README.qmd

---
format: gfm
---

<!-- README.md is generated from README.qmd. Please edit that file -->

```{r}
#| include: false
#| eval: false
# Create pdf and png version of template
library(tidyverse)
library(quarto)
library(magick)

# Render template
quarto_render(input = "index.qmd")
# Convert rendered PDF to PNG
image_read_pdf("_book/Awesome-thesis.pdf", pages = 1) |>
  image_montage(geometry = "x1000+25+35", tile = 1, bg = "grey92", shadow = TRUE) |>
  image_convert(format = "png") |>
  image_write("figures/cover.png")
# Move pdf to examples folder
fs::file_copy("_book/Awesome-thesis.pdf", "examples/template.pdf", overwrite = TRUE)
```

# uOttawa (biology) Thesis Template

This is a Quarto (<https://quarto.org/>) template that assists you in creating a University of Ottawa thesis. You can fork or download the repository to get started but the recommended way is simply to use the quarto function within R or the system shell to install and use the template


## How to get it
``` r
#  You might need the development version of the quarto R package that you can install with
remotes::install_github("quarto-dev/quarto-r")

quarto::quarto_use_template("juliengamartin/quarto-bio-uo-thesis")
```

or in a terminal

``` bash
quarto use template juliengamartin/quarto-bio-uo-thesis
```

## how to use it 

The template can generate a pdf document as well as an associated website to be hosted on github

Edit and add files as necessary see folder structure below

### Template structure

<!-- obtained with tree -L 2 and reorganised -->
```
* indicates files with thesis content (i.e. to modify and rename as you see fit)
+ indicates files to modify for your thesis but do NOT rename (needed by quarto)

.
├── * App-A.qmd                               <- first appendix
├── * App-B.qmd                               <- second appendix
├── * chap_1.qmd                              <- first chapter
├── * chap_2.qmd                              <- second chapter
├── * conclusion.qmd                          <- conclusion
├── *+ index.qmd                              <- thesis front matter
├── * introduction.qmd                        <- introduction
├── LICENSE                                   <- License file for sharing
├── + _quarto.yml                             <- specifying project building /rendering with quarto
├── README.md                                 <- github description how to use
├── * references.qmd                          <- references chapter
├── biblio                                    <- folder for biblio
│   ├── american-statistical-association.csl  <- biblio style
│   ├── * packages.bib                        <- bib files of references (generated by grateful)
│   ├── quarto.bib                            <- bib files with quarto reference
│   └── * thesisrefs.bib                      <- bib files of references
├── data                                      <- folder for data used in thesis
│   └── sales.csv                             <- example data
├── examples                                  <- folder with example (can be removed)
│   └── template.pdf                          <- example in pdf
├── figures                                   <- folder for figures/images
│   └── cover.png                             <- example cover image
└── _extensions                               <- folder with template info (don't modify or at your own risks)
    └── juliengamartin
        └── bio-uo-thesis
            ├── before-title.tex
            ├── end_frontmatter.tex
            ├── _extension.yml
            ├── thesis.scss
            ├── title.tex
            ├── toc.tex
            ├── uOttawa-crop-large.png
            └── uOttawa-crop.png


```

## Example

Here is the source code for a minimal sample document: [template.qmd](template.qmd) with the [generated pdf output](examples/template.pdf) and the [website](https://juliengamartin.github.io/quarto-bio-uO-thesis/)