Update and cleanup

README.md

@@ -1,41 +1,19 @@
-<img src="/figures/logo/TUOS_PRIMARY_LOGO_FULL COLOUR.png" width=300>
-
-
 # Thesis Template - Astronomy students
-_Updated: 20 March 2019_
 
-This repository contains a thesis template for the use of PhD students at the University of Sheffield. 
-Official guidelines can be found on the website and summarised below. 
+This repository contains a thesis template for the use of PhD astronomy students at the University of Sheffield. 
 
-## Latex template
-The latex template provided here is a cleaned version for the template that has been passed down generations of Astronomy PhD students. Students from other subjects (and other Universities) are welcome to use it if they so wish, although we recommend you check with your supervisor. 
+## LaTeX template
+The LaTeX template provided here is a cleaned version of the files that have been passed down generations of Astronomy PhD students. Students from other subjects (and other Universities) are welcome to use it if they so wish, although we recommend you check with your supervisor. 
 
 ## Formatting Guidelines
 
 The format guidelines (beyond the sections included in the template) are far and few between. There are two you need to bear in mind:
-* Although single-spacing is acceptable it is much more comment for people to either use **double-space** or **one and a half** spacing for the main body of the Thesis in order to give ample room for the examiners to comment (the template uses one and a half by default but it is commented appropriately to tell you what to change).
+* Although single-spacing is acceptable it is much more comment for people to either use **double-space** or **one and a half** spacing for the main body of the Thesis in order to give ample room for the examiners to comment.
 * Your **summary** page should not exceed **300 words**. 
-* Theses should preferably be printed double-sided.
-
-## Submission Guidelines
-
-* Submit to: **Research Services, New Spring House, 231 Glossop Road, Sheffield, S10 2GW.**
-* You need to submit **3 copies** of your thesis: **2 bound copies** (ring biders are *not* acceptable, but you can use comb binders) and **one on CD**.
-* You also need to submit your thesis to **Turnitin** to check for plagiarism. See below for a link to the Univesity Guidelines. 
-
-* **PHD STUDENTS SHOULD NOT UNDER ANY CIRCUMSTANCES SEND A COPY OF THEIR THESIS TO THEIR EXAMINERS BEFORE SUBMISSION**
-
-
-## Disclaimer
-_This summary is provided for convenience and quick access to essential information. The authors take no responsibility for the accuracy of this information and we strongly recommend that you refer to the guidelines provided on the University of Sheffield website (see reference links below) before you start writting your thesis and double-check before you submit_
-
-
-### References
-
-[General submission guidelines](https://www.sheffield.ac.uk/rs/code/submission)
-
-[Formatting guidelines](https://www.sheffield.ac.uk/rs/code/formatting)
+* Theses should preferably be printed double-sided, in which case you want to change the page layout to have the headers alternate between pages. How to do this is commented in the main thesis.tex file.
 
-[Guide to the thesis examination process for candidates of research degree programmes ](https://www.sheffield.ac.uk/polopoly_fs/1.688400!/file/Guidance_Notes_for_Candidates_final_updated_Sept18.pdf)
+## Useful links:
 
-[Submitting to Turnitin](https://www.sheffield.ac.uk/rs/code/turnitin)
+* Preparation guidelines: https://www.sheffield.ac.uk/research-services/code/thesis/preparation
+  * Formatting: https://www.sheffield.ac.uk/research-services/code/thesis/preparation/formatting
+* Submission guidelines: https://www.sheffield.ac.uk/research-services/code/thesis/submission

