MLImpute

Simple tool to run Machine Learning based imputation techniques

Prerequisites

• pixi (v0.5+)
• NVIDIA-based GPU hardware with CUDA (v12+)
  • For gpu environment only (see next section)
• Linux or macOS OS environment preferred

Setup

Retrieve project code

git clone https://github.com/maize-genetics/MLImpute.git
cd MLImpute

Option A (preferred) - set up virtual environment (pixi)

# For CPU only
pixi install

# For Linux + GPU machines
pixi install --environment gpu

Option B - set up virtual environment (conda)

conda env create -f environment.yml

Run (CLI tool)

Conda:

python impute.py --input <input_file> --output <output_file> --model <imputation_method>

Pixi:

pixi run -- python impute.py --input <input_file> --output <output_file> --model <imputation_method>

Development (GUI app - experimental)

Prerequisites

• Node.js
• Rust

Run Tauri dev container

npm run tauri dev

Testing

Run python unit tests with HTML output (CLI)

pytest --cov=src --cov-report=term-missing --cov-report=html