Merge branch 'themikesmith-master'

README.md

@@ -1,3 +1,6 @@
+Note: this README needs to be updated, as of 2020-03-02, but as of this commit, all LaTeX formatting is correct and confirmed by the GW library.
+
+
 | Build Status                             | Latest Release                                      | Version                                             | Last Commit                                                     | Activity                                                      | CTAN                         | Citation |
 | :--------------------------------------: | :--------------------------:                        | :----:                                              | :------:                                                        | :------:                                                      | :----:                       | :-----: |
 | [![Travis][travis_shield]][travis]       | [![Github Release][release_shield]][github_release] | [![Github Version][version_shield]][github_version] | [![Github Last Commit][last_commit_shield]][github_last_commit] | [![Github commit activity][activity_shield]][github_activity] | [![CTAN][ctan_shield]][ctan] | [![DOI][ doi_shield ]][ doi ]
@@ -20,7 +23,7 @@
 
 ## [GWU Thesis](https://skulumani.github.io/2016/10/thesis-gwu)
 
-This is a [GWU SEAS](https://library.gwu.edu/seas) thesis template, it conforms to the University and SEAS formatting guidelines as of May 21 2018.
+This is a [GWU SEAS](https://library.gwu.edu/seas) thesis template, it conforms to the University and SEAS formatting guidelines as of March 3, 2020.
 
 ![screenshot](./doc/etd.png)
 
@@ -84,7 +87,7 @@ Installing everything means you can work without being connected to the internet
 You also have total control over the various intricacies of LaTeX as it's on your system.
 This also means you have the responsibility of ensuring it's working properly, and fixing it when it goes horribly wrong.
 
-Using and online service frees you from dealing with downloading, installing, updating, etc. 
+Using an online service frees you from dealing with downloading, installing, updating, etc. 
 At the same time, you also are dependent on the internet and a working website in order to write your thesis. 
 If their website is compromised, crashes, gets DDoS'ed or the like, you may be in a difficult situation. 
 
@@ -133,10 +136,11 @@ For example, there are a variety of frontmatter pages, i.e. prologue, preface, a
 Simply, by removing the command or using the macros `\hidepreface` you can automatically remove them. 
 
 Your text can be included in individual `/tex/*.tex` files and included in the main document using `\include{./tex/chapter1.tex}`. 
-This gives you the added benefit of using `\includeonly{chapter1.tex}` to compile only specific sections of your much larger thesis. 
+This gives you the added benefit of using `\includeonly{chapter1.tex}` to compile only specific sections of your much larger thesis.
 
 The class file already loads several common packages such as, `amsmath, graphicx, cleveref, hyperref` and others. 
-You can add more packages but be aware that all package interactions **HAVE NOT** been tested. 
+
+If you need to load other or more packages, we've split off a `required-packages.tex` file for you to edit; it gets `input`ted into the class file. However, be aware that all package interactions **HAVE NOT** been tested. 
 
 There is also some demonstration of typical commands, such as equations, figures, cross-referencing. 
 

