This submission template is for a markdown-based publication with additional supporting notebook and markdown files, as well as supporting data, bibliography, and Quarto build configuration. It is based upon a new type of project in Quarto, Manuscripts.
Get started with Quarto and Manuscript projects here: https://quarto.org/docs/manuscripts/.
The source file for this template is a Jupyter notebook. There is not necessarily anything special about this notebook. It may contain markdown cells, code cells, and outputs from common Python packages, including pandas, matplotlib, plotly, seaborn, and altair.
The notebook has an additional markdown cell at the top of the document which configures Quarto to render the notebook.
By convention, all data should be saved in data/ directory. There is nothing magic about this directory; references to your data from your notebook must still specify the correct relative path.
Similar to the data/ directory, images for figures should be specified in images/ directory.
Bibliography entries may be specific in the document as described in the Quarto documentation.
Configuration for the example is provided by the Quarto project file, _quarto.yml, and the YAML block (front matter) that appears with the article markdown document.
To build PDF/JATS output from your source data, you must have the Quarto CLI installed - you can download or learn about installation at https://quarto.org/docs/download/
Then render the article using
quarto render article.ipynb