tufte-common-local.tex

%!TEX root = ./main.tex

%%% Default imports

% mock text
\usepackage{lipsum}

% For figure displays
\usepackage{graphicx}
\graphicspath{{images/}}
\usepackage{caption}
\usepackage{subcaption}

% basic math display
\usepackage{amssymb}
% define a mathnote which is equivalent to marginnote but inside an align env
\def\mathnote#1{%
  \tag*{\rlap{\hspace\marginparsep\smash{\parbox[t]{\marginparwidth}{%
  \footnotesize#1}}}}
}

%%%%%%%%%
% Index %
%%%%%%%%%
% Generates the index https://en.wikibooks.org/wiki/LaTeX/Indexing
% https://www.overleaf.com/learn/latex/Indices
% To make clickable links with hyperref
% pass nohyper option to tufte documentclass
% and load hyperref after imakeidx
\usepackage{imakeidx}
\indexsetup{level=\chapter*, toclevel=chapter}
\makeindex[title=Index, columns=1, intoc]

\usepackage[svgnames]{xcolor}
\definecolor{mydarkblue}{rgb}{0,0.08,0.45}
\definecolor{myblue}{RGB}{18,75,126}
\definecolor{burgundy}{RGB}{128,0,32}

\usepackage{hyperref}
\hypersetup{
    linktoc=all,
    breaklinks=true,
    colorlinks=true,
    linkcolor=mydarkblue,
    citecolor=mydarkblue,
    filecolor=mydarkblue,
    urlcolor=mydarkblue
}

%%%%%%%%%%%%
% Glossary %
%%%%%%%%%%%%

% https://www.overleaf.com/learn/latex/Glossaries
% Terminal: makeglossaries main
% rebuild main.tex
% To make clickable links with hyperref
% load hyperref before glossaries
\usepackage[acronym, toc, section=chapter]{glossaries}
% https://tex.stackexchange.com/a/73768 disable hyperref for glossary
\usepackage{xparse}
\DeclareDocumentCommand{\newdualentry}{ O{} O{} m m m m } {%
  \newglossaryentry{gls-#3}{name={#5},text={#5\glsadd{#3}},
      description={#6},#1
  }%
  \newacronym[see={gls-#3},description={#5},#2]{#3}{#4}{#5\glsadd{gls-#3}}%
}
% \glsdisablehyper
\makeglossaries



%%%%%%%%%%%%%%%%
% Nomenclature %
%%%%%%%%%%%%%%%%

% to build nomenclature
% makeindex main.nlo -s nomencl.ist -o main.nls
% rebuild main.tex
\usepackage{etoolbox}  % required in input_files/nomenclature.tex
\usepackage[intoc]{nomencl}
\makenomenclature
\nomlabelwidth=30mm
\setlength{\nomitemsep}{.5\parsep}
\renewcommand{\nomname}{Notations}
\newcommand{\nomunit}[1]{%
\renewcommand{\nomentryend}{\hspace*{\fill}#1}}

% Add appendix to each chapter
\usepackage{appendix}
% You may need to comment the next import depending on your version of LaTeX
% see https://tex.stackexchange.com/q/425600
\let\counterwithout\relax
\let\counterwithin\relax
\usepackage{chngcntr}

\AtBeginEnvironment{subappendices}{%
\newpage
\section*{Appendices}
\phantomsection
\addtocontents{toc}{\vspace{1ex}} % small vertical space
\addtocontents{toc}{\protect\contentsline{section}{\protect\textsc{Appendices}}{}{}}
\counterwithin{equation}{section}
\counterwithin{figure}{section}
\counterwithin{table}{section}
}
\AtEndEnvironment{subappendices}{%
\counterwithin{equation}{section}
\counterwithout{figure}{section}
\counterwithout{table}{section}
}

% chapter format
\titleformat{\chapter}
  [display]%
  {\bfseries\huge}
  {\marginnote[0em]{\resizebox{!}{1.2cm}{\fboxsep=1pt%
  \colorbox{black!60}{\color{white}{\thechapter}}
  }\filright}}
  {-2em}
  {\raggedleft}
  []

