+ (defun org-mode-reftex-search ()
+ (interactive)
+ (org-open-link-from-string (format "[[notes:%s]]" (first (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 "$HOME/bin/bibtex_to_paper") bibtexkey)))
+ (org-add-link-type "papers" 'open-research-paper)
+ (defun open-research-paper-pdf (bibtexkey)
+ "Open a paper pdf by bibtex key"
+ (interactive "bibtex key: ")
+ (shell-command
+ (format "%s -p evince_annot %s"
+ (substitute-in-file-name "$HOME/bin/bibtex_to_paper") bibtexkey)))
+ (org-add-link-type "papers-pdf" 'open-research-paper-pdf)
+
+ (add-to-list 'org-link-abbrev-alist
+ '("notes" .
+ "~/projects/research/paper_notes.org::#%s"))
+
+ ; I pretty much always want hiearchical checkboxes
+ (setq org-hierachical-checkbox-statistics nil)
+
+ ;; Add \begin{equation}\end{equation} templates to the org mode easy templates
+ (add-to-list 'org-structure-template-alist
+ '("E" "\\begin{equation}\n?\n\\end{equation}"))
+
+ ;; 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)
+
+
+#+END_SRC
+** Org Mobile Configuration
+#+BEGIN_SRC emacs-lisp
+ (setq-default org-mobile-directory "/linnode.donarmstrong.com:/sites/dav.donarmstrong.com/root/org/")
+ (when (string= system-name "linnode")
+ (setq-default org-mobile-directory "/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")
+
+#+END_SRC
+** Org iCal Support
+#+BEGIN_SRC emacs-lisp
+ ;; org mode ical export
+ (setq org-icalendar-timezone "America/Los_Angeles")
+ (setq org-icalendar-use-scheduled '(todo-start event-if-todo))
+ ;; we already add the id manually
+ (setq org-icalendar-store-UID t)
+
+#+END_SRC
+** General Org Babel Configuration
+#+BEGIN_SRC emacs-lisp
+ ;; org babel support
+ (org-babel-do-load-languages
+ 'org-babel-load-languages
+ '((emacs-lisp . t )
+ (R . t)
+ (latex . t)
+ (ditaa . t)
+ (dot . t)
+ ))
+ ;; use graphviz-dot for dot things
+ (add-to-list 'org-src-lang-modes '("dot" . graphviz-dot))
+ ;; org-babel-by-backend
+ (defmacro org-babel-by-backend (&rest body)
+ `(case (if (boundp 'backend)
+ (org-export-backend-name backend)
+ nil) ,@body))
+
+ (defun my/fix-inline-images ()
+ (when org-inline-image-overlays
+ (org-redisplay-inline-images)))
+
+ (add-hook 'org-babel-after-execute-hook
+ 'my/fix-inline-images)
+
+#+END_SRC
+** LaTeX configuration
+ :PROPERTIES:
+ :ID: 7135ba17-6a50-4eed-84ca-b90afa5b12f8
+ :END:
+#+BEGIN_SRC emacs-lisp
+ (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}")))
+
+ (setq org-beamer-outline-frame-options "")
+ (add-to-list 'org-latex-classes
+ '("beamer"
+ "\\documentclass[ignorenonframetext]{beamer}
+ [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}")))
+
+ (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}")))
+
+ (add-to-list 'org-latex-classes
+ '("dlacv"
+ "\\documentclass{dlacv}
+ [NO-DEFAULT-PACKAGES]
+ [NO-PACKAGES]
+ [NO-EXTRA]"
+ ("\\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
+ '("dlaresume"
+ "\\documentclass{dlaresume}
+ [NO-DEFAULT-PACKAGES]
+ [NO-PACKAGES]
+ [NO-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 -f -pdflatex=xelatex -bibtex -use-make -pdf %f"))
+
+ ;; Default packages included in /every/ tex file, latex, pdflatex or xelatex
+ (setq org-latex-default-packages-alist
+ '(("" "amsmath" t)
+ ("" "unicode-math" t)
+ ))
+ (setq org-latex-packages-alist
+ '(("" "graphicx" t)
+ ("" "fontspec" t)
+ ("" "xunicode" t)
