Added Makefile
This commit is contained in:
parent
3d81d2a451
commit
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# This is the Makefile
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#
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# 4/2/18, PH
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# project name
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PROJ = org-mode-poster
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#####################################
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# Usually no edits below this line
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#####################################
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# Output directory
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# Source directory
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SRC = src
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# External
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EXT = ext
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# directory for additional pdf files
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LIB = lib
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POSTER = $(SRC)/$(PROJ)_poster.pdf
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# executables
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RM = rm -Rf
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TEX = xelatex -interaction nonstopmode -shell-escape
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BIBTEX = bibtex
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EMACSINIT = $(EXT)/$(PROJ)_dotemacs
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EMACS = emacs -l ../$(EMACSINIT)
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EMACSMSARGS = --batch -f org-latex-export-to-latex --kill
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EMACSPARGS = --batch -f org-beamer-export-to-latex --kill
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VIEWBIN = pdfview
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PDFMERGEBIN = ext/pdfmerge
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CPBIN = cp
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MKDIRBIN = mkdir
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# list org files
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ORGFILES = $(SRC)/$(PROJ)_poster.org
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# list tex files
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TEXFILES = $(ORGFILES:$(SRC)/$(PROJ)_poster.org=$(SRC)/$(PROJ)_poster.tex)
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# list additional library files
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PDFLIB = $(wildcard $(LIB)/$(PROJ)*.*)
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# indicator files to show tex has run
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TEXOUTFILES = $(TEXFILES:$(SRC)/%.tex=$(SRC)/%.aux)
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# replace tex with pdf to get pdf tex files
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PDFTEXFILES = $(TEXOUTFILES:$(SRC)/%.aux=$(SRC)/%.pdf)
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# Rule for $(TEXFILES)
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# Convert every org file to LaTeX this is done from within the subfolder
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# so be careful with relative paths
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$(SRC)/%.tex: $(SRC)/%.org $(PDFLIB) $(SRC)/beamerthemeph.sty
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@if [ "$(notdir $<)" = "$(PROJ)_poster.org" ]; then \
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echo "Exporting poster from org to LaTeX" \
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&& cd $(SRC) && $(EMACS) $(PROJ)_poster.org $(EMACSPARGS); \
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fi
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# Rule for $(TEXOUTFILES)
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# Run every tex file this is done from within the subfolder so be
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# careful with relative paths
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$(SRC)/%.aux: $(SRC)/%.tex $(PDFLIB)
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cd $(SRC) && $(TEX) $(notdir $<)
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cd $(SRC) && $(TEX) $(notdir $<)
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# Default entry
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all: poster
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# make poster
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poster: tex
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# run tex files
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tex: $(TEXOUTFILES) $(TEXFILES)
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viewposter: poster
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pdfview $(POSTER)
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.PHONY: clean texclean Rclean
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clean: texclean
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texclean:
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$(RM) $(TEXOUT)/$(PROJ)*.tex
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$(RM) $(TEXOUT)/$(PROJ)*.aux
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test:
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@echo $(POSTER) $(TEXFILES) $(ORGFILES)
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;; This is the .emacs configuration file
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;; Large parts of this have been copied from other people
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;; PH, 12/1/16
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;;----------------------------------------------------------------------
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;; Global
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;;----------------------------------------------------------------------
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;; get rid of yes or no
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(fset 'yes-or-no-p 'y-or-n-p)
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;; package archives
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(require 'package)
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(add-to-list 'package-archives
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'("org" . "http://orgmode.org/elpa/"))
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(add-to-list 'package-archives
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'("melpa" . "http://melpa.org/packages/"))
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(add-to-list 'package-archives
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'("melpa-stable" . "http://stable.melpa.org/packages/"))
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(setq package-enable-at-startup nil)
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(package-initialize)
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(unless (package-installed-p 'use-package)
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(package-refresh-contents)
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(package-install 'use-package))
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(setq use-package-verbose t)
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(setq use-package-always-ensure t)
