuffer-setup-hook ()
- (my-keys-minor-mode 0))
-
-(add-hook 'minibuffer-setup-hook 'my-minibuffer-setup-hook)
-(defadvice load (after give-my-keybindings-priority)
- "Try to ensure that my keybindings always have priority."
- (if (not (eq (car (car minor-mode-map-alist)) 'my-keys-minor-mode))
- (let ((mykeys (assq 'my-keys-minor-mode minor-mode-map-alist)))
- (assq-delete-all 'my-keys-minor-mode minor-mode-map-alist)
- (add-to-list 'minor-mode-map-alist mykeys))))
-(ad-activate 'load)
+(add-to-list 'load-path '"~/lib/emacs_el/configuration/")
+(require 'don-configuration)
projects / emacs.git / blobdiff