revisited appendices environment

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% ******************************* Thesis Appendix A ********************************
\chapter{How to install \LaTeX}
\chapter{Appendix A\texorpdfstring{\\ }{: }Installing the CUED Class file}
\section*{Windows OS}
\LaTeX.cls files can be accessed system-wide when they are placed in the
<texmf>/tex/latex directory, where <texmf> is the root directory of the users \TeX installation. On systems that have a local texmf tree (<texmflocal>), which
may be named ``texmf-local'' or ``localtexmf'', it may be advisable to install packages in <texmflocal>, rather than <texmf> as the contents of the former, unlike that of the latter, are preserved after the \LaTeX system is reinstalled and/or upgraded.
\subsection*{TeXLive package - full version}
\begin{enumerate}
\item Download the TeXLive ISO (2.2GB) from\\
\href{https://www.tug.org/texlive/}{https://www.tug.org/texlive/}
\item Download WinCDEmu (if you don't have a virtual drive) from \\
\href{http://wincdemu.sysprogs.org/download/}{http://wincdemu.sysprogs.org/download/}
\item To install Windows CD Emulator follow the instructions at\\
\href{http://wincdemu.sysprogs.org/tutorials/install/}{http://wincdemu.sysprogs.org/tutorials/install/}
\item Right click the iso and mount it using the WinCDEmu as shown in \\
\href{http://wincdemu.sysprogs.org/tutorials/mount/}{http://wincdemu.sysprogs.org/tutorials/mount/}
\item Open your virtual drive and run setup.pl
\end{enumerate}
It is recommended that the user create a subdirectory <texmf>/tex/latex/CUED for all CUED related \LaTeX class and package files. On some \LaTeX systems, the directory look-up tables will need to be refreshed after making additions or deletions to the system files. For \TeX Live systems this is accomplished via executing ``texhash'' as root. MIK\TeX users can run ``initexmf -u'' to accomplish the same thing.
or
Users not willing or able to install the files system-wide can install them in their personal directories, but will then have to provide the path (full or relative) in addition to the filename when referring to them in \LaTeX.
\subsection*{Basic MikTeX - TeX distribution}
\begin{enumerate}
\item Download Basic-MiK\TeX (32bit or 64bit) from \href{http://miktex.org/download}{http://miktex.org/download}
\item Run the installer
\item To add a new package go to Start >> All Programs >> MikTex >> Maintenance (Admin) and choose Package Manager
\item Select or search for packages to install
\end{enumerate}
\subsection*{TexStudio - Tex Editor}
\begin{enumerate}
\item Download TexStudio from \href{http://texstudio.sourceforge.net/\#downloads}{http://texstudio.sourceforge.net/\#downloads}
\item Run the installer
\end{enumerate}
\section*{Mac OS X}
\subsection*{MacTeX - TeX distribution}
\begin{enumerate}
\item Download the file from \href{http://mirror.ctan.org/systems/mac/mactex/MacTeX.pkg}{http://mirror.ctan.org/systems/mac/mactex/MacTeX.pkg}
\item Extract and double click to run the installer. It does the entire configuration, sit back and relax.
\end{enumerate}
\subsection*{TexStudio - Tex Editor}
\begin{enumerate}
\item Download TexStudio from \href{http://texstudio.sourceforge.net/\#downloads}{http://texstudio.sourceforge.net/\#downloads}
\item Extract and Start
\end{enumerate}
\section*{Unix/Linux}
\subsection*{TeXLive - TeX distribution}
\subsubsection*{Getting the distribution:}
\begin{enumerate}
\item TexLive can be downloaded from \href{http://www.tug.org/texlive/acquire-netinstall.html}{http://www.tug.org/texlive/acquire-netinstall.html}. You might require wget to download through proxies.
