#+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: Research Chapter
: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: