History

0.3.0

  • Added --weighted_edgelist flag to enable generation of a single weighted edge list with cosine similarity values as a third column, instead of multiple cutoff-based edge lists. When this flag is set, only the first cutoff value from --ppi_cutoffs is used (defaults to parent cutoff if not specified), and the resulting edge list includes edge weights that can be utilized by HiDeF for hierarchy generation.

    • Added test suite for verifying weighted edgelist behavior.

0.2.5 (2025-10-08)

  • Remove leading spaces from name of hierarchy.

0.2.4 (2025-05-15)

  • Updated to PEP 517 compliant build system

0.2.3 (2025-03-19)

  • Update requirements versions

  • Increase timeout for cmd run

  • Fix ‘k’ argument type

0.2.2 (2024-11-25)

  • Added default argument for password.

0.2.1 (2024-11-08)

  • Fixed types of arguments.

0.2.0 (2024-10-16)

  • Added the --bootstrap_edges flag, which allows specifying the percentage of edges to be randomly removed from each PPI network (across networks at different PPI cutoffs).

  • Added a style for proteins specified as bait.

  • Refactored code and expose more methods for hierarchy generation from edgelists.

0.1.0 (2024-09-06)

  • First release on PyPI.