Taha’s PhD thesis

Nanostructured ZnO and metal chalcogenide films for solar photocatalysis Taha Ahmed PDF (DiVA)    Source code repository on Codeberg  and GitHub . Publicly defended on Monday, Dec 18, 13.15 at the Ångström laboratory, Uppsala University (errata ).

Thesis advisors: prof. Tomas Edvinsson and assoc. prof. Jiefang Zhu .
Uppsala University, Uppsala, 2023.

Source code and reproducibility

In addition to the PDF of the thesis, I have chosen to also share the code I wrote (LuaLaTeX and R) and data that make up my thesis, in the form of a git repository shared using a libre license, making it easy for you to inspect the code, recompile the whole thesis or any parts of it on your own, or adapt all or part of it for your own work.

You are of course more than welcome to reach out to me with comments, criticism, or just to let me know you found some part of the thesis source code useful.

To maintain all the source files and other dependencies of this thesis I used git (what’s git? find out!). The source code repository (note that the Codeberg and Github repositories are identical, use whichever host you prefer) contain the dependencies, the data (larger datasets have been packaged as binary rda archives to save disk space and compilation speed; you could reconstruct the original text files from them using R), and the code required to reproduce the thesis as-published on DiVA.

I have cleaned up this repository from zombie code, orphaned files, and other stuff that crept into the work over the years but which is no longer necessary, but no one is perfect, so do let me know if you find any discrepancies between the PDF compiled from the repository (make sure the document was set to final mode) and the PDF on DiVA.

The README in the repository contains more hands-on information on how to download the repository and compile the thesis on your own computer.

Links and notes

I am far from the first to share the source code of their PhD thesis. Here are only a few others that have crossed my path:

• Laurent P. René de Cotret, McGill University (Markdown and LuaLaTeX).
• Katrin Leinweber, Universität Konstanz (Markdown and LaTeX).
• Edouard Leurent, Université des Sciences et des Technologies de Lille (LaTeX).
• Iñaki Ucar, Universidad Carlos III de Madrid (R bookdown).¹
• Raphael Vallat, Lyon University (LaTeX).
• Malcolm Ramsay, University of Sydney (LaTeX).
• Fernando Bevilacqua, University of Skövde (LaTeX).
• T. W. Hughes, Stanford University (LaTeX).
• Julian Valentin, University of Stuttgart (LaTeX).
• Lilian Besson, Universite Bretagne Loire (LaTeX).
• Jill-Jênn Vie, Université Paris-Saclay (XeLaTeX or LuaLaTeX).
• Filip Dominec, Czech Technical University (LaTeX).
• Yani Ioannou, University of Cambridge (LaTeX).
• Egon Geerardyn, Vrije Universiteit Brussel (LaTeX).
• Michael Hall, European Bioinformatics Institute (LaTeX).
• Michael F. Herbst, Ruprecht-Karls-Universität Heidelberg (LaTeX with Python).
• Tomás di Domenico, Università Degli Studi di Padova (LaTeX).
• Henrique Becker, Universidade Federal do Rio Grande do Sul (LaTeX).
• Aalborg University LaTeX template collection.

Most repos on GitHub use the phd-thesis tag, but so far none of the above repos on Codeberg use any tags.

Thesis templates

It seems every university or college with some self-respect has published a LaTeX-based thesis template. Simply too many to list. Below, a non-representative list:

• http://cleanthesis.der-ric.de
• https://libguides.ub.uu.se/avhandling/latex XeLaTeX template for Uppsala University
• https://github.com/kks32/phd-thesis-template LaTeX/XeLaTeX/LuaLaTeX template for Cambridge University
• https://github.com/ismayc/thesisdown R Markdown using bookdown
• https://codeberg.org/slumber/phd-latex-template LaTeX template for Université Paris 8 - Vincennes Saint-Denis (poorly documented)
• https://codeberg.org/bnass/PhD_shared_scripts scripts for data management, analysis, visualization

---

1. Ucar is the author of the awesome errors package. ↩︎