Talmolab Sleap Investigation

name: investigation description: > Scaffolds a structured investigation in scratch/ for empirical research and documentation. Use when the user says "start an investigation" or wants to: trace code paths or data flow ("trace from X to Y", "what touches X", "follow the wiring"), document system architecture comprehensively ("document how the system works", "archeology"), investigate bugs ("figure out why X happens"), explore technical feasibility ("can we do X?"), or explore design options ("explore the API", "gather context", "design alternatives"). Creates dated folder with README. NOT for simple code questions or single-file searches.

Set up an investigation

Instructions

1. Create a folder in {REPO_ROOT}/scratch/ with the format {YYYY-MM-DD}-{descriptive-name}:

   mkdir scratch/$(uv run python -c "import datetime; print(datetime.date.today().isoformat())")-{descriptive-name}
   

2. Create a README.md in this folder with: task description, background context, task checklist. Update with findings as you progress.
3. Create scripts and data files as needed for empirical work.
4. For complex investigations, split into sub-documents as patterns emerge.

Investigation Patterns

These are common patterns, not rigid categories. Most investigations blend multiple patterns.

Tracing - "trace from X to Y", "what touches X", "follow the wiring"

• Follow call stack or data flow from a focal component to its connections
• Can trace forward (X → where does it go?) or backward (what leads to X?)
• Useful for: assessing impact of changes, understanding coupling

System Architecture Archeology - "document how the system works", "archeology"

• Comprehensive documentation of an entire system or flow for reusable reference
• Start from entry points, trace through all layers, document relationships exhaustively
• For complex systems, consider numbered sub-documents (01-cli.md, 02-data.md, etc.)

Bug Investigation - "figure out why X happens", "this is broken"

• Reproduce → trace root cause → propose fix
• For cross-repo bugs, consider per-repo task breakdowns

Technical Exploration - "can we do X?", "is this possible?", "figure out how to"

• Feasibility testing with proof-of-concept scripts
• Document what works AND what doesn't

Design Research - "explore the API", "gather context", "design alternatives"

• Understand systems and constraints before building
• Compare alternatives, document trade-offs
• Include visual artifacts (mockups, screenshots) when relevant
• For iterative decisions, use numbered "Design Questions" (DQ1, DQ2...) to structure review

Best Practices

• Use uv with inline dependencies for standalone scripts; for scripts importing local project code, use python directly (or uv run python if env not activated)
• Use subagents for parallel exploration to save context
• Write small scripts to explore APIs interactively
• Generate figures/diagrams and reference inline in markdown
• For web servers: npx serve -p 8080 --cors --no-clipboard &
• For screenshots: use Playwright MCP for web, Qt's grab() for GUI
• For external package API review: clone to scratch/repos/ for direct source access

Important: Scratch is Gitignored

The scratch/ directory is in .gitignore and will NOT be committed.

• NEVER delete anything from scratch - it doesn't need cleanup
• When distilling findings into PRs, include all relevant info inline
• Copy key findings, code, and data directly into PR descriptions
• PRs must be self-contained; don't reference scratch files

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