bibliography.bib

@@ -1,10 +1,66 @@
 % Encoding: UTF-8
 
-@Article{example,
-  author = 	 {Albert Norman Example},
-  title = 	 {An Analysis of the Titles of Example Journal Articles},
-  journal = 	 {MNRAS},
-  volume =       1,
-  pages =        {101-104},
-  year = 	 {1999}
+@ARTICLE{example,
+       author = {{Example}, A.~N. and {Nother}, A.~N.},
+        title = "{An example paper to be cited in this thesis.}",
+      journal = {\nat},
+         year = 2000,
+        month = jan,
+       volume = {1},
+        pages = {1-999},
 }
+
+@PHDTHESIS{1993PhDT.......301C,
+       author = {{Crowther}, Paul Adrian},
+        title = "{Model atmosphere studies of Wolf-Rayet stars}",
+       school = {University College London, UK},
+         year = 1993,
+        month = jan,
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1993PhDT.......301C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@ARTICLE{1984MNRAS.208..955F,
+       author = {{Fosbury}, R.~A.~E. and {Tadhunter}, C.~N. and {Bland}, J. and {Danziger}, I.~J.},
+        title = "{Very extended ionized gas in radio galaxies - III. emission along the radio axis of PKS 0634-20.}",
+      journal = {\mnras},
+     keywords = {Elliptical Galaxies, Emission Spectra, Forbidden Transitions, Interstellar Gas, Ionized Gases, Oxygen Spectra, Radio Galaxies, Radial Velocity, Spectral Line Width, Astrophysics},
+         year = 1984,
+        month = jun,
+       volume = {208},
+        pages = {955-959},
+          doi = {10.1093/mnras/208.4.955},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1984MNRAS.208..955F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{1992MolPh..75..917G,
+       author = {{Goodwin}, S.~P. and {Boughey}, J.~D. and {Heritage}, J.~R.},
+        title = "{Calculation of the hard sphere radial distribution function}",
+      journal = {Molecular Physics},
+         year = 1992,
+        month = jan,
+       volume = {75},
+       number = {4},
+        pages = {917-923},
+          doi = {10.1080/00268979200100691},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1992MolPh..75..917G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+@ARTICLE{1991MNRAS.252..342D,
+       author = {{Dhillon}, V.~S. and {Marsh}, T.~R. and {Jones}, D.~H.~P.},
+        title = "{A spectrophotometric study of the eclipsing nova-like variable V 1315 Aquilae.}",
+      journal = {\mnras},
+     keywords = {Cataclysmic Variables, Eclipsing Binary Stars, Stellar Spectrophotometry, Accretion Disks, Light Curve, Ubv Spectra, Astrophysics},
+         year = 1991,
+        month = oct,
+       volume = {252},
+        pages = {342},
+          doi = {10.1093/mnras/252.3.342},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1991MNRAS.252..342D},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+

chapters/appendix.tex

@@ -1,10 +1,21 @@
-%Appenndix for line measurements in IRTF + other spectra
+\chapter{Example Appendix}
+\label{appendix:example}
+% ~~~~~~~~~~~~~~~~~~~~
 
-%\label{app:line_measure}
+Here is a table:
 
-\chapter{Appendix}
-\label{app:my_appendix}
-
-\lhead{\emph{My appendix}}
-
-Your blabla
+\begin{table}
+	\centering
+	\caption{This is an example table. Captions appear above each table.
+	Remember to define the quantities, symbols and units used.}
+	\label{tab:example_table}
+	\begin{tabular}{lccr} % four columns, alignment for each
+		\hline
+		A & B & C & D\\
+		\hline
+		1 & 2 & 3 & 4\\
+		2 & 4 & 6 & 8\\
+		3 & 5 & 7 & 9\\
+		\hline
+	\end{tabular}
+\end{table}

chapters/chapter1.tex

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+\chapter{Example Chapter}
+\label{chap:chapter1}
+% ~~~~~~~~~~~~~~~~~~~~
+
+Astronomy
+
+Sheffield helped build the \acro{goto} telescope on La Palma.
+
+There is also a second \acro{goto} site in Australia, at Siding Spring Observatory.
+
+The full name is the \acrofull{goto}.

chapters/chapter2.tex

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+\chapter{Example Chapter}
+\label{chap:chapter2}
+% ~~~~~~~~~~~~~~~~~~~~
+
+Did you know you can nicely format units with the \texttt{siunitx} package? For instance, \SI{100}{\solarmass\per\second} or $F_\lambda = 5.5 \times 10^{6}/\lambda_\text{eff}~\si{\photon\per\second\per\centi\metre\squared\per\angstrom}$. You use \texttt{\textbackslash{}SI\{value\}\{unit\}}, or just \texttt{\textbackslash{}si\{unit\}} if you want the unit on its own.

