MainPackages.tex

% -------- Packages --------

% This package just gives you a quick way to dump in some sample text.
% You can remove it -- it's just here for the examples.
\usepackage{blindtext}

% This package means empty pages (pages with no text) won't get stuff
%  like chapter names at the top of the page. It's mostly cosmetic.
\usepackage{emptypage}

% The graphicx package adds the \includegraphics command,
%  which is your basic command for adding a picture.
\usepackage{graphicx}

% The float package improves LaTeX's handling of floats,
%  and also adds the option to *force* LaTeX to put the float
%  HERE, with the [H] option to the float environment.
\usepackage{float}

% The amsmath package enhances the various ways of including
%  maths, including adding the align environment for aligned
%  equations.
\usepackage{amsmath}

% Use these two packages together -- they define symbols
%  for e.g. units that you can use in both text and math mode.
\usepackage{gensymb}
\usepackage{textcomp}
% You may also want the units package for making little
%  fractions for unit specifications.
%\usepackage{units}


% The setspace package lets you use 1.5-sized or double line spacing.
\usepackage{setspace}
\setstretch{1.5}

% That just does body text -- if you want to expand *everything*,
%  including footnotes and tables, use this instead:
%\renewcommand{\baselinestretch}{1.5}


% PGFPlots is either a really clunky or really good way to add graphs
%  into your document, depending on your point of view.
% There's waaaaay too much information on using this to cover here,
%  so, you might want to start here:
%   http://pgfplots.sourceforge.net/
%  or here:
%   http://pgfplots.sourceforge.net/pgfplots.pdf
%\usepackage{pgfplots}
%\pgfplotsset{compat=1.3} % <- this fixed axis labels in the version I was using

% PGFPlotsTable can help you make tables a little more easily than
%  usual in LaTeX.
% If you're going to have to paste data in a lot, I'd suggest using it.
%  You might want to start with the manual, here:
%  http://pgfplots.sourceforge.net/pgfplotstable.pdf
%\usepackage{pgfplotstable}

% These settings are also recommended for using with pgfplotstable.
%\pgfplotstableset{
%	% these columns/<colname>/.style={<options>} things define a style
%	% which applies to <colname> only.
%	empty cells with={--}, % replace empty cells with '--'
%	every head row/.style={before row=\toprule,after row=\midrule},
%	every last row/.style={after row=\bottomrule}
%}


% The mhchem package provides chemistry formula typesetting commands
%  e.g. \ce{H2O}
%\usepackage[version=3]{mhchem}

% And the chemfig package gives a weird command for adding Lewis 
%  diagrams, for e.g. organic molecules
%\usepackage{chemfig}

% The linenumbers command from the lineno package adds line numbers
%  alongside your text that can be useful for discussing edits 
%  in drafts.
% Remove or comment out the command for proper versions.
%\usepackage[modulo]{lineno}
%\linenumbers 
%\renewcommand\linenumberfont{\normalfont\itshape\footnotesize}


% Alternatively, you can use the ifdraft package to let you add
%  commands that will only be used in draft versions
%\usepackage{ifdraft}

% For example, the following adds a watermark if the draft mode is on.
%\ifdraft{
%  \usepackage{draftwatermark}
%  \SetWatermarkText{\shortstack{\textsc{Draft Mode}\\ \strut \\ \strut \\ \strut}}
%  \SetWatermarkScale{0.5}
%  \SetWatermarkAngle{90}
%}


% The multirow package adds the option to make cells span 
%  rows in tables.
\usepackage{multirow}


% Subfig allows you to create figures within figures, to, for example,
%  make a single figure with 4 individually labeled and referenceable
%  sub-figures.
% It's quite fiddly to use, so check the documentation.
%\usepackage{subfig}
% DG comment: subfig is broken. https://tex.stackexchange.com/questions/13625/subcaption-vs-subfig-best-package-for-referencing-a-subfigure

% The natbib package allows book-type citations commonly used in
%  longer works, and less commonly in science articles (IME).
% e.g. (Saucer et al., 1993) rather than [1]
% More details are here: http://merkel.zoneo.net/Latex/natbib.php
\usepackage[numbers,sort&compress]{natbib}

% The bibentry package (along with the \nobibliography* command)
%  allows putting full reference lines inline.
%  See: 
%   http://tex.stackexchange.com/questions/2905/how-can-i-list-references-from-bibtex-file-in-line-with-commentary
%\usepackage{bibentry} 

% The isorot package allows you to put things sideways 
%  (or indeed, at any angle) on a page.
% This can be useful for wide graphs or other figures.
%\usepackage{isorot}

% The caption package adds more options for caption formatting.
% This set-up makes hanging labels, makes the caption text smaller
%  than the body text, and makes the label bold.
% Highly recommended.
\usepackage[format=hang,font=small,labelfont=bf]{caption}

% If you're getting into defining your own commands, you might want
%  to check out the etoolbox package -- it defines a few commands
%  that can make it easier to make commands robust.
\usepackage{etoolbox}

% Loads Libertine and Biolinum fonts
\usepackage[sb]{libertine}

% I hoped this would allow me to reference the Krinov data properly, but it didn't work
%\usepackage{libertinegc} 
\usepackage[utf8]{inputenc}
%\usepackage[russian]{babel}

% Introduces a few neat typographic tricks
\usepackage[stretch = 16]{microtype}

% Package to set images to be maximum text width
\usepackage[export]{adjustbox}

% for making lettered lists
\usepackage{enumitem}

% Highlighting
\usepackage{color,soul}
\definecolor{lightgray}{gray}{0.85}
\sethlcolor{lightgray}

% for insering full pdf pages (used by me for making ethics applications into appendices
\usepackage{pdfpages} 
\includepdfset{offset= 0cm -3cm}

% For full page figures with the caption on the previous page
\usepackage{phffullpagefigure}

% %for code chunks
\usepackage{listings} 
\usepackage[framed]{matlab-prettifier}


%for multi-line equations
\usepackage{amsmath} 

% For quoting hack
\usepackage{xparse}
\usepackage{quoting}

\NewDocumentEnvironment{citequote}{m}
 {%
  \begin{quoting}[indentfirst=false,font=itshape]
  \bigquotes{r}{``} \centering 
 }
 {%
  \bigquotes{l}{''}%
  \item\relax\hspace*{\fill}\citeauthor{#1}\ \textup{\cite{#1}}%
   \end{quoting}
 }
\newcommand{\bigquotes}[2]{%
  {%
    \raisebox{\dimexpr\fontcharht\font`A-\height}{\Large\bfseries#2}%
  }%
}

\NewDocumentEnvironment{itquote}{m} %as above but without the ref. I can't get rid of the {m} and I don't know why
 {%
  \begin{quoting}[indentfirst=false,font=itshape]
  \bigquotes{r}{``} \centering 
 }
 {%
  \bigquotes{l}{''}%
   \end{quoting}
 }
 
% For rounding numbers
\usepackage{numprint}
% https://tex.stackexchange.com/questions/9132/rounding-numbers-in-a-table-truncating-text-in-table