This submission template is for a simple notebook-based publication with one source file, supporting data, bibliography, and MyST build configuration.
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. Specific markdown cells may be tagged in their metadata as "part": "abstract", or "part": "availability" - these cells will be extracted from the document and included as the specified part in the built output.
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 specified two ways, both described in the MyST docs. They may be listed explicitly in bibtex format, by convention in the file references.bib, and referenced by key using a cite MyST role. They may also be specified as inline DOI links. These do not require full bibliographic information; the data is fetched implicitly on build from the DOI.
A myst.yml file must be provided to configure notebook metadata and exports. This includes authors, affiliations, licenses, keywords, and much more.
To build PDF/JATS output from your source data, you must have the MyST Markdown CLI installed
npm install -g mystmdThen build all exports defined in the myst.yml file:
myst build --all