Disclaimer: This is work in progress, I will be updating this post as I standardize and create a separate template/extension repository.

I wrote my master thesis in LaTeX, but given that markdown is a bit nicer to write, so I decided to switch with my PhD thesis to Markdown.
I was trying with Pandoc but last year I switched to Quarto, as it is more flexible, and it is easier to customize.

Nicer Fonts and Better Handling of Figures #

I am sharing with you a fragment of my _quarto.yml file, with some tweaks I am using to make my PDF output nicer.

 format:
  pdf:
    link-citations: true  # <1>
    number-sections: false
    reference-section-title: "References"
    pdf-engine: xelatex
    include-in-header:
      text: |
        \usepackage{epigraph} 
        %%
        %% Code related to fonts and how the output looks
        %%
        \usepackage{mathpazo}   % <2>
        \usepackage[T1]{fontenc}
        \usepackage[sups,osf]{fbb} % osf (or tosf) for text, not math # <2>
        \usepackage[scaled=.95]{cabin} % sans serif # <2>
        \usepackage[varqu,varl]{inconsolata} % sans serif typewriter # <2>
        %%
        %% Code related to figures in document
        %%
        \usepackage{float}  % <3>
        \graphicspath{{figures}{chapters/figures}{../figures}{chapters}} # <4>
        \let\origfigure\figure
        \let\endorigfigure\endfigure
        \renewenvironment{figure}[1][2] {
            \expandafter\origfigure\expandafter[H]
        } {
            \endorigfigure
        }        

I put number as comments, so you can better understand specific lines.

1. Some options for PDF output (more or less self-explanatory)>
2. The font use by default template are ugly format, this look similar but are nicer.
3. Forcing figures to be placed where they are in the text
4. Allowing to use figures from different folders, and allowing to use relative paths to figures.

Use Profiles to Compile either Whole Book or Thesis or Single Chapter #

Since quarto 1.2 profiles are introduced ¹ In my use case I have on profile _quarto-thesis.yml which include all chapters and preambles, and another _quarto.yml which I can use just to compile the current markdown file; If I want to render whole thesis I just use quarto render --profile thesis; you could have as many as you want of those profiles (I was procrastinating that way with different look and templates for my thesis 🙂 )

Roman Numbering for front Matter and Arabic for Main Matter #

I am inserting roman numbering for front matter and arabic for main matter.

 format:
  pdf:
    include-before-body:
        text: |
           \pagestyle{plain}
           \pagenumbering{roman}           

In main tex I switch back to arabic numbering:

\pagenumbering{arabic}

Problem with index.md and Inserted Blank Page #

As you write complex project, you want might want to have separate files for each chapter.
When you are using quarto to render your project, you could put them inside index.md in your root folder:

{{include "chapters/chapter1.qmd"}}
{{include "chapters/chapter2.qmd"}}

Using include filter will add the content of the files to the index.md file when compiling.
This is nice solution, but I have a problem when I want to use quarto preview to update and monitor resulting pdf when I change something in source files.
Unfortunately, quarto preview does not update output .pdf file when files added with include change, so I needed to choose another solution.

Alternative solution is to add chapters into you _quarto.yml file:

project:
  output-dir: _output
  execute-dir: file

book:
  title: Title of my  thesis or book
  author:
    name: Author Name
  chapters:
    - index.qmd
    - chapters/chapter1.md
    - chapters/chapter1.md

I want to all of my content of to live in the ‘chapters’ folder.
Unfortunately currently in quatro users always need to include index.md (it makes sense when generating html as output, but not always when generating pdf).

I can leave the index.md file empty, but then I will have an empty page between my table of content and first chapter.
I can include the first chapter into index.md but then we were hitting the same problem on smaller scale again.

My Solution #

By default, latex is adding a page break after each chapter, and the index.md file is treated as a chapter, even if empty.
As a hack, I am hiding the problem by relaxing \clearpage behaviour in latex.

I am leaving my index.md file almost empty, I’m just adding this latex code ²:

\let\standardclearpage\clearpage
\let\clearpage\relax 

Then within my first chapter when my content start, I am returning to standard behaviour of \clearpage:

\let\clearpage\standardclearpage

This way I am not adding any extra page between my table of content and first chapter, and I can use quarto preview to monitor my changes.
In future the quatro behaviour might change regarding inclusion of `index.md``, you can follow discussion here:

Useful Materials #

I just saw this post published on the blog of Cameron Patrick, it contains more useful information about writing thesis with quarto: https://cameronpatrick.com/post/2023/07/quarto-thesis-formatting/.

I am personally using modified quarto-thesis template for my thesis, you can find it here: https://github.com/nmfs-opensci/quarto-thesis
If you don’t use quarto, but you want to play with it, you can modify it online on the Posit virtual Rstudio instance https://rstudio.cloud/content/4383755 (free account required)

References #