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(eval-when-compile (require 'use-package))
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(setq default-fill-column 72)
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;; Tell emacs where is your personal elisp lib dir
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;; keyboard binding to replace M-x
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(global-set-key "\C-x\C-m" 'execute-extended-command)
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(global-set-key "\C-c\C-m" 'execute-extended-command)
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;;----------------------------------------------------------------------
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;; org mode
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;;----------------------------------------------------------------------
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;; remove comments from org document for use with export hook
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;; https://emacs.stackexchange.com/questions/22574/orgmode-export-how-to-prevent-a-new-line-for-comment-lines
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(defun delete-org-comments (backend)
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(loop for comment in (reverse (org-element-map
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(org-element-parse-buffer)
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'comment 'identity))
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do
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(setf (buffer-substring (org-element-property :begin comment)
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(org-element-property :end comment))
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"")))
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;; add to export hook
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(add-hook 'org-export-before-processing-hook 'delete-org-comments)
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;;----------------------------------------------------------------------
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;; ess
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;;----------------------------------------------------------------------
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(require 'ess)
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(require 'ess-site)
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(setq tab-width 2)
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;(whitespace-mode t)
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; let ess not ask for starting directory
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(setq ess-ask-for-ess-directory nil)
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; disable auto complete (takes too long)
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(setq ess-use-auto-complete nil)
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;(linum-mode t)
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(add-hook 'ess-mode-hook
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(lambda ()
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(whitespace-mode t)
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(linum-mode t)
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; if you uncomment this and reload .emacs from within an R buffer,
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; it should work as a hack
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(setq ess-indent-with-fancy-comments nil)
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(setq ess-style nil)))
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;;----------------------------------------------------------------------
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;; Org
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;;----------------------------------------------------------------------
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(require 'org)
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(require 'org-element)
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;; window setup
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(setq org-agenda-restore-windows-after-quit t)
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(setq org-agenda-skip-scheduled-if-done t)
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;; use ox-extra to ignore certain headings
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(require 'ox-extra)
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(ox-extras-activate '(ignore-headlines))
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;; disable indenting
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(require 'org-indent)
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(org-indent-mode -1)
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;; we don't want raw inline calls to include a newline
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;;(setq org-babel-inline-result-wrap "well, %s")
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;; indentation
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(defun my-tab-related-stuff ()
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; (setq indent-tabs-mode t)
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; (setq tab-stop-list (number-sequence 4 200 4))
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; (setq default-tab-width 2)
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(setq tab-width 2))
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; (setq indent-line-function 'insert-tab))
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(add-hook 'org-mode-hook 'my-tab-related-stuff)
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;; inline results wrapping
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(setq org-babel-inline-result-wrap "%s")
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;; active Babel languages
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(org-babel-do-load-languages
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'org-babel-load-languages
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'((R . t)
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(latex . t)
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(dot . t)
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(shell . t)
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(ditaa . t)
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))
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;; we trust our own R code so we do not need to confirm
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(defun my-org-confirm-babel-evaluate (lang body)
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(not (string-match "[Rlatexdotditaashell]" lang ))) ; don't ask for R
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(setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)
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(require 'ox-latex)
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;;; XeLaTeX customisations
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;; remove "inputenc" from default packages as it clashes with xelatex
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(setf org-latex-default-packages-alist
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(remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))
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;(setq org-latex-pdf-process '("latexmk -pdf
