v1.1.0

Added

• Added the representative attribute to the Gene class and the is_isoform keyword argument to the add_gene method of the
  Genome class, allowing for the management of gene isoforms.

• Added the synteny module to initiate a SyntenyEngine object written in Rust to accelerate the analysis and minimize memory
  overhead.

Changed

• calculate_synteny_ratio and get_window are now implemented in Rust.

• Use disjoint set union (DSU) instead of BFS search for finding clusters after refinement.

• Use ThreadPool instead of Pool to minimize memory overhead.

• Sort the final refined clusters to ensure consistent results across runs.

Removed

• SOG, attribute and Refine method from lib.orthogroup.Orthogroup class.

• compare_gene_sets functions from lib.orthogroup module.

Fixed

• Resolved an issue identified in #2, specifically a bug within the compare_gene_sets function in the orthogroup module. (incorporated into lib.rs)

• Fixed the visualization script that was previously unable to correctly label and color orthogroups.

v1.0.0

Added

• Translate OrthoRefine logic in Python.
• Multiprocessing support for refinement steps.
• Companion script to visualize the refined orthologs.