AI Assistants

PhysioTwin4D is developed with AI coding assistants in the loop (Claude Code, Codex, Cursor, and others). Two repository conventions make that work well.

Repository Instructions

AGENTS.md holds the role-based guidance that applies across every assistant; CLAUDE.md adds Claude-specific instructions. Role subagents live in .agents/agents/ and slash-command skills in .agents/skills/. Read those before hand-writing a prompt that repeats project conventions.

graphify

The recommended way to explore this codebase with an AI assistant is the graphify knowledge graph in graphify-out/, which indexes god nodes, community structure, and cross-file relationships.

A graph query returns a scoped subgraph. That is dramatically smaller and more accurate than pasting whole files or raw grep output into a prompt, which matters here: the source tree spans segmentation, registration, statistical modeling, and USD export, and the relevant call chain for a question is rarely in one file.

graphify query "how does a labelmap become a USD stage?"
graphify path "WorkflowConvertImageToVTK" "ConvertVTKToUSD"
graphify explain "anatomy taxonomy"

Recommended use:

  • Ask graphify query before searching manually, whenever graphify-out/graph.json exists.

  • Use graphify path to see how two classes relate, and graphify explain to focus on a single concept.

  • Browse graphify-out/wiki/index.md for broad navigation; read graphify-out/GRAPH_REPORT.md only for whole-architecture review.

  • Run graphify update . after changing code. The update is AST-only, so it costs no API calls, and it keeps assistants from resolving symbols against a stale graph.

See Also