Initial Commit
Daniel Gomez
commit
77d048ef60
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*.aux
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*.glo
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*.idx
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*.log
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*.toc
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*.ist
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*.acn
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*.acr
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*.alg
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*.bbl
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*.blg
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*.dvi
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*.glg
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*.gls
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*.ilg
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*.ind
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*.lof
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*.lot
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*.maf
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*.mtc
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*.mtc1
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*.out
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*.synctex.gz
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*.tex~
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_minted*
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auto
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*-blx.bib
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*.tex
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*.pdf
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*.docx
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*ltximg*
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#+TITLE: Org-thesis
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#+AUTHOR: Daniel Gomez
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* Introduction
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This repository contains the skeleton of a Ph.D. thesis written in Org Mode. It does not aim to be an authoritative guide on writing thesis with Org Mode, i.e., it only represents the solution that I found most convenient within the time frame of my Ph.D.
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The goal of this setup was to allow the seamless inclusion of research chapters into the thesis *without* having to modify the included files at all. In other words, chapters can live as standalone repositories with completely different export settings. In other words, this setup separates content from form and allows content to move freely between the thesis and a chapter.
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* Installation & Requirements
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You will need at least Emacs 26 and Org 9.2 for this to work because it relies on Org's #+INCLUDE derivative, which is broken for files containing relative paths and links in earlier versions. You will also need a recent version of LaTeX. Details on my LaTeX setup are described in the [[./latex-setup.org]] file in the root of this repository. The information was extracted automatically using =scimax-latex.el=. Information about scimax-latex is also described in the end of the latex setup file.
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You will also need org-ref for links to equations and citations to work as expected.
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And to compile the thesis as is you'd require the [[https://github.com/Pseudomanifold/latex-mimosis][mimosis]] latex class. It'll probably work if you change class, but YMMV.
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* Usage
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More usage details can be found under [[https://write.as/dani/writing-a-phd-thesis-with-org-mode][this blog post.]] For more information, feel free to open an issue.
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* Possible improvements
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** Repository maybe tied to my class choices?
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The setup files and LaTeX classes seen here are those that I use. It'd be nice to have a more minimalistic example that didn't require such dependencies.
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** Bibliography management
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Currently the bibliography management is not properly modular. I use Zotero for bibliography management and I have Zotero export a master file for the thesis and individual files for each chapter. It works well, but I cannot simply include a new chapter into the thesis without first adapting Zotero as well
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** Manual management of lines to skip
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For each included file, I skip LaTeX derivatives by constraining the number of lines to be included. This is manual work and couple probably be improved.
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#+TITLE: LaTeX setup
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This file describes how LaTeX is setup on your computer.
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* Executables
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latex: /Library/TeX/texbin/latex
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pdflatex: /Library/TeX/texbin/pdflatex
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bibtex: /Library/TeX/texbin/bibtex
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biber: /Library/TeX/texbin/biber
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tlmgr: /Library/TeX/texbin/tlmgr
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kpsewhich: /Library/TeX/texbin/kpsewhich
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texdoc: /Library/TeX/texbin/texdoc
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Configuration:
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texmf configuration values (from /usr/local/texlive/2016/texmf.cnf):
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TEXMFVAR = ~/Library/texlive/2016/texmf-var
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TEXMFHOME = ~/Library/texmf
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TEXMFCONFIG = ~/Library/texlive/2016/texmf-config
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* Latex classes org-mode knows about
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Here are some relevant variables
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help:org-format-latex-header
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help:org-latex-default-packages-alist
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help:org-latex-packages-alist
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help:org-latex-pdf-process
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Note: Not every class has a corresponding style file. Click on the texdoc link to learn more about the class.
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Missing files should be installed in the TEXMFHOME directory listed above. See https://en.wikibooks.org/wiki/LaTeX/Installing_Extra_Packages for help.
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** elsarticle creates documents with this LaTeX documentclass: elsarticle
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This is the header that is expanded.
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\documentclass{elsarticle}
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[NO-DEFAULT-PACKAGES]
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[PACKAGES]
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[EXTRA]
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LaTeX path for class: [[/usr/local/texlive/2016/texmf-dist/tex/latex/elsarticle/elsarticle.cls]]
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[[elisp:(shell-command "texdoc elsarticle"][texdoc elsarticle]]
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Latex style path: [[]]
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** mimosis creates documents with this LaTeX documentclass: mimosis
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This is the header that is expanded.
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\documentclass{mimosis}
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[NO-DEFAULT-PACKAGES]
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[PACKAGES]
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[EXTRA]
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\newcommand{\mboxparagraph}[1]{\paragraph{#1}\mbox{}\\}
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\newcommand{\mboxsubparagraph}[1]{\subparagraph{#1}\mbox{}\\}
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LaTeX path for class: [[/Users/user/Library/texmf/tex/latex/local/mimosis.cls]]
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[[elisp:(shell-command "texdoc mimosis"][texdoc mimosis]]
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Latex style path: [[]]
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** mimore creates documents with this LaTeX documentclass: mimore
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This is the header that is expanded.
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\documentclass{mimore}
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[NO-DEFAULT-PACKAGES]
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[PACKAGES]
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[EXTRA]
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LaTeX path for class: [[/Users/user/Library/texmf/tex/latex/local/mimore.cls]]
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[[elisp:(shell-command "texdoc mimore"][texdoc mimore]]
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Latex style path: [[]]
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** article creates documents with this LaTeX documentclass: article
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This is the header that is expanded.
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\documentclass[11pt]{article}
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LaTeX path for class: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/article.cls]]
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[[elisp:(shell-command "texdoc article"][texdoc article]]
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Latex style path: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/article.sty]]
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** report creates documents with this LaTeX documentclass: report
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This is the header that is expanded.
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\documentclass[11pt]{report}
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LaTeX path for class: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/report.cls]]
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[[elisp:(shell-command "texdoc report"][texdoc report]]
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Latex style path: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/report.sty]]
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** book creates documents with this LaTeX documentclass: book
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This is the header that is expanded.
