\documentclass[12pt]{article}
%\usepackage{booktabs}
\usepackage{maybemath, xspace, setspace, fancyvrb, a4wide, url, relsize}
\usepackage[colorlinks=true,pdfpagemode=FullScreen,bookmarks=true]{hyperref}
\newcommand{\maybemath}{\texttt{maybemath}\xspace}
\newcommand{\hepthesis}{\texttt{hepthesis}\xspace}

\let\OldCite\cite
\renewcommand{\cite}[1]{\mbox{\!\!\OldCite{#1}}}


\onehalfspacing
\DefineShortVerb{\|}

\author{Andy Buckley, \texttt{andy@insectnation.org}}
\title{The \hepthesis \LaTeX{} class}

\newcommand{\Or}{\ensuremath{\vert}\xspace}
\newcommand{\manifestsAs}{\ensuremath{\Rightarrow\quad}\xspace}
\newcommand{\texcmd}[1]{\texttt{\char`\\#1}} 
\newcommand{\texenv}[1]{\texttt{\char`#1}} 
\newcommand{\texopt}[1]{\texttt{\char`#1}}
\newcommand{\texarg}[1]{\texttt{\char`#1}}
\newcommand{\texcommand}[1]{\texcmd{#1}} 
\newcommand{\texoption}[1]{\texopt{#1}}
\newenvironment{snippet}{\Verbatim}{\endVerbatim}

\begin{document}
\maketitle

\abstract{%
  The \hepthesis package provides an attractive framework in which to write a
  PhD or Masters' degree dissertation. The commands provided by this package
  permit most structural aspects of the thesis to be defined more or less
  semantically, rather than in terms of raw text sizings and position shifts.
  Special equation, figure and table environments are provided, along with
  pre-defined figure widths and macros for typesetting chapter quotes, 
  introductory paragraphs and incliner section headings.
}

\section{Introduction}
When I began my PhD, I was surprised to find that there was no standard \LaTeX
thesis class used by students in my field (high-energy particle physics, hence
the ``hep''). In retrospect, this is not so surprising --- groups tend to have
an informal system of handing down slightly tailored thesis templates (complete
with in line \texcommand{vspace}s, \texcommand{Huge}s and all the rest) through
generations of students without ever formalising the style and attempting to do
it ``properly''. By the time it came to write my own thesis it was obvious that
I would only retain my sanity through measures of extreme procrastination and so
this package came to be. It has now been edited and hacked for about 2 years,
taking stylistic features from other theses that I've thought attractive. As my
own thesis has been recently submitted, this seems an apt time to release the
first official version of \hepthesis upon the world.

This document will document the structure of \hepthesis and how to make it work
with you rather than against you. I may be unable to resist including other
hints and tips on how to make your thesis-writing go smoothly. Please contact me
with suggested improvements, either to the package or to this documentation.


\section{Features}
Why would you want to use \hepthesis? Here's a list of features, so you can
decide for yourself:

\begin{itemize}
\item Semantic macros for defining the front page, abstract, preface, acknowledgements, etc.
\item Macros for quotes, including a full-page quote and chapter-wise quotes
\item Attractive header and footer structures
\item Pre-set margins suitable for binding or for screen viewing
\item Nicely (re-)defined figure, table and equation environments
\item Optional mode for generating hyper-links when building PDF files
\item Built-in draft copy mode with line numbering
\end{itemize}


\section{Recommended usage}
The basic usage mode for \hepthesis is to place
%
\begin{snippet}
\documentclass{hepthesis}
\end{snippet}
%
in the preamble of your document. This will then set up the document's appearance and
provide the \hepthesis macros as do the standard \LaTeX{} classes like |article|
and |report|. A more sophisticated and flexible approach is described in 
Appendix~\ref{app:DerivedClass}.

Although strictly unrelated to \hepthesis, it is usual to write each thesis
chapter as a separate |.tex| file and to include it with
\texcommand{include} or \texcommand{input}. You may find it useful to set your
|LATEXINPUTS| environment variable to ensure that the \texcommand{input}'d
files are found by \LaTeX.

