# Installation

**Gunz-CM** is a high-performance library for genomic contact matrix manipulation. It requires Python 3.11 or higher.

## Standard Installation

Install the library directly from GitHub:

```bash
pip install git+https://github.com/sXperfect/gunz-cm.git
```

## Recommended: Mamba/Conda Environment

We recommend using a dedicated `mamba` environment to ensure high-performance linear algebra libraries (like OpenBLAS or MKL) are correctly linked:

```bash
# Create the environment
mamba create -n gunz-cm python=3.11

# Activate it
mamba activate gunz-cm

# Install in editable mode for research
pip install -e .
```

## Optional Dependencies

Genomics data processing often requires specialized file formats and visualization tools. Install them using the following tags:

*   **`[conv]`**: Support for `.hic` to `.cool` conversion.
*   **`[vis]`**: Matplotlib, Plotly, and Interactive widgets.
*   **`[all]`**: Recommended for full research capability.

```bash
pip install "gunz-cm[all]"
```

## System Dependencies

Some components (like `pybedtools`) require C++ compilers and compression libraries:

*   **Ubuntu/Debian:** `sudo apt-get install g++ libcurl4-openssl-dev`