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; -pdflatex='xelatex -shell-escape -interaction nonstopmode' -bibtex -f %f "))
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(setq org-latex-pdf-process
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'("latexmk -pdflatex='xelatex -interaction nonstopmode' -pdf -bibtex -f %f"))
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;; avoid hypersetup
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(setq org-latex-with-hyperref nil)
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;; latex templates
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;\\usepackage[authoryear]{natbib}
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(add-to-list 'org-latex-classes
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'("myarticle"
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"\\documentclass[12pt]{article}
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\\usepackage[labelfont=bf]{caption}
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\\usepackage{times}
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[NO-DEFAULT-PACKAGES]"
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("\\section{%s}" . "\\section*{%s}")
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("\\subsection{%s}" . "\\subsection*{%s}")
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("\\subsubsection{%s}" . "\\subsubsection*{%s}")
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("\\paragraph{%s}" . "\\paragraph*{%s}")
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("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
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;; latex templates
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(add-to-list 'org-latex-classes
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'("mybeamerxl"
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"\\documentclass[presentation,20pt]{beamer}
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\\usetheme{default}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("mybeamerposter"
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"\\documentclass[final]{beamer}
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\\usetheme{ph}
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\\usepackage[orientation=portrait,size=a0,scale=1.4]{beamerposter}
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\\usepackage[absolute,overlay]{textpos}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("mybeamerm"
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"\\documentclass[presentation]{beamer}
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\\usetheme{default}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(add-to-list 'org-latex-classes
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'("cv"
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"\\documentclass[10pt]{extarticle}
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\\usepackage[authoryear]{natbib}
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[NO-DEFAULT-PACKAGES]"))
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(setq org-latex-listings 'minted)
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'(org-export-latex-listings-langs
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(quote ((emacs-lisp "Lisp")
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(lisp "Lisp")
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(clojure "Lisp")
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(c "C")
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(cc "C++")
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(fortran "fortran")
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(perl "Perl")
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(cperl "Perl")
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(python "Python")
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(ruby "Ruby")
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(html "HTML")
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(xml "XML")
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(tex "TeX")
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(latex "TeX")
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(shell-script "bash")
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(gnuplot "Gnuplot")
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(ocaml "Caml")
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(caml "Caml")
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(sql "SQL")
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(sqlite "sql")
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(R-mode "R"))))
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(setq org-latex-minted-options
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'(("linenos=true") ("bgcolor=lightgray")))
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; set timestamp format
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;;----------------------------------------------------------------------
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;; bibtex
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;;----------------------------------------------------------------------
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(require 'bibtex)
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(require 'org-ref)
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(require 'org-ref-pubmed)
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(require 'org-ref-wos)
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(require 'org-ref-scopus)
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(setq reftex-default-bibliography '("master.bib"))
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(setq org-ref-default-bibliography '("master.bib"))
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@ -0,0 +1,163 @@
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;; This is the .emacs configuration file
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;; Large parts of this have been copied from other people
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;; PH, 12/1/16
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;;----------------------------------------------------------------------
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;; Global
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;;----------------------------------------------------------------------
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;; get rid of yes or no
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(fset 'yes-or-no-p 'y-or-n-p)
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;; package archives
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(require 'package)
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(add-to-list 'package-archives
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'("org" . "http://orgmode.org/elpa/"))
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(add-to-list 'package-archives
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'("melpa" . "http://melpa.org/packages/"))
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(add-to-list 'package-archives
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'("melpa-stable" . "http://stable.melpa.org/packages/"))
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(setq package-enable-at-startup nil)
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(package-initialize)
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(unless (package-installed-p 'use-package)
