packages.tex

%% REMEMBER: The order of package imports is sometimes important

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%% Language and font encodings
%%
\usepackage[english]{babel}
% NB https://tex.stackexchange.com/a/49613
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}


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%% Page size and margins etc.
%%
\usepackage[a4paper,top=2cm,bottom=4cm,inner=4cm,outer=2.5cm,twoside]{geometry}
\usepackage{layout}
\usepackage{lineno}
\usepackage{setspace}

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%% Mathematics and lists
%%
\usepackage{amsmath}
\usepackage{bm}
\usepackage{enumitem}
% Compact lists; https://stackoverflow.com/a/4974583
\setlist{noitemsep,topsep=0pt,parsep=0pt,partopsep=0pt}


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%% Graphics
\usepackage{graphicx}
% Tikz setup
% https://www.sharelatex.com/blog/2013/08/29/tikz-series-pt3.html
% https://tex.stackexchange.com/a/342227
\usepackage{tikz}
\usetikzlibrary{shapes,arrows}
\tikzstyle{startstop} = [rectangle, rounded corners, minimum width=3cm, minimum height=1cm,text centered, draw=black, fill=red!30]
\tikzstyle{io} = [trapezium, trapezium left angle=80, trapezium right angle=100, trapezium stretches=true, minimum width=3cm, minimum height=1cm, text centered, draw=black, fill=blue!30]
\tikzstyle{process} = [rectangle, minimum width=3cm, minimum height=1cm, text centered, draw=black, fill=orange!30]
\tikzstyle{decision} = [diamond, minimum width=3cm, minimum height=1cm, text centered, draw=black, fill=green!30]
\tikzstyle{arrow} = [thick,->,>=stealth]


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%% Hyperlinks
% Re: print version, see https://tex.stackexchange.com/a/95009
\usepackage[colorlinks=true, allcolors=blue]{hyperref}
% \usepackage[colorlinks=true, allcolors=blue, hidelinks=true]{hyperref}


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%% For TO-DO notes in margins
%%
\usepackage[colorinlistoftodos]{todonotes}
% put todo notes on the inner (larger) margin:
\reversemarginpar


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%% More mathematics and other things...
%%
\usepackage{amssymb}
\usepackage{siunitx}
% gensymb provides \degree
\usepackage{textcomp, gensymb}
% For sidewaystable and sidewaysfigure
\usepackage{rotating}
\usepackage[toc,acronym,nonumberlist]{glossaries}
\usepackage[toc,page]{appendix}
% Make figure captions smaller
\usepackage[textfont={small},labelfont={small,bf}]{caption}
% Makes list of figures, tables appear in table of contents
\usepackage[nottoc]{tocbibind}


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% %% DEPRECATED
% %% Bibliography using natbib
% %% https://www.overleaf.com/learn/latex/Bibliography_management_with_natbib
% %% http://merkel.texture.rocks/Latex/natbib.php
% %% https://tex.stackexchange.com/a/39457
% %% agsm provides Harvard style
% \usepackage{doi}     % clickable doi's, must be loaded before natbib
% \usepackage{natbib}
% \bibliographystyle{abbrvnat}
% % \bibliographystyle{agsm}
% % \bibliographystyle{humannat}
% % \bibliographystyle{alpha}
% % \bibliographystyle{apalike}
% % \setcitestyle{authoryear}
% % \setcitestyle{authoryear,open={((},close={))}}
% % Must use \bibliography{references} in main.tex
%% http://merkel.texture.rocks/Latex/natbib.php
%% https://tex.stackexchange.com/a/39457
%% agsm provides Harvard style


