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quarto-thesis

Quarto extension for a masters or PhD thesis based on Masters/Doctoral Thesis, LaTeX Template, Version 2.5 (27 Aug 2017). You can play with it on RStudio Cloud without installing anything: https://rstudio.cloud/content/4383755 Go to the Build tab (upper right panel) and click Render Book.

Quick Start!

  • Show me how to download a zip and open in RStudio: Video
  • Show me how to use this repo as a template and then clone to my computer with RStudio: Video
  • Show me how to render in Visual Studio Code (see previous videos for how to get the repo onto your computer): Video
  • Scroll to the bottom for information on customizing the look of your thesis.

Installing the extension

You will need to do this to get all the folders with tex files. Start in the directory where you will create the directory that will contain your thesis files. Run this from a terminal in that directory.

quarto use template nmfs-opensci/quarto-thesis

It will ask for an empty directory name where to put the files, give it a new directory name.

Once you do that you can cd to the new directory and render from within the directory.

quarto render

Installation or updating for an existing document

You may also use this format with an existing Quarto project or document. But you will need to have all the tex folders already (see above).

quarto install extension nmfs-opensci/quarto-thesis

Usage

Customizing the look

For a LaTeX document, the class file MasterDoctoralThesis.cls in the _extensions/quarto-thesis determines the look and LaTeX environments available. To make any changes to the layout, change the MasterDoctoralThesis.cls in the _extensions folder. The MastersDoctoralThesis.cls file in the main folder will be overwritten by the one in the _extensions folder when you re-rerender. To get info on the MasterDoctoralThesis document class, do a web search for MasterDoctoralThesis.cls. You'll find some documentation.

Adding content

  • start adding Chapters in qmd format to the Chapters folder.
  • then add the chapter (or appendix) to the _quarto.yml file
image

Getting and giving help

First try the Discussion link because there may be a solution there. Have a solution to post or want to show how you have used this template? Post to the discussion forum too! You'll find links to other Quarto thesis templates there too.

If you think it's a bug, then definitely post an issue and I'll look into it!

Contributors

Contributors

This template is based on the Masters/Doctoral Thesis, LaTeX Template, Version 2.5 (27 Aug 2017). Other Quarto thesis examples:

Problems

  • All the stuff in Frontmatter is mandatory LaTeX since it is being injected into the tex document after the qmd is processed. Probably need to learn how to write a lua filter to render the Frontmatter qmd to LaTeX via Pandoc.

  • I doubt that passing in classoptions in your _quarto.yml will work. The elsevier lua filter suggests that the classoptions need to be added on.

  • Why does index-blx.bib keep appearing?

Warning. Chapter 1 has R code

Python and Julia users: After you install the extension, search for {r} in Chapters/Chapter1.qmd and get rid of the R code (for a table and a figure) or replace with Python or Julia code.

quarto-thesis's People

Contributors

eeholmes avatar theorashid avatar

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quarto-thesis's Issues

References are not beeing rendered anymore.

Description

References of my thesis project are not being rendered correctly anymore. This only applies to the citations in the text body, the reference section at the end of the document is rendered fine. So the .bib file seems to be working.

When rendering, xelatex runs multiple loops, aborting after reaching the maximum number of runs. I found an old GitHub Issue from the Quarto Repository, suggesting that this might have something to do with LaTex packages not working correctly (see here quarto-dev/quarto-cli#3518 (comment).

This also happens with previous version of my project, of which I'm sure, that they were working before. I assume that this is related to the new Quarto version 1.4, since this is the only thing I can think of that has changed since then. However, when not working with this project, e.g. basic Quarto scripts with pdf Output, references work fine.

I tried reproducing the error with the example of this repository, but here I got a different error:

ERROR: 
compilation failed- missing packages (automatic installed disabled)      
LaTeX Error: Something's wrong--perhaps a missing \item.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...

l.872 \end{CSLReferences}

Is anyone else having this problem?

Issues with the abstract

How can I add new paragraphs to the abstract? I have added the abstract in the _quarto.yml but I cant figure out how to get it into paragraphs. I have tried \n and breaking it up with quotation marks but it isnt working.

Also, my abstract is long and the 'title page' for the abstract now renders at the bottom of a new page and then abstract content is on a second page. I have tried to figure out how to change this in the yml, cls etc but I cant seem to do it and save the cls.

