notebooks

npx skills add BioTender-max/awesome-bio-agent-skills --skill notebooks --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Notebooks A single skill for authoring, validating, and delivering reproducible analysis notebooks. Marimo is the default format; Jupyter is supported for existing `.ipynb` files and when a downstream tool requires JSON. Conversion between the two formats is part of this skill. A notebook is not "done" until it has been executed end-to-end on a fresh kernel and every figure is embedded in the delivered file. ## Instructions 1. **Pick the format.** - New notebook: write a marimo `.py` notebook. Use the canonical cell layout (one concept per cell, final expression renders, no `if` guards around outputs, no `try/except` for control flow). - Existing `.ipynb` to extend or polish: keep it as Jupyter unless the user asks to convert. - Conversion: see "Convert between marimo and Jupyter" below. 2. **Outline before coding.** Write the notebook plan (purpose, data sources, analysis steps, expected outputs/plots) as the first markdown cell, then implement against that plan. 3. **Keep marimo cells clean.** These are hard rules for every `.py` notebook: - Markdown cells use one plain triple-quoted string: `mo.md(r"""...""")` or `mo.md(f"""...""")` only when interpolation is required. Put the

pixi run python -m ipykernel install --user --name <project> --display-name "<project> (pixi)"
uvx marimo check notebook.py
uv run marimo export ipynb notebook.py -o notebook.executed.ipynb
One-time kernel registration in the project root:
pixi run python -m ipykernel install --user --name myproject --display-name "myproject (pixi)"
After authoring, run end-to-end on a fresh kernel:
python skills/notebooks/scripts/execute_notebook.py notebooks/analysis.ipynb \
uvx marimo convert notebooks/legacy.ipynb -o notebooks/legacy.py
uvx marimo check notebooks/legacy.py
uv run marimo export ipynb notebooks/legacy.py -o notebooks/legacy.executed.ipynb