Reproducible quarto manuscript for "Title"

This is a template for generating a reproducible quarto manuscript.

Steps to reproduce:

Clone this repo

gh repo clone WeberLab/Reproducible_Manuscript_Template

rv package manager for r

You will find an rproject.toml file in the main directory and the notebooks directory. These define the R version and the package to install.

You will need to install rv

Then run:

rv init .
rv sync

And do the same in Notebooks/RStats:

cd notebooks/RStats
rv init .
rv sync

uv for Figures.ipynb

cd notebooks/PythonFigures
uv sync

add packages with uv add <packagename>

Then you can create/edit your .ipynb file with uv run --with jupyter jupyter lab

Quarto

Now you can first preview, then render

quarto preview --no-browser #You don't need this flag; it just suppresses the browser from opening
quarto render

If you get some broken figure links, run quarto preview again

For publishing to github, your .github/workflow will fail until you run quarto publish gh-pages

Snippets

Reminders

When your paper is published, edit the index.qmd front matter:

citation:
  container-title: Unpublished # change when published