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 primary source file for this template is a Quarto markdown article. This file may embed notebook cells from other sub-articles to use the output of these cells as figures. It may also reference content from other markdown sub-articles. All of these supplementary source notebooks/articles should be saved in the notebooks/ folder.
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