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nbscuid 🦑

Notebook-Based, Super CUstomizable Infrastructure for Diagnostics

This is a package to enable running notebook-based diagnostic workflows. Based on my-cesm-experiment by matt-long: https://github.com/matt-long/my-cesm-experiment.

See some examples of workflows at https://github.com/rmshkv/nbscuid-examples.

Capabilities

  • Integration with data catalogs
  • Inject custom parameters into code and Markdown cells
  • Run many notebooks at once on a parameter set, or different parameters per notebook
  • Run different notebooks in different environments
  • Cache intermediate data products
  • Quickly build a Jupyter book with results

Installation

  1. Clone this repo

  2. Activate the environment you want to install nbscuid in. Within the cloned nbscuid directory, run:

    pip install .

    Alternatively, to install the commands nbscuid-run and nbscuid-build without installing all of nbscuid's dependencies, first install pipx with pip install pipx, then run:

    pipx install .

Running a notebook collection

Create a new folder that contains a config.yml file. (A guide to what goes in a config.yml file is coming soon!) This will be the run directory for your collection of notebooks, where all the computed notebooks will appear.

To run all the notebooks you've specified, execute:

nbscuid-run path/to/config.yml

To build the jupyter book if desired, execute:

nbscuid-build path/to/config.yml