+ ("" "hyperref" t)
+ ("" "url" t)
+ ("" "rotating" t)
+ ("" "longtable" nil)
+ ("" "float" )))
+
+ ;; make equations larger
+ (setq org-format-latex-options (plist-put org-format-latex-options :scale 2.0))
+
+ (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))
+
+ ;; keep latex logfiles
+
+ (setq org-latex-remove-logfiles nil)
+
+ ;; Resume clocking task when emacs is restarted
+ (org-clock-persistence-insinuate)
+ ;;
+ ;; Show lot of clocking history so it's easy to pick items off the C-F11 list
+ (setq org-clock-history-length 23)
+ ;; Resume clocking task on clock-in if the clock is open
+ (setq org-clock-in-resume t)
+ ;; Change tasks to NEXT when clocking in; this avoids clocking in when
+ ;; there are things like PHONE calls
+ (setq org-clock-in-switch-to-state 'bh/clock-in-to-next)
+ ;; Separate drawers for clocking and logs
+ (setq org-drawers (quote ("PROPERTIES" "LOGBOOK")))
+ ;; Save clock data and state changes and notes in the LOGBOOK drawer
+ (setq org-clock-into-drawer t)
+ (setq org-log-into-drawer t)
+ ;; Sometimes I change tasks I'm clocking quickly - this removes clocked tasks with 0:00 duration
+ (setq org-clock-out-remove-zero-time-clocks t)
+ ;; Clock out when moving task to a done state
+ (setq org-clock-out-when-done t)
+ ;; Save the running clock and all clock history when exiting Emacs, load it on startup
+ (setq org-clock-persist t)
+ ;; Do not prompt to resume an active clock
+ (setq org-clock-persist-query-resume nil)
+ ;; Enable auto clock resolution for finding open clocks
+ (setq org-clock-auto-clock-resolution (quote when-no-clock-is-running))
+ ;; Include current clocking task in clock reports
+ (setq org-clock-report-include-clocking-task t)
+
+ ;; the cache seems to be broken
+ (setq org-element-use-cache nil)
+
+ (defvar bh/keep-clock-running nil)
+
+ (defun bh/is-task-p ()
+ "Any task with a todo keyword and no subtask"
+ (save-restriction
+ (widen)
+ (let ((has-subtask)
+ (subtree-end (save-excursion (org-end-of-subtree t)))
+ (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
+ (save-excursion
+ (forward-line 1)
+ (while (and (not has-subtask)
+ (< (point) subtree-end)
+ (re-search-forward "^\*+ " subtree-end t))
+ (when (member (org-get-todo-state) org-todo-keywords-1)
+ (setq has-subtask t))))
+ (and is-a-task (not has-subtask)))))
+ (defun bh/is-project-p ()
+ "Any task with a todo keyword subtask"
+ (save-restriction
+ (widen)
+ (let ((has-subtask)
+ (subtree-end (save-excursion (org-end-of-subtree t)))
+ (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
+ (save-excursion
+ (forward-line 1)
+ (while (and (not has-subtask)
+ (< (point) subtree-end)
+ (re-search-forward "^\*+ " subtree-end t))
+ (when (member (org-get-todo-state) org-todo-keywords-1)
+ (setq has-subtask t))))
+ (and is-a-task has-subtask))))
+
+ (defun bh/is-subproject-p ()
+ "Any task which is a subtask of another project"
+ (let ((is-subproject)
+ (is-a-task (member (nth 2 (org-heading-components)) org-todo-keywords-1)))
+ (save-excursion
+ (while (and (not is-subproject) (org-up-heading-safe))
+ (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
+ (setq is-subproject t))))
+ (and is-a-task is-subproject)))
+
+
+ (defun bh/clock-in-to-next (kw)
+ "Switch a task from TODO to NEXT when clocking in.
+ Skips capture tasks, projects, and subprojects.
