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Author, execute, and deliver reproducible analysis notebooks in marimo (default) or Jupyter, with all cells run end-to-end and figures embedded. Also converts between marimo and Jupyter on request.
fmschulz/omics-skills · ★ 3 · Data & Documents · score 67
Install: claude install-skill fmschulz/omics-skills
# 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 prose directly inside the string; never paste quoted string fragments such as `" ... "` lines inside the markdown body. - Do not leave empty generated cells, whitespace-only cells, or `@app.cell def _(): return` placeholders. Remove them before final verification. - Do not a