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Contributing to lif-figure

Development Setup

git clone https://github.com/half-adder/lif-figure.git
cd lif-figure
uv sync --group dev

To run the tool locally:

uv run lif-figure input.lif --channels "DAPI,GFP,mCherry"

Running Tests

uv run python -m pytest

Linting and Formatting

This project uses Ruff for linting and formatting.

uv run ruff check .        # Check for lint errors
uv run ruff check --fix .  # Auto-fix lint errors
uv run ruff format .       # Format code

VS Code Setup

For the best development experience, install the Ruff extension. The project includes .vscode/settings.json which enables format-on-save.

Project Structure

lif-figure/
├── src/lif_figure/
│   ├── cli.py       # Command-line interface
│   ├── reader.py    # LIF file reading and metadata extraction
│   ├── figure.py    # Matplotlib figure generation
│   └── config.py    # Configuration handling
├── tests/           # Test files
└── docs/            # Documentation

Documentation