\hepthesis takes several optional arguments. Personally, I use
%
\begin{snippet}
\documentclass[hyperpdf,bindnopdf]{hepthesis}
\end{snippet}
%
which produces page-centered, hyper-linked PDF files and PostScript files with
margins suitable for binding and no hyper-links, depending on whether you build
the document using |latex| or |pdflatex|. The details of the \hepthesis options
are described in Section~\ref{sec:Options} of this document.


\section{Requirements}
As \hepthesis aims to allow produce a fairly final version of a thesis without
much additional tweaking, there are quite a few required packages. Most should
be natively available in your \TeX{} distribution; the rest from CTAN.

Here's the mandatory packages:
\begin{itemize}
\item \textbf{cite~\cite{cite}}
\item \textbf{setspace~\cite{setspace}}
\item \textbf{fancyhdr~\cite{fancyhdr}}
\item \textbf{tocbibind~\cite{tocbibind}}
\item \textbf{rotating~\cite{rotating}}
\item \textbf{subfigure~\cite{subfigure}} (needs updating to use |subfig| instead)
\item \textbf{ccaption~\cite{ccaption}}
\item \textbf{caption~\cite{caption}} (need updating to be able to use |caption2| instead).
\end{itemize}

Additionally, there are several packages which are only required depending on
the class options:

\begin{itemize}
\item \textbf{a4wide~\cite{a4wide}:} very standard. Disabled with any paper size option other than |a4paper|
\item \textbf{amsmath~\cite{amsmath}:} very, \emph{very} standard. Disabled with the |noams| option
\item \textbf{hyperref~\cite{hyperref}:} very standard. Enabled with the |hyper| option
\item \textbf{booktabs~\cite{booktabs}:} non-standard. Disable with the |nobooktabs| option
\item \textbf{draftcopy~\cite{draftcopy}:} very standard. Enable with the |draft| option
\item \textbf{lineno~\cite{lineno}:} non-standard (?). Enable with the |draft| option
\end{itemize}

Some other handy packages (which aren't required at all for compatibility with
|hepthesis| but may well help you to write your thesis) are summarised in
Section~\ref{sec:ExtraPackages}.


\section{Class options}
\label{sec:Options}

\subsection{\texoption{oneside} \Or \texoption{twoside}}
Typeset the thesis for printing in one- or two-sided format: for example, you
may wish to present preview and draft copies in two-sided format, but the final
submission may be required to be single-sided. Changing to single-sided form
will remove the blank facing pages and only use the margins and header/footer
format specified for right-hand pages.

\subsection{\texoption{bind} \Or \texoption{nobind} \Or \texoption{bindnopdf}}
Set the margins to be suitable for printing or screen-viewing. Using the
\texoption{bind} option produces larger inner margins, so that left- and
right-facing pages have LR-reflection symmetry. Using the \texoption{nobind}
option makes the margins equal, so that the pages don't jump around when you
flick through them in |gv| or Adobe Acrobat. The \texoption{bindnopdf} option
will use binding margins when making a PostScript document and screen-view
margins when building a PDF. Note that this option requires some carefulness
with the |.aux| files: this is described in Appendix \ref{app:AuxFileProblem}.

\subsection{\texoption{ams} \Or \texoption{noams}}
Make use of the AMS mathematical package. This re-defines several \hepthesis
mathematical environments using more powerful macros and is enabled by default.
If you don't plan on having any maths in your thesis, then disabling this option
may speed up your build-time a little.

\subsection{\texoption{alphafoot}}
Use alphanumeric footnote markers.

\subsection{\texoption{hidefront} \Or \texoption{hideback} \Or \texoption{hidefrontback}}
Useful for draft builds, these options respectively hide the front matter, the
back matter or both from the \LaTeX{} compilation, giving a faster build time
and meaning you don't have to flick through 20 pages of garbage before
proof-checking the first real content. Note that hiding the back matter will
fail to include the bit where you generate your bibliography, so unless you make
a work-around, all your citations will break.

