Jupyter Notebook Best Practices
by oimiragieo
Guidelines for structuring and documenting Jupyter notebooks for reproducibility and clarity.
Skill Details
Repository Files
3 files in this skill directory
name: jupyter-notebook-best-practices description: Guidelines for structuring and documenting Jupyter notebooks for reproducibility and clarity. version: 1.0.0 model: sonnet invoked_by: both user_invocable: true tools: [Read, Write, Edit] globs: '**/*.ipynb' best_practices:
- Follow the guidelines consistently
- Apply rules during code review
- Use as reference when writing new code error_handling: graceful streaming: supported
Jupyter Notebook Best Practices Skill
- Structure notebooks with clear sections using markdown cells.
- Use meaningful cell execution order to ensure reproducibility.
- Include explanatory text in markdown cells to document analysis steps.
- Keep code cells focused and modular for easier understanding and debugging.
- Use magic commands like %matplotlib inline for inline plotting.
- Document data sources, assumptions, and methodologies clearly.
- Use version control (e.g., git) for tracking changes in notebooks and scripts.
Memory Protocol (MANDATORY)
Before starting:
cat .claude/context/memory/learnings.md
After completing: Record any new patterns or exceptions discovered.
ASSUME INTERRUPTION: Your context may reset. If it's not in memory, it didn't happen.
Related Skills
Dbt Transformation Patterns
Master dbt (data build tool) for analytics engineering with model organization, testing, documentation, and incremental strategies. Use when building data transformations, creating data models, or implementing analytics engineering best practices.
Clinical Decision Support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug develo
Scientific Schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
Mermaid Diagrams
Comprehensive guide for creating software diagrams using Mermaid syntax. Use when users need to create, visualize, or document software through diagrams including class diagrams (domain modeling, object-oriented design), sequence diagrams (application flows, API interactions, code execution), flowcharts (processes, algorithms, user journeys), entity relationship diagrams (database schemas), C4 architecture diagrams (system context, containers, components), state diagrams, git graphs, pie charts,
Diagram Generation
Mermaid diagram generation for architecture visualization, data flow diagrams, and component relationships. Use for documentation, PR descriptions, and architectural analysis.
Scientific Schematics
Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
Clinical Decision Support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug develo
Materialize Docs
Materialize documentation for SQL syntax, data ingestion, concepts, and best practices. Use when users ask about Materialize queries, sources, sinks, views, or clusters.
Dbt Transformation Patterns
Master dbt (data build tool) for analytics engineering with model organization, testing, documentation, and incremental strategies. Use when building data transformations, creating data models, or implementing analytics engineering best practices.
Mermaidjs V11
Create diagrams and visualizations using Mermaid.js v11 syntax. Use when generating flowcharts, sequence diagrams, class diagrams, state diagrams, ER diagrams, Gantt charts, user journeys, timelines, architecture diagrams, or any of 24+ diagram types. Supports JavaScript API integration, CLI rendering to SVG/PNG/PDF, theming, configuration, and accessibility features. Essential for documentation, technical diagrams, project planning, system architecture, and visual communication.
