packages.sty

\usepackage[a4paper,bottom=1in]{geometry}
% Fix fancyhdr warnings
\setlength{\headheight}{14.5pt}

\usepackage[english]{babel}

% Only used for text generation in the template
%
\usepackage{lipsum}
%%

\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{csquotes}

\usepackage[final]{microtype}

\usepackage[ttscale=.75]{libertine}
\usepackage[libertine]{newtxmath}
\usepackage{relsize}

% Set nicer (= less bold, less vertical spacing) mathcal font
\usepackage[cal=cm]{mathalpha}

% Set up the opening page for the chapters
\usepackage{titlesec}
\titleformat{\chapter}[display]
{\Huge}
{\filleft\textsc{\chaptertitlename} \thechapter}
{4ex}
{\bfseries
  \titlerule%
  \vspace{2ex}%
\filright}
[\vspace{2ex}%
\titlerule]

% Set up the headers and footers
\usepackage{fancyhdr}
\usepackage{ifthen}
\pagestyle{fancy}
\fancyhf{}
% Use ifthenelse to work around the fact that we wish to have alternate headers
% but a onesided document
% (https://tex.stackexchange.com/questions/69100/distinguish-even-odd-pages-in-header-with-oneside-option)
\fancyhead[R]{\ifthenelse{\isodd{\value{page}}}{\thepage\hfill\textsc{\nouppercase\leftmark}}{}}
\fancyhead[L]{\ifthenelse{\isodd{\value{page}}}{}{\textsc{\nouppercase\rightmark}\hfill\thepage}}
\fancyfoot{}

% Remove page numbers on the first page of a chapter
% https://tex.stackexchange.com/questions/278420/remove-page-number-on-chapter-page
\fancypagestyle{plain}{%
  \renewcommand{\headrulewidth}{0pt}%
  \fancyhf{}%
}

% See the excellent biblatex documentation for more information
\usepackage[
backend=biber,%
style=alphabetic,%
block=ragged,%
backref=true,%
useprefix=true,%
maxnames=8,%
minnames=7,%
minalphanames=3,%
maxalphanames=4,%
backrefstyle=two]%
{biblatex}
\addbibresource{references.bib}
\renewcommand{\subtitlepunct}{\addcolon\addspace}

% Enumerations and tables
\usepackage{calc}
\usepackage[shortlabels]{enumitem}
\setlist{nosep}
\setlist[description]{font={\textnormal},labelindent=\parindent}

\usepackage{booktabs}
\usepackage{longtable}
\usepackage[width=.8\textwidth]{caption}
\captionsetup[table]{skip=1em}

% Math packages
\usepackage{mathtools}

\usepackage{savesym}
\usepackage{amsmath}
\savesymbol{openbox}
\usepackage{amsthm}

\usepackage{thmtools}
\savesymbol{Bbbk}
\usepackage{amssymb}
\usepackage{stmaryrd}


% tocbibind allows us to have the toc in the toc
\usepackage[notbib,notindex]{tocbibind}
% Supposedly it should also allow us to have the index and the bibliography in
% the toc, but it has some bugs (e.g. displaying the right page number in the
% toc, but getting the wrong link with hyperref), so we disable those options
% here and use corresponding separate options for the index, index of symbols
% (nomenclature) and bibliography instead.
%
% The whole is rather finicky and it is somehow crucial that tocbibind is loaded
% *before* imakeidx.

\usepackage{imakeidx}
\makeindex[intoc,columns=2]
\usepackage[refpage,intoc,noprefix]{nomencl}
% Set fixed width so that descriptions in the index of symbols are aligned.
\setlength{\nomlabelwidth}{5cm}
\renewcommand{\nomname}{Index of symbols}
% Make page numbers links
\renewcommand*{\pagedeclaration}[1]{\unskip, \hyperpage{#1}}
\makenomenclature%

% Used in hyperref's setup, and must be loaded before tikz-cd.
\usepackage[dvipsnames]{xcolor}
\usepackage[most]{tcolorbox}
\usepackage{tikz-cd}

\usepackage[
  colorlinks=true  % Remove the boxes
, linktocpage=true % Make page numbers (not section titles) links in ToC
, linkcolor=NavyBlue    % Colour for internal links
, citecolor=Green  % Colour for bibliographical citations
, urlcolor=BrickRed % Colour for (external) urls
]{hyperref}


% Metadata setup (define using \subject, \degree, \institution, etc. in main.tex)
\makeatletter

\newcommand{\subject}[1]{\gdef\@subject{#1}}%
\newcommand{\@subject}{PhD thesis} 
\newcommand{\degree}[1]{\gdef\@degree{#1}}%
\newcommand{\@degree}{Doctor of Philosophy}
\newcommand{\institution}[1]{\gdef\@institution{#1}}%
\newcommand{\@institution}{University of Foo}
\newcommand{\school}[1]{\gdef\@school{#1}}%
\newcommand{\college}[1]{\gdef\@college{#1}}%
\newcommand{\keywords}[1]{\gdef\@keywords{#1}}%
\newcommand{\@keywords}{some, descriptive, keywords} 

