main.tex

\documentclass{article}

\usepackage{graphicx} % Required for inserting images
\usepackage{authblk} % For affiliations
\usepackage{enumerate} % For ordered lists
\usepackage{parskip} % Adds white space between paragraphs
\usepackage{orcidlink} % Insert ORCID links
\usepackage{abstract} % Customise abstract
\usepackage{xurl} % To add URLs (which will line break)
\usepackage{hyperref} % To add URLs
\usepackage{geometry} % Tables
\usepackage{booktabs} % Tables (styling)
\usepackage{tabulary,lipsum} % Tables (e.g. J/C/L/R column types)
\usepackage{float} % Tables (prevent repositioning)
\usepackage{enumitem} % Use alternatives to 123 in ordered list
\usepackage{forest} % To create directory tree
\usepackage{xcolor} % For highlights and shading
\usepackage{soul} % For highlights
\usepackage{framed} % To make shaded abstract
\usepackage{enumitem,amssymb} % To make check box lists
\usepackage{multicol} % Columns
\usepackage{titlesec} % To make alternative section titles
\usepackage{clock} % Create clock symbol
\usepackage[clock]{ifsym} % Create clock symbol
\usepackage{amsmath} % Create tick symbol
\usepackage{makecell} % To add forced line breaks within table cells
\usepackage{changepage} % For adjustwidth

% Checkboxes
\newlist{todolist}{itemize}{2}
\setlist[todolist]{label=$\square$}

% Change font
\usepackage{cmbright}

% References using biblatex
\usepackage[
    sorting=none,
    autocite=superscript
]{biblatex}
\bibliography{references}

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

% Blue highlight
\definecolor{highlightblue}{HTML}{e8f2f6}
\DeclareRobustCommand{\hlblue}[1]{{\sethlcolor{highlightblue}\hl{#1}}}
    
% Create shaded abstract
% ---------------------------------------------------
% Credit to JamesT (https://tex.stackexchange.com/questions/675419/text-is-not-centered-with-colorbox)
\definecolor{abstractcolour}{HTML}{D1E6EE}
\colorlet{shadecolor}{abstractcolour}
\renewenvironment{abstract} 
     {
    \vfill%
      \list{}{
        \setlength{\leftmargin}{.3cm}%
        \setlength{\rightmargin}{\leftmargin}%
      \vfill%
      }%
      \item\relax}
 {\endlist}
\setlength{\parindent}{0mm} 
% ---------------------------------------------------

% Create shaded headings
% ---------------------------------------------------
% Logo is #1982AB. Chose paler colous for the heading shading.
\definecolor{section}{HTML}{A3CDDD}
\newcommand{\colorsection}[1]{\colorbox{section}{\parbox{\dimexpr\textwidth-11\fboxsep}{#1}}}
\titleformat
    {name=\section} % Command
    [block] % Shape
    {\normalfont\Large\bfseries} % Format
    {\thesection} % Label
    {1em} % Space between number and title
    {\colorsection} % Before code
    [] % After code

\definecolor{subsection}{HTML}{A3CDDD}
\newcommand{\colorsubsection}[1]{\colorbox{subsection}{\parbox{\dimexpr\textwidth-13\fboxsep}{#1}}}
\titleformat{name=\subsection}[block]
    {\normalfont\large\bfseries}
    {\thesubsection}
    {1em}
    {\colorsubsection}

\definecolor{subsubsection}{HTML}{D1E6EE}
\newcommand{\colorsubsubsection}[1]{\colorbox{subsubsection}{\parbox{\dimexpr\textwidth-14\fboxsep}{#1}}}
\titleformat{name=\subsubsection}[block]
    {\normalfont\normalsize\bfseries}
    {\thesubsubsection}
    {1em}
    {\colorsubsubsection}
% ---------------------------------------------------

\begin{document}

% Title page and TOC
\include{sections/title}

% Main body of protocol
\include{sections/protocol_intro}
\include{sections/protocol_reproduction}
\include{sections/protocol_guidelines}
\include{sections/protocol_end}

% Sections after this point are Appendices
\appendix
\include{sections/email}
\include{sections/badges}
% \include{sections/stars}

% Print bibliography and include in table of contents
\printbibliography[heading=bibintoc]

\end{document}