cu-dbmi / center-notebooks

Python Jupyter notebooks for pre-production or one-off experiments.

Center Notebooks

Python Jupyter notebooks for pre-production or one-off experiments.

Installation

Use Python poetry to run and install related packages.

# installation
poetry install

Running Notebooks

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

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
...

center-notebooks's Issues

Create Monthly Cites from PMC Lookups Notebook

Create "Monthly Cites from PMC Lookups" notebook based on existing yearly notebook content.

Package and schedule the "set integration task status" notebook

Please package and schedule the "set task integration status" notebook to run daily.

I'll set up a kick-off meeting to discuss more. :)

Use Poetry for Dependency and Environment Management

Migrate from requirements.txt (along with other structure) to Poetry for dependency and environment management.

Package and schedule the undone task journal notebook

Please package and schedule the "undone task journal" notebook to run every seven days.

That notebook name isn't accurate anymore, but I presume I'll change it when we sort out the packaging steps.

Migrate Dendron Vault Content to set-notegraph

Where appropriate, migrate Dendron content to set-notegraph repo.