% % section format
\titleformat{\section}%
  [hang]%
  {\color{myblue}\Large\normalfont\scshape}%
  {\makebox[30pt][r]{\smallcaps{\thesection}}}{15pt}{}

% subsection format
\titleformat{\subsection}%
  [hang]%
  {\normalfont\scshape\color{myblue}}%
  {\makebox[30pt][r]{\thesubsection}}{15pt}{\normalfont\itshape\color{Black}}

  \titlespacing*{\chapter}
    {0pt}
    {30pt}
    {20pt}
\titlespacing*{\section}
  {-45pt}
  {3.5ex plus 1ex minus .2ex}
  {2.3ex plus .2ex}
\titlespacing*{\subsection}
  {-45pt}
  {3.5ex plus 1ex minus .2ex}
  {2.3ex plus .2ex}

% ------------------------------------- %
%           Table of content
% ------------------------------------- %

% TOC at the beginning of each chapter as marginnote
\newcommand{\dochaptoc}{\marginnote{\startcontents\vbox{\noindent\scshape\normalsize}\vskip1ex\printcontents{l}{1}{}}}

% Part
\titlecontents{part}
  [0em]
  {\vskip12pt\scshape \hypersetup{linkcolor=myblue}\Large}
  {\hypersetup{linkcolor=myblue}\thecontentslabel\enspace}
  {}
  {\hspace{0.5em}\color{burgundy}\contentspage}
  [\vskip 6pt]

% Chapter
\newcounter{chapcntr}
\setcounter{chapcntr}{-1}

\titlecontents{chapter}
  [0em]
  {\vskip12pt\scshape \stepcounter{chapcntr} \large}
  {\thecontentslabel\enspace}
  {}
  {\hspace{0.5em}\color{burgundy}\contentspage}[\vskip 6pt]

% Section
\titlecontents{section}
  [1em]
  {\ifboolexpr{test {\ifnumequal{\thechapcntr}{0}}}
                    {\color{white}}
                    {\ifboolexpr{test {\ifnumequal{\thechapcntr}{8}}}
                                {\color{white}}
                                {\color{black}}}}
  {\hypersetup{linkcolor=black}\thecontentslabel\enspace}
  {}
  {\hspace{0.5em}\color{burgundy}\contentspage}[\vskip 4pt]

% Sub-section
\titlecontents{subsection}
  [2em]
  {}
  {\hypersetup{linkcolor=black}\itshape\thecontentslabel\enspace}
  {}
  {\hspace{0.5em}\color{burgundy}\contentspage}
  [\vskip 3pt]

% \subsubsection
\titlecontents{subsubsection}
  [3em]
  {}
  {\hypersetup{linkcolor=black}\itshape\thecontentslabel\enspace}
  {}
  {\hspace{0.5em}\color{burgundy}\contentspage}[\vskip 3pt]

%%%%%%%% MINITOCs for Chapters
\newcommand\partialtocname{Chapter contents}

\titlecontents{lsection}
  [2em]
  {\footnotesize\normalfont}
  {\contentslabel{2em}}
  {}
  {\hfill\color{burgundy}\contentspage}

\titlecontents{lsubsection}[0pt]
  {\scriptsize}
  {\space}
  {}
  {\hfill}% \space\textbullet

%%%%%%%%%%%%
% Biblatex % (Custom)
%%%%%%%%%%%%

% Biblatex cheatsheet
% http://tug.ctan.org/info/biblatex-cheatsheet/biblatex-cheatsheet.pdf
\usepackage[utf8]{inputenc}
\usepackage{csquotes,xpatch}% recommended
\usepackage[authordate,
    isbn=false,
    url=false,
    backref=true,
    backrefstyle=none,
    backend=biber,
    % natbib=true,
    eprint=true,
    doi=false,
    maxcitenames=3,
    defernumbers=true,
    ibidtracker=false,
    uniquename=false,
    giveninits=true
]{biblatex-chicago}
% Using backref=true, backrefstyle=none, the following sets backrefs display
\DefineBibliographyStrings{english}{%
  backrefpage = {\lowercase{s}ee p.\!},%
  backrefpages = {\lowercase{s}ee pp.\!}%
}
% For a chapterwise biblio see https://tex.stackexchange.com/q/403421
% use refsection=chapter at import
% \printbibliography[heading=subbibliography]

