v0.4.0

What's New

Updated documentation with new file structure and TOML-first workflow.

Install

curl -fsSL https://github.com/eloualiche/ResearchSetup/releases/latest/download/install.py | uv run --script -

File Structure

_tools/
├── scripts/
│   └── link_json.py           # Main linker script
└── nickel/
    ├── link_contracts.ncl     # Type contracts
    └── links_template.ncl     # Your config (edit this)

Usage

# Edit your links
vim _tools/nickel/links_template.ncl

# Export and link
nickel export --format toml _tools/nickel/links_template.ncl > links.toml
uv run _tools/scripts/link_json.py links.toml

See README for Snakemake integration examples.