Python Jupyter notebooks for pre-production or one-off experiments.
Use Python poetry to run and install related packages.
# installation
poetry install
To run a notebook using Papermill:
# navigate to Notebooks dir
cd center-notebooks/Notebooks
# run a notebook using papermill cmd
papermill --log-output "Create Cites from PMC Lookups.ipynb" -
Development is assisted by procedures using Dagger via the development.cue
file within this repo. These are also related to checks which are performed related to CI/CD. See the following page for more information on installing Dagger: https://docs.dagger.io/install
Afterwards, use the following commands within the project directory to perform various checks. Warnings or errors should show the related file and relevant text from the related tool which may need to be addressed.
# clean various files using formatting standards
dagger do clean
# lint the files for formatting or other issues
dagger do lint
...