mathesis.sty

\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{mathesis}
\usepackage[utf8]{inputenc}
\RequirePackage[l2tabu, orthodox]{nag}
\RequirePackage{etoolbox}
\usepackage{pgfkeys}
\usepackage{pgfopts}
\pgfkeys{
	/mathesis/.cd,
	biblatex/.store in = \mathesis@biblatex,
	bib/.store in = \mathesis@bib,
	initials/.store in = \mathesis@initials,
	initials=ma,
}
\ProcessPgfPackageOptions*

%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LAYOUT AND LOOKS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Bibliography with ToC entry %%%%
\ifdef{\mathesis@biblatex}{
	\ifdef{\mathesis@bib}{
		\usepackage[backend=bibtex,url=false,isbn=false,doi=false,firstinits=true,maxbibnames=99,style=numeric]{biblatex}
		\addbibresource{\mathesis@bib}
		\@ifclassloaded{book}{
			\AtEndEnvironment{document}{%
                \printbibliography[heading=bibintoc]%
            }{}{}
		}{
			\AtEndEnvironment{document}{%
                \addcontentsline{toc}{section}{\refname}\printbibliography%
            }{}{}
		}
	}{}
}{
    \ifdef{\mathesis@bib}{
         \AtEndEnvironment{document}{%
             \bibliography{\mathesis@bib}{}\bibliographystyle{plain}%
         }
     }{}
}

%%% Page size %%%%
\@ifclassloaded{book}{
	\usepackage[inner=1.4in, outer=1.1in]{geometry}	
}{
	\@ifclassloaded{sciposter}{}{
		\usepackage[bottom=1in, top=1.5in,right=2cm,left=2cm]{geometry}
	}
}

%%%% Headers and footers %%%%
\usepackage{fancyhdr}
\fancyhead{}
\fancyfoot{}
\renewcommand{\headrulewidth}{0pt}
\fancyfoot[C]{\thepage} 
\usepackage{setspace}

%%%% Chapter headings %%%%
\@ifclassloaded{book}{
	\usepackage{titlesec}
	\titleformat{\chapter}[display]{\normalfont\huge\bfseries}{}{0pt}{\Huge}%Put stuff before title in last brackets
	\titlespacing*{\chapter}{0pt}{20pt}{40pt}
}{}

%%%% Figures %%%%
\usepackage{scalerel}
\@ifclassloaded{sciposter}{}{
	\usepackage[labelfont=bf]{caption}
	\captionsetup[algorithm]{labelfont=rm,labelsep=period}
	\usepackage{subcaption}
}

%%%% Typography %%%%
\usepackage{microtype}
\usepackage{lmodern}
\usepackage[USenglish]{babel}
\usepackage[T1]{fontenc}

%%%% Float placement %%%%
\usepackage{flafter}

%%%%%%%%%%%%%%%%%%%%%%%%%%%% STRUCTURE COMMANDS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% Theorems %%%%
%% The actual theorem, corollary,... definitions need to be after cleverref 
%% according to the documentaiton of cleverref.
\usepackage{amsthm} 

%%%% Abstract  %%%%
\@ifclassloaded{book}{
    \newenvironment{abstract}{%
            \clearpage\null \vfill\begin{center}% 
            \bfseries \abstractname \end{center}%
    }{%
        \vfill\null%
    }%
}

%%%% Emphasized matter by frame with left bar %%%%
\usepackage{framed}
\renewenvironment{leftbar}[1][\hsize]%
{%
	\def\FrameCommand%
	{%    
		\vrule width 3pt \hspace{-4pt}              
		\fboxsep=\FrameSep\colorbox{Lavender!25}%
	}%
	\MakeFramed{\hsize#1\advance\hsize-\width\FrameRestore}%
}%
{\endMakeFramed}

%%%% Align with left tags %%%%
\usepackage{environ}
\NewEnviron{Lalign}{\tagsleft@true\begin{align}\BODY\end{align}}

%%%% Blank page %%%%
\newcommand{\blankpage}{\clearpage\mbox{}\thispagestyle{empty}\clearpage}

%%%%%%%%%%%%%%%%%%%%% MORE COMMANDS AND PACKAGES %%%%%%%%%%%%%%%%%%%%%
%%%% Math  %%%%
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{madefs}

%%%% Algorithms %%%%
\usepackage{algorithm}
\usepackage{algpseudocode}

%%%% Various %%%%
\usepackage{blindtext}

%%%% Graphics %%%%
\usepackage{pgfplots,tikz}
\usetikzlibrary{matrix,arrows}
\usepackage{epstopdf}

%%%% Counting %%%%
\usepackage{chngcntr}

%%%% Float placement %%%%
\usepackage{afterpage}

%%%% Various %%%%
\usepackage{etoolbox} % Needed for \pretocmd{\chapter} %% CHECK UNUSED
\usepackage{bm} % Bold math symbols. Just as good as textbf and mathbf. Never use bfseries
\usepackage{bbm} % Blackboard Numbers \mathbbm{1}
\usepackage{csquotes} % \enquote 
\usepackage{enumerate} % change to enumitem

%%%% Structuring  %%%%
\usepackage{appendix} %%CHECK USAGE

%%%% Typing superscript numbers %%%%
\usepackage{nth}

%%%% Typing Roman Numbers %%%%
\newcommand{\romath}[1]{%
  \textup{\uppercase\expandafter{\romannumeral#1}} % Roman numbers from input
}

%%%% Adding %%%%
\newcommand\add[2]{\the\numexpr(#1)+(#2)\relax}

%%%% Miscellaneous %%%%
\newcommand{\condinput}[1]{
	\ifcsname#1\endcsname%
	\input{#1}
	\fi%
}


%%%%%%%%%%%%%%%%%%%%%% THINGS THAT MUST COME AT THE END %%%%%%%%%%%%%%%%%%%%%%
%%%% Links %%%%
%% Must come before cleveref accoring to cleveref, but at the end according 
%% to hyperref. It seems to work here
\usepackage{hyperref}

%%%% Referencing %%%%
\usepackage[capitalize]{cleveref}

%%%% Annotations, must come after amsthm %%%%
\usepackage[mode=multiuser]{fixme}
\fxsetup{layout=pdfcnote,targetlayout=color} 
\fxusetheme{signature}
\FXRegisterAuthor{\mathesis@initials}{an\mathesis@initials}{\mathesis@initials}
\crefname{definition}{Definition}{Definitions}
\crefname{remark}{Remark}{Remarks}
\crefname{corollary}{Corollary}{Corollaries}
\crefname{theorem}{Theorem}{Theorems}
\crefname{algo}{Algorithm}{Algorithms}
\crefname{lemma}{Lemma}{Lemmas}
\crefname{example}{Example}{Examples}
\crefname{proposition}{Proposition}{Propositions}
\crefname{defpro}{Definition and Proposition}{}
\crefname{equation}{Equation}{Equations}

%%%% Theorem definitions %%%%
%% Must come after cleveref, according to cleveref 
\theoremstyle{plain}
\@ifclassloaded{book}{
	\newtheorem{definition}{Definition}[chapter]
}{
	\newtheorem{definition}{Definition}[section]
}
\newtheorem{remark}{Remark}
\newtheorem{example}{Example}
\theoremstyle{plain}
\newtheorem{corollary}[definition]{Corollary}
\newtheorem{theorem}[definition]{Theorem}
\newtheorem{algo}[definition]{Algorithm}
\newtheorem{lemma}[definition]{Lemma}
\newtheorem{proposition}[definition]{Proposition}
\newtheorem{defpro}[definition]{Definition and Proposition}