jupyter-notebook
Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.
- License 许可
- MIT
- 最近更新
- 2026-11-02
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01 前言 Front Matter
- name
- jupyter-notebook
- description
- Use when the user asks to create, scaffold, or edit Jupyter notebooks (`.ipynb`) for experiments, explorations, or tutorials; prefer the bundled templates and run the helper script `new_notebook.py` to generate a clean starting notebook.
03 SKILL.md 正文
Jupyter Notebook Skill
Create clean, reproducible Jupyter notebooks for two primary modes:
- Experiments and exploratory analysis
- Tutorials and teaching-oriented walkthroughs
Prefer the bundled templates and the helper script for consistent structure and fewer JSON mistakes.
When to use
- Create a new
.ipynbnotebook from scratch. - Convert rough notes or scripts into a structured notebook.
- Refactor an existing notebook to be more reproducible and skimmable.
- Build experiments or tutorials that will be read or re-run by other people.
Decision tree
- If the request is exploratory, analytical, or hypothesis-driven, choose
experiment. - If the request is instructional, step-by-step, or audience-specific, choose
tutorial. - If editing an existing notebook, treat it as a refactor: preserve intent and improve structure.
Skill path (set once)
export CODEX_HOME="${CODEX_HOME:-$HOME/.codex}"
export JUPYTER_NOTEBOOK_CLI="$CODEX_HOME/skills/jupyter-notebook/scripts/new_notebook.py"
User-scoped skills install under $CODEX_HOME/skills (default: ~/.codex/skills).
Workflow
-
Lock the intent. Identify the notebook kind:
experimentortutorial. Capture the objective, audience, and what "done" looks like. -
Scaffold from the template. Use the helper script to avoid hand-authoring raw notebook JSON.
uv run --python 3.12 python "$JUPYTER_NOTEBOOK_CLI" \
--kind experiment \
--title "Compare prompt variants" \
--out output/jupyter-notebook/compare-prompt-variants.ipynb
### Templates and helper script
### Temp and output conventions
### Dependencies (install only when needed)
### Environment
### Reference map
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clarify-requirements
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openmm-md
Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein / protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.
visual-review
Take screenshots of web pages and UI using Playwright for visual review and iteration
status
Diagnostic status report — shows metaswarm installation state, project setup, and potential issues
start
Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work
setup
Interactive project setup — detects your project, configures metaswarm, writes project-local files