Installation guide

Prerequisites

Before installing annnet, please ensure you have the following tools installed:

Tool	Minimum Version	Description	Installation Guide
Python	3.10	Programming language	Install Python 3
uv	—	Python packaging & dependency manager	Install uv
git	—	Version control system	Install git

Tip

If you are missing any of those pre-requisites, please follow the installation guide in each resource before you continue.

Checking prerequisites

Verify that everything is installed by running:

python --version   # Should be 3.10 or higher
uv --version
git --version

Installation

From PyPI

pip install annnet

# Optional extras
pip install "annnet[networkx,igraph]"   # backends
pip install "annnet[io]"                # JSON/Parquet/Zarr, Excel, Narwhals
pip install "annnet[all]"               # common extras (graph‑tool not on PyPI)

Graph‑tool is supported if installed via your OS/package manager.

From source (editable dev install)

This package is under active development. To try the latest, clone and install in editable mode so changes reflect immediately without reinstalling.

Clone the repository:

git clone https://github.com/saezlab/annnet.git

Navigate into the project directory:
```
cd annnet
```
Install the package in editable mode using uv:
```
uv pip install -e .
```

You can now start using annnet in your Python environment. Any changes you make to the source code will take effect immediately.