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(package-refresh-contents)
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(package-install 'use-package))
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(setq use-package-verbose t)
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(setq use-package-always-ensure t)
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(eval-when-compile (require 'use-package))
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(setq default-fill-column 72)
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;; Tell emacs where is your personal elisp lib dir
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;(add-to-list 'load-path "~/.emacs.d/lisp/")
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;; keyboard binding to replace M-x
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(global-set-key "\C-x\C-m" 'execute-extended-command)
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(global-set-key "\C-c\C-m" 'execute-extended-command)
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;;----------------------------------------------------------------------
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;; org mode
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;;----------------------------------------------------------------------
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;; remove comments from org document for use with export hook
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;; https://emacs.stackexchange.com/questions/22574/orgmode-export-how-to-prevent-a-new-line-for-comment-lines
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(defun delete-org-comments (backend)
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(loop for comment in (reverse (org-element-map
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(org-element-parse-buffer)
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'comment 'identity))
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do
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(setf (buffer-substring (org-element-property :begin comment)
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(org-element-property :end comment))
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"")))
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;; add to export hook
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(add-hook 'org-export-before-processing-hook 'delete-org-comments)
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;;----------------------------------------------------------------------
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;; ess
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;;----------------------------------------------------------------------
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(require 'ess)
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(require 'ess-site)
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(setq tab-width 2)
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;(whitespace-mode t)
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; let ess not ask for starting directory
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(setq ess-ask-for-ess-directory nil)
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; disable auto complete (takes too long)
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(setq ess-use-auto-complete nil)
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;(linum-mode t)
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(add-hook 'ess-mode-hook
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(lambda ()
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(whitespace-mode t)
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(linum-mode t)
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; if you uncomment this and reload .emacs from within an R buffer,
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; it should work as a hack
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(setq ess-indent-with-fancy-comments nil)
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(setq ess-style nil)))
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;;----------------------------------------------------------------------
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;; Org
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;;----------------------------------------------------------------------
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(require 'org)
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(require 'org-element)
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;; window setup
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(setq org-agenda-restore-windows-after-quit t)
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(setq org-agenda-skip-scheduled-if-done t)
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;; use ox-extra to ignore certain headings
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(require 'ox-extra)
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(ox-extras-activate '(ignore-headlines))
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;; disable indenting
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(require 'org-indent)
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(org-indent-mode -1)
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;; we don't want raw inline calls to include a newline
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;;(setq org-babel-inline-result-wrap "well, %s")
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;; indentation
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(defun my-tab-related-stuff ()
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; (setq indent-tabs-mode t)
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; (setq tab-stop-list (number-sequence 4 200 4))
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; (setq default-tab-width 2)
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(setq tab-width 2))
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; (setq indent-line-function 'insert-tab))
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(add-hook 'org-mode-hook 'my-tab-related-stuff)
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;; inline results wrapping
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(setq org-babel-inline-result-wrap "%s")
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;; active Babel languages
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(org-babel-do-load-languages
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'org-babel-load-languages
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'((R . t)
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(latex . t)
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(dot . t)
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(shell . t)
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(ditaa . t)
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))
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;; we trust our own R code so we do not need to confirm
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||||
(defun my-org-confirm-babel-evaluate (lang body)
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(not (string-match "[Rlatexdotditaashell]" lang ))) ; don't ask for R
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(setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)
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|
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(require 'ox-latex)