chapters/conclusion.tex

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+\chapter{Conclusion}
+\label{chap:conclusion}
+
+Here are some interesting papers: \citep{1984MNRAS.208..955F, 1991MNRAS.252..342D, 1992MolPh..75..917G, 1993PhDT.......301C}.

chapters/introduction.tex

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+\chapter{Introduction}
+\label{chap:intro}
+
+% ~~~~~~~~~~~~~~~~~~~~
+\section{Why Astronomy is Great}
+\label{sec:why}
+
+Astronomy is all about looking up at the sky.
+
+% ~~~~~~~~~~~~~~~~~~~~
+\subsection{Examples of astronomy}
+\label{sec:examples}
+
+Some astronomy is observational and some is theoretical. There is a lot of debate on which is better.
+
+\begin{figure}[t]
+    \begin{center}
+        \includegraphics[width=0.9\linewidth]{images/m31.jpg}
+    \end{center}
+    \caption[An image of M31]{
+        This is a picture of M31, the Andromeda Galaxy.
+        }\label{fig:m31}
+\end{figure}
+
+% ~~~~~~~~~~~~~~~~~~~~
+\section{Thesis outline}
+\label{sec:outline}
+
+This thesis is going to show just how great astronomy is. In \nref{chap:chapter1} I describe my main findings. In \nref{chap:chapter2} I prove my theory. Finally in \nref{chap:conclusion} I present concluding remarks and some suggestions for future work.
+
+\newpage
+
+Here's some more test just to see if the headers are working.

structure/acronyms.tex

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+\makeglossaries{}
+
+% set the length of the glossary description on the acronym page
+\setlength{\glsdescwidth}{0.8\linewidth}
+
+% define \acro commands
+% using \acro will automatically add the full name when first referenced, then use the short version on later calls
+% if you want to force the full name with the acronym in brackets then use \acrofull
+\newcommand{\acro}{\gls}
+\newcommand{\acrofull}{\glsfirst}
+
+% if you want hyperlinks from each reference to the acronym list then comment out this line
+%\glsdisablehyper{} % no hyperlinks
+
+% ~~~~~~~~~~~~~~~~~~~~
+% Add any acronyms below this point:
+\newacronym{goto}{GOTO}{Gravitational-wave Optical Transient Observer}

structure/colours.tex

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+% This file defines colours to use for section headings, links etc
+
+% Colours are used in various places. The main ones are:
+% - section heading colours, defined under "heading colours" in format.txt
+% - link colours, defined in the "hyperref" package configuration (see packages.txt)
+% - caption colours, defined in the "caption" package configuration (see packages.txt)
+
+% If you just want to make coloured text use "\textcolor{red}{THIS TEXT IS RED}"
+
+% The "xcolors" package includes a lot of default colours, see the documentation
+% at https://ctan.org/pkg/xcolor for a full list.
+% Here we define various custom colours, for formatting or just in case they are useful.
+
+% Example colours, can used for headers
+\definecolor{StevanceBlue}{RGB}{46,116,181}
+\definecolor{SheffieldPurple}{RGB}{68,0,153} % < this is the current default, based on the Uni logo (https://www.sheffield.ac.uk/brand-toolkit/colour)
+
+% Tableau colours (matplotlib defaults)
+% https://www.tableau.com/about/blog/2016/7/colors-upgrade-tableau-10-56782
+\definecolor{tab_blue}{HTML}{4E79A7}
+\definecolor{tab_orange}{HTML}{F28E2B}
+\definecolor{tab_red}{HTML}{E15759}
+\definecolor{tab_cyan}{HTML}{76B7B2}
+\definecolor{tab_green}{HTML}{59A14F}
+\definecolor{tab_yellow}{HTML}{EDC948}
+\definecolor{tab_purple}{HTML}{B07AA1}
+\definecolor{tab_pink}{HTML}{FF9DA7}
+\definecolor{tab_brown}{HTML}{9C755F}
+\definecolor{tab_grey}{HTML}{BAB0AC}