\subsection{\texoption{draft}}
Prints ``DRAFT'' diagonally across the pages and numbers the lines, suitable for
proof-reading. This makes use of the standard |draftcopy| and the less-standard
|lineno| packages.

\subsection{\texoption{booktabs} \Or \texoption{nobooktabs}}
Use the |booktabs| package to define the \hepthesis tabular environment.
|booktabs| produces publication quality tables, as opposed to \TeX's rather
ropey defaults, and so this option is enabled by default. You can disable it if
your thesis doesn't have any tables and get a slightly faster build, but it is
strongly encouraged that any table presentation uses the |booktabs| look and
feel because it's so much better!

\subsection{\texoption{hyper}}
The |hyper| option is used to activate the |hyperref| package, with some reasonably]
sensible default options. Essentially, it's equivalent to putting
%
\begin{snippet}
\usepackage[colorlinks=true,pdfpagemode=FullScreen, \
            bookmarks=true]{hyperref}
\end{snippet}
%
in the preamble of your document.

\subsection{\texoption{hyperpdf}}
|hyperpdf| has the effect of the |hyper| option when building PDF output, and no
effect at all if building PostScript. This can be handy if you consider the PDFs
to be for screen-reading purposes and the PS for printing: you probably don't
want to print a version where all the references and URLs are coloured! Note
that this option requires some carefulness with the |.aux| file, since
alternating between PS and PDF builds involves repeatedly writing and removing
hyperref tokens. A solution to this is described in Appendix \ref{app:AuxFileProblem}.

\subsection{\texoption{index}}
Include the |makeidx| package, to allow an index to be built. Note that you have
to do this by hand and that it's probably best done as a retrospective feature
after you've written the thesis. Not many people want to spend \emph{more} time
with their thesis when they've done enough to pass!

\subsection{\texoption{a4paper} \Or \texoption{a4narrow} \Or \texoption{letterpaper} \Or \dots}
Choose the paper size. Duh.

%\subsection{\texoption{hep} \Or \texoption{hep\{fd,layout,hyper,float,all\}}}

\section{Environments and commands}
The \hepthesis environments and commands are a mix of new macros and tweaked
versions of existing standard ones. The ones that re-define standard macros
can't be disabled (at least, not in this version), so if you don't like them
then you can either hack \hepthesis to be the way you'd like (preferably in a
nice way which I can integrate into a future release) or use something else. The
choice is yours!

Here are the environments and commands, roughly in the order that you'd use them:

\subsection{\texcmd{definethesis}}
This command should be placed in the preamble, and is used to define
the thesis title and the author (you!). In future, maybe I'll find a nice way to
use the built-in \texcmd{author} and \texcmd{title} commands for this. Use it like:
%
\begin{snippet}
\definethesis%
  {A study of \BToKPi decays with the \LHCb experiment}%
  {Andrew Gordon Buckley}
...
\begin{document}
...
\end{snippet}

Once this command has been executed, the title and author strings are available
via the \texcommand{thetitle} and \texcommand{theauthor} commands.

\subsection{\texenv{frontmatter} \Or \texenv{mainmatter} \Or \texenv{appendices} \Or \texenv{backmatter}}
Use these to delimit the auxiliary parts of your thesis from the main feature
(being all that clever work you spent years working on). In practice, these
commands change the page-numbering style and set/reset some section counters
appropriately: the frontmatter and backmatter environments will not use chapter
numbering but will insert the un-numbered chapter titles in the table of
contents. Note that this means appendices should be placed in the appendices
environment between mainmatter and backmatter, rather than in the back matter
itself, which is intended for such things as the bibliography, colophon etc.