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\documentclass[11pt]{book}
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|
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LaTeX path for class: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.cls]]
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|
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[[elisp:(shell-command "texdoc book"][texdoc book]]
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Latex style path: [[/usr/local/texlive/2016/texmf-dist/tex/latex/base/book.sty]]
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* org-mode default latex packages
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|
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- inputenc (options=AUTO) [[elisp:(shell-command "texdoc inputenc"][texdoc inputenc]]
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- fontenc (options=T1) [[elisp:(shell-command "texdoc fontenc"][texdoc fontenc]]
|
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- graphicx (options=) [[elisp:(shell-command "texdoc graphicx"][texdoc graphicx]]
|
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- grffile (options=) [[elisp:(shell-command "texdoc grffile"][texdoc grffile]]
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- longtable (options=) [[elisp:(shell-command "texdoc longtable"][texdoc longtable]]
|
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- wrapfig (options=) [[elisp:(shell-command "texdoc wrapfig"][texdoc wrapfig]]
|
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- rotating (options=) [[elisp:(shell-command "texdoc rotating"][texdoc rotating]]
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- ulem (options=normalem) [[elisp:(shell-command "texdoc ulem"][texdoc ulem]]
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- amsmath (options=) [[elisp:(shell-command "texdoc amsmath"][texdoc amsmath]]
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- textcomp (options=) [[elisp:(shell-command "texdoc textcomp"][texdoc textcomp]]
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- amssymb (options=) [[elisp:(shell-command "texdoc amssymb"][texdoc amssymb]]
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- capt-of (options=) [[elisp:(shell-command "texdoc capt-of"][texdoc capt-of]]
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- hyperref (options=) [[elisp:(shell-command "texdoc hyperref"][texdoc hyperref]]
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* org-mode defined latex packages
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* org-mode LaTeX compiling setup
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org-latex-pdf-process = "(latexmk -pdflatex='pdflatex -shell-escape -interaction nonstopmode' -pdf -bibtex -f %f)"
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* Generate LaTeX setup
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Install scimax-latex and then run =scimax-latex-setup=.
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#+begin_src emacs-lisp
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(use-package scimax-latex
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:straight (scimax-latex :type git
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:host github
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:repo "jkitchin/scimax"
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:files ("scimax-latex.el"))
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:commands (scimax-latex-setup
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kpsewhich
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texdoc))
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#+end_src
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Binary file not shown.
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After Width: | Height: | Size: 18 KiB |
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#+TITLE: A research chapter
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#+LATEX_CLASS: elsarticle
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#+LATEX_CLASS_OPTIONS: [authoryear,preprint,5p,times,twocolumn,11pt]
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#+SETUPFILE: manuscript.setup
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#+LATEX_HEADER:\bibliography{./ref/bibliography}
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* Frontmatter :ignore:journal:
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#+LATEX: \begin{frontmatter}
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** Author List :ignore:
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#+BEGIN_EXPORT latex
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\author[add1]{First Author\corref{cor1}}
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\ead{first@author.edu}
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\author[add1,add2]{Senior Author}
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\ead{senior@author.edu}
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\address[add1]{Center of Org Studies, GNUniversity, The Earth}
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\address[add2]{Institute of Freedom, The Land of Lisp}
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\cortext[cor1]{Corresponding author}
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#+END_EXPORT
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** Abstract :ignore:
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#+begin_abstract
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This file exemplifies how I write a research chapter with Org Mode. Bibliographical references are stored in the =/bib= directory and images in =/img=.
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Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec hendrerit tempor tellus. Donec pretium posuere tellus. Proin quam nisl, tincidunt et, mattis eget, convallis nec, purus. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Nulla posuere. Donec vitae dolor. Nullam tristique diam non turpis. Cras placerat accumsan nulla. Nullam rutrum. Nam vestibulum accumsan nisl.
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#+end_abstract
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** Keywords :ignore:
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#+begin_keyword
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lorem \sep ipsum \sep dolor \sep sit \sep amet
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#+end_keyword
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#+LATEX: \end{frontmatter}
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* Introduction
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Aliquam erat volutpat. parencite:big Nunc eleifend leo vitae magna, as discussed in cite:small. In id erat non orci commodo lobortis. Proin neque massa, cursus ut, gravida ut, lobortis eget, lacus. Sed diam. Praesent fermentum tempor tellus. Nullam tempus. Mauris ac felis vel velit tristique imperdiet. Donec at pede. Etiam vel neque nec dui dignissim bibendum. Vivamus id enim. Phasellus neque orci, porta a, aliquet quis, semper a, massa. Phasellus purus. Pellentesque tristique imperdiet tortor. Nam euismod tellus id erat.
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Pellentesque dapibus suscipit ligula. Donec posuere augue in quam. Etiam vel tortor sodales tellus ultricies commodo. Suspendisse potenti. Aenean in sem ac leo mollis blandit. Donec neque quam, dignissim in, mollis nec, sagittis eu, wisi. Phasellus lacus. Etiam laoreet quam sed arcu. Phasellus at dui in ligula mollis ultricies. Integer placerat tristique nisl. Praesent augue. Fusce commodo. Vestibulum convallis, lorem a tempus semper, dui dui euismod elit, vitae placerat urna tortor vitae lacus. Nullam libero mauris, consequat quis, varius et, dictum id, arcu. Mauris mollis tincidunt felis. Aliquam feugiat tellus ut neque. Nulla facilisis, risus a rhoncus fermentum, tellus tellus lacinia purus, et dictum nunc justo sit amet elit.
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Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
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* Methods
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** Data Acquisition
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We can have links everywhere. This [[https://www.gnu.org/software/emacs/][link]], for example, points to the Emacs website.
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Aliquam erat volutpat. Nunc eleifend leo vitae magna. In id erat non orci commodo lobortis. Proin neque massa, cursus ut, gravida ut, lobortis eget, lacus. Sed diam. Praesent fermentum tempor tellus. Nullam tempus. Mauris ac felis vel velit tristique imperdiet. Donec at pede. Etiam vel neque nec dui dignissim bibendum. Vivamus id enim. Phasellus neque orci, porta a, aliquet quis, semper a, massa. Phasellus purus. Pellentesque tristique imperdiet tortor. Nam euismod tellus id erat.
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It can contain tables as well, with captions, of course, as seen in ref:example-table.
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#+name: example-table
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#+caption: Table with a custom caption.
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| foo | bar | baz |
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| 1 | 2 | 3 |
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Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Donec hendrerit tempor tellus. Donec pretium posuere tellus. Proin quam nisl, tincidunt et, mattis eget, convallis nec, purus. Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Nulla posuere. Donec vitae dolor. Nullam tristique diam non turpis. Cras placerat accumsan nulla. Nullam rutrum. Nam vestibulum accumsan nisl.
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* Results
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Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
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Results can contain some images as well.
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# In this no-op origin tag I just put the name of the code that generated the fig. for bookkeeping.
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#+origin: ~/projects/directory/with/code/that/generated/this/figure.py
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#+name: figure-example
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#+caption: This is an example figure.
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[[./img/img.png]]
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||||
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* Conclusion
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||||
Awesome.
