SAWNERGY: A Python framework for dynamic residue-interaction networks and walk-based embeddings from molecular dynamics simulations

This paper was submitted to the Journal of Open Source Software in December of 2025. Pre-review began in January of 2026, and due to the new requirements (https://blog.joss.theoj.org/2026/01/preparing-joss-for-a-generative-ai-future) that were released right before the pre-review but after the submission, we need to make some additional changes and re-submit.