\subsection{\texcmd{titlepage}}
The \texcmd{titlepage} macro generates a title page for the thesis and as such
should probably be the first item in the front matter. It takes two arguments:
the institution and the description of the award for which the thesis is being
submitted. You may need to hack this or use a different macro if your
institution has a very different prescribed format for the layout of thesis
title pages. Here's an example:
%
\begin{snippet}
\thesistitlepage
{Churchill College}
{A dissertation submitted to the University 
 of Cambridge\\ for the degree of Doctor of Philosophy}
\end{snippet}

\subsection{\texenv{abstract}}
Where you present the summary of your thesis: this should be within the
\texenv{frontmatter} environment. The \texenv{abstract} environment takes one
optional argument, which will be the heading above the abstract. If this isn't
specified, the heading will simply be ``Abstract''. This may be useful for
providing a stand-alone summary page, with a snippet like:
%
\begin{snippet}
\begin{abstract}%
  [\smaller\thetitle\\ \vspace*{1cm} \smaller{\theauthor}]
\thispagestyle{empty}
This thesis describes all the really cool work I did on...
\end{abstract}
\end{snippet}

\subsection{\texenv{declaration}}
Where you declare that the thesis was all your own work, lies within word
limits, etc. Use it in the front matter area, of course, with something like
%
\begin{snippet}
\begin{declaration}
  This dissertation is the result of my own work...
  \vspace*{1cm}
  \begin{flushright}
    Andy Buckley
  \end{flushright}
\end{declaration}
\end{snippet}

\subsection{\texenv{acknowledgements}}
A nice little environment for putting all those gushing thank-you's (and the
obligatory thanks to a supervisor). Use it (in the front matter again) like:
%
\begin{snippet}
\begin{acknowledgements}
  Of the many people who deserve thanks, some are 
  particularly prominent, for example...
\end{acknowledgements}
\end{snippet}

\subsection{\texenv{preface}}
Here's where you summarise the structure of the thesis to come, just before the
main matter starts, with something like:
%
\begin{snippet}
\begin{preface}
  This thesis describes my research on various aspects of...
\end{preface}
\end{snippet}

\subsection{\texcmd{dedication}}
Dedicate your thesis to someone/something:
%
\begin{snippet}
\begin{mainmatter}
  \dedication{For Jo}
  ...
  \end{frontmatter}
\end{snippet}


\subsection{\texcmd{frontquote}}
Use this at the start of the main matter if you want to encapsulate your thesis
in a few choice words, for example:
%
\begin{snippet}
  \frontquote%
  {Writing in English is the most ingenious torture\\
   ever devised for sins committed in previous lives.}%
  {James Joyce}
  ...
  \end{frontmatter}
\end{snippet}

\subsection{\texcmd{chapterquote}}
Something flippant/emotive to put at the start of chapters:
%
\begin{snippet}
\chapter{\CP violation in the \Bmeson system}
\label{chap:basictheory}
\thesischapterquote{Laws were made to be broken.}%
  {Christopher North 1785--1854}
  ...
\end{snippet}

\subsection{\texenv{colophon}}
A colophon is an inscription placed at the end of a book or other work that
talks about how the work was created and what things were used in its creation.
This should go in the back matter of your thesis and is completely optional.
If you use this, please mention \hepthesis' r\^ole in making your thesis! Here's 
an example:
%
\begin{snippet}
  \begin{backmatter}
  \begin{colophon}
    This thesis was made with ``hepthesis'' and it was really cool...
  \end{colophon}
  ...
\end{snippet}


\subsection{\texenv{table}}
Tables --- use like any other table (probably combined with the tabular
environment). It has been slightly modified to be horizontally centered and have
an slightly increased vertical spacing at the top.

\subsection{\texenv{tabular}}
If the |booktabs| package is used (enabled by default), then the tabular
environment is re-defined to have a horizontal bar at top and bottom, which
looks much nicer than \TeX's default tables.

\subsection{\texenv{figure} and \texenv{sidewaysfigure}}
The \texenv{figure}, \texenv{figure*} and \texenv{sidewaysfigure} environments
are re-defined to be automatically centered.