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||||
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||||
* Acknowledgements :journal:
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||||
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Pellentesque dapibus suscipit ligula. Donec posuere augue in quam. Etiam vel tortor sodales tellus ultricies commodo. Suspendisse potenti. Aenean in sem ac leo mollis blandit. Donec neque quam, dignissim in, mollis nec, sagittis eu, wisi. Phasellus lacus. Etiam laoreet quam sed arcu. Phasellus at dui in ligula mollis ultricies. Integer placerat tristique nisl. Praesent augue. Fusce commodo. Vestibulum convallis, lorem a tempus semper, dui dui euismod elit, vitae placerat urna tortor vitae lacus. Nullam libero mauris, consequat quis, varius et, dictum id, arcu. Mauris mollis tincidunt felis. Aliquam feugiat tellus ut neque. Nulla facilisis, risus a rhoncus fermentum, tellus tellus lacinia purus, et dictum nunc justo sit amet elit.
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||||
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||||
|
||||
* Bibliography :ignore:journal:
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||||
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||||
#+BEGIN_EXPORT latex
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||||
\printbibliography
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||||
#+END_EXPORT
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||||
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||||
# For HTML export. Just a hack to avoid triggering org-ref's regexp search.
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#+INCLUDE: ./ref/bib-html-setup.org
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||||
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||||
* Build :noexport:
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||||
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||||
Feel free to add some more config in here, if necessary. This can be useful if you want to use a single =paper.setup=, but still want some per file configuration.
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# -*- mode: org; -*-
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||||
#+STARTUP: content
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||||
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||||
* COMMENT Paper Setup
|
||||
|
||||
The paper setup controls the export of content for publication. Using a dedicated paper setup makes it simpler to include the content later in a thesis, simply by swapping or ignoring the setup of the individual file and using and overarching =thesis.setup=.
|
||||
Additionally, for publication we can remove any setup at all to get a clean export using whatever class provided by the publisher. If NeuroImage is the target, for example, then we should use the elsarticle class. Support for multiple classes for publication, within Emacs Org-Mode, can be found [[https://github.com/jkitchin/scimax/blob/master/ox-manuscript/ox-manuscript.el][in the scimax starters package]].
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||||
To make the main file inclusion simpler, only use the first 5 lines of the paper file for extra configuration. All the rest should go in the setup file.
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||||
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||||
Remember that #+OPTIONS are parsed even from =:noexport:= headings.
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||||
|
||||
* Options :noexport:
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||||
|
||||
The options are intended to remove default clutter that Org adds automatically to the export.
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||||
#+OPTIONS: title:nil date:nil ^:{} toc:nil num:nil d:t author:nil tags:nil
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||||
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||||
* LaTeX headers :noexport:
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||||
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||||
#+latex_header: \usepackage[T1]{fontenc}
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||||
#+latex_header: \usepackage[utf8]{inputenc}
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||||
#+latex_header: \DeclareUnicodeCharacter{200B}{}
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||||
#+latex_header: \usepackage{booktabs}
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||||
#+latex_header: \renewcommand{\arraystretch}{1.1}
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||||
#+latex_header: \usepackage{graphicx}
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||||
#+latex_header: \usepackage{float}
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||||
#+latex_header: \usepackage{amsmath}
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||||
#+latex_header: \usepackage[linktocpage, pdfstartview=FitH, colorlinks, linkcolor=black, anchorcolor=black, citecolor=black, filecolor=black, menucolor=black, urlcolor=black]{hyperref}
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||||
#+latex_header: \usepackage[autocite=plain, backend=biber, doi=true, url=false, hyperref=true, style=apa, maxcitenames=2]{biblatex}
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||||
#+latex_header: \AtEveryBibitem{%
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||||
#+latex_header: \clearfield{issn} % Remove issn
|
||||
#+latex_header: \clearfield{doi} % Remove doi
|
||||
#+latex_header: \ifentrytype{online}{}{% Remove url except for @online
|
||||
#+latex_header: \clearfield{url}
|
||||
#+latex_header: }
|
||||
#+latex_header: }
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||||
#+latex_header: \usepackage[binary-units=true]{siunitx}
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||||
#+latex_header: \DeclareSIUnit\px{px}
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||||
#+latex_header: \usepackage{textcomp}% for '\textdegree' macro
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||||
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||||
|
||||
* HTML headers :noexport:
|
||||
|
||||
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/htmlize.css"/>
|
||||
#+HTML_HEAD: <link rel="stylesheet" type="text/css" href="http://www.pirilampo.org/styles/readtheorg/css/readtheorg.css"/>
|
||||
|
||||
#+HTML_HEAD: <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js"></script>
|
||||
#+HTML_HEAD: <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js"></script>
|
||||
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/lib/js/jquery.stickytableheaders.min.js"></script>
|
||||
#+HTML_HEAD: <script type="text/javascript" src="http://www.pirilampo.org/styles/readtheorg/js/readtheorg.js"></script>
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
#+MACRO: if-not-latex (eval (unless (org-export-derived-backend-p org-export-current-backend 'latex) "$1"))
|
||||
# Print bibliography in other exports that are not LaTeX.
|
||||
{{{if-not-latex(bibliographystyle:apalike)}}}
|
||||
{{{if-not-latex(bibliography:./ref/bibliography.bib)}}}
|
||||
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
% A sample bibliography file from the internets.
|
||||
%
|
||||
|
||||
@article{small,
|
||||
author = {Freely, I.P.},
|
||||
title = {A small paper},
|
||||
journal = {The journal of small papers},
|
||||
year = 1997,
|
||||
volume = {-1},
|
||||
note = {to appear},
|
||||
}
|
||||
|
||||
@article{big,
|
||||
author = {Jass, Hugh},
|
||||
title = {A big paper},
|
||||
journal = {The journal of big papers},
|
||||
year = 7991,
|
||||
volume = {MCMXCVII},
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
% A sample bibliography file from the internets.
|
||||
%
|
||||
|
||||
@article{small,
|
||||
author = {Freely, I.P.},
|
||||
title = {A small paper},
|
||||
journal = {The journal of small papers},
|
||||
year = 1997,
|
||||
volume = {-1},
|
||||
note = {to appear},
|
||||
}
|
||||
|
||||
@article{big,
|
||||
author = {Jass, Hugh},
|
||||
title = {A big paper},
|
||||
journal = {The journal of big papers},
|
||||
year = 7991,
|
||||
volume = {MCMXCVII},
|
||||
}
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
#+TITLE: An introduction
|
||||
|
||||
* Introduction
|
||||
|
||||
We can have equations and reference them using =eqref=, as seen in eqref:larmor.
