biahub-uv.md

Plan: Migrate biahub packaging from setuptools to uv

Goal

Convert biahub from setuptools to uv as the package manager. Single package — no workspaces.

Changes

1. Replace build system in pyproject.toml

• Replace [build-system] from setuptools to hatchling (uv's default)
• Remove [tool.setuptools] and [tool.setuptools.dynamic] sections
• Set a static version or use hatch-vcs for versioning
• Keep all existing dependencies, scripts, optional-dependencies unchanged

2. Add uv-specific configuration

• Add [tool.uv] section if needed (e.g., for git dependency overrides)
• Handle git dependencies (stitch, waveorder) — may need [tool.uv.sources] for these

3. Generate lockfile

• Run uv lock to generate uv.lock
• Add uv.lock to version control

4. Verify

uv sync --all-extras
biahub --help
pytest tests/

Notes

• No directory moves — biahub/ package stays where it is
• All imports unchanged
• Click CLI entry point unchanged
• Existing settings/ YAML configs unchanged