\subsection{\texenv{equation \Or displaymath}}
These environments and their starred versions are re-defined so that
\texenv{equation} behaves like the normal \texenv{displaymath} environment. If
the AMS package is used (which it is by default) then both are redefined to use
the AMS \texenv{align} environment, which is much more powerful: it supports
more intelligent label-placement, sub-equations and boasts a better alignment
syntax than the default \LaTeX{} displayed math environments. The AMS re-defined
\texenv{equation} is suitable for most purposes --- \emph{all} my purposes, in
fact.

\subsection{\texcmd{verysubsection}}
A little command for in-line mini section headings, consisting of a boldened
phrase specified by the argument, a bold colon and a space. Just for
convenience, really, when all you want to do is label a paragraph without
incurring all the vertical space of \texcmd{subsubsub...subsection}s. Use it
like:
%
\begin{snippet}
\verysubsection{\Tevatron Run II experiments}
Since 1983 and until the commissioning of the \LHC is complete...
\end{snippet}

\subsection{Semantic figure widths}
Rather than specifying figure widths in raw terms, like centimetres, or document
parameters like \texcmd{textwidth}, it's nice to be able to have a more semantic
reference. Having a few standard width also helps to keep things looking
consistent through the document. For these reasons, |hepthesis| provides four
standard figure widths, \texcmd{smallfigwidth}, \texcmd{mediumfigwidth},
\texcmd{largefigwidth} and \texcmd{hugefigwidth}, which are defined in terms of
the text width and chosen to avoid overflows. Use them like this:
%
\begin{snippet}
\begin{figure}
  \includegraphics[width=\largefigwidth]{ckmfitter-alpha-combined}
  \caption{CKM Fitter constraints on \alphaCKM.}
  \label{fig:CKMFitter}
\end{figure}
\end{snippet}
  
Note also that this way of including images will automatically look for an
|.eps| file when building PostScript and a |.pdf| file when building PDF. You
may find the |eps2pdf| and |pdf2eps| utilities useful.

\subsection{Standard in-document reference terms}
It's nice to be able to refer to portions of your document with standard names,
capitalisation, etc. For this reason, I've defined a bunch of macros which give
consistent and sensible capitalisations. Using them systematically will ensure
consistency in your references:
%
\begin{itemize}
\item \texcmd{Chapter} \manifestsAs Chapter
\item \texcmd{Section} \manifestsAs Section
\item \texcmd{Appendix} \manifestsAs Appendix
\item \texcmd{Figure} \manifestsAs Figure
\item \texcmd{Table} \manifestsAs Table
\item \texcmd{Equation} \manifestsAs equation
\item \texcmd{Reference} \manifestsAs reference
\item \texcmd{Page} \manifestsAs page
\end{itemize}

Taking this consistency thing a step further, here are versions of the same
commands which take the reference label as a argument:
%
\begin{itemize}
\item \texcmd{ChapterRef}
\item \texcmd{SectionRef}
\item \texcmd{AppendixRef}
\item \texcmd{FigureRef}
\item \texcmd{TableRef}
\item \texcmd{EquationRef}
\item \texcmd{ReferenceRef}
\item \texcmd{PageRef}
\end{itemize}
%
Using these forms will ensure that the spacing between e.g. the worked
``Chapter'' and the chapter number is always the same, and that it won't wrap
over line breaks. The equation, reference and page forms will call the
\texcmd{eqref}, \texcmd{cite} and \texcmd{pageref} reference macros rather than
\texcmd{ref}, which is used for all others.

\subsection{``thesis---'' prefix versions}
Additionally, all \hepthesis environments and commands have an alternative name,
which is the version described above, prefixed with ``thesis''\footnote{This
  is a hang-over from early versions of my thesis, when I didn't know how to
  robustly extend and re-define environments and commands.}. These forms are
frankly a bit of a pain to use, so use the short versions, please. The
``thesis---'' versions should be considered deprecated and may be removed in
future releases.