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;;; XeLaTeX customisations
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;; remove "inputenc" from default packages as it clashes with xelatex
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(setf org-latex-default-packages-alist
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(remove '("AUTO" "inputenc" t) org-latex-default-packages-alist))
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;(setq org-latex-pdf-process '("latexmk -pdf
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; -pdflatex='xelatex -shell-escape -interaction nonstopmode' -bibtex -f %f "))
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(setq org-latex-pdf-process
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'("latexmk -pdflatex='xelatex -interaction nonstopmode' -pdf -bibtex -f %f"))
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;; avoid hypersetup
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(setq org-latex-with-hyperref nil)
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;; latex templates
|
||||
;\\usepackage[authoryear]{natbib}
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(add-to-list 'org-latex-classes
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'("myarticle"
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"\\documentclass[12pt]{article}
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\\usepackage[labelfont=bf]{caption}
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\\usepackage{times}
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[NO-DEFAULT-PACKAGES]"
|
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("\\section{%s}" . "\\section*{%s}")
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("\\subsection{%s}" . "\\subsection*{%s}")
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("\\subsubsection{%s}" . "\\subsubsection*{%s}")
|
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("\\paragraph{%s}" . "\\paragraph*{%s}")
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("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
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;;----------------------------------------------------------------------
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;; bibtex
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||||
;;----------------------------------------------------------------------
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(require 'bibtex)
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(require 'org-ref)
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(require 'org-ref-pubmed)
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(require 'org-ref-wos)
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(require 'org-ref-scopus)
|
||||
(setq reftex-default-bibliography '("master.bib"))
|
||||
(setq org-ref-default-bibliography '("master.bib"))
|
||||
|
|
@ -111,7 +111,7 @@
|
|||
% \centering
|
||||
\vskip7.6ex
|
||||
|
||||
\usebeamercolor{title in headline}{\color{fg}\textbf{\huge{\inserttitle}}\\[1ex]}
|
||||
\usebeamercolor{title in headline}{\color{fg}\textbf{\Huge{\inserttitle}}\\[1ex]}
|
||||
\usebeamercolor{author in headline}{\color{fg}\large{\insertauthor}\\[1ex]}
|
||||
\vskip2.4ex
|
||||
\end{beamercolorbox}
|
||||
|
@ -146,7 +146,7 @@
|
|||
\begin{columns}[c,onlytextwidth]
|
||||
\column{.35\textwidth}
|
||||
%\begin{beamercolorbox}[leftskip=-0.5cm,wd=\columnwidth, ht=3cm]{logo}
|
||||
\begin{beamercolorbox}[leftskip=-0.5cm,\columnwidth, ht=4cm]{logo}
|
||||
\begin{beamercolorbox}[leftskip=-0.5cm,wd=\columnwidth, ht=4cm]{logo}
|
||||
\includegraphics[width=0.9\textwidth,right]{logo_feinstein.pdf}
|
||||
%\vskip1.6ex
|
||||
\end{beamercolorbox}
|
||||
|
@ -169,10 +169,11 @@
|
|||
|
||||
|
||||
\begin{tabular}{rllrll}
|
||||
\textbf{Philipp Homan, MD, PhD} & & & & & \\
|
||||
phoman1@northwell.edu & &
|
||||
\includegraphics[width=0.5in]{twitter.pdf} & @philipphoman &
|
||||
\includegraphics[width=0.5in]{github.pdf} & github.com/philipphoman \\
|
||||
%\textbf{Philipp Homan, MD, PhD} & & & & & \\
|
||||
\textbf{\auth} & & & & & \\
|
||||
\authemail & &
|
||||
\includegraphics[width=0.5in]{twitter.pdf} & \authtwitter &
|
||||
\includegraphics[width=0.5in]{github.pdf} & \authgithub \\
|
||||
\end{tabular}
|
||||
\vspace{-0.2ex}
|
||||
|
||||
|
|
|
@ -1,5 +1,5 @@
|
|||
#+startup: beamer
|
||||
#+TITLE: Using org-mode to produce scientific posters
|
||||
#+TITLE: Using org-mode for scientific posters
|
||||
* Preamble :ignore:
|
||||
** General comments :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
|
@ -10,6 +10,8 @@
|
|||
# ----------------------------------------------------------------------
|
||||
** Specific comments for this manuscript :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
# This is a comment
|
||||
# ----------------------------------------------------------------------
|
||||
** org specific settings :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
#+OPTIONS: email:nil toc:nil num:nil author:nil date:t tex:t title:nil
|
||||
|
@ -39,12 +41,16 @@
|
|||
#+LATEX_HEADER: \newcommand{\Xoi}[1]{#1(i)}
|
||||
#+LATEX_HEADER: \newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}}
|
||||
#+LATEX_HEADER: \newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)}
|
||||
#+LATEX_HEADER: \newcommand{\auth}{Philipp Homan, MD, PhD}
|
||||
#+LATEX_HEADER: \newcommand{\authemail}{phoman1@northwell.edu}
|
||||
#+LATEX_HEADER: \newcommand{\authtwitter}{@philipphoman}
|
||||
#+LATEX_HEADER: \newcommand{\authgithub}{github.com/philipphoman}
|
||||
#+LATEX_HEADER: \date{}
|
||||
# ----------------------------------------------------------------------
|
||||
** Authors and affiliations :ignore:
|
||||
# ----------------------------------------------------------------------
|
||||
#+LATEX_HEADER: \author{
|
||||
#+LATEX_HEADER: Philipp Homan$^{1}$,
|
||||
#+LATEX_HEADER: Philipp Homan$^{1}$
|
||||
#+LATEX_HEADER: \\
|
||||
#+LATEX_HEADER: \normalsize{$^{1}$Department of Psychiatry,}
|
||||
#+LATEX_HEADER: \normalsize{The Donald and Barbara Zucker}
|
||||
|
@ -148,16 +154,16 @@
|
|||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
- Org-mode is not only useful for producing blog posts and even
|
||||
scientific manuscripts; it is also perfectly suitable to make
|
||||
- Here we show how org-mode (version src_elisp{org-version}
|
||||
{{{results(9.1.7)}}}) together with emacs (version
|
||||
src_elisp{emacs-version} {{{results(25.2.2)}}}) can be used to make
|
||||
decent looking scientific posters
|
||||
- We combine a relatively simple custom \LaTeX style file and common
|
||||
org-mode syntax
|
||||
- The nice thing about org-mode is that we can populate the poster with
|
||||
code, graphs and numbers from inline code in languages such as R,
|
||||
python, Matlab and even shell scripting
|
||||
- Inline code would look like this, which will produce a graph
|
||||
(Fig. [[figcode1]]):
|
||||
- With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
- For example, this poster was created on {{{time(%Y-%m-%d %H:%M)}}}
|
||||
- Inline code could look like this (which will produce a graph;
|
||||
Fig. [[figcode1]]):
|
||||
|
||||
**** Block
|
||||
:PROPERTIES:
|
||||
|
@ -337,6 +343,6 @@ plot(d2, col="blue", lwd=3)
|
|||
:PROPERTIES:
|
||||
:BEAMER_env: block
|
||||
:END:
|
||||
- This little example is meant to show how incredibly versatile
|
||||
org-mode is
|
||||
- This little example is meant to show how versatile org-mode is
|
||||
- Scientific posters can be produced with a simple text editor
|
||||
|
||||
|
|
Binary file not shown.
