v0.3.0

Changes

New file structure

_tools/
├── scripts/
│   └── link_json.py
└── nickel/
    ├── link_contracts.ncl
    └── links_template.ncl

Improvements

• link_json.py: Refactored with dataclass, better error handling, cleaner output
• Removed link.py wrapper: Use Snakemake or run commands directly
• TOML-first: Examples now show TOML export (cleaner than JSON)

Install

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

Usage

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

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

Or with Snakemake - see README for examples.