\item TexLive DVD is also available in the Grad Suite
\item TexLive is provided by most operating system you can use (rpm,apt-get or yum) to get TexLive distributions
\end{enumerate}
\subsubsection*{Installation}
\begin{enumerate}
\item Mount the ISO file in the mnt directory
\begin{verbatim}
mount -t iso9660 -o ro,loop,noauto /your/texlive####.iso /mnt
\end{verbatim}
\item Install wget on your OS (use rpm, apt-get or yum install)
\item Run the installer script install-tl.
\begin{verbatim}
cd /your/download/directory
./install-tl
\end{verbatim}
\item Enter command `i' for installation
\item Post-Installation configuration:\\ \href{http://www.tug.org/texlive/doc/texlive-en/texlive-en.html\#x1-320003.4.1}{http://www.tug.org/texlive/doc/texlive-en/texlive-en.html\#x1-320003.4.1}
\item Set the path for the directory of TexLive binaries in your .bashrc file\\
\textbf{For 32Bit OS}\\
For Bourne-compatible shells such as bash, and using Intel x86 GNU/Linux and a default directory setup as an example, the file to edit might be \begin{verbatim}
edit $~/.bashrc file and add following lines
PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH;
export PATH
MANPATH=/usr/local/texlive/2011/texmf/doc/man:$MANPATH;
export MANPATH
INFOPATH=/usr/local/texlive/2011/texmf/doc/info:$INFOPATH;
export INFOPATH
\end{verbatim}
\textbf{For 64Bit}
\begin{verbatim}
edit $~/.bashrc file and add following lines
PATH=/usr/local/texlive/2011/bin/x86_64-linux:$PATH;
export PATH
MANPATH=/usr/local/texlive/2011/texmf/doc/man:$MANPATH;
export MANPATH
INFOPATH=/usr/local/texlive/2011/texmf/doc/info:$INFOPATH;
export INFOPATH
\end{verbatim}
\end{enumerate}
%\subsection{Installing directly using Linux packages}
\subsubsection*{Fedora/RedHat/CENTOS:}
\begin{verbatim} sudo yum install texlive \end{verbatim}
\subsubsection*{SUSE:}
\begin{verbatim} sudo zypper install texlive \end{verbatim}
\subsubsection*{Debian/Ubuntu:}
\begin{verbatim} sudo apt-get install texlive \end{verbatim}

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@ -1,110 +1,12 @@
% ******************************* Thesis Appendix B ********************************
\chapter{Appendix B: How to install \LaTeX}
\chapter{Installing the CUED Class file}
\section*{Windows OS}
\LaTeX.cls files can be accessed system-wide when they are placed in the
<texmf>/tex/latex directory, where <texmf> is the root directory of the users \TeX installation. On systems that have a local texmf tree (<texmflocal>), which
may be named ``texmf-local'' or ``localtexmf'', it may be advisable to install packages in <texmflocal>, rather than <texmf> as the contents of the former, unlike that of the latter, are preserved after the \LaTeX system is reinstalled and/or upgraded.
\subsection*{TeXLive package - full version}
\begin{enumerate}
\item Download the TeXLive ISO (2.2GB) from\\
\href{https://www.tug.org/texlive/}{https://www.tug.org/texlive/}
\item Download WinCDEmu (if you don't have a virtual drive) from \\
\href{http://wincdemu.sysprogs.org/download/}{http://wincdemu.sysprogs.org/download/}
\item To install Windows CD Emulator follow the instructions at\\
\href{http://wincdemu.sysprogs.org/tutorials/install/}{http://wincdemu.sysprogs.org/tutorials/install/}
\item Right click the iso and mount it using the WinCDEmu as shown in \\
\href{http://wincdemu.sysprogs.org/tutorials/mount/}{http://wincdemu.sysprogs.org/tutorials/mount/}
\item Open your virtual drive and run setup.pl
\end{enumerate}
It is recommended that the user create a subdirectory <texmf>/tex/latex/CUED for all CUED related \LaTeX class and package files. On some \LaTeX systems, the directory look-up tables will need to be refreshed after making additions or deletions to the system files. For \TeX Live systems this is accomplished via executing ``texhash'' as root. MIK\TeX users can run ``initexmf -u'' to accomplish the same thing.
or
Users not willing or able to install the files system-wide can install them in their personal directories, but will then have to provide the path (full or relative) in addition to the filename when referring to them in \LaTeX.