|
||||
|
||||
#+begin_export latex
|
||||
\begin{equation}
|
||||
\omega_{0} = \gamma B_{0} \label{larmor}
|
||||
\end{equation}
|
||||
#+end_export
|
||||
|
||||
Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
|
||||
|
||||
Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
|
||||
|
||||
Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
|
||||
|
||||
* Theoretical Background
|
||||
|
||||
Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
|
||||
|
||||
|
|
@ -0,0 +1,11 @@
|
|||
#+TITLE: Summary
|
||||
|
||||
* Summary
|
||||
|
||||
Aliquam erat volutpat. Nunc eleifend leo vitae magna. In id erat non orci commodo lobortis. Proin neque massa, cursus ut, gravida ut, lobortis eget, lacus. Sed diam. Praesent fermentum tempor tellus. Nullam tempus. Mauris ac felis vel velit tristique imperdiet. Donec at pede. Etiam vel neque nec dui dignissim bibendum. Vivamus id enim. Phasellus neque orci, porta a, aliquet quis, semper a, massa. Phasellus purus. Pellentesque tristique imperdiet tortor. Nam euismod tellus id erat.
|
||||
|
||||
Nullam eu ante vel est convallis dignissim. Fusce suscipit, wisi nec facilisis facilisis, est dui fermentum leo, quis tempor ligula erat quis odio. Nunc porta vulputate tellus. Nunc rutrum turpis sed pede. Sed bibendum. Aliquam posuere. Nunc aliquet, augue nec adipiscing interdum, lacus tellus malesuada massa, quis varius mi purus non odio. Pellentesque condimentum, magna ut suscipit hendrerit, ipsum augue ornare nulla, non luctus diam neque sit amet urna. Curabitur vulputate vestibulum lorem. Fusce sagittis, libero non molestie mollis, magna orci ultrices dolor, at vulputate neque nulla lacinia eros. Sed id ligula quis est convallis tempor. Curabitur lacinia pulvinar nibh. Nam a sapien.
|
||||
|
||||
Pellentesque dapibus suscipit ligula. Donec posuere augue in quam. Etiam vel tortor sodales tellus ultricies commodo. Suspendisse potenti. Aenean in sem ac leo mollis blandit. Donec neque quam, dignissim in, mollis nec, sagittis eu, wisi. Phasellus lacus. Etiam laoreet quam sed arcu. Phasellus at dui in ligula mollis ultricies. Integer placerat tristique nisl. Praesent augue. Fusce commodo. Vestibulum convallis, lorem a tempus semper, dui dui euismod elit, vitae placerat urna tortor vitae lacus. Nullam libero mauris, consequat quis, varius et, dictum id, arcu. Mauris mollis tincidunt felis. Aliquam feugiat tellus ut neque. Nulla facilisis, risus a rhoncus fermentum, tellus tellus lacinia purus, et dictum nunc justo sit amet elit.
|
||||
|
||||
Aliquam erat volutpat. Nunc eleifend leo vitae magna. In id erat non orci commodo lobortis. Proin neque massa, cursus ut, gravida ut, lobortis eget, lacus. Sed diam. Praesent fermentum tempor tellus. Nullam tempus. Mauris ac felis vel velit tristique imperdiet. Donec at pede. Etiam vel neque nec dui dignissim bibendum. Vivamus id enim. Phasellus neque orci, porta a, aliquet quis, semper a, massa. Phasellus purus. Pellentesque tristique imperdiet tortor. Nam euismod tellus id erat.
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
% A sample bibliography file from the internets.
|
||||
%
|
||||
|
||||
@article{small,
|
||||
author = {Freely, I.P.},
|
||||
title = {A small paper},
|
||||
journal = {The journal of small papers},
|
||||
year = 1997,
|
||||
volume = {-1},
|
||||
note = {to appear},
|
||||
}
|
||||
|
||||
@article{big,
|
||||
author = {Jass, Hugh},
|
||||
title = {A big paper},
|
||||
journal = {The journal of big papers},
|
||||
year = 7991,
|
||||
volume = {MCMXCVII},
|
||||
}
|
||||
|
|
@ -0,0 +1,115 @@
|
|||
#+TITLE: Writing a Thesis with Org Mode
|
||||
#+latex_class: mimosis
|
||||
#+latex_header: \KOMAoptions{headings=small,fontsize=12,DIV=12}
|
||||
#+setupfile: ./thesis.setup
|
||||
#+latex_header: \bibliography{./thesis}
|
||||
#+EXCLUDE_TAGS: journal noexport
|
||||
|
||||
* Acronym and Glossary :ignore:
|
||||
|
||||
# {{{glossaryentry(LaTeX,\LaTeX,A document preparation system,LaTeX)}}}
|
||||
# {{{glossaryentry(Real Numbers,$\real$,The set of Real numbers,Real Numbers)}}}
|
||||
|
||||
# #+latex_header: \makeglossaries
|
||||
|
||||
* Frontmatter :ignore:
|
||||
#+BEGIN_EXPORT latex
|
||||
\frontmatter
|
||||
#+END_EXPORT
|
||||
|
||||
#+INCLUDE: ./title.org
|
||||
|
||||
* Mainmatter :ignore:
|
||||
|
||||
#+BEGIN_EXPORT latex
|
||||
\tableofcontents
|
||||
\mainmatter
|
||||
#+END_EXPORT
|
||||
|
||||
* A General Introduction
|
||||
|
||||
This work demonstrates how to use Org Mode to write a Ph.D. thesis.
|
||||
|
||||
#+INCLUDE: "./introduction/introduction.org" :lines "2-"
|
||||
|
||||
* A Research Chapter
|
||||
:PROPERTIES:
|
||||
:ALT_TITLE: Pulse Sequence Development for Cognitive Neuroscience
|
||||
:END:
|
||||
|
||||
#+INCLUDE: "../research-chapter/manuscript.org::*Abstract" :only-contents t
|
||||
|
||||
{{{fourstar}}}
|
||||
#+latex: \noindent
|
||||
#+begin_small
|
||||
Junior Author & Senior Author.
|
||||
#+end_small
|
||||
#+latex: \vspace*{\fill}
|
||||
#+begin_flushright
|
||||
/Contents published as Author et al., Org Science 2019/
|
||||
#+end_flushright
|
||||
{{{clearpage}}}
|
||||
|
||||
#+INCLUDE: "../research-chapter/manuscript.org" :lines "6-"
|
||||
|
||||
* Summary and general discussion
|
||||
|
||||
#+INCLUDE: "./summary/summary.org" :lines "2-"
|
||||
|
||||
|
||||
* Bibliography :ignore:
|
||||
|
||||
#+BEGIN_EXPORT latex
|
||||
\begingroup
|
||||
\sloppy
|
||||
\setstretch{1}
|
||||
\setlength\bibitemsep{3pt}
|
||||
\printbibliography
|
||||
\endgroup
|
||||
#+END_EXPORT
|
||||
|
||||
* Backmatter :ignore:
|
||||
|
||||
#+BEGIN_EXPORT latex
|
||||
% This ensures that the subsequent sections are being included as root
|
||||
% items in the bookmark structure of your PDF reader.