required-packages.tex

@@ -0,0 +1,127 @@
+% this will speed up your tikz figures by building them once to another directory
+\usepackage{pgfplots}
+\usepgfplotslibrary{external}
+\pgfplotsset{compat=1.16}
+%\tikzexternalize
+%\tikzsetexternalprefix{cache/}
+
+% This class uses the geometry.sty package to set the margins.
+\if@gwu@debug
+  % Show margins 
+  \RequirePackage[top=1in,bottom=1in,left=1.25in, right=1.25in,
+  showframe]{geometry}
+\else
+ % Use the standard margins for the thesis version.
+ \RequirePackage[top=1in,bottom=1in,left=1.25in, right=1.25in]{geometry}
+\fi
+
+% Obsolete package check
+\RequirePackage[l2tabu,orthodox]{nag}
+
+% This loads the required math packages.
+\RequirePackage[binary-units=true]{siunitx}
+\RequirePackage{amsmath}
+\RequirePackage{amsfonts}
+\RequirePackage{amssymb}
+\RequirePackage{mathtools}
+\RequirePackage{amsthm}
+
+% This loads the proper graphics package.
+\RequirePackage{graphicx}
+
+% Better spacing for text
+\RequirePackage[utf8]{inputenc}
+\RequirePackage[T1]{fontenc}
+\RequirePackage{lmodern}
+\RequirePackage{microtype}
+\RequirePackage{bm}
+
+\RequirePackage{mathptmx}
+
+% Add package for managing section headings
+\RequirePackage[]{titlesec}
+
+% This is useful for complex figures.
+\RequirePackage{subcaption}
+
+% Compress multiple citations
+% \RequirePackage{cite}
+
+% This package allows the ability to create a 'code' environment.
+\RequirePackage{verbatim}
+
+% This hopefully tells verbatim to leave my damn quotes alone.
+% \RequirePackage{upquote}
+
+% This package enables the use of proper single quotes in text.
+% \RequirePackage{textcomp}
+
+% This package is used to set line spacing.
+\RequirePackage{setspace}
+
+% This package is used to make nomenclature tables that can span pages.
+% \RequirePackage{longtable}
+
+% This package allows conditional testing of varibles.
+\RequirePackage{ifthen}
+
+% This package is used for silly letter spacing
+\RequirePackage{soul}
+
+% This package is used to generate alternate environments.
+\RequirePackage{float}
+
+% This package is for the index, if it is to be used.
+\if@gwu@index
+ \RequirePackage{makeidx}
+ \makeindex
+\fi
+
+% This is the package for special headers and footers.
+\RequirePackage{fancyhdr}
+
+% some extra packages to help with debugging
+\if@gwu@debug
+  \RequirePackage[final]{showlabels} % show labels for referencing
+  \RequirePackage{refcheck} % check for unused references/labels
+\fi
+
+%% ---- HYPERREF ----------------------------------------------------------
+% This loads a package that allows extra colors for links.
+\RequirePackage[]{color}
+% Custom color for references.
+% \definecolor{DarkGreen}{rgb}{0,0.6,0}
+
+% This will make labels and references hyperlinks.
+\if@gwu@backref%
+ % Use references in the bibliography.
+ \RequirePackage[pagebackref=true]{hyperref}%
+\else%
+ % Do not use back references.
+ \RequirePackage{hyperref}%
+\fi
+
+  \hypersetup{%
+    unicode=false,          % non-Latin characters in Acrobat’s bookmarks
+    pdftoolbar=true,        % show Acrobat’s toolbar?
+    pdfmenubar=true,        % show Acrobat’s menu?
+    pdffitwindow=false,     % window fit to page when opened
+    pdfstartview={FitV},    % fits the width of the page to the window
+    pdfnewwindow=true,      % links in new PDF window
+    colorlinks=false,       % false: boxed links; true: colored links
+    bookmarksdepth=3,
+    bookmarksopen=true,
+  }%
+
+% Cleveref referencing - must happen after hyperref
+\AtEndOfClass{\RequirePackage[noabbrev,capitalize]{cleveref}}%
+
+% Glossaries package - must come after hypperef
+% This package is used for the list of abbreviations
+\RequirePackage[printonlyused]{acronym}%
+\RequirePackage[abbreviations,symbols,shortcuts=none,automake]{glossaries-extra}%
+
+\glsxtrRevertTocMarks % remove warning from tocloft about starttoc
+
+\RequirePackage{tocloft}
+\RequirePackage{calc}

tex/appendix-ex.tex

@@ -0,0 +1,38 @@
+% !TEX root = ../thesis-sample.tex
+\appendix
+\doublespacing
+\chapter{Appendix}
+This is an example of an appendix. 
+The only difference is the use of \verb+\appendix+ command at the start of this \texttt{tex} file. 
+This automatically changes the chapter and section headings.
+
+\section{A section}
+The easiest method.
+
+\begin{equation}\label{eq:sum}
+    x_k = \frac{a_k+b_k}{2}
+\end{equation}
+
+\section{False Position}
+\lipsum[20]
+
+
+\section{Starting the Appendices}
+Actually, using appendices is quite simple.  Immediately after the end
+of the last chapter and before the start of the first appendix, simply
+enter the command \verb|\appendix|.  This will tell \LaTeX~to change
+how it interprets the commands \verb|\chapter|, \verb|\section|,
+\textit{etc.}
+
+Each appendix is actually a chapter, so once the \verb|\appendix|
+command has been called, start a new appendix by simply using the
+\verb|\chapter| command.
+
+Note that the \verb|\appendix| command should be called only
+once--not before the start of each appendix.
+
+All the fancy referencing and tools still work.
+You only need to add the appendix command and all will be as it should be.
+
+\chapter{Another Appendix}
+\lipsum[24]

tex/conclusion.tex

@@ -0,0 +1,4 @@
+
+\chapter{Conclusions: four contributions related to measuring trust in vaccines} \label{chap:conclusions}
+
+asdf

tex/discussion.tex

@@ -0,0 +1,9 @@
+% !TEX root = ../thesis-sample.tex
+
+\chapter{Discussion} \label{chap:discussion}
+
+\section{Practical discussion: Potential for low-cost targeting and tailoring}
+
+\section{Theoretical discussion: how to increase validity for measure of complex constructs}
+
+\section{Limitations and future work: context, improve part 3, links to behavior}