+ Switch projects and subprojects from NEXT back to TODO"
+ (when (not (and (boundp 'org-capture-mode) org-capture-mode))
+ (cond
+ ((and (member (org-get-todo-state) (list "TODO"))
+ (bh/is-task-p))
+ "NEXT")
+ ((and (member (org-get-todo-state) (list "NEXT"))
+ (bh/is-project-p))
+ "TODO"))))
+
+ (defun bh/punch-in (arg)
+ "Start continuous clocking and set the default task to the
+ selected task. If no task is selected set the Organization task
+ as the default task."
+ (interactive "p")
+ (setq bh/keep-clock-running t)
+ (if (equal major-mode 'org-agenda-mode)
+ ;;
+ ;; We're in the agenda
+ ;;
+ (let* ((marker (org-get-at-bol 'org-hd-marker))
+ (tags (org-with-point-at marker (org-get-tags-at))))
+ (if (and (eq arg 4) tags)
+ (org-agenda-clock-in '(16))
+ (bh/clock-in-organization-task-as-default)))
+ ;;
+ ;; We are not in the agenda
+ ;;
+ (save-restriction
+ (widen)
+ ; Find the tags on the current task
+ (if (and (equal major-mode 'org-mode) (not (org-before-first-heading-p)) (eq arg 4))
+ (org-clock-in '(16))
+ (bh/clock-in-organization-task-as-default)))))
+
+ (defun bh/punch-out ()
+ (interactive)
+ (setq bh/keep-clock-running nil)
+ (when (org-clock-is-active)
+ (org-clock-out))
+ (org-agenda-remove-restriction-lock))
+
+ (defun bh/clock-in-default-task ()
+ (save-excursion
+ (org-with-point-at org-clock-default-task
+ (org-clock-in))))
+
+ (defun bh/clock-in-parent-task ()
+ "Move point to the parent (project) task if any and clock in"
+ (let ((parent-task))
+ (save-excursion
+ (save-restriction
+ (widen)
+ (while (and (not parent-task) (org-up-heading-safe))
+ (when (member (nth 2 (org-heading-components)) org-todo-keywords-1)
+ (setq parent-task (point))))
+ (if parent-task
+ (org-with-point-at parent-task
+ (org-clock-in))
+ (when bh/keep-clock-running
+ (bh/clock-in-default-task)))))))
+
+ (defvar bh/organization-task-id "e22cb8bf-07c7-408b-8f60-ff3aadac95e4")
+
+ (defun bh/clock-in-organization-task-as-default ()
+ (interactive)
+ (org-with-point-at (org-id-find bh/organization-task-id 'marker)
+ (org-clock-in '(16))))
+
+ (defun bh/clock-out-maybe ()
+ (when (and bh/keep-clock-running
+ (not org-clock-clocking-in)
+ (marker-buffer org-clock-default-task)
+ (not org-clock-resolving-clocks-due-to-idleness))
+ (bh/clock-in-parent-task)))
+
+ ; (add-hook 'org-clock-out-hook 'bh/clock-out-maybe 'append)
+
+ (require 'org-id)
+ (defun bh/clock-in-task-by-id (id)
+ "Clock in a task by id"
+ (org-with-point-at (org-id-find id 'marker)
+ (org-clock-in nil)))
+
+ (defun bh/clock-in-last-task (arg)
+ "Clock in the interrupted task if there is one
+ Skip the default task and get the next one.
+ A prefix arg forces clock in of the default task."