\section{Recommended extra packages}
\label{sec:ExtraPackages}
Here are some other packages it might be good to know about:
\begin{itemize}
\item \textbf{SIunits~\cite{SIunits}:} \emph{the} way to do units and get it right.
\item \textbf{hepunits~\cite{hepunits}:} my extension of |SIunits| to include some common HEP units not used elsewhere.
\item \textbf{hepnames~\cite{hepnames} and hepparticles~\cite{hepparticles}:} my packages for typesetting HEP particle names \emph{properly}, with |hepnames| defining macros for a lot of the standard ones. Requires |maybemath|~\cite{maybemath}
\item \textbf{braket~\cite{braket}:} decent implementation of Dirac bra and ket notation
\item \textbf{cancel~\cite{cancel}:} the best way to do Feynman slashes (in my opinion)
\item \textbf{feynmf/feynmp~\cite{feynmf} and axodraw~\cite{axodraw}:} various approaches to doing Feynman diagrams, especially in equations, inline contexts and so-on.
\end{itemize}
%
and some related software:
%
\begin{itemize}
\item \textbf{FeynDiagram~\cite{feyndiagram} and Jaxodraw~\cite{jaxodraw}}: for Feynman diagrams outside \TeX. You might also
  be interested in my |pyfeyn|~\cite{pyfeyn} program, once it's publically released.
\item \textbf{SLAC SPIRES' biblio tools service:} see \url{www.slac.stanford.edu/spires/}
\end{itemize}



\section{An example \texttt{hepthesis} thesis}
Here are some selected snippets from my thesis, which hopefully demonstrate the
features described. I split my thesis into |thesis.cls|, |thesis.sty| and
|thesis.tex| files, with the front matter, back matter and chapters
\texcommand{input}'d into |thesis.tex|. The output was built by running e.g.
%
\begin{snippet}
latex thesis.tex && bibtex thesis && latex thesis.tex
\end{snippet}
%
(though I used a Makefile rather than do it directly). You should note that you
might not be able to build this exact thesis due to missing packages: if you're
writing an HEP thesis then I'd encourage you to use the |hepnames| \LaTeX{}
package for typesetting particle names --- it depends on the extra
|hepparticles| and |maybemath| packages, which you'll also have to download. The
examples used here also rely on the |hepunits| package: you can all these extra
packages from the CTAN~\cite{CTAN}. See Appendix~\ref{app:InstallingPackages} for
a quick guide on how to install personal copies of \LaTeX{} packages.


\subsection{\texttt{thesis.cls}}
{\smaller \VerbatimInput{example/thesis.cls}}

\subsection{\texttt{thesis.sty}}
{\smaller \VerbatimInput{example/thesis.sty}}

\subsection{\texttt{thesis.tex}}
{\smaller \VerbatimInput{example/example.tex}}

\subsection{\texttt{frontmatter.tex}}
{\smaller \VerbatimInput{example/frontmatter.tex}}

\subsection{\texttt{chap1.tex}}
{\smaller \VerbatimInput{example/chap1.tex}}

\subsection{\texttt{chap2.tex}}
{\smaller \VerbatimInput{example/chap2.tex}}

\subsection{\texttt{backmatter.tex}}
{\smaller \VerbatimInput{example/backmatter.tex}}


\section{Wishlist / TODO}
I'm not planning on writing another thesis, but maybe I'll add features if
there's demand. If you add a nice feature, pass it on to me and I'll think about
including it in the package (and will give you some credit, of course). But anyway, 
here's the TODO:
%
\begin{itemize}
\item Make |hepthesis| use |subfig| in place of |subfigure| and check out compatibility between |caption| and |caption2|.
\item Make the spacing in the \texcmd{SectionRef} etc. commands customisable.
\item Make the vertical spacings on the quote, dedication and title pages appropriate for the paper size
\end{itemize}


\section{Feedback}
|hepthesis| has taken a lot of work\dots I hope you think it was worthwhile and
that you enjoy using it. Or at least, I hope you enjoy writing your thesis more
than you would have done without it! If you're feeling appreciative, then a teeny
credit in your thesis acknowledgements would be hugely appreciated.