|
||||
\bookmarksetup{startatroot}
|
||||
\backmatter
|
||||
% \begingroup
|
||||
% \let\clearpage\relax
|
||||
% \glsaddall
|
||||
% \printglossary[type=\acronymtype]
|
||||
% \newpage
|
||||
% \printglossary
|
||||
% \endgroup
|
||||
% \printindex
|
||||
#+END_EXPORT
|
||||
|
||||
* Appendix :ignore:
|
||||
|
||||
#+latex: \appendix
|
||||
|
||||
* COMMENT Acknowledgments
|
||||
:PROPERTIES:
|
||||
:UNNUMBERED: t
|
||||
:END:
|
||||
|
||||
|
||||
* Build :noexport:
|
||||
|
||||
Bind derivatives change variable values *locally* on export.
|
||||
|
||||
These two are because I'm defining the title and toc manually using latex, so I don't want org-latex to take care of that.
|
||||
#+BIND: org-latex-title-command ""
|
||||
#+BIND: org-latex-toc-command ""
|
||||
This is so that src code blocks get src highlighting from the minted package.
|
||||
#+BIND: org-latex-listings minted
|
||||
This beautifies table borders. It will only work if the booktabs package is loaded, which I do in the setup file.
|
||||
#+BIND: org-latex-tables-booktabs t
|
||||
And this configuration increases the default width of images, so that they are larger and more readable on print.
|
||||
#+BIND: org-latex-image-default-width ".97\\linewidth"
|
||||
|
||||
# Local Variables:
|
||||
# mode: org
|
||||
# org-export-allow-bind-keywords: t
|
||||
# End:
|
||||
Binary file not shown.
|
|
@ -0,0 +1,317 @@
|
|||
# -*- mode: org; -*-
|
||||
# Daniel Gomez
|
||||
# Ph.D. Thesis Org Mode + LaTeX thesis.setup
|
||||
|
||||
* Org Mode Export Options :noexport:
|
||||
|
||||
** Macros
|
||||
#+MACRO: acronym #+latex_header: \newacronym[description={$1}]{$2}{$2}{$3}
|
||||
#+MACRO: glossaryentry #+latex_header: \newglossaryentry{$1}{name={$2},description={$3},sort={$4}}
|
||||
#+MACRO: newline @@latex:\hspace{0pt}\\@@ @@html:<br>@@
|
||||
#+MACRO: fourstar @@latex:\bigskip{\centering\color{BrickRed}\FourStar\par}\bigskip@@
|
||||
#+MACRO: clearpage @@latex:\clearpage@@@@odt:<text:p text:style-name="PageBreak"/>@@
|
||||
|
||||
** Options
|
||||
#+OPTIONS: toc:nil H:4 tags:nil
|
||||
|
||||
* LaTeX Export Headers and Options :noexport:
|
||||
|
||||
** Geometry
|
||||
|
||||
The thesis page size should be 17,21 cm vs 24,41 cm.
|
||||
# #+latex_header: \usepackage[paperheight=24.41cm,paperwidth=17.21cm,bottom=3cm,left=1.4cm,right=2cm,heightrounded]{geometry}
|
||||
But instead of setting it manually, I can leave it at A4 size and have the printshop reduce the A4 to 81%.
|
||||
|
||||
** Floating images configuration
|
||||
|
||||
By default, if a figure consumes 60% of the page it will get its own float-page. To change that we have to adjust the value of the floatpagefraction derivative.
|
||||
#+latex_header: \renewcommand{\floatpagefraction}{.8}%
|
||||
|
||||
See more information [[https://tex.stackexchange.com/questions/68516/avoid-that-figure-gets-its-own-page][here]].
|
||||
|
||||
** Etoolbox package
|
||||
#+latex_header: \usepackage{etoolbox}
|
||||
|
||||
** SI Units X package
|
||||
|
||||
The siunitx package is already required and configured properly in the mimosis class.
|
||||
# #+latex_header: \usepackage[binary-units=true]{siunitx}
|
||||
#+latex_header: \DeclareSIUnit\px{px}
|
||||
|
||||
This package allows setting SI units using the SI macro. It ensures that no line breaks happen between numbers and their units.
|
||||
|
||||
** Hyperref
|
||||
|
||||
Self-explanatory.
|
||||
#+latex_header: \usepackage[colorlinks=true, citecolor=BrickRed, linkcolor=BrickRed, urlcolor=BrickRed]{hyperref}
|
||||
|
||||
** Bookmarks
|
||||
|
||||
The bookmark package implements a new bookmark (outline) organisation for package hyperref. This lets us change the "tree-navigation" associated with the generated pdf and constrain the menu only to H:2.
|
||||
#+latex_header: \usepackage{bookmark}
|
||||
#+latex_header: \bookmarksetup{depth=2}
|
||||
|
||||
** BBding
|
||||
|
||||
Symbols such as diamond suit, which can be used for aesthetically separating paragraphs, could be added with the package =fdsymbol=. I'll use bbding which offers the more visually appealing =\FourStar=. I took this idea from seeing the thesis of the mimosis package author.
|
||||
#+latex_header: \usepackage{bbding}
|
||||
|
||||
** CS Quotes
|
||||
|
||||
The [[https://ctan.org/pkg/csquotes][csquotes]] package offers context sensitive quotation facilities, improving the typesetting of inline quotes.
|
||||
|
||||
Already imported by mimosis class.
|
||||
# #+latex_header: \usepackage{csquotes}
|
||||
|
||||
To enclose quote environments with quotes from csquotes, see [[https://tex.stackexchange.com/questions/365231/enclose-a-custom-quote-environment-in-quotes-from-csquotes][the following TeX SE thread]].