|
@ -1,4 +1,4 @@
|
|||
% Created 2018-04-02 Mon 22:17
|
||||
% Created 2018-04-03 Tue 15:36
|
||||
% Intended LaTeX compiler: pdflatex
|
||||
\documentclass[final]{beamer}
|
||||
\usetheme{ph}
|
||||
|
@ -23,9 +23,13 @@
|
|||
\newcommand{\Xoi}[1]{#1(i)}
|
||||
\newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}}
|
||||
\newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)}
|
||||
\newcommand{\auth}{Philipp Homan, MD, PhD}
|
||||
\newcommand{\authemail}{phoman1@northwell.edu}
|
||||
\newcommand{\authtwitter}{@philipphoman}
|
||||
\newcommand{\authgithub}{github.com/philipphoman}
|
||||
\date{}
|
||||
\author{
|
||||
Philipp Homan$^{1}$,
|
||||
Philipp Homan$^{1}$
|
||||
\\
|
||||
\normalsize{$^{1}$Department of Psychiatry,}
|
||||
\normalsize{The Donald and Barbara Zucker}
|
||||
|
@ -33,25 +37,25 @@ Philipp Homan$^{1}$,
|
|||
\normalsize{Hempstead, NY}
|
||||
}
|
||||
\usetheme{default}
|
||||
\date{2018-04-02 22:17}
|
||||
\title{Using org-mode to produce scientific posters}
|
||||
\date{2018-04-03 15:35}
|
||||
\title{Using org-mode for scientific posters}
|
||||
\begin{document}
|
||||
|
||||
\begin{frame}[fragile,label={sec:orgec21ff0}]{}
|
||||
\begin{frame}[fragile,label={sec:orge330f04}]{}
|
||||
\begin{columns}
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Background}
|
||||
\begin{itemize}
|
||||
\item Org-mode is not only useful for producing blog posts and even
|
||||
scientific manuscripts; it is also perfectly suitable to make
|
||||
\item Here we show how org-mode (version
|
||||
9.1.7) together with emacs (version
|
||||
25.2.2) can be used to make
|
||||
decent looking scientific posters
|
||||
\item We combine a relatively simple custom \LaTeX style file and common
|
||||
org-mode syntax
|
||||
\item The nice thing about org-mode is that we can populate the poster with
|
||||
code, graphs and numbers from inline code in languages such as R,
|
||||
python, Matlab and even shell scripting
|
||||
\item Inline code would look like this, which will produce a graph
|
||||
(Fig. \ref{fig:org498cf2b}):
|
||||
\item With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
\item For example, this poster was created on 2018-04-03 15:35
|
||||
\item Inline code could look like this (which will produce a graph;
|
||||
Fig. \ref{fig:org646b9c5}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -67,7 +71,7 @@ hist(x2, col="blue", add=TRUE)
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:org498cf2b}
|
||||
\caption{\label{fig:org646b9c5}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -81,7 +85,7 @@ This is the output.}
|
|||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:org80b4f16}) :
|
||||
table (Table \ref{tab:org2f8852f}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -100,6 +104,8 @@ mutate(name=c("x1", "x2"))
|
|||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\caption{\label{tab:org2f8852f}
|
||||
A table summarizing the two distributions.}
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
\hline
|
||||
|
@ -109,9 +115,6 @@ minimum & q1 & median & mean & q3 & maximum & name\\
|
|||
-2.17 & -0.45 & 0.07 & 0.13 & 0.85 & 2.23 & x2\\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\caption{\label{tab:org80b4f16}
|
||||
A table summarizing the two distributions.}
|
||||
|
||||
\end{table}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
|
@ -122,7 +125,7 @@ A table summarizing the two distributions.}
|
|||
\begin{block}{Graphics}
|
||||
\begin{itemize}
|
||||
\item We can use shell scripting to grab an image with curl from the