Other than that, any feedback on the package is very welcome, especially if it's
constructive criticism! Email your thoughts to
\texttt{hepthesis@insectnation.org}, please.


\appendix

\section{Using your own derived document class}
\label{app:DerivedClass}
If you're feeling sophisticated, then you can make your own document class based on 
\hepthesis by placing
%
\begin{snippet}
\LoadClass{hepthesis}
\end{snippet}
%
in your own class definition file. This is a rather nice way of working, since
it allows you to tweak the \hepthesis defaults without cluttering your
|.tex| file with preamble junk.


\section{Installing personal copies of \LaTeX{} packages}
\label{app:InstallingPackages}
Since |hepthesis| depends on several non-standard \LaTeX{} packages, you may have to
download and install them yourself. If you don't have |root| access to the computer
on which you're working then you'll probably have to install them into your own home
directory or similar. Since I expect quite a few prospective users of |hepthesis| will
be non-experts in the ways of \TeX{}, this is a quick guide on what to do.

\begin{enumerate}
\item Make a \TeX{} directory tree in your home directory (or any other area you can write to), e.g.
\begin{snippet}
$ mkdir -p $HOME/local/texmf/tex/latex
$ mkdir -p $HOME/local/texmf/bibtex/bib
$ mkdir -p $HOME/local/texmf/bibtex/bst
\end{snippet}
\item Download the packages from CTAN~\cite{CTAN} or wherever.
\item Follow the packages' installation instructions to install them into the \\
  |$HOME/local/texmf/tex/latex| %$
  directory you made above (or an appropriately-named sub-directory of it if you
  want to be neat). For simple |.sty| or |.cls| files, this will just involve
  copying them into your directory of choice. |.dtx| files will probably require
  running |latex| to build the files to be installed.
\item If you use the |bash| shell, add the following to your |~/.bashrc| file:
\begin{snippet}
export TEXINPUTS="$HOME/local/texmf/tex//:$TEXINPUTS"
export LATEXINPUTS="$HOME/local/texmf/tex/latex//:$LATEXINPUTS"
export BIBINPUTS="$HOME/local/texmf/bibtex//:$BIBINPUTS"
\end{snippet}
or, if you use the |(t)csh| shell, add the following to your |~/.cshrc| file:
\begin{snippet}
setenv TEXINPUTS "$HOME/local/texmf/tex//:$TEXINPUTS"
setenv LATEXINPUTS "$HOME/local/texmf/tex/latex//:$LATEXINPUTS"
setenv BIBINPUTS "$HOME/local/texmf/bibtex//:$BIBINPUTS"
\end{snippet}
\item That's all: the lines above mean that  \LaTeX{} will look for input files
such as classes, packages, images, \texcmd{input}'d |.tex| files etc. recursively under \\
|$HOME/local/texmf/tex/latex| %$
 and that BibTeX will look for its style and database files recursively under
|$HOME/local/texmf/bibtex|.%$
You can probably see how this can be extended to keep your thesis development
directories neat, too!
\end{enumerate}


\section{Distinguishing PS/PDF output in thesis builds}
\label{app:AuxFileProblem}

The options \texopt{bindnopdf} and \texopt{hyperpdf} change the behaviour
depending on whether you're building PDF or PostScript output. This is fine if
you only ever do one, but if you want to switch rapidly between these output
formats then you'll have problems. This is because the |.aux| file, which
records the reference keys and suchlike changes depending on whether you're
making hyper-refs and if the changes of margins force sections on to different
pages.

