autopaper.sty

%MIT License
\ProvidesPackage{autopaper}
% uploading packages
\RequirePackage[table]{xcolor} % https://tex.stackexchange.com/a/83102/224861, https://tex.stackexchange.com/a/54925/224861
\RequirePackage{kvoptions}
\RequirePackage{setspace}
\RequirePackage{graphicx}
\RequirePackage{amssymb}
\RequirePackage{textcomp} % https://latex.org/forum/viewtopic.php?f=4&t=3364#p13124, https://tex.stackexchange.com/questions/165115
\RequirePackage{gensymb}
\RequirePackage{lineno}
\RequirePackage{mathtools}
\RequirePackage[title]{appendix}
% \RequirePackage{pgfmath}
\newcommand{\calcnum}[2][1]{%
    \pgfmathparse{#2}%
    \num[round-mode=places,round-precision=#1]{\pgfmathresult}%
}
\newcommand{\percReduction}[3][1]{\calcnum[#1]{(#3-#2)/#3*100}}
\newcommand{\absReduction}[3][4]{\calcnum[#1]{#3-#2}}
\RequirePackage[separate-uncertainty=true]{siunitx}
% \RequirePackage{xr-hyper} %needs to  be before hyperref
% \RequirePackage{numprint} %tex.stackexchange.com/a/9139/224861
\RequirePackage{enumitem}
\RequirePackage{caption}
\RequirePackage{subcaption}
\newcommand{\NA}{---} % holds an m-dash
\graphicspath{{figures/}} %Setting the graphicspath
% ---------to deal with the double quotes-----------
\usepackage [english]{babel}
\usepackage [autostyle, english = american]{csquotes}
\MakeOuterQuote{"}
\RequirePackage{listings}[breakatwhitespace=true,escapechar=\%]
\RequirePackage{pythonhighlight}
\RequirePackage{matlab-prettifier}

\RequirePackage{mathrsfs}
\RequirePackage{chemformula}
\RequirePackage{tabulary}
\RequirePackage{multirow}
\RequirePackage{makecell} % https://tex.stackexchange.com/questions/2441/how-to-add-a-forced-line-break-inside-a-table-cell
\newcommand{\matlab}[1]{\mbox{\lstinline[style=Matlab-editor]{#1}}}
%alternatively can use `` '' format for double quotes
\RequirePackage{csvsimple}
\RequirePackage{booktabs}
% \RequirePackage{widetext} % kept running into bugs with disappearing text, maybe due to multicol - never could quite figure out
% \usepackage{breqn} % wasn't working as intended with the Mathematica output
\RequirePackage{cuted}
\setlength {\marginparwidth}{2cm}
\setlength{\abovetopsep}{1ex}

\RequirePackage{placeins}

\RequirePackage{xurl} %needs to be before hyperref
\RequirePackage{hyperref}
% \PassOptionsToPackage{hyphens}{url} \RequirePackage{hyperref} %allow URLs to break across lines
\hypersetup{
    colorlinks,
    linkcolor={red!50!black},
    citecolor={blue!50!black},
    urlcolor={blue!80!black}
} %https://tex.stackexchange.com/a/847/224861
\RequirePackage[nameinlink,capitalise]{cleveref} %needs to appear after hyperref, https://tex.stackexchange.com/questions/396728/my-equations-referencing-not-working
\Crefname{figure}{Figure}{Figures} %needs to appear after hyperref and cleveref
\crefname{appsec}{Appendix}{Appendices}
\newcommand\crefrangeconjunction{--} % modify the reference style

\RequirePackage[shortcuts]{glossaries-extra} %needs to appear after hyperref
% \RequirePackage[shortcuts,abbreviations]{glossaries-extra} %for some reason, abbreviations seemed to be messing with automatic regeneration of Glossary and the counting stuff

\newcommand*{\TCac}[1]{\ecapitalisewords{\glsentrylong{#1}}}
% remove the "Preprint submitted to Elsevier" footer on the first page
% \makeatletter %conflicts with
\def\ps@pprintTitle{%
   \let\@oddhead\@empty
   \let\@evenhead\@empty
   \def\@oddfoot{\reset@font\hfil\thepage\hfil}
   \let\@evenfoot\@oddfoot
}
% \makeatother