|
||||
internet (Fig. \ref{fig:orge0395cc}):
|
||||
internet (Fig. \ref{fig:org0ba80fb}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -139,7 +142,7 @@ curl -0 https://www.gnu.org/software/emacs/images/emacs.png
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[page=9,width=0.2\textwidth]{emacs.png}
|
||||
\caption{\label{fig:orge0395cc}
|
||||
\caption{\label{fig:org0ba80fb}
|
||||
This is the downloaded image.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -185,7 +188,7 @@ derived as follows:
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4l.png}
|
||||
\caption{\label{fig:org9158640}
|
||||
\caption{\label{fig:org9542cf7}
|
||||
This is the left figure of a two-column block, showing the density of \(x1\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -195,7 +198,7 @@ This is the left figure of a two-column block, showing the density of \(x1\).}
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4r.png}
|
||||
\caption{\label{fig:org4bc9c2a}
|
||||
\caption{\label{fig:org3813d21}
|
||||
This is the right figure. It shows the density of \(x2\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -204,8 +207,7 @@ This is the right figure. It shows the density of \(x2\).}
|
|||
|
||||
\begin{block}{Conclusions}
|
||||
\begin{itemize}
|
||||
\item This little example is meant to show how incredibly versatile
|
||||
org-mode is
|
||||
\item This little example is meant to show how versatile org-mode is
|
||||
\item Scientific posters can be produced with a simple text editor
|
||||
\end{itemize}
|
||||
\end{block}
|
||||
|
|
|
@ -1,4 +1,4 @@
|
|||
% Created 2018-04-02 Mon 22:15
|
||||
% Created 2018-04-03 Tue 15:32
|
||||
% Intended LaTeX compiler: pdflatex
|
||||
\documentclass[final]{beamer}
|
||||
\usetheme{ph}
|
||||
|
@ -23,9 +23,13 @@
|
|||
\newcommand{\Xoi}[1]{#1(i)}
|
||||
\newcommand{\frakPQ}[2]{\frac{\Xoi{#1}}{\Xoi{#2}}}
|
||||
\newcommand{\DKLPQ}[3]{D_{\mathrm{KL}}(#1 #3 #2)}
|
||||
\newcommand{\auth}{Philipp Homan, MD, PhD}
|
||||
\newcommand{\authemail}{phoman1@northwell.edu}
|
||||
\newcommand{\authtwitter}{@philipphoman}
|
||||
\newcommand{\authgithub}{github.com/philipphoman}
|
||||
\date{}
|
||||
\author{
|
||||
Philipp Homan$^{1}$,
|
||||
Philipp Homan$^{1}$
|
||||
\\
|
||||
\normalsize{$^{1}$Department of Psychiatry,}
|
||||
\normalsize{The Donald and Barbara Zucker}
|
||||
|
@ -33,25 +37,25 @@ Philipp Homan$^{1}$,
|
|||
\normalsize{Hempstead, NY}
|
||||
}
|
||||
\usetheme{default}
|
||||
\date{2018-04-02 22:15}
|
||||
\title{Using org-mode to produce scientific posters}
|
||||
\date{2018-04-03 15:31}
|
||||
\title{Using org-mode for scientific posters}
|
||||
\begin{document}
|
||||
|
||||
\begin{frame}[fragile,label={sec:org1571d9a}]{}
|
||||
\begin{frame}[fragile,label={sec:org04c7cf4}]{}
|
||||
\begin{columns}
|
||||
\begin{column}[t]{0.45\columnwidth}
|
||||
\begin{block}{Background}
|
||||
\begin{itemize}
|
||||
\item Org-mode is not only useful for producing blog posts and even
|
||||
scientific manuscripts; it is also perfectly suitable to make
|
||||
\item Here we show how org-mode (version
|
||||
9.1.7) together with emacs (version
|
||||
25.2.2) can be used to make
|
||||
decent looking scientific posters
|
||||
\item We combine a relatively simple custom \LaTeX style file and common
|
||||
org-mode syntax
|
||||
\item The nice thing about org-mode is that we can populate the poster with
|
||||
code, graphs and numbers from inline code in languages such as R,
|
||||
python, Matlab and even shell scripting
|
||||