% You can add as many bib file as you want
% \addbibresource{bibliography.bib}

% for full names in fullcite
\preto\fullcite{\AtNextCite{\defcounter{maxnames}{99}}}
\renewcommand*{\nameyeardelim}{\addcomma\space}
\usepackage{csquotes}

% make title clickable
% https://tex.stackexchange.com/a/48409
\newbibmacro{string+doiurlisbn}[1]{%
  \iffieldundef{doi}{%
    \iffieldundef{url}{%
      \iffieldundef{isbn}{%
        \iffieldundef{issn}{%
          #1%
        }{%
          \href{http://books.google.com/books?vid=ISSN\thefield{issn}}{#1}%
        }%
      }{%
        \href{http://books.google.com/books?vid=ISBN\thefield{isbn}}{#1}%
      }%
    }{%
      \href{\thefield{url}}{#1}%
    }%
  }{%
    \href{http://dx.doi.org/\thefield{doi}}{#1}%
  }%
}
\DeclareFieldFormat*{title}{\usebibmacro{string+doiurlisbn}{\mkbibemph{#1}}}

% Process the fields of each bib entry
\DeclareSourcemap{
    \maps{
        \map{
        % Replaces '{\_}', '{_}' or '\_' with just '_'
        \step[fieldsource=url,
              match=\regexp{\{\\\_\}|\{\_\}|\\\_},
              replace=\regexp{\_}]
        % Replaces '{'$\sim$'}', '$\sim$' or '{~}' with just '~'
        \step[fieldsource=url,
              match=\regexp{\{\$\\sim\$\}|\{\~\}|\$\\sim\$},
              replace=\regexp{\~}]
        % Replaces '{\$}'
        \step[fieldsource=url,
              match=\regexp{\{\\\x{26}\}},
              replace=\regexp{\x{26}}]
        \step[fieldset=abstract, null]
        \step[fieldset=annotation, null]
        \step[fieldset=volume, null]
        \step[fieldset=number, null]
        \step[fieldset=eid, null]
        \step[fieldset=pages, null]
        \step[fieldset=issue, null]
        \step[fieldset=location, null]
        \step[fieldset=month, null]
    }
  }
}

\DeclareFieldFormat*{journaltitle}{#1}
\DeclareFieldFormat*{booktitle}{#1}

% if babel english
% write dissertation instead of diss
\DefineBibliographyStrings{english}{phdthesis = {PhD dissertation}}

% create link to arXiv:<arxivId>
% inspired by https://tex.stackexchange.com/a/419890
% \makeatletter (uncomment when using in another class like beamer)
\DeclareFieldFormat{eprint:arxiv}{%
  arXiv\addcolon%
  \ifhyperref%
    {\href{http://arxiv.org/\abx@arxivpath/\iffieldundef{eprintclass}
                                            {#1}
                                            {\thefield{eprintclass}/#1}}
          {\iffieldundef{eprintclass}
                        {}
                        {\textsf{\thefield{eprintclass}/}}\textsf{#1}}}%
    {\iffieldundef{eprintclass}
                  {}
                  {\textsf{\thefield{eprintclass}/}}\textsf{#1}}%
}
% \makeatother (uncomment when using in another class like beamer)

\usepackage{silence}
\WarningFilter{biblatex}{Patching footnotes failed}
\WarningFilter{biblatex}{Attempt to redefine deprecated}
\WarningFilter{latex}{Marginpar on page}
\WarningFilter{latexfont}{Font shape}
\WarningFilter{latexfont}{Some font}
\WarningFilter{latexfont}{Size substitutions}
\WarningFilter{hyperref}{Token not allowed in a PDF string}