rmnldwg / lythesis Goto Github PK

• University: University of Zurich (UZH)
• Department: Department of Physics
• Supervisor: Prof. Jan Unkelbach
• Time: September 2019 - December 2022

This repository contains the source code for my PhD dissertation. It is set up to be - above all - modular and reproducible. I have created two versions of it: An online version, optimized for screens and without lengthy URLs or empty pages, and a print version, where chapters start on right pages and every link is written out. You can download them via the buttons below:

To compile this thesis, one needs a TeX distribution. Ideally TeX Live 2022, I have noticed some errors with TeXt Live 2019.

All figures in the thesis are compiled using scripts that are contained in this repository. This means, given the correct data, one can recreate all plots. This is not necessary for compiling the thesis, because the figures are also contained in the repository, but if anyone wants to check if I have done everything correctly, feel free to do so.

To recreate all figures, in addition to a TeX Live distribution, one needs...

1. Python 3.8 or later installed. Ideally one has also created a virtual environment.
2. an installation of Inkscape to convert .svg plots into a .pdf and a .pdf_tex file each.

The section below lays out the steps for recreating the figures.

If you want to reproduce the thesis, i.e. recompile it and recreate all the figures, do the following (ideally inside a virtual environment, like venv):

First, install the dependencies:

pip install -U pip setuptools wheel
pip install -r requirements.txt

Then, update all the data sources. You could go through all data folders inside every chapter's directory and execute dvc update -R ., but there is a faster way. At the root of the repository, call

find -iname "*.dvc" -exec dvc update {} \;

Next, the plots can be reproduced by telling the tool DVC to rerun the pipelines that were defined with its help. Again, this could be done chapter by chapter, but the shorthand command is

find -iname "dvc.yaml" -exec dvc repro {} \;

And after this, you can build the entire document by running

latexmk -synctex=1 -interaction=nonstopmode -file-line-error -pdf -outdir=_build main

Now your _build directory at the root of the repo should contain a beautifully rendered main.pdf 👍

Of course, you can also build the print version of the document. Simply replace main with print in the last command above.

The thesis itself is obviously copyrighted by default, meaning you cannot sell or distribute it under your name. But the basic structure of this repository may be used freely as a sort of template under the MIT license. If you base your thesis on the scaffolding of mine, you can use the "Cite this repository" button to give credit.

To cite the thesis itself, you can use this BibTeX entry:

@thesis{ludwig_modelling_2022,
    title = {Modelling {{Lymphatic Metastatic Progression}} in {{Head}} and {{Neck Cancer}}},
    author = {Ludwig, Roman},
    date = {2022-10},
    institution = {{University of Zurich}},
    location = {{Zurich, Switzerland}},
    langid = {english},
    pagetotal = {181},
}

I make heavy use of LaTeX's subfiles package to make everything as modular as possible. The main.tex and print.tex files contain no content, except the thesis title, author and date. They only load in other files and directories.

1. First, it loads the preamble.tex, where I define all the packages and set up the document. There I also load the math_operators.tex I defined for myself and an extensive glossary.tex of abbreviations.
2. After that comes a simple subfile call to the actual content that I store inside content/_content.tex. This file in turn includes other files via subfile calls:
   1. The abstract, acknowledgements, ToC, etc. are all in the content/frontmatter.tex.
   2. Written chapters are pulled in from subdirectories within the content folder. However, not as large content files directly, but via content/<title>/_chapter.tex files, that - like the main.tex - don't have much content in them. These chapter TeX files, too, use subfiles to include the sections within the respective chapter. This makes it super easy to in- or exclude entire sections and chapters. Only besides the _chapter.tex files in the corresponding directory can one find the "leafs" of this thesis' structure tree.
   3. Lastly, like the content/frontmatter.tex a file content/backmatter.tex defines what follows after the main body. Like a table of figures and stuff like that.

Since it is set up such that every .tex file that has a document environment in it compiles into a working PDF, this repo should have _build directories on every level. I have configured VS Code such that it always puts intermediate files and compiled PDFs there. These folders can then just be ignored by git to keep the repo uncluttered.

In every chapter folder I placed data directories that hold data that will be plotted in some form or another. The data is imported and versioned using DVC.

I do not intend to put raw data here which then runs in an hours long inference process to produce a single figure in the end, but rather outputs of such inference processes. In my case, the inference pipelines are stored in the repository lynference.

The root and every chapter folder also have figures directories in them. This is the place to store...

1. static images to be displayed in the thesis
2. scripts that produce plots of computed results

For the second point, I again rely heavily on DVC. This tool defines which files in the respective data folder to use with which (Python) script to produce exactly which version (using MD5 hashes) of a plot.

In order to use this thesis as a template, first delete the content of all _build folders. Then, delete all the directories inside the content folder and replace them with your chapters.

You also need to adapt some stuff in the frontmatter.tex, backmatter.tex and of course the title, author and date in the main.tex.

Finally, replace the references.bib with your list of references and adapt/extend the math_operators.tex and glossary.tex to what you need.

I often stumbled over the graphicspath setting and how it interacts with the subfiles package. If the build fails because some figure has not been found, this is likely the issue.

In that case, make sure that in the preamble.tex the path to all figures directories is listed (each in their own {} bracket pair and not separated by commas). Also make sure each _chapter.tex lists \subfix{./figures/} in their graphicspath setting. And the same goes for the other section files in each chapter's directory.

That should fix all errors regarding LaTeX not being able to find figures.