\item Inline code would look like this, which will produce a graph
|
||||
(Fig. \ref{fig:org6629f8c}):
|
||||
\item With org-mode we can populate the poster with code, graphs and numbers
|
||||
from inline code in languages such as R, python, Matlab and even shell
|
||||
scripting
|
||||
\item For example, this poster was created on 2018-04-03 15:31
|
||||
\item Inline code could look like this (which will produce a graph;
|
||||
Fig. \ref{fig:orgbc6b6ab}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -67,7 +71,7 @@ hist(x2, col="blue", add=TRUE)
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{3.png}
|
||||
\caption{\label{fig:org6629f8c}
|
||||
\caption{\label{fig:orgbc6b6ab}
|
||||
This is the output.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -81,7 +85,7 @@ This is the output.}
|
|||
capabilities
|
||||
\item Some code to process the first vector from above to make a table out
|
||||
of its summary could look like this, which would result in a little
|
||||
table (Table \ref{tab:org74ecade}) :
|
||||
table (Table \ref{tab:org62ea45d}) :
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -100,6 +104,8 @@ mutate(name=c("x1", "x2"))
|
|||
\vspace{2cm}
|
||||
|
||||
\begin{table}[htbp]
|
||||
\caption{\label{tab:org62ea45d}
|
||||
A table summarizing the two distributions.}
|
||||
\centering
|
||||
\begin{tabular}{rrrrrrl}
|
||||
\hline
|
||||
|
@ -109,9 +115,6 @@ minimum & q1 & median & mean & q3 & maximum & name\\
|
|||
-2.17 & -0.45 & 0.07 & 0.13 & 0.85 & 2.23 & x2\\
|
||||
\hline
|
||||
\end{tabular}
|
||||
\caption{\label{tab:org74ecade}
|
||||
A table summarizing the two distributions.}
|
||||
|
||||
\end{table}
|
||||
\end{column}
|
||||
\end{columns}
|
||||
|
@ -122,7 +125,7 @@ A table summarizing the two distributions.}
|
|||
\begin{block}{Graphics}
|
||||
\begin{itemize}
|
||||
\item We can use shell scripting to grab an image with curl from the
|
||||
internet (Fig. \ref{fig:org966972d}):
|
||||
internet (Fig. \ref{fig:org45de491}):
|
||||
\end{itemize}
|
||||
|
||||
\begin{columns}
|
||||
|
@ -139,7 +142,7 @@ curl -0 https://www.gnu.org/software/emacs/images/emacs.png
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[page=9,width=0.2\textwidth]{emacs.png}
|
||||
\caption{\label{fig:org966972d}
|
||||
\caption{\label{fig:org45de491}
|
||||
This is the downloaded image.}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -185,7 +188,7 @@ derived as follows:
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4l.png}
|
||||
\caption{\label{fig:orga3a0e13}
|
||||
\caption{\label{fig:org2b19bfd}
|
||||
This is the left figure of a two-column block, showing the density of \(x1\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -195,7 +198,7 @@ This is the left figure of a two-column block, showing the density of \(x1\).}
|
|||
\begin{figure}[htbp]
|
||||
\centering
|
||||
\includegraphics[width=.9\linewidth]{4r.png}
|
||||
\caption{\label{fig:org6c7191a}
|
||||
\caption{\label{fig:org03df045}
|
||||
This is the right figure. It shows the density of \(x2\).}
|
||||
\end{figure}
|
||||
\end{column}
|
||||
|
@ -204,8 +207,7 @@ This is the right figure. It shows the density of \(x2\).}
|
|||
|
||||
\begin{block}{Conclusions}
|
||||
\begin{itemize}
|
||||
\item This little example is meant to show how incredibly versatile
|
||||
org-mode is
|
||||
\item This little example is meant to show how versatile org-mode is
|
||||
\item Scientific posters can be produced with a simple text editor
|
||||
\end{itemize}
|
||||
\end{block}
|
||||
|
|
Loading…
Reference in New Issue