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%% Bibliography using biblatex
%% https://www.overleaf.com/learn/latex/Bibliography_management_in_LaTeX
%% https://www.overleaf.com/learn/latex/Articles/Getting_started_with_BibLaTeX
%% https://tex.stackexchange.com/a/5105
%% MANUAL: http://mirrors.ibiblio.org/CTAN/macros/latex/exptl/biblatex/doc/biblatex.pdf
\usepackage{csquotes}
\usepackage[
    % Provide compatibility with natbib's \citet and \citep commands
    natbib=true,
    backend=biber,
    bibstyle=authoryear,
    citestyle=authoryear-comp,
    % sorting=nyt,
    % Don't replace repeated author name with dash
    %  see manual page 72 (authoryear)
    dashed=false, 
    % Don't print the url fields (will be a problem for referencing websites)
    url=false,
    % Only print forename initials
    %  https://tex.stackexchange.com/a/128823
    % NB: doesn't affect sorting (beware of mix of names and initials)
    giveninits=true,
    % Don't print initials in citations
    %  https://tex.stackexchange.com/a/134544
    uniquename=false,
    uniquelist=false,
    % Show at most 6 names, followed by et al.
    %  https://tex.stackexchange.com/a/76251
    minbibnames=6,
    maxbibnames=6,
    % Show at most 2 names in citations
    %  https://tex.stackexchange.com/a/368042
    maxcitenames=2,
    % Sort list by (first author) name, year, title
    % https://tex.stackexchange.com/a/203270
    % Why doesn't maxsortnames do this?
    % maxalphanames=1,
    % labelalpha=true,
    % sorting=anyt,
    % Sort set members
    % sortsets=true,
    % must be set after maxbibnames, maxcitenames
    % minsortnames=1,
    % maxsortnames=1,     % DOESN'T APPEAR TO BE WORKING?
    % sortfirstinits=True,
    % Sort citations in the same way as the bibliography (default?)
    % sortcites=true,
]{biblatex}
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%% PROVIDE YOUR REFERENCES LOCATION HERE
%%
\addbibresource{references.bib}
%%
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%% More complicated biblatex stuff
%
% 1)
% Sort bibliography (and citations) by first author name only
% https://tex.stackexchange.com/a/434947
% NB: bibtex file (from Mendeley) must not contain mix of first names and initials like:
%  Last, First;   Last, F.
% (that will interfere with the sorting)
% 2)
% Undo Mendeley's auto-escaping of special characters in url/doi fields
% https://tex.stackexchange.com/a/309995
\DeclareSourcemap{
  \maps[datatype=bibtex]{
    \map{
      \step[fieldsource=author, match=\regexp{(.*?)\s+and\s+}]
      \step[fieldset=sortname, fieldvalue={$1}]
    }
    % % Undo Mendeley's auto-escaping of special characters in url/doi fields
    % % https://tex.stackexchange.com/a/309995
    \map{ % Replaces '{\_}', '{_}' or '\_' with just '_'
        \step[fieldsource=doi,
              match=\regexp{\{\\\_\}|\{\_\}|\\\_},
              replace=\regexp{\_}]
        }
    \map{ % Replaces '{'$\sim$'}', '$\sim$' or '{~}' with just '~'
        \step[fieldsource=doi,
              match=\regexp{\{\$\\sim\$\}|\{\~\}|\$\\sim\$},
              replace=\regexp{\~}]
    }
  }
}
%
% Print url if no doi
% https://tex.stackexchange.com/a/424775
\renewbibmacro*{doi+eprint+url}{%
    \printfield{doi}%
    \newunit\newblock%
    \iftoggle{bbx:eprint}{%
        \usebibmacro{eprint}%
    }{}%
    \newunit\newblock%
    \iffieldundef{doi}{%
        \usebibmacro{url+urldate}}%
        {}%
    }
%
% Get rid of ISSNs
% https://tex.stackexchange.com/a/40107
\AtEveryBibitem{\clearfield{issn}}
%
% fix period before brackets in citation
%  https://tex.stackexchange.com/a/312565
\DeclareDelimFormat[cbx@textcite]{nameyeardelim}{\addspace}
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