\subsection*{Basic MikTeX - TeX distribution}
\begin{enumerate}
\item Download Basic-MiK\TeX (32bit or 64bit) from \href{http://miktex.org/download}{http://miktex.org/download}
\item Run the installer
\item To add a new package go to Start >> All Programs >> MikTex >> Maintenance (Admin) and choose Package Manager
\item Select or search for packages to install
\end{enumerate}
\subsection*{TexStudio - Tex Editor}
\begin{enumerate}
\item Download TexStudio from \href{http://texstudio.sourceforge.net/\#downloads}{http://texstudio.sourceforge.net/\#downloads}
\item Run the installer
\end{enumerate}
\section*{Mac OS X}
\subsection*{MacTeX - TeX distribution}
\begin{enumerate}
\item Download the file from \href{http://mirror.ctan.org/systems/mac/mactex/MacTeX.pkg}{http://mirror.ctan.org/systems/mac/mactex/MacTeX.pkg}
\item Extract and double click to run the installer. It does the entire configuration, sit back and relax.
\end{enumerate}
\subsection*{TexStudio - Tex Editor}
\begin{enumerate}
\item Download TexStudio from \href{http://texstudio.sourceforge.net/\#downloads}{http://texstudio.sourceforge.net/\#downloads}
\item Extract and Start
\end{enumerate}
\section*{Unix/Linux}
\subsection*{TeXLive - TeX distribution}
\subsubsection*{Getting the distribution:}
\begin{enumerate}
\item TexLive can be downloaded from \href{http://www.tug.org/texlive/acquire-netinstall.html}{http://www.tug.org/texlive/acquire-netinstall.html}. You might require wget to download through proxies.
\item TexLive DVD is also available in the Grad Suite
\item TexLive is provided by most operating system you can use (rpm,apt-get or yum) to get TexLive distributions
\end{enumerate}
\subsubsection*{Installation}
\begin{enumerate}
\item Mount the ISO file in the mnt directory
\begin{verbatim}
mount -t iso9660 -o ro,loop,noauto /your/texlive####.iso /mnt
\end{verbatim}
\item Install wget on your OS (use rpm, apt-get or yum install)
\item Run the installer script install-tl.
\begin{verbatim}
cd /your/download/directory
./install-tl
\end{verbatim}
\item Enter command `i' for installation
\item Post-Installation configuration:\\ \href{http://www.tug.org/texlive/doc/texlive-en/texlive-en.html\#x1-320003.4.1}{http://www.tug.org/texlive/doc/texlive-en/texlive-en.html\#x1-320003.4.1}
\item Set the path for the directory of TexLive binaries in your .bashrc file\\
\textbf{For 32Bit OS}\\
For Bourne-compatible shells such as bash, and using Intel x86 GNU/Linux and a default directory setup as an example, the file to edit might be \begin{verbatim}
edit $~/.bashrc file and add following lines
PATH=/usr/local/texlive/2011/bin/i386-linux:$PATH;
export PATH
MANPATH=/usr/local/texlive/2011/texmf/doc/man:$MANPATH;
export MANPATH
INFOPATH=/usr/local/texlive/2011/texmf/doc/info:$INFOPATH;
export INFOPATH
\end{verbatim}
\textbf{For 64Bit}
\begin{verbatim}
edit $~/.bashrc file and add following lines
PATH=/usr/local/texlive/2011/bin/x86_64-linux:$PATH;
export PATH
MANPATH=/usr/local/texlive/2011/texmf/doc/man:$MANPATH;
export MANPATH
INFOPATH=/usr/local/texlive/2011/texmf/doc/info:$INFOPATH;
export INFOPATH
\end{verbatim}
\end{enumerate}
%\subsection{Installing directly using Linux packages}
\subsubsection*{Fedora/RedHat/CENTOS:}
\begin{verbatim} sudo yum install texlive \end{verbatim}
\subsubsection*{SUSE:}
\begin{verbatim} sudo zypper install texlive \end{verbatim}
\subsubsection*{Debian/Ubuntu:}
\begin{verbatim} sudo apt-get install texlive \end{verbatim}

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@ -2,7 +2,7 @@
%*********************************** First Chapter ***************************************
%*****************************************************************************************
\chapter{Background} %Title of the First Chapter
\chapter{Getting Started} %Title of the First Chapter
\ifpdf
\graphicspath{{Chapter1/Figs/Raster/}{Chapter1/Figs/PDF/}{Chapter1/Figs/}}

