Usage

Installation

# Clone the repository
git clone https://github.com/linum-uqam/linumpy.git
cd linumpy

# Install with uv (recommended)
uv sync

# Or with pip in an existing environment
pip install -e .

For GPU acceleration (CuPy, plus optional PyTorch for BaSiCPy), install the matching CUDA extra:

uv sync --extra gpu          # CUDA 12
uv sync --extra gpu-cuda13   # CUDA 13

See GPU Acceleration for details on the GPU code paths.

Running scripts

All command-line tools are installed as linum_* entry points. List them with:

linum_aip --help

For an inventory of every script, see Command-line scripts (auto-generated from the argparse definitions) or Scripts Reference (curated overview).

Pipelines

For end-to-end processing, use the Nextflow workflows shipped with the repository — see Pipeline Overview and Nextflow Workflows Guide.