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quarto-phd-thesis

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Quarto Template PhD Thesis - The University of Edinburgh

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# Quarto PhD Data Science Thesis Template: Edinburgh University

[PDF preview click here](_book/quarto-phd-template.pdf), select pages:

# Install & Usage

Follow the steps below to clone, customize, and build the document.

### Prerequisites

1. Install Python: Download and install Python from the official website: https://www.python.org/downloads
2. Install JupyterLab: Follow the installation instructions on the official JupyterLab website: https://jupyter.org/install
3. Install Git: Download and install Git from the official website: https://git-scm.com/downloads
4. Install Quarto: Follow the installation instructions on the official Quarto website: https://quarto.org/docs/installation.html
5. Install Cormorant Garamond, JetBrains Mono and STIX 2 for font styling available at https://github.com/JetBrains/JetBrainsMono or Google Fonts. You may need to reset your matplotlib font cache.

### Clone the Repository
1. Open a terminal or command prompt.
2. Navigate to the directory where you want to clone the repository.
3. Run the following command to clone the repository:

```python
git clone https://github.com/james-d-h/quarto-phd-thesis.git
```

### Customize the Document
1. Navigate to the cloned repository directory:

```python
cd quarto-phd-thesis
```

2. Open the source files (e.g., `.qmd` files) with a text editor, an integrated development environment (IDE) that supports Quarto or Markdown, or with JupyterLab.
3. Customize the content by editing the source files, adding your own text, figures, tables, and citations. More details in the dir walkthrough below quarto.org
4. Customize the template to fit your specific requirements by modifying the content in the frontmatter, if necessary. 
3. Modify the _configs file to format graph or figure styling (see Chapter 1 for examples)
4. Run the create-chapter.ipynb notebook to generate new chapter folders and resource folders as needed.
5. Use the ascii-dir script to visualize the structure of your repository at single or full levels.
6. Call quarto render in the terminal in the main directory.
### Build the Document

1. In the terminal or command prompt, make sure you are in the `quarto-phd-thesis` directory.
2. Run the following command to build the document:

```python
quarto render
```

3. This will generate the output files in the `_book` directory within the `quarto-phd-thesis` folder.
4. Open the output files (such as `uoe-thesis.pdf`) with your preferred PDF viewer or web browser to see the final result.

### Make Changes and Rebuild
1. After making changes to the source files, run `quarto render` again to update the output files.

# Further Details for Customising

This Thesis template uses Roman numeral page numbering for front matter sections and Arabic numeral page numbering for the main content. Page numbering counter starts on page 3 to skip the cover sheet, you can comment that out in before-body.tex. Dedication, Title-page, declaration, abstract and acknowledgements are optional. The template also allows glossaries to be written in Markdown (I find it much simpler), but distributes TOCs, LOTs, LOFs to latex (also simplere/more flexible). Example Glossary of abbreviations, symbols, and definitions are within. The table of contents, list of figures, and list of tables can be commented out within the toc.tex file. before-body.tex can be used to drop whatever preamble sections you won't need.

## Repository / Thesis Structure
The repository is organized to mirror the structure of the thesis document. The index.qmd and _quarto.yml files can be edited as needed, but they cannot be deleted or renamed. The following diagram provides an overview of the template structure. Consult the code in the repository for a better understanding of how Quarto ties everything together. You can call the code-cell in create-chapter.ipynb to generate new chapters and associated resource folders (see Chapter 1 example). The ascii-dir script reates repository structure drawingls like that below.

```python
├── _book/
│   └── uoe-thesis.pdf         # calling quarto render from terminal produces your thesis here
├── _configs/                  # A folder for global config files; reproducible/consistent plots all Thesis 
│   └── matplotlibrc.txt       # I just use matplotlibrc.txt as an example for nice graphs 
├── chapter-00/                # Chapter content is organised into chapter folders, this introduction chapter is unnumbered
│   └── _introduction.qmd      # _chapter-name.qmd are the files I use to compile sections, figures, tables etc.
├── chapter-01/                # Chapter 1 folder; example of breaking up .qmd files into sections
│   ├── 01-intro.qmd           # Chapter 1: Section 1
│   ├── 02-wq.qmd              # Chapter 1: Section 2, and so on...
│   ├── 03-eo.qmd              # Sections use figures, code, notebook-outputs, etc. from /figs, /tables below
│   ├── 05-ai.qmd
│   ├── _literature-review.qmd # Sections are compiled in _literature-review.qmd
│   ├── figs/                  # Figures resource for Chapter 1
│   ├── images/
│   ├── litreview.qmd
│   ├── notebooks/             # .ipynb notebooks generate outputs -> /tables or /figs -> sections -> _lit-review.qmd
│   └── tables/                # You can skip any or all steps
├── chapter-02/                # Not everyone will need the full suite of Quarto abilities in chapter-01, that's okay
│   └── _materials&methods.qmd # Chapter 2 demonstrates simple use cases
├── chapter-03/                # Delete any folders or sections you don't need, except...
│   ├── _chapter-title.qmd     # ...this one; _chapter-title file is where the content goes
│   ├── _chapter-title.md      # The .qmd files can be changed to your preferred code format
│   ├── _chapter-title.ipynb   # Mix .tex, .md, .py in a single JupyterLab
│   ├── _chapter-title.tex     # Or pick your favorite, such as .tex
├── _quarto.yml                # Define the correct _chapter-title files in the right order in this .yml file
├── endmatter/                 # Includes appendix and .bibs for references or bibliographies needed
│   ├── appendices/            # Folder for appenices. Below bibliography folder holds the .bib file(s) and references.qmd
│   ├── bibliography/          # References.qmd simple calls the references to be made, you can decide where in the _quarto.yml
├── frontmatter/               # The frontmatter will be more familiar to most
│   ├── 01-dedication.txt
│   ├── 02-declaration.txt
│   ├── 03-abstract.txt
│   ├── 04-acknowledgements.txt
│   ├── before-body.tex        # This folder's content defines the template styling, similar to Overleaf
│   ├── figs/                  # This /figs contains title page images, etc.
│   ├── header.tex             # This is the LaTeX preamble called before "/begindocument{}"
│   ├── title.tex              # Defines variables from the .yml file for use in the title page
│   └── toc.tex                # Contains the TOC, LOF, LOTs, which you can delete as required
```

## License

This template is released under the MIT License.

## Disclaimer

This repository is a datascience product and is not official communication of the Edinburgh University, nor any of the cited contributors.

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