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CLAUDE.md

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

Project Overview

This is the BIOP team's extension catalog for QuPath (an open-source bioimage analysis application). The catalog is a catalog.json file that QuPath's built-in extension manager reads to let users discover, install, and manage BIOP extensions.

Repository Structure

  • catalog.json — The catalog file consumed by QuPath. This is the primary artifact of the repo. It follows the schema defined by qupath/extension-catalog-model.
  • biop-catalog-generator.groovy — A Groovy script meant to be run inside QuPath's script editor to regenerate catalog.json. Before running, the savingFolder path at the top must be updated to your local checkout.
  • .github/workflows/validate-catalog.yml — CI workflow that validates catalog.json against the extension_catalog_model Python package on push to main and on PRs.

Catalog JSON Schema

Each extension entry has: name, description, author, homepage, starred, and a list of releases. Each release has:

  • name — version tag (e.g. "v0.12.0")
  • main_url — download URL for the extension JAR or ZIP
  • required_dependency_urls / optional_dependency_urls — Maven or GitHub URLs for dependency JARs
  • version_range — { min, max, excludes } specifying compatible QuPath versions

Common Tasks

Validate the catalog locally

pip install git+https://github.com/qupath/extension-catalog-model.git
python -c "from extension_catalog_model.model import *; Catalog.model_validate_json(open('catalog.json').read())"

Regenerate catalog.json from the Groovy script

Open biop-catalog-generator.groovy in QuPath's script editor (requires QuPath v0.7.0+), update the savingFolder variable to point to your local catalog.json path, and run it.

Key Conventions

  • Extensions target QuPath version ranges: v0.6.0–v0.6.0, v0.6.0–v0.7.0, or v0.7.0–v0.7.0. When adding a new release, pick the appropriate range.
  • Some extensions (Warpy, ABBA) have shared Maven dependencies (imglib2, imglib2-realtransform, jitk-tps, ejml, jama) listed in required_dependency_urls. Keep dependency versions consistent across extensions that share them.
  • Simple extensions (Cellpose, Spotiflow, BIOP) ship as self-contained ZIPs or JARs with no extra dependencies.
  • ABBA bundles Warpy as a required dependency — when Warpy's version changes, ABBA's dependency URL must be updated to match.
  • Version tags use a v prefix in the catalog (e.g. "v0.12.0"), but some older Warpy/ABBA download URLs omit the v in the path segment.