GaugeFixer

GaugeFixer is a lightweight Python package that allows interpretation of the parameters of linear models for sequence-function relationships by removing unconstrained degrees of freedom in their values, an operation known as "fixing the gauge".

Installation

Create a new python environment with conda and activate it

conda create -n gaugefixer python=3.10
conda activate gauge

Users

Install the latest stable from PyPI using the pip package manager

pip install gaugefixer

Online documentation is available at readthedocs

Developers

Download the lastest version from GitHub

git clone https://github.com/jbkinney/gaugefixer.git

and install the package in development model

pip install -e gaugefixer

Run tests with:

pytest test 

To build the documentation of the package:

cd docs
pip install -r requirements.txt
bash build_docs.sh

License

See the LICENSE file for details.

Cite GaugeFixer

Carlos Martí-Gómez, David M. McCandlish, Justin B. Kinney (2025). GaugeFixer: Removing unconstrained degrees of freedom in sequence-function relationships. In preparation.