|
||||
|
||||
#+latex_header: \def\signed #1{{\leavevmode\unskip\nobreak\hfil\penalty50\hskip1em
|
||||
#+latex_header: \hbox{}\nobreak\hfill #1%
|
||||
#+latex_header: \parfillskip=0pt \finalhyphendemerits=0 \endgraf}}
|
||||
|
||||
#+latex_header: \newsavebox\mybox
|
||||
#+latex_header: \newenvironment{aquote}[1]
|
||||
#+latex_header: {\savebox\mybox{#1}\begin{quote}\openautoquote\hspace*{-.7ex}}
|
||||
#+latex_header: {\unskip\closeautoquote\vspace*{1mm}\signed{\usebox\mybox}\end{quote}}
|
||||
|
||||
And then use quotes as:
|
||||
#+begin_example
|
||||
# The options derivative adds text after the environment. We use it to add the author.
|
||||
#+ATTR_LATEX: :options {\cite{Frahm1994}}
|
||||
#+begin_aquote
|
||||
/Current (fMRI) applications often rely on "effects" or "statistically significant differences", rather than on a proper analysis of the relationship between neuronal activity, haemodynamic consequences, and MRI physics./
|
||||
#+end_aquote
|
||||
#+end_example
|
||||
|
||||
Note that org-ref links won't work here because the attr latex will be pasted as-is in the .tex file.
|
||||
|
||||
** Hyphenat
|
||||
|
||||
Words that have are manually hyphenated do not hyphenate. The fix is to use the hyphenate package and use \hyp instead of -.
|
||||
#+latex_header: \usepackage{hyphenat}
|
||||
#+latex_header: \hyphenation{deoxy-hemo-glo-bin}
|
||||
#+latex_header: \hyphenation{Sie-mens}
|
||||
#+latex_header: \hyphenation{multi-band multi-echo}
|
||||
|
||||
** Date Time
|
||||
|
||||
The date time package allows us to specify a "formatted" date object, which will print different formats according to the current locale & language. I use this in my title page.
|
||||
#+latex_header: \usepackage[level]{datetime}
|
||||
|
||||
** BibLaTeX
|
||||
|
||||
General configuration.
|
||||
#+latex_header: \usepackage[autocite=plain, backend=biber, doi=true, url=true, hyperref=true,uniquename=false, maxbibnames=99, maxcitenames=2, sortcites=true, style=authoryear-comp]{biblatex}
|
||||
|
||||
Improvements provided with the Mimosis class.
|
||||
#+latex_header: \input{bibliography-mimosis}
|
||||
|
||||
# And fix the andothers to show et al in English as well:
|
||||
# #+latex_header: \DefineBibliographyStrings{english}{andothers={\textit{et\, al\adddot}}}
|
||||
# #+latex_header:\DefineBibliographyStrings{english}{and={\textit{and}}}}
|
||||
|
||||
|
||||
Remove ISSN, DOI and URL to shorten the bibliography.
|
||||
#+latex_header: \AtEveryBibitem{%
|
||||
#+latex_header: \clearfield{urlyear}
|
||||
#+latex_header: \clearfield{urlmonth}
|
||||
#+latex_header: \clearfield{note}
|
||||
#+latex_header: \clearfield{issn} % Remove issn
|
||||
#+latex_header: \clearfield{doi} % Remove doi
|
||||
#+latex_header: \ifentrytype{online}{}{% Remove url except for @online
|
||||
#+latex_header: \clearfield{url}
|
||||
#+latex_header: }
|
||||
#+latex_header: }
|
||||
|
||||
And increase the spacing between the entries, as per default they are too small.
|
||||
#+latex_header: \setlength\bibitemsep{1.1\itemsep}
|
||||
|
||||
Also reduce the font-size
|
||||
#+latex_header: \renewcommand*{\bibfont}{\footnotesize}
|
||||
|
||||
** Fonts: Libertine, Garamond and Source Code Pro
|
||||
|
||||
The sf font is a nice sans serif font for tables.
|
||||
#+latex_header: \usepackage[sf,scaled=0.9]{quattrocento}
|
||||
#+latex_header: \ifxetexorluatex
|
||||
#+latex_header: \setmainfont{Minion Pro}
|
||||
#+latex_header: \else
|
||||
# #+latex_header: \usepackage[lf]{ebgaramond}
|
||||
Minion Pro has to be installed for this to work. See instructions below.
|
||||
#+latex_header: \usepackage[]{MinionPro}
|
||||
|
||||
The Source Code Pro font for code.
|
||||
#+latex_header: \usepackage[oldstyle, scale=0.7]{sourcecodepro}
|
||||
# #+latex_header: \singlespacing
|
||||
#+latex_header: \fi
|
||||
#+latex_header: \setkomafont{sectioning}{\normalfont\bfseries}
|
||||
|
||||
** Fix the th for dates.
|
||||
#+latex_header: \renewcommand{\th}{\textsuperscript{\textup{th}}\xspace}
|
||||
|
||||
** Improve chapter font colors and font size
|
||||
|
||||
The following commands make chapter numbers BrickRed, which look like the Donders color.
|
||||
#+latex_header: \makeatletter
|
||||
#+latex_header: \renewcommand*{\chapterformat}{ \mbox{\chapappifchapterprefix{\nobreakspace}{\color{BrickRed}\fontsize{40}{45}\selectfont\thechapter}\autodot\enskip}}
|
||||
#+latex_header: \renewcommand\@seccntformat[1]{\color{BrickRed} {\csname the#1\endcsname}\hspace{0.3em}}
|
||||
#+latex_header: \makeatother
|
||||
|
||||
** Define a new dummy abstract environment
|
||||
|
||||
Because some of the publications were written using the Elsevier =elsarticle= class, which provides an abstract env, we need to define a dummy one for the thesis as well so that INCLUDEs don't break. This here is an important part of getting the thesis/part multi-setup working. This would not be required for html exports, as "abstract" would end up as a div class, and that's ok if there is no CSS targetting it. For LaTeX, non-existing envrionments lead to compilation failure.
|
||||
|
||||
#+latex_header: \newenvironment*{abstract}{}{}
|
||||
|
||||
** Setspace for controlling line spacing
|
||||
|
||||
Already imported when using mimosis.
|
||||
# #+latex_header: \usepackage{setspace}
|
||||
#+latex_header: \setstretch{1.25}
|
||||
|
||||
** Parskip
|
||||
|
||||
Fine tuning of spacing between paragraphs. See [[https://tex.stackexchange.com/questions/161254/smaller-parskip-than-half-for-koma-script][thread here]].
|
||||
|
||||
#+latex_header: \setparsizes{0em}{0.1\baselineskip plus .1\baselineskip}{1em plus 1fil}
|
||||
|
||||
** Table of Contents improvements
|
||||
|
||||
TOC only the chapters, not their content.
|
||||
#+latex_header: \setcounter{tocdepth}{1}
|
||||
|
||||
** Thesis specific commands to monkey-patch paper commands.
|
||||
|
||||
I added this commands because I was using them with the PNAS class.
