Installation

Requirements

Python 3.11.x (tested with 3.11.7)
UV (recommended) or Conda

Option 1: UV (Recommended - Fastest ⚡)

Install UV

# macOS/Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

# Windows
powershell -c "irm https://astral.sh/uv/install.ps1 | iex"

Setup SIMBA

Installation takes approximately 2-5 minutes:

# Clone the repository
git clone https://github.com/bittremieux-lab/simba.git
cd simba

# Create virtual environment and install dependencies
uv sync

# Activate the environment
source .venv/bin/activate  # macOS/Linux
# or
.venv\Scripts\activate     # Windows

For Jupyter notebooks

# Install notebook dependencies
uv sync --extra notebooks

# Register the kernel
python -m ipykernel install --user --name=simba --display-name="SIMBA (UV)"

To use notebooks in VS Code:

Open any .ipynb file in the notebooks/ folder
Click “Select Kernel” in the top-right corner
Choose “SIMBA (UV)” or “Python 3.11 (.venv: venv)”
If the kernel doesn’t appear, reload VS Code window (Cmd+Shift+P → “Developer: Reload Window”)

Option 2: Conda (Alternative)

# Create and activate environment
conda env create -f environment.yml
conda activate simba

# Install the module
pip install -e .

Note for macOS users:

brew install xz

Verify Installation

simba --version