Use them when contributing to napari-chatgpt, including setup, installation, testing, code checks, formatting, building, cleaning, and publishing.

They provide the background and repeatable commands needed to develop and check the plugin. This makes it clearer how to install it, run tests, format code, lint, build, and publish it.

How royerlab/napari-chatgpt configures Claude Code

Q: What is napari-chatgpt CLAUDE.md?

Project instructions for napari-chatgpt, a napari plugin that adds an AI agent for interactive image processing and analysis. They describe the project, its dependencies, and its Makefile commands.

Reuse

Borrowing it

Nothing to install: this file belongs to royerlab/napari-chatgpt. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file

curl -O https://raw.githubusercontent.com/royerlab/napari-chatgpt/main/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/royerlab/napari-chatgpt

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/royerlab/napari-chatgpt/claude-md/github.svg)](https://agentmods.dev/instructions/royerlab/napari-chatgpt/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/royerlab/napari-chatgpt/claude-md"><img src="https://agentmods.dev/badge/instructions/royerlab/napari-chatgpt/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/royerlab/napari-chatgpt/claude-md"><img src="https://agentmods.dev/badge/instructions/royerlab/napari-chatgpt/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 1,077 This file is loaded in full into every session.

When invoked 1,077 The same file — it is already loaded in full.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.01077	$0.01077
Opus 5.5	$0.00431	$0.00431
Sonnet 5.5	$0.00215	$0.00215
Haiku 4.5	$0.00108	$0.00108

Measured 2mo ago against content hash b8aa0b0c3338, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

napari-chatgpt CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

CLAUDE.md · 99 lines

How it starts

The opening of the file, as written. The whole thing — 99 lines — stays where its author put it; the contents beside it link to each section on GitHub.

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

napari-chatgpt is a napari plugin providing Omega, an LLM-powered autonomous agent for interactive image processing and analysis. It uses the LiteMind library to support multiple LLM providers (OpenAI, Anthropic, Gemini) and enables conversational image analysis within the napari viewer.

Publication: https://doi.org/10.1038/s41592-024-02310-w

Build & Development Commands

The project uses a Makefile for common development tasks:

make help          # Show all available commands
make setup         # Install with all dev dependencies + pre-commit hooks
make install       # Install with minimal dependencies
make install-dev   # Install with test dependencies only
make test          # Run all tests
make test-cov      # Run tests with coverage report
make check         # Run all code checks (format + lint)
make format        # Format code with black and isort
make lint          # Run flake8 linter
make pre-commit    # Run all pre-commit hooks
make build         # Build package
make clean         # Clean build artifacts
make publish       # Bump version to today's date, tag, and push (triggers PyPI)
make publish-patch # Same-day patch release (e.g., 2025.2.1 -> 2025.2.1.1)

# Documentation (requires Claude Code CLI for readme/wiki updates)
make update-readme      # Review & update README.md relative to codebase
make update-screenshots # Regenerate widget screenshots for wiki (uses hatch docs env)
make update-wiki        # Review & update wiki pages relative to codebase

Hatch Environments

default: Main development environment with all project dependencies
hatch-test: Testing environment with pytest, cellpose, stardist, tensorflow
docs: Documentation environment for screenshot generation (hatch run docs:screenshots)

Manual Commands

# Run a single test file
pytest src/napari_chatgpt/llm/api_keys/tests/api_key_vault_test.py -v

# Run tests via tox (multi-environment)
tox
tox -e py311-linux  # specific environment

Read the full file on GitHub · 99 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

2mo ago First seen · 99 lines · 1,077 tokens per session scan A b8aa0b0c3338

Subscribe to this mod's changes

napari-chatgpt CLAUDE.md is an instructions file published in the GitHub repository royerlab/napari-chatgpt (306 stars, last pushed 8mo ago), licensed BSD-3-Clause. It adds 1,077 tokens to every session, about $0.0043 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

napari-chatgpt CLAUDE.md next to 6 instructions from other repositories
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napari-chatgpt: Instructions file for Claude Code