Changelog

All notable changes to NeKo are documented here. The format follows Keep a Changelog and the project adheres to Semantic Versioning.

---

[1.1.0] – 2025

Added

• Branching NetworkHistory with automatic state snapshots and HTML/SVG rendering
• NetworkState class for point-in-time network snapshots
• BFS / DFS graph traversal algorithms in neko.core.algorithms
• connect_to_upstream_nodes method
• Performance benchmarking scripts

Changed

• Interaction lookup tables pre-processed for O(1) neighbour queries
• connect_nodes signature updated for clarity
• pandas pinned to 2.2.2 for stability

Fixed

• Edge colouring bug in NetworkVisualizer.vis_comparison
• Handling of complex node names containing colons

---

[1.0.0] – 2024

Added

• Initial public release on PyPI as nekomata
• Core Network class with add_node, add_edge, remove_node
• connect_nodes, connect_subgroup, connect_component, complete_connection
• connect_genes_to_phenotype via Gene Ontology
• NetworkVisualizer with Graphviz and yFiles backends
• Exports class: BNet and SIF formats
• Ontology class for GO-term and tissue mapping
• 11 tutorial notebooks
• Sphinx documentation hosted on GitHub Pages

---

[0.x] – Pre-release

Internal development versions at Institut Curie / Sysbio-Curie.