The PhD thesis template

A (unofficial) LaTeX template for creating a PhD thesis at the Department of Mathematics, Stockholm University.

The structure of a PhD thesis

A cumulative dissertation style thesis at the Department of Mathematics, Stockholm University, consists of the following parts:

The cover page
The "spikblad" or "nailing page" containing publication information and the abstract
A series of frontmatter pages including the title, the dirt title, a dedication page and an optional quote
The list of papers
Acknowledgements
Table of contents
Part I: Introduction (the "kappa")
A summary in Swedish
A bibliography for the introduction
Part II: The papers (including the papers themselves)
A back cover page with a summary and author biography

Items 1, 3, and 11 are handled in the thesis publication tool Verktyg för visuell identitet. Item 2 will be provided by the Avhandlingsstöd department after registering the thesis, whereafter it can be included by uploading the pdf to the thesis publication tool. Item 10 is handled by uploading the individual papers to the thesis publication tool. The rest is handled by this LaTeX template.

The structure of this template

The main file for items 4-9 is main.tex. It is structured in order to make it graspable by utilizing the input command to include the various parts of the thesis as well as loading the necessary packages and defining the necessary commands. This guide will go through everything you need to use the template and compile everything into a series of pdf files that can be uploaded to the thesis publication tool.

Note that the template now contains a set of dummy papers, sections, figures, and commands in order to make it easier to grasp. The texts and images are AI-generated nonsense and should be replaced with your own content.

`bibliography.bib`

This is where to put the references for the introduction and the papers. This guide will assume that you are using bibtex with the biber as your bibliography backend. If you prefer some other setup, make sure to change the citation commands in the source files, e.g. in src/sections/list_of_papers.tex which utilizes the custom fullciteall command. There are comment lines detailing where to put your own papers, book sources and article sources. These are merely guidelines and can be changed to fit your needs - the document will compile as long as the references are in the file and the citation commands are correct.

`src`

This folder is meant to contain the source code for the entire thesis. It is split into a number of folders.

`src/packages.tex`

This is where all LaTeX packages are loaded. The current setup is quite minimal, but it is easy to add more packages here. If you remove any package from here, make sure this does not cause issues elsewhere in the document. I recommend adding all relevant packages here, as it makes it easier to keep track of what is loaded.

`src/setup_layout.tex`

This is where the layout of the document is set up. This is done by using commands from some of the packages loaded in src/packages. A lot of this is customizable, but the current setup aligns with what most previous theses have looked like.

`src/custom_commands.tex`

This contains a few custom commands used in the thesis.

For example, it sets up the official Stockholm University color scheme, using the definitions from Digital färgpalett. These can be used in figures for a nice and consistent look, but it is not mandatory. For their names, see the file. Some other commands included are for solving some issues with page numbering. These are pretty hacky and work for the current setup, but might need to be changed for future use. The fullciteall command defined here is used in the list of papers to print all references in the bibliography. This is also where you could add your own custom commands, like Definitions, Proofs, etc. Currently, the "Remark" environment is defined here as an example.

`src/sections`

This is where to put the source code for the various sections of the thesis. These can preferably be split into chapter- or section-wise folders, but it is up to the author to decide how to structure this. Some files included in this folder are:

list_of_papers.tex - The list of papers. This should outline the papers included in the thesis, and assign them roman numerals. A template for this is included, using the custom fullciteall command. The contribution of the thesis author should be outlined for all co-authored papers.
acknowledgements.tex - The acknowledgements for the thesis.
sammanfattning.tex - The summary in Swedish. Most theses use a translation of the abstract.

`src/algorithms`, `src/figures`, `src/tables`

These are only suggested directories for the source code for algorithms, figures, and tables. Change it up if you prefer a different structure.

`src/papers`

This is where one can put the pdf files for the papers included in the thesis. This is not mandatory and will only matter if you want the page numbering of the thesis to be consistent throughout the entire thesis, which will require a bit of extra work (see Step 4 in the usage section below).

Usage

This guide will go through the steps to use the template, from opening it up to compiling the final document and uploading it to the thesis publication tool.