Many thanks

Scoping of `setspace` classoption

Prerequisites

  • Run quarto --version and report the Quarto version you are using: 1.0.36
  • Tell us your OS: 5.15.74-3-MANJARO x86_64

Having trouble rendering to PDF?

  • Tell us how you are rendering Quarto docs (RStudio, VS Code, command line, etc): Rstudio terminal quarto render
  • Tell us what TeX and version you are using tex --version: TeX 3.141592653 (TeX Live 2022/Arch Linux)
  • Are you using tinytex (note tinytex is a version of TeX Live)?: tinytex 0.42 library not in use

Description

Alternative classoptions for line spacing have the effect of increasing all spacing, including of front matter, tables and code chunks (see Table 1.1 of the rendered A-doctoral-thesis-title.pdf file.

Steps to Reproduce

  1. Edit ./_extensions/quarto-thesis/_extension.yml
  2. Change classoption from singlespacing to either onehalfspacing or doublespacing
  3. quarto render to render PDF

Additional Information

Shouldn't user alterations to setspace be confined in their scope to paragraph text within the main body?
Relevant Stack Overflow discussions here, here, and here

Adding the following to ./_quarto.yml protects single line spacing within code (shaded environment) and tabular environments. I'm not sure if all of these tabular environments are relevant : in my test (with keep-tex: true) Table 1.1 was located within a longtable environment.

format:
  quarto-thesis-pdf: 
    urlcolor: red
    toclinkcolor: black
    toc-depth: 2
    classoption: [onehalfspacing, oneside]
    header-includes: |
      \usepackage{etoolbox}
      \AtBeginEnvironment{Shaded}{\singlespace}
      \AtBeginEnvironment{tabular}{\singlespacing}
      \AtBeginEnvironment{lltable}{\singlespacing}
      \AtBeginEnvironment{longtable}{\singlespacing}
      \AtBeginEnvironment{tablenotes}{\doublespacing}
      \captionsetup[table]{font={stretch=1.5}}
      \captionsetup[figure]{font={stretch=1.5}}

minor error in section reference of example

First of all thanks for this great template! I appreciate your work that you share this!

I just wanted to hint at a minor error in the section reference of the example. I saw that you stumbled upon this in your video and that it is still included in the example. So I thought I'd let you know.

Description

The header of section 1.9 Thesis Features and Conventions is rendered as 1.9 Thesis Features and Conventions {sec-ThesisConventions}

This is due to the missing '#' ({#sec-ThesisConventions} instead of {sec-ThesisConventions}).

Displaying university logo

Discussed in #18

Originally posted by XtayCalmEco August 16, 2023
I input a file location and yet nothing appears to show - do you have any advice?

Multiple supervisors

Feature request

Hi there, I have 3 (!) supervisors. Is it possible to extend this template for multiple supervisors

How to add support for Chinese?

Question

I'm trying to add support for Chinese in Quarto, but I'm encountering some issues. I've tried several methods, but none seem to give me the desired results. I want to be able to use Chinese text in my Quarto project and ensure that Chinese characters are handled and formatted correctly. Are there any specific configurations or steps to achieve this? I would greatly appreciate any advice or guidance on this matter.

maybe add \usepackage{ctex} somewhere in MastersDoctoralThesis.cls?

TKS!!!

Math not rendering correctly in pdf

Description

Hi @eeholmes, I inserted a basic equation into the template Chapter 1. It renders fine on quarto equation preview in VSCode, but it does not render in the pdf. If I change the output to html, the equation renders as expected.

Steps to Reproduce

$$
\int_{A_i}{\lambda (\mathbf{x})}
$$

Does quarto not natively support math such as \int?

From html output:
Screenshot 2023-01-20 at 17 06 47

From pdf:
Screenshot 2023-01-20 at 17 04 51

Include a pdf

Question

Hello
I am a new quarto (but old R user) who was going to use Overleaf for my thesis because I know I can include pdfs of my published papers in Overleaf. https://stackoverflow.com/questions/2739159/inserting-a-pdf-file-in-latex
However, I would like to use Quarto and this template instead. Do you know of a way to include pdfs into quarto? I cant find an answer for doing it in documents yet. I am going to raise it as a question on the Quarto site.
Thank you

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