X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=.emacs;h=5fe719e7df4f3b2c956cdbf4110edee178664398;hb=be7768a74ce2c3531dfa47094e4d6c3344cec7ca;hp=f37d936892081ae7023327f571051168e121091a;hpb=5d29561746b27218b3832146ce00cc75077360a9;p=emacs.git diff --git a/.emacs b/.emacs index f37d936..5fe719e 100644 --- a/.emacs +++ b/.emacs @@ -1,15 +1,15 @@ (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) @@ -97,6 +97,7 @@ "~/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"))) @@ -133,6 +134,10 @@ (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) @@ -174,6 +179,15 @@ "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)) @@ -279,12 +293,15 @@ Argument DESCRIPTION MIME description." 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"))) @@ -318,6 +335,11 @@ Argument DESCRIPTION MIME description." (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 () @@ -331,30 +353,47 @@ Argument DESCRIPTION MIME description." ;; ) (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) @@ -431,10 +470,10 @@ Argument DESCRIPTION MIME description." (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) @@ -516,10 +555,12 @@ Argument DESCRIPTION MIME description." (reftex-set-cite-format '((?b . "[[bib::%l][%l-bib]]") (?n . "[[note::%l][%l-notes]]") - (?h . "** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l-paper]]"))) + (?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) @@ -527,11 +568,123 @@ Argument DESCRIPTION MIME description." (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") +;; 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}"))) + +;; Originally taken from Bruno Tavernier: http://thread.gmane.org/gmane.emacs.orgmode/31150/focus=31432 +;; but adapted to use latexmk 4.22 or higher. +(defun my-auto-tex-cmd () + "When exporting from .org with latex, automatically run latex, + pdflatex, or xelatex as appropriate, using latexmk." + (let ((texcmd))) + ;; default command: pdflatex + (setq texcmd "latexmk -pdflatex='pdflatex -synctex=1 --shell-escape --' -pdf %f") + ;; pdflatex -> .pdf + (if (string-match "LATEX_CMD: pdflatex" (buffer-string)) + (setq texcmd "latexmk -pdflatex='pdflatex -synctex=1 --shell-escape' -pdf %f")) + ;; xelatex -> .pdf + (if (string-match "LATEX_CMD: xelatex" (buffer-string)) + (setq texcmd "latexmk -pdflatex='xelatex -syntex=1 --shell-escape' -bibtex -use-make -pdf %f")) + ;; LaTeX compilation command + (setq org-latex-to-pdf-process (list texcmd))) + +(add-hook 'org-latex-after-initial-vars-hook 'my-auto-tex-cmd) + +;; Default packages included in /every/ tex file, latex, pdflatex or xelatex +(setq org-latex-packages-alist + '(("" "graphicx" t) + ("" "longtable" nil) + ("" "float" ))) + +;; Custom packages +(defun my-auto-tex-parameters () + "Automatically select the tex packages to include. See https://github.com/kjhealy/latex-custom-kjh for the support files included here." + ;; default packages for ordinary latex or pdflatex export + (setq org-latex-default-packages-alist + '(("AUTO" "inputenc" t) + ("minted,minion" "org-preamble-pdflatex" t))) + ;; Packages to include when xelatex is used + (if (string-match "LATEX_CMD: xelatex" (buffer-string)) + (setq org-latex-default-packages-alist + '(("minted" "org-preamble-xelatex" t) )))) + +(add-hook 'org-latex-after-initial-vars-hook 'my-auto-tex-parameters) + +; 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") @@ -612,6 +765,101 @@ want to use in the modeline *in lieu of* the original.") (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" tkey))) + (define-key key-translation-map (kbd (format "M-[ 1 ; %d B" x)) (kbd (format "%s" tkey))) + (define-key key-translation-map (kbd (format "M-[ 1 ; %d C" x)) (kbd (format "%s" tkey))) + (define-key key-translation-map (kbd (format "M-[ 1 ; %d D" x)) (kbd (format "%s" tkey))) + ;; home + (define-key key-translation-map (kbd (format "M-[ 1 ; %d H" x)) (kbd (format "%s" tkey))) + ;; end + (define-key key-translation-map (kbd (format "M-[ 1 ; %d F" x)) (kbd (format "%s" tkey))) + ;; page up + (define-key key-translation-map (kbd (format "M-[ 5 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; page down + (define-key key-translation-map (kbd (format "M-[ 6 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; insert + (define-key key-translation-map (kbd (format "M-[ 2 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; delete + (define-key key-translation-map (kbd (format "M-[ 3 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f1 + (define-key key-translation-map (kbd (format "M-[ 1 ; %d P" x)) (kbd (format "%s" tkey))) + ;; f2 + (define-key key-translation-map (kbd (format "M-[ 1 ; %d Q" x)) (kbd (format "%s" tkey))) + ;; f3 + (define-key key-translation-map (kbd (format "M-[ 1 ; %d R" x)) (kbd (format "%s" tkey))) + ;; f4 + (define-key key-translation-map (kbd (format "M-[ 1 ; %d S" x)) (kbd (format "%s" tkey))) + ;; f5 + (define-key key-translation-map (kbd (format "M-[ 15 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f6 + (define-key key-translation-map (kbd (format "M-[ 17 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f7 + (define-key key-translation-map (kbd (format "M-[ 18 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f8 + (define-key key-translation-map (kbd (format "M-[ 19 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f9 + (define-key key-translation-map (kbd (format "M-[ 20 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f10 + (define-key key-translation-map (kbd (format "M-[ 21 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f11 + (define-key key-translation-map (kbd (format "M-[ 23 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f12 + (define-key key-translation-map (kbd (format "M-[ 24 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f13 + (define-key key-translation-map (kbd (format "M-[ 25 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f14 + (define-key key-translation-map (kbd (format "M-[ 26 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f15 + (define-key key-translation-map (kbd (format "M-[ 28 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f16 + (define-key key-translation-map (kbd (format "M-[ 29 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f17 + (define-key key-translation-map (kbd (format "M-[ 31 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f18 + (define-key key-translation-map (kbd (format "M-[ 32 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f19 + (define-key key-translation-map (kbd (format "M-[ 33 ; %d ~" x)) (kbd (format "%s" tkey))) + ;; f20 + (define-key key-translation-map (kbd (format "M-[ 34 ; %d ~" x)) (kbd (format "%s" 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