Step 1: Copy the template

The first step is to download the template and copy it to a new folder. This can be done using a terminal command like this:

git clone https://github.com/henningzakrisson/su-math-thesis
copy -r su-math-thesis my_thesis
cd my_thesis

Or by downloading the repository as a zip file (Press the green "Code" button and select "Download ZIP"), extracting it, and renaming the folder to something like my_thesis. The my_thesis folder is where you will work on your thesis.

Step 2: Compile the dummy document

In order to make sure everything works on your system, compile the dummy document. I recommend using pdflatex for this, using biber for the bibliography. I also recommend using a interim folder for the compilation, as this will generate a lot of files. The interim folder is added in the .gitignore file, so it will not be included in the repository. The same goes for the out folder, which will be touched upon later.

Compile using whatever software you prefer, but here is a suggestion for the terminal:

mkdir interim
pdflatex -output-directory=interim main.tex
biber interim/main
pdflatex -output-directory=interim main.tex
pdflatex -output-directory=interim main.tex

This will generate a main.pdf file in the interim folder. Check that this looks good and that the references are correct.

For future compilations, use the same commands without the mkdir command. Also, unless you change the references, you only need to run

pdflatex -output-directory=interim main.tex

for a recompilation.

Step 3: Write the thesis

This is probably the hardest part. The src folder is where to put all the source code for the thesis. I suggest using a folder structure that makes sense to you, and that you are consistent with it. Add chapters, sections, and subsections to the thesis by using the input command in main.tex. You can see in the dummy example how this is done.

If you add new sources, make sure to add them to the bibliography.bib file.

The page numbering of the frontmatter will be (non-printed) roman numerals (meaning they only show up in the table of contents and not on the pages themselves). The rest of the thesis will have arabic numerals, with the numbering stopping at the end of Part I unless Step 4 is performed. Note that the number of pages between the abstract and List of papers will differ depending on whether or not you have a dedication page and an optional quote. On line 32 in main.tex, the command

\setcounter{page}{X}

adjusts the page numbering to account for this. If you do not use a dedication page or a quote, this should be set to 4. If you use one of them, it should be set to 6, and if you use both, it should be set to 8.

Step 4: Preprocess the papers (optional)

If you want the page numbering to be consistent throughout the entire thesis, you can add the papers to the src/papers folder. Performing this step will also include the individual papers in the table of contents. What this means is that if you just upload the papers to the thesis publication tool, the page numbering will use whatever page numbering the pdf files have, typically that of the journal they were published in, or the page numbering of the preprint.

If you do not care for this, you can remove the papers folder and the input command in main.tex that includes a paper. Do however not remove the Part II section named Papers, since this should still separate the introduction from the papers.

To remove the page numbering from the papers, open their source tex files and add the following command at the beginning of the document:

\pagenumbering{gobble}

Then, add the compiled papers to the src/papers folder, and add it to the thesis using these two lines:

\part*{Paper I\addcontentsline{toc}{section}{Paper X}}
\includepdf[pages=-, pagecommand={\thispagestyle{plain}}]{src/papers/paper_x.pdf}

in main.tex, replacing Paper X with the roman numeral number of the paper and paper_x.pdf with the name of the pdf file. An example for this is included in the dummy document.

Step 4.1 Removing pages from already compiled papers (optional)

In case you do not have access to the source files of the papers, the situation is a little more complicated since you will have to remove the page numbers from the pdf files. My suggestion is to create a new LaTeX document that includes the papers using the pdfpages package, but uses tikz to create a white overlay on top of the page numbers. It takes a bit of manual work, but it is doable. I have not finished my general implementation of this to add to this template. Note that this way you can also remove annoying headers and footers that are often included in digitally published papers.

Step 4.2 Removing colored hyperlinks from the papers (optional)

When printing the thesis, the library will ask you to specify on what pages to print in color. This is in order to make figures and plots look good. However, many digital publications use colored hyperlinks. Thus, if pages with figures are printed in colors, and pages without figures are printed in black and white, the hyperlinks will only be visibly colored on some pages, looking inconsistent.