|
||||
#+latex_header: \newcommand{\dropcap}[1]{#1}
|
||||
#+latex_header: \newcommand{\matmethods}[1]{#1}
|
||||
#+latex_header: \newcommand{\showmatmethods}[1]{}
|
||||
#+latex_header: \newcommand{\acknow}[1]{#1}
|
||||
#+latex_header: \newcommand{\showacknow}[1]{}
|
||||
#+latex_header: \newcommand{\thesisnoop}[1]{}
|
||||
|
||||
** Table improvements (reduce font and make sans serif)
|
||||
|
||||
I reduce the size of tables so that longer tables can still fit into an A4.
|
||||
#+latex_header: \usepackage{floatrow}
|
||||
#+latex_header: \floatsetup[table]{font={footnotesize,sf},capposition=top}
|
||||
|
||||
** Possible Equation improvements
|
||||
|
||||
Make the equation numbers follow the chapter, not the whole thesis.
|
||||
#+latex_header: \numberwithin{equation}{chapter}
|
||||
|
||||
** Minted
|
||||
|
||||
The minted package is used for highlighting source code.
|
||||
#+latex_header: \usepackage{listings}
|
||||
#+latex_header: \usepackage{minted}
|
||||
#+latex_header: \setminted{autogobble=true,fontsize=\small,baselinestretch=0.8}
|
||||
#+latex_header: \setminted[python]{python3=true,tabsize=4}
|
||||
#+latex_header: \usemintedstyle{trac}
|
||||
#+latex_header: \lstset{abovecaptionskip=0}
|
||||
|
||||
Also make the listing numbers follow the chapter, not the whole thesis.
|
||||
#+latex_header: \numberwithin{listing}{chapter}
|
||||
And reduce the distance between a minted listing and its caption.
|
||||
# #+latex_header: \captionsetup[listing]{skip=-10pt}
|
||||
#+latex_header: \renewcommand{\listingscaption}{Code Snippet}
|
||||
# This here is to bring the caption closer to the environment.
|
||||
#+latex_header: \AtEndEnvironment{listing}{\vspace{-16pt}}
|
||||
# #+latex_header: \captionsetup{skip=-20pt}
|
||||
|
||||
** Scrhack
|
||||
|
||||
This package fixes some incompatibility errors between KOMAScript and other packages (namely minted). It has to be loaded at the end.
|
||||
#+latex_header: \usepackage{scrhack}
|
||||
|
||||
** COMMENT Background cover page
|
||||
|
||||
Add the cover image as background to the first page. Only do so when outputting a final version, because it significantly slows down the compilation times.
|
||||
|
||||
# #+latex_header: \usepackage[pages=some]{background}
|
||||
# #+latex_header: \backgroundsetup{
|
||||
# #+latex_header: scale=1,
|
||||
# #+latex_header: color=black,
|
||||
# #+latex_header: opacity=0.9,
|
||||
# #+latex_header: angle=0,
|
||||
# #+latex_header: contents={%
|
||||
# #+latex_header: \includegraphics[width=\paperwidth,height=\paperheight]{/Users/user/Desktop/TectonicPlatesXVI.png}
|
||||
# #+latex_header: }%
|
||||
# #+latex_header: }
|
||||
|
||||
* COMMENT Thesis Writing Org Mode Setup
|
||||
|
||||
A PhD thesis in the Netherlands consists more or less of a title page, an introduction, a collection of publications gathered as Chapters, and a summary in Dutch. the graduate student makes stylistic choices on how to format it.
|
||||
I chose to use Org Mode's markup language to write my thesis, since it offers direct export facilities to LaTeX but does not require me to remember details from the arcane LaTeX syntax. In addition, it keeps track of headings and references in the background, so that i don't have to do that myself.
|
||||
|
||||
The setup consists of a thesis.org file. Here we define the org and latex setup for the complete thesis and write glue code to include separate chapters. The magic here is that the chapters may be compiled on its own for submission, independent of the thesis. This gives us quite a bit of flexibility and modularity.
|
||||
|
||||
|
||||
** Installation
|
||||
The complete setup requires only the following steps:
|
||||
|
||||
*** Install latex-mimosis
|
||||
|
||||
Latex-mimosis is a KOMA derived minimal LaTeX template class. To install it we only have to clone [[https://github.com/Submanifold/latex-mimosis][the original repository]].
|
||||
To make the files visible by our TeX installation, we can put them (the .cls file and the bibliography setup files) in the following directory:
|
||||
|
||||
#+BEGIN_SRC sh :eval never
|
||||
kpsewhich -var-value=TEXMFHOME
|
||||
#+END_SRC
|
||||
|
||||
#+RESULTS:
|
||||
: /Users/user/Library/texmf
|
||||
|
||||
And then run =texhash $DIR=, where =$DIR= is the directory returned by the command above.
|
||||
Alternatively the class file can be place in the same directory as the main =Thesis.org= document.
|
||||
|
||||
*** Create the thesis directory and main files
|
||||
|
||||
The thesis directory has to contain a main thesis.org file, a thesis.setup file (a copy of this file), and the subdirectories with the chapters.
|
||||
|
||||
*** Add the mimosis class to your Emacs
|
||||
|
||||
The following code makes the org-latex export aware of the mimosis class. It also configures it so that headings start at chapter, followed by sections, subsections, etc.
|
||||
#+BEGIN_SRC emacs-lisp :eval never
|
||||
(add-to-list 'org-latex-classes
|
||||
'("mimosis"
|
||||
"\\documentclass{mimosis}
|
||||
[NO-DEFAULT-PACKAGES]
|
||||
[PACKAGES]
|
||||
[EXTRA]"
|
||||
("\\chapter{%s}" . "\\addchap{%s}")
|
||||
("\\section{%s}" . "\\section*{%s}")
|
||||
("\\subsection{%s}" . "\\subsection*{%s}")
|
||||
("\\subsubsection{%s}" . "\\subsubsection*{%s}")
|
||||
("\\paragraph{%s}" . "\\paragraph*{%s}")
|
||||
("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
|
||||
#+END_SRC
|
||||
|
||||
Note that to be able to use subsubsections and lower hierarchical levels we have to change an export variable called =org-export-headline-levels=. Every level below what is defined by said variable will be exported within an enumeration environment, i.e., as a list. This is why we set the option H:4 in this setup file.
|
||||
|
||||
** Usage
|
||||
|
||||
|
||||
*** Contextual export
|
||||
|
||||
As mentioned before, a PhD thesis in the Netherlands is composed of thesis specific content plus a collection of journal publications, each of which consists of chapter.
