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Repository Guidelines

Project Structure & Module Organization

nnInteractive/ is the main Python package for promptable 3D medical-image segmentation.

  • nnInteractive/inference/: local sessions, remote client support, server code, and the CVPR 2025 baseline wrapper
  • nnInteractive/interaction/: interaction primitives such as point prompts
  • nnInteractive/utils/: bbox, crop, morphology, checkpoint, OS, and inference helpers
  • nnInteractive/trainer/: lightweight checkpoint reconstruction stub
  • nnInteractive/supervoxel/: optional SAM/SAM2 supervoxel subproject with separate packaging and CLIs

Top-level docs include readme.md, SERVER_CLIENT.md, and API_CHANGES_v2.md. Documentation images live in imgs/.

Build, Test, and Development Commands

The repo builds two distributions sharing the nnInteractive namespace: nninteractive-client (torch-free remote client, source under client/) and nnInteractive (full stack, root; depends on the client). See "Two-distribution layout" in CLAUDE.md.

  • pip install -e ./client && pip install -e .: editable dev install (client first, then the full stack which depends on it).
  • pip install -e ".[dev]": add Black, Ruff, and pre-commit tooling.
  • pip install nninteractive-client: install only the lightweight torch-free remote client (no torch / nnU-Net). pip install nnInteractive installs the full stack and pulls the client in automatically.
  • nninteractive-server --model-dir /path/to/checkpoint --fold all --host 0.0.0.0 --port 1527 --device cuda:0: run the inference server.
  • black nnInteractive/: format Python code; the pre-commit hook uses line length 120.
  • ruff check nnInteractive/ --fix: lint and apply safe fixes.
  • codespell --skip='.git,*.pdf,*.svg': check spelling in source and docs.
  • pre-commit run --all-files: run configured hooks before submitting changes.

For supervoxel work, install both layers: cd nnInteractive/supervoxel/src/sam2 && pip install -e ., then cd ../.. && pip install -e ..

Coding Style & Naming Conventions

Use Python 3.10+ for the main package and Python 3.9+ in nnInteractive/supervoxel/. Follow Black formatting with 4-space indentation and 120-character lines. Prefer typed, explicit public inference/session APIs. Use snake_case for modules, functions, and variables; PascalCase for classes; and UPPER_SNAKE_CASE for constants.

Testing Guidelines

There is no dedicated automated test suite. Validate changes with the narrowest reproducible smoke path:

  • local inference through nnInteractiveInferenceSession using the readme.md flow
  • remote inference by starting nninteractive-server, checking /healthz, and exercising nnInteractiveRemoteInferenceSession
  • supervoxel CLI execution on a small sample volume when touching nnInteractive/supervoxel/

Also run formatting, linting, and spelling checks for touched areas.

Commit & Pull Request Guidelines

Recent history uses short, imperative subjects such as disable compile on cpu, reduce threshold for blosc2, and bump version. Keep commits focused and include body context for behavior changes, compatibility breaks, or dependency assumptions.

Pull requests should state what changed, why it changed, exact validation commands, related issues or integrations, and any GPU, PyTorch, checkpoint, server/client, or API-compatibility assumptions. Do not commit local model checkpoints, API keys, or generated large outputs.