% Cross referencing with the xr package in Overleaf (https://www.overleaf.com/learn/how-to/Cross_referencing_with_the_xr_package_in_Overleaf)

% \makeatletter
\newcommand*{\addFileDependency}[1]{% argument=file name and extension
  \typeout{(#1)}
  \@addtofilelist{#1}
  \IfFileExists{#1}{}{\typeout{No file #1.}}
}
% \makeatother

% \newcommand*{\myexternaldocument}[2]{%
%   \externaldocument{#1/#2}%
%     \addFileDependency{#2.tex}%
%     \addFileDependency{#1/#2.aux}% https://tex.stackexchange.com/a/590837/224861 % couldn't get to work, left a comment

\newcommand*{\myexternaldocument}[1]{%
    \externaldocument{#1}%
    \addFileDependency{#1.tex}%
    \addFileDependency{#1.aux}%
}

\RequirePackage{nameref,zref-xr}
\zxrsetup{toltxlabel}
% \zexternaldocument*{supp} %https://tex.stackexchange.com/questions/77774/undefined-control-sequence-when-cross-referencing-with-xr-hyper
% \myexternaldocument{supp}
\ifcsname biboptions\endcsname
  \biboptions{sort&compress} %only use if defined
\else
  % do nothing
\fi
% https://tex.stackexchange.com/questions/46223/if-document-class-is-equal-to-something-then-do-not-use-package

\interfootnotelinepenalty=10000 %prevent footnotes from getting split across columns/pages
%\patchcmd{\emailauthor}{(#2)}{(S.G. Baird).}{}{} %Removes/Abbreviates corresponding author name after Email address so that the footnote doesn't take up 2 lines.
% Double Spacing
% \doublespacing

\newcommand*{\glsentrytitlecasefull}[1]{\glsentrytitlecase{#1}{long} (\glsentryshort{#1}) }

\newcommand*{\glsentrytitlecasefullplural}[1]{\glsentrytitlecase{#1}{longpl} (\glsentryshort{#1}s) }

%Options
\DeclareBoolOption[true]{refcheck}

\DeclareBoolOption[true]{todonotes}
\ProcessKeyvalOptions*{}
% \newif\ifmypackage@todonotes
% \DeclareOption{todonotes}{\mypackage@todonotestrue}
% \DeclareOption{notodonotes}{\mypackage@todonotesfalse}
% \ExecuteOptions{todonotes}

% \ProcessOptions\relax

\ifautopaper@refcheck
    \RequirePackage{refcheck} %checks for unused labels - comment when done
    %%% Infrastructure
    % \makeatletter
    \newcommand{\refcheckize}[1]{%
      \expandafter\let\csname @@\string#1\endcsname#1%
      \expandafter\DeclareRobustCommand\csname relax\string#1\endcsname[1]{%
        \csname @@\string#1\endcsname{##1}\wrtusdrf{##1}}%
      \expandafter\let\expandafter#1\csname relax\string#1\endcsname
    }
    % \makeatother
    %%%
    %%% Now we add the reference commands we want refcheck to be aware of
    \refcheckize{\cref}
    \refcheckize{\Cref}
    %https://tex.stackexchange.com/questions/87610/making-refcheck-work-with-cleveref

    \let\orig@subcaption@@label\subcaption@@label
\def\subcaption@@label#1#2{\usedref{sub@#2}\orig@subcaption@@label{#1}{#2}} % https://tex.stackexchange.com/a/412598/224861
\fi

\ifautopaper@todonotes
    \RequirePackage[colorinlistoftodos]{todonotes}
\else
    \RequirePackage[disable]{todonotes}
\fi

% https://tex.stackexchange.com/questions/369559/how-to-force-new-page-if-paragraph-will-break
\newcommand{\uComment}[3]{%
  \filbreak
  \begin{commentTextFont}#1\end{commentTextFont}%
  \vspace*{0.5cm}
  \begin{userFont}\textit{#2}\hspace*{\fill}%
  \begin{dateFont}#3\end{dateFont}\end{userFont}%
  \vspace*{0.8cm}
}