bio-reporting-jupyter-reports

80 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Runs parameterized Jupyter notebooks as reproducible batch report generators with papermill, renders them to HTML/PDF with nbconvert, aggregates results across samples, and makes notebook outputs trustworthy. Use when generating per-sample analysis reports, executing a notebook template across many datasets, or fixing notebooks that do not reproduce.

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this.

Found in 3 places.

skills/bio-reporting-jupyter-reports/SKILL.md, line 59- papermill reads/writes notebooks from `s3://`, `gs://`, `adl://`/`abs://`, and `http(s)://` out of the box (cloud connectors are extras: `pip install papermil
skills/bio-reporting-jupyter-reports/SKILL.md, line 72- `--to pdf` needs a LaTeX toolchain (xelatex + pandoc) - the classic CI pain. `--to webpdf` renders HTML then prints via headless Chromium (`pip install nbconv
skills/bio-reporting-jupyter-reports/usage-guide.md, line 10pip install papermill nbconvert scrapbook jupytext nbstripout

Runs commands on your computer

The author does not mention this.

Found in 2 places.

skills/bio-reporting-jupyter-reports/SKILL.md, line 67jupyter nbconvert --to html --no-input out/sampleA.ipynb # code-hidden stakeholder report
skills/bio-reporting-jupyter-reports/examples/papermill_batch.py, line 24subprocess.run(['jupyter', 'nbconvert', '--to', 'html', '--no-input', str(notebook)], check=True)

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-reporting-jupyter-reports' ] || [ -L ~/.agents/skills/'bio-reporting-jupyter-reports' ]; then echo 'A skill folder named bio-reporting-jupyter-reports already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-reporting-jupyter-reports' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-reporting-jupyter-reports' ~/.agents/skills/'bio-reporting-jupyter-reports' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-reporting-jupyter-reports' ~/.claude/skills/'bio-reporting-jupyter-reports' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-11	`908229c`	80