README.md

Python Bindings for FlatGFA

This is a Python interface for the FlatGFA library, which provides an efficient representation for pangenomic variation graphs in the Graphical Fragment Assembly (GFA) format.

You can install it from PyPI:

$ pip install flatgfa

Then, read the API documentation for details about what it can do so far.

Development

To build this library, first install Maturin:

$ pipx install maturin

Next, we'll build and install the Python library in our virtualenv. Starting from the repository root:

$ uv venv  # Unless you already created the virtualenv.
$ uv pip install pip  # Maturin depends on pip.
$ source .venv/bin/activate
$ cd flatgfa-py
$ maturin develop

Now the flatgfa module is available to Python programs. Try our example:

$ python example.py

Or run the tests:

$ uv pip install pytest
$ pytest