A nice solution to this involves using a Makefile, which you probably want to be
doing anyway. You'll have to read up on the details of Makefiles (and possibly
GNU automake) elsewhere, but to save on Make-newbie angst, I'll tell you that
the indents in the following snippet \emph{must} be tabs, rather than spaces!
Here goes --- put the following into a file called |Makefile|, change the
|DOCNAME| variable to something which suits your project and run |make thesis| or |make thesispdf|:
\begin{snippet}
# For a main thesis LaTeX file called ``thesis.tex''
DOCNAME = thesis

thesis: $(TEXSOURCES) $(DOCNAME).bbl
    test -f $(DOCNAME).aux.ps && cp $(DOCNAME).aux.ps \
      $(DOCNAME).aux || true
    latex $(DOCNAME)
    cp $(DOCNAME).aux $(DOCNAME).aux.ps
    ./thesisstats.sh >> buildlog.dat

thesispdf: $(TEXSOURCES) $(DOCNAME).bbl
    test -f $(DOCNAME).aux.pdf && cp $(DOCNAME).aux.pdf \
      $(DOCNAME).aux || true
    pdflatex $(DOCNAME)
    cp $(DOCNAME).aux $(DOCNAME).aux.pdf
    ./thesisstats.sh >> buildlog.dat
\end{snippet}

Otherwise you can just delete the |.aux| file when you change between using
|latex| and |pdflatex|, but this will require more passes, since the
|.aux| file has to be replaced each time.

\begin{thebibliography}{99}
\bibitem{CTAN}{CTAN: \url{http://www.ctan.org}. \url{http://www.tex.ac.uk/tex-archive} is shortened to |ctan:| below.}
\bibitem{cite}{cite: \url{ctan:/macros/latex/contrib/cite/}}
\bibitem{setspace}{setspace: \url{ctan:/macros/latex/setspace/}}
\bibitem{fancyhdr}{fancyhdr: \url{ctan:/macros/latex/contrib/fancyhdr/}}
\bibitem{rotating}{rotating: \url{ctan:/macros/latex/contrib/rotating/}}
\bibitem{tocbibind}{tocbibind: \url{ctan:/macros/latex/contrib/tocbibind/}}
\bibitem{subfigure}{subfigure: \url{ctan:/obsolete/macros/latex/contrib/subfigure/}}
\bibitem{ccaption}{ccaption: \url{ctan:/macros/latex/contrib/ccaption/}}
\bibitem{caption}{caption: \url{ctan:/macros/latex/contrib/caption/}}
\bibitem{a4wide}{a4wide: \url{ctan:/macros/latex/contrib/misc/a4wide.sty}}
\bibitem{amsmath}{amsmath: \url{ctan:/macros/latex/required/amslatex/math/}}
\bibitem{hyperref}{hyperref: \url{ctan:/macros/latex/contrib/hyperref/}}
\bibitem{booktabs}{booktabs: \url{ctan:/macros/latex/contrib/booktabs/}}
\bibitem{draftcopy}{draftcopy: \url{ctan:/macros/latex/contrib/draftcopy/}}
\bibitem{lineno}{lineno: \url{ctan:/macros/latex/contrib/lineno/}}
\bibitem{SIunits}{SIunits: \url{ctan:/macros/latex/contrib/SIunits/}}
\bibitem{hepunits}{hepunits: \url{ctan:/macros/latex/contrib/hepunits/}}
\bibitem{hepnames}{hepnames: \url{ctan:/macros/latex/contrib/hepnames/}}
\bibitem{hepparticles}{hepparticles: \url{ctan:/macros/latex/contrib/hepparticles/}}
\bibitem{maybemath}{maybemath: \url{ctan:/macros/latex/contrib/maybemath/}}
\bibitem{braket}{braket: \url{ctan:/macros/latex/contrib/misc/braket.sty}}
\bibitem{cancel}{cancel: \url{ctan:/macros/latex/contrib/misc/cancel.sty}}
\bibitem{feynmf}{feynmf: \url{ctan:/macros/latex/contrib/feynmf/}}
\bibitem{axodraw}{axodraw: \url{http://www.nikhef.nl/~form/FORMdistribution/axodraw/}}
\bibitem{feyndiagram}{feyndiagram: \url{http://www.feyndiagram.com}}
\bibitem{jaxodraw}{jaxodraw: \url{http://http://jaxodraw.sourceforge.net/}}
\bibitem{pyfeyn}{|pyfeyn|: \url{http://hepforge.cedar.ac.uk/pyfeyn/}}
\end{thebibliography}

\end{document}
