pantree-setup

name	pantree-setup
description	Install, validate, repair, or explain the Pantree development and runtime environment. Use for uv setup, Python compatibility, dependency problems, package installation, or initial command and test validation.

Pantree setup

Use this skill for environment work. Use pantree-usage for GFA-to-VCF, simplification, consolidation, or format questions.

Install the locked environment from the repository root:

uv sync

Validate the package and command surface:

uv run python -c "import pantree"
uv run pantree --help
uv run pytest

Pantree supports Python 3.10 or newer. Prefer the checked-in uv.lock; do not replace the project environment with ad hoc pip installation unless requested.

When a fixture or dependency under Dropbox is zero bytes, treat it as potentially unsynced. Tell the user which file needs syncing rather than regenerating or overwriting it.

For a focused smoke check, run uv run pytest tests/test_imports.py tests/test_cli.py. Run the full suite before declaring an environment repair complete.