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@ -232,11 +232,11 @@ supported!}
\RequirePackage{ifpdf} % Check for pdfLaTeX
% *********************** Table of Contents and Appendix************************
% *********************** Table of Contents & Appendices ***********************
% add Bibliography, List of figures and tables to contents
\RequirePackage{tocbibind}
\RequirePackage{appendix} % add appendix
% Add appendices
\RequirePackage[title,titletoc]{appendix}
% *************************** Graphics and Figures *****************************
\RequirePackage[usenames, dvipsnames]{color}
@ -663,6 +663,9 @@ font in preamble by specifying `customfont' in the class options}
}
% ******************************** Line Spacing ********************************
% Set spacing as 1.5 line spacing for the PhD Thesis
\onehalfspace
% ******************** To compute empty space in title page ********************

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% ******************* Fonts (like different typewriter fonts etc.)*************
% Add `customfont' in the document class option to use this section
%\renewcommand\rmdefault{psb}
\ifsetFont
\else
% Set your custom font here and use `customfont' in options. Leave empty to
@ -25,8 +24,9 @@
% *****************************************************************************
% *************************** Bibliography and References ********************
% Add `custombib' in the document class option to use this section
\usepackage{cleveref} %Referencing without need to explicitly state fig /table
% Add `custombib' in the document class option to use this section
\ifsetBib % True, Bibliography option is chosen in class options
\else % If custom bibliography style chosen then load bibstyle here
\RequirePackage[square, sort, numbers, authoryear]{natbib} % CustomBib
@ -34,7 +34,7 @@
% *****************************************************************************
% **************************** Custom Packages *********************************
% **************************** Custom Packages ********************************
% *****************************************************************************
@ -83,19 +83,20 @@
% ************************* User Defined Commands ******************************
% ******************************************************************************
% Set spacing as 1.5 line spacing for the PhD Thesis
\onehalfspace
% ********************** Adding TOC and List of Figures ************************
% ********************** TOC depth and numbering depth *************************
\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}
% To hide sections from appearing in TOC use:
% \tochide\section{Section name} in the section
% ******************************* Nomenclature *********************************
% To change the name of the Nomenclature section, uncomment the following line
% \renewcommand\nomname{Symbols}
% ********************************* Appendix ***********************************
% The default value of both \appendixtocname and \appendixpagename is `Appendices'. These names can all be changed via:
%\renewcommand{\appendixtocname}{List of appendices}
%\renewcommand{\appendixname}{Appndx}

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%\include{Chapter4/chapter4} \include{Chapter5/chapter5}
%\include{Chapter6/chapter6} \include{Chapter7/chapter7}
% ********************************* Back Matter ********************************
\backmatter \appendix \include{Appendix1/appendix1}
% ********************************** Appendices ********************************
\begin{appendices} % Using appendices environment for more functunality
\include{Appendix1/appendix1}
\include{Appendix2/appendix2}
\end{appendices}
% ********************************** Back Matter *******************************
% ********************************** Bibliography ******************************
\backmatter
\begin{spacing}{0.9}
% Bibliography style