While this is extremely minor, there is a simple solution to this, which is to run the ghostscript included in the scripts folder on the pdf files of the papers. Run the command in the terminal like this:

./scripts/remove_hyperlinks.sh src/papers/output.pdf src/papers/input.pdf

where output.pdf is the name of the new file and input.pdf is the name of the original file. Check that the result looks good, and if it does, use the new file in the thesis.

Step 5: Compile the final document

When you are done writing the thesis, it is time to compile the final document and split it into the various parts that can be uploaded to the thesis publication tool. This can be done by compiling as normal and then manually splitting the resulting pdf file, but an easier way is to use the python script included in the scripts folder, that splits the pdf file into the various parts by examining the table of contents. Note that this requires the PyPDF2 package, which can be installed using pip:

pip install PyPDF2

If you have changed the format of the table of contents, or drastically changed the structure of the thesis, the script likely won't work, and you will have to split the pdf manually. It also won't work if you have more than 9 papers, but that is easily adjusted manually in the script.

To compile and split the final document, use the following commands (all included in the scripts/compile_and_split.sh shell script):

# Navigate to the root directory
cd "$(dirname "$0")/.."

# Ensure interim and out directories exist
mkdir -p interim out

# Compile the document
pdflatex -interaction=batchmode --output-directory=interim main.tex
biber interim/main.aux
pdflatex -interaction=batchmode --output-directory=interim main.tex
pdflatex -interaction=batchmode --output-directory=interim main.tex

# Split it into pieces
python3 scripts/split_document.py --toc_path interim/main.toc --pdf_path interim/main.pdf --out_path out/

This will create a number of files in the out folder.

abstract.pdf - For publication purposes, this file can be discarded, as it will be replaced by the spikblad. It is however useful to include when sending the thesis to internal revision or to the opponent and grading committee.
frontmatter.pdf - This is the part of the frontmatter that is not included in the thesis publication tool. It contains the List of papers, Acknowledgements, and Table of contents.
introduction.pdf - This is the introduction, or the "kappa". It starts with the "Part I" title page and ends with the "Part II" title page.
paper_i.pdf, paper_ii.pdf, ... - These are the papers included in the thesis. If you did not perform Step 4, these files won't be included in the out folder.

Step 6: Upload to the thesis publication tool

When you have the pdf files, you can upload them to the thesis publication tool.

The spikblad/nailing page/abstract will be provided by the Avhandlingsstöd department after registering the thesis and should be uploaded as a separate file under the "Spikblad"/"Nailing page" section in the tool

The frontmatter.pdf and introduction.pdf files should be uploaded under the "Kappa/Thesis" section in the tool, in that order.

The papers paper_i.pdf, paper_ii.pdf, ... should be uploaded under the "Papers" section in the tool. Make sure to upload them in the correct order. If you did not perform Step 4, upload the original pdf files of the papers instead.

Check the preview in the tool and make sure that the numberings in the pages and table of contents are correct. If anything is wrong with these, the easiest solution is probably to go back to the source files and manually add the command

\setcounter{page}{X}

where X is the correct page number, and recompile the document. Hopefully, this will not be necessary.

Troubleshooting

Sometimes the page numbering will be off, especially in the frontmatter which should feature unlabeled, roman, page numberings. To supress page numberings in the frontmatter when it pops up, use the command

\thispagestyle{empty}

\afterpage{\null\thispagestyle{empty}
\newpage}

until you reach a satisfactory page numbering. This will likely happen if some section in the frontmatter extends beyond one page.

If at any point in the thesis you end up with Chapter titles or new papers on the left-hand side, you can use the command

\cleardoublepage

\newpage

until you reach a satisfactory page numbering. Also, if the number is just plain wrong anywhere, use

\setcounter{page}{X}

where X is the correct page number.

Not implemented

A solution to the fact the frontmatter pages are occasionally visibly numbered and have to be supressed manually
Reimplementing the template as a cls file for easier use
A straight-forward way to remove page numbers from pdf files

Contact

If you have any questions or suggestions, feel free to contact me here. I do not guarantee that I will be able to help or have time to help, but hopefully this template will get a life of its own and be improved on by future PhD students.

Good luck with your thesis!

henningzakrisson/su-math-thesis