|
||||
That means that ideally we'd like to be able to reuse the same content (org mode file) but exclude or modify certain parts depending on whether the file is being used to generate a journal report or being included in the thesis.
|
||||
|
||||
To achieve that, this thesis package proposes the following convention:
|
||||
|
||||
The main Thesis.org file will not export any headline with a tag of =:journal:=.
|
||||
Therefore, to selectively exclude a heading from the thesis, simply mark it as =:journal:=.
|
||||
A usage example is to avoid printing bibliography multiple times, or to avoid including journal specific frontmatter into the thesis.
|
||||
|
||||
Another issue pertaining contextual export relates to relative file paths, especially those pointing to images that are included in each Chapter. To solve this problem and have Org Mode correctly adapt paths independent of where the files get included from, I've had to "monkey-patch" some of Org's include functions. This means that, if you are not willing to monkey-patch your Org, you'll have to write absolute paths for all figures to be included.
|
||||
|
||||
The [[https://code.orgmode.org/bzg/org-mode/commit/d81a1d088c74e605c99e90a2835c55df5144f43e][patch has landed]] in Org mode master, so no need for further monkey-patching.
|
||||
|
||||
** Fonts
|
||||
|
||||
To install the MinionPro fonts used in the current thesis, please refer to https://github.com/sebschub/FontPro.
|
||||
|
||||
* COMMENT Org Mode Thesis Structuring Decisions
|
||||
|
||||
I decided to use =:ignore:= headers to define Frontmatter, Mainmatter and Backmatter because this makes the ox-latex parser work without annoyances. If I remove these headings then some LATEX exports fail to appear. This may be a bug, but I'm happy to work around it for now.
|
||||
|
|
@ -0,0 +1,125 @@
|
|||
# -*- mode: org; -*-
|
||||
|
||||
* COMMENT Titlepage regulations
|
||||
|
||||
Here some info about the title page. Feel free to add the documentation of your own University as a reminder to self. Comment headings own be exported.
|
||||
|
||||
* Relevant Variables :ignore:
|
||||
#+latex_header: \newcommand{\ThesisTitle}{{Writing a Thesis with Org Mode}}
|
||||
#+latex_header: \newcommand{\ThesisSubTitle}{is nice.}
|
||||
#+latex_header: \newcommand{\FormattedThesisDefenseDate}{\mbox{\formatdate{1}{1}{2100}}}
|
||||
#+latex_header: \newcommand{\FormattedAuthorDateOfBirth}{\mbox{\formatdate{1}{1}{2000}}}
|
||||
#+latex_header: \newcommand{\FormattedThesisDefenseTime}{\mbox{10:00}}
|
||||
#+latex_header: \newcommand{\AuthorShortName}{\mbox{Author}}
|
||||
#+latex_header: \newcommand{\AuthorFullName}{\mbox{The Author}}
|
||||
#+latex_header: \newcommand{\AuthorPlaceOfBirth}{\mbox{Earth}}
|
||||
#+latex_header: \newcommand{\ThesisISBN}{\mbox{}}
|
||||
|
||||
* Title Page -- LaTeX :ignore:
|
||||
|
||||
#+BEGIN_EXPORT latex
|
||||
\begin{titlepage}
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% First page: Thesis Title and Author Name
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
% Uncomment when adding the background figure to the cover.
|
||||
%\BgThispage
|
||||
|
||||
\cleardoublepage
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{center}
|
||||
\null\vfill
|
||||
{\LARGE{\bfseries \ThesisTitle}\par}
|
||||
\vspace{\stretch{0.5}}
|
||||
{\large \ThesisSubTitle \par}
|
||||
\vspace{\stretch{2}}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\stretch{2}}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\stretch{1}}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\stretch{1}}
|
||||
{\large\AuthorShortName}\\
|
||||
\vspace{\stretch{1}}
|
||||
\vspace{\baselineskip}
|
||||
\vspace{\baselineskip}
|
||||
\vfill
|
||||
\end{center}
|
||||
|
||||
\clearpage
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Second page: Copyright and ISSN Number
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\null
|
||||
\noindent
|
||||
The work presented in the current demonstration could not have been possible without wonderful blog posts on Org mode usage found on the internet, and without the GNU Emacs documentation.
|
||||
|
||||
\vfill
|
||||
\noindent\textcopyright\ \number\year, \AuthorFullName\\
|
||||
\ThesisTitle\\
|
||||
Thesis, GNUniversity, The Earth\\
|
||||
Illustrated; with bibliographic information
|
||||
|
||||
\bigskip
|
||||
|
||||
\cleardoublepage
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Fifth page: Defense Information (English)
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{center}
|
||||
\null\vfill
|
||||
{\LARGE{\bfseries \ThesisTitle}\par}
|
||||
\vspace{\stretch{0.5}}
|
||||
{\large \ThesisSubTitle \par}
|
||||
\vspace{\stretch{2}}
|
||||
{Doctoral Thesis}\\
|
||||
\vspace{\stretch{2}}
|
||||
to obtain the degree of doctor\\
|
||||
from GNUniversity\\
|
||||
to be defended in public \\
|
||||
on \FormattedThesisDefenseDate\\\
|
||||
at \FormattedThesisDefenseTime\ hours\\
|
||||
\vspace{\stretch{1}}
|
||||
by\\
|
||||
\vspace{\stretch{1}}
|
||||
{\large\AuthorFullName}\\
|
||||
\vspace{\stretch{1}}
|
||||
born on \FormattedAuthorDateOfBirth\\
|
||||
in \AuthorPlaceOfBirth
|
||||
\vfill
|
||||
\end{center}
|
||||
|
||||
\clearpage
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% Sixth page: Corona Information (English)
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\noindent
|
||||
\begin{tabular}{@{}l@{\hspace{22pt}}l}
|
||||
\textbf{Supervisor}: & Prof.\ dr. Doc Doctor\\
|
||||
|
||||
\\
|
||||
\\
|
||||
|
||||
\textbf{Doctoral Thesis Committee}: & Prof.\ dr.\ Doctor Doc \hspace*{1cm} (chair) \\ [0.5em]
|
||||
& Prof.\ dr.\ Doctor Doctor \\
|
||||
& \hspace*{1cm} \textit{University of VS, not Earth} \\[0.5em]
|
||||
& Dr.\ Doctor von Doc \\
|
||||
& \hspace*{1cm} \textit{University of VIM} \\[0.5em]
|
||||
|
||||
\end{tabular}
|
||||
\cleardoublepage
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
% End Titlepage
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\end{titlepage}
|
||||
#+END_EXPORT
|
||||
|
||||
Loading…
Reference in New Issue