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Papermill parameterized notebook starter

Skill ma-compbio-lab/SkillFoundry/skills/reproducible-workflows/papermill-parameterized-notebook-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill papermill-parameterized-notebook-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.2 KB, 264 tokens by cl100k_base, as published. Nobody here has run it

Papermill Parameterized Notebook Starter

Use this skill to execute a tiny parameterized notebook with Papermill and capture a deterministic summary plus the rendered output notebook.

What This Skill Does

  • runs a toy notebook with injected parameters
  • materializes an executed .ipynb
  • extracts the final JSON result from notebook cell outputs

When To Use It

  • when you need a runnable reproducible-notebooks starter
  • when you want a lightweight parameterized notebook pattern before scaling to a real analysis notebook
  • when you need a local smoke path for notebook execution

Run

./slurm/envs/reporting/bin/python skills/reproducible-workflows/papermill-parameterized-notebook-starter/scripts/run_papermill_parameterized_notebook.py --input skills/reproducible-workflows/papermill-parameterized-notebook-starter/examples/toy_parameters.ipynb --output-notebook scratch/papermill/toy_parameters_executed.ipynb --summary-out scratch/papermill/toy_parameters_summary.json --x 5 --y 7

Notes

  • The example notebook stays intentionally small and arithmetic-only so execution remains stable on a generic python3 kernel.
  • Replace the toy notebook after the starter passes locally and in the repository test surface.

Keep looking

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