+ (interactive "p")
+ (let ((clock-in-to-task
+ (cond
+ ((eq arg 4) org-clock-default-task)
+ ((and (org-clock-is-active)
+ (equal org-clock-default-task (cadr org-clock-history)))
+ (caddr org-clock-history))
+ ((org-clock-is-active) (cadr org-clock-history))
+ ((equal org-clock-default-task (car org-clock-history)) (cadr org-clock-history))
+ (t (car org-clock-history)))))
+ (widen)
+ (org-with-point-at clock-in-to-task
+ (org-clock-in nil))))
+
+
+ (defun org-export-to-ods ()
+ (interactive)
+ (let ((csv-file "data.csv"))
+ (org-table-export csv-file "orgtbl-to-csv")
+ (org-odt-convert csv-file "ods" 'open)))
+
+ ; allow for zero-width-space to be a break in regexp too
+ ; (setcar org-emphasis-regexp-components " [:space:] \t('\"{")
+ ; (setcar (nthcdr 1 org-emphasis-regexp-components) " [:space:]- \t.,:!?;'\")}\\")
+ ; (org-set-emph-re 'org-emphasis-regexp-components org-emphasis-regexp-components)
+
+ ;; support inserting screen shots
+ (defun my/org-insert-screenshot ()
+ "Take a screenshot into a time stamped unique-named file in the
+ same directory as the org-buffer and insert a link to this file."
+ (interactive)
+ (defvar my/org-insert-screenshot/filename)
+ (setq my/org-insert-screenshot/filename
+ (read-file-name
+ "Screenshot to insert: "
+ nil
+ (concat (buffer-file-name) "_" (format-time-string "%Y%m%d_%H%M%S") ".png")
+ )
+ )
+ (call-process "import" nil nil nil my/org-insert-screenshot/filename)
+ (insert (concat "[[" my/org-insert-screenshot/filename "]]"))
+ (org-display-inline-images))
+
+ (defun my/fix-inline-images ()
+ (when org-inline-image-overlays
+ (org-redisplay-inline-images)))
+
+ (add-hook 'org-babel-after-execute-hook 'my/fix-inline-images)
+
+ ;; use xelatex to preview with imagemagick
+ (add-to-list 'org-preview-latex-process-alist
+ '(xelateximagemagick
+ :programs ("xelatex" "convert")
+ :description "pdf > png"
+ :message "you need to install xelatex and imagemagick"
+ :use-xcolor t
+ :image-input-type "pdf"
+ :image-output-type "png"
+ :image-size-adjust (1.0 . 1.0)
+ :latex-compiler ("xelatex -interaction nonstopmode -output-directory %o %f")
+ :image-converter ("convert -density %D -trim -antialias %f -quality 100 %O"))
+ )
+ ;; use xelatex by default
+ (setq org-preview-latex-default-process 'xelateximagemagick)
+
+ ; from http://orgmode.org/Changes.html
+ (defun my/org-repair-property-drawers ()
+ "Fix properties drawers in current buffer.
+ Ignore non Org buffers."
+ (interactive)
+ (when (eq major-mode 'org-mode)
+ (org-with-wide-buffer
+ (goto-char (point-min))
+ (let ((case-fold-search t)
+ (inline-re (and (featurep 'org-inlinetask)
+ (concat (org-inlinetask-outline-regexp)
+ "END[ \t]*$"))))
+ (org-map-entries
+ (lambda ()
+ (unless (and inline-re (org-looking-at-p inline-re))
+ (save-excursion
+ (let ((end (save-excursion (outline-next-heading) (point))))
+ (forward-line)
+ (when (org-looking-at-p org-planning-line-re) (forward-line))
+ (when (and (< (point) end)
+ (not (org-looking-at-p org-property-drawer-re))
+ (save-excursion
+ (and (re-search-forward org-property-drawer-re end t)
+ (eq (org-element-type
+ (save-match-data (org-element-at-point)))
+ 'drawer))))
+ (insert (delete-and-extract-region
+ (match-beginning 0)
+ (min (1+ (match-end 0)) end)))
+ (unless (bolp) (insert "\n"))))))))))))
+
+#+END_SRC
+** Org-Gcal
+#+BEGIN_SRC emacs-lisp
+ (use-package calfw
+ :ensure f
+ )
+ (use-package calfw-org
+ :ensure f
+ )
+ (use-package org-gcal
+ :ensure f
+ :config '((if (file-readable-p "~/.hide/org_gcal.el")
+ (load-file "~/.hide/org_gcal.el"))
+ )
+ )
+#+END_SRC
+** End use-package
+#+BEGIN_SRC emacs-lisp
+ )
+#+END_SRC