\AtBeginDocument{
  \hypersetup{
    pdftitle = {\@title},
    pdfauthor = {\@author},
    pdfsubject = {\@subject},
    pdfkeywords = {\@keywords}
  }
}
\makeatother

\usepackage[noabbrev,capitalize]{cleveref}
\creflabelformat{equation}{#2\textup{#1}#3} % Write Equation x.y.z instead of Equation (x.y.z)

% Label tables just like equations, theorems, definitions, etc.
%
% NB: This can be confusing if LaTeX does not place the table at the point of
% writing (e.g. for lack of space)!
\numberwithin{equation}{section}
\numberwithin{table}{section}
\makeatletter
\let\c@equation\c@table
\makeatother

% Setting up the coloured environments
%
\newbool{shade-envs}
% This can be used to toggle the coloured environments on or off.
\setboolean{shade-envs}{true}

%%
\ifthenelse{\boolean{shade-envs}}{%
  % Colours are as in Andrej Bauer's notes on realizability:
  % https://github.com/andrejbauer/notes-on-realizability
  \colorlet{ShadeOfPurple}{blue!5!white}
  \colorlet{ShadeOfYellow}{yellow!5!white}
  \colorlet{ShadeOfGreen} {green!5!white}
  \colorlet{ShadeOfBrown} {brown!10!white}
  % But we also shade proofs
  \colorlet{ShadeOfGray}  {gray!10!white}
}
% If we don't want to have shaded environments, then we use a closing symbol
% \lozenge to mark the end of remarks, definitions and examples.
{%
  \declaretheoremstyle[
      spaceabove=6pt,
      spacebelow=6pt,
      bodyfont=\normalfont,
      qed=\(\lozenge\)
  ]{definitionwithbox}
  \declaretheoremstyle[
      headfont=\itshape,
      bodyfont=\normalfont,
      qed=\(\lozenge\)
      ]{remarkwithbox}
}

\ifthenelse{\boolean{shade-envs}}{%
  \declaretheorem[sibling=equation]{theorem}
  \declaretheorem[sibling=theorem]{lemma,proposition,corollary}
  \declaretheorem[sibling=theorem,style=definition]{definition}
  \declaretheorem[sibling=theorem,style=definition]{example}
  \declaretheorem[sibling=theorem,style=remark]{remark}
  % Now we set the shading using the tcolorbox package.
  %
  % The related thmtools' option "shaded" and the package mdframed seem to have
  % issues: the former does not allow for page breaks in shaded environments and
  % the latter puts double spacing between two shaded environments.
  %
  % Since tcolorbox puts stuff inside a minipage or \parbox (according to this
  % stackexchange answer: https://tex.stackexchange.com/a/250170), new
  % paragraphs aren't indented. We can fix this by grabbing the parindent
  % value and passing it to tcbset.
  \newlength{\normalparindent}
  \AtBeginDocument{\setlength{\normalparindent}{\parindent}}
  \tcbset{shadedenv/.style={
      colback={#1},
      frame hidden,
      enhanced,
      breakable,
      boxsep=0pt,
      left=2mm,
      right=2mm,
      % LaTeX thinks this is too wide (as becomes clear from the many "Overfull
      % \hbox" warnings, but optically it looks spot on.
      add to width=1.1mm,
      enlarge left by=-0.6mm,
      before upper={\setlength{\parindent}{\normalparindent}}}
  }
  \newcommand{\setenvcolor}[2]{%
      \tcolorboxenvironment{#1}{shadedenv={#2}}
      \addtotheorempreheadhook[#1]{\tikzcdset{background color=#2}}
  }
  %
  \setenvcolor{theorem}{ShadeOfPurple}
  \setenvcolor{lemma}{ShadeOfPurple}
  \setenvcolor{proposition}{ShadeOfPurple}
  \setenvcolor{corollary}{ShadeOfPurple}
  \setenvcolor{definition}{ShadeOfYellow}
  \setenvcolor{example}{ShadeOfGreen}
  \setenvcolor{remark}{ShadeOfBrown}
  \setenvcolor{proof}{ShadeOfGray}
}{% Use closing symbols if we don't have colours
  \declaretheorem[sibling=equation]{theorem}
  \declaretheorem[sibling=theorem]{lemma,proposition,corollary}
  \declaretheorem[sibling=theorem,style=definitionwithbox]{definition}
  \declaretheorem[sibling=theorem,style=definitionwithbox]{example}
  \declaretheorem[sibling=theorem,style=remarkwithbox]{remark}
  }
\declaretheorem[sibling=theorem,style=remark,numbered=no]{claim}

% Note that proofs will still have the \qed symbol at the end, even when shaded,
% because we prefer to keep up the tradition.


% Set table of contents depth
\setcounter{tocdepth}{2}