Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Types of changes:

• Added for new features.
• Changed for changes in existing functionality.
• Deprecated for soon-to-be removed features.
• Removed for now removed features.
• Fixed for any bug fixes.
• Security in case of vulnerabilities.

[1.1.3] - (Unreleased)

[1.1.2] - (2025-09-29)

• Fix symmetry correction factor in the acceptance probability for MCMC sampling. (#78)

[1.1.1] - (2025-09-29)

• Yield per network instead of returning all in one list. (#77)
• Update github workflow pytest to use variable ubuntu version per python version. (#77)

[1.1.0] - (2024-07-15)

• Improve navigability of docs. (#64)

[1.0.5] - (2024-05-15)

• Rerelease because of failed pypi upload.

[1.0.4] - (2024-05-15)

• Fixed main example from the documentation. (#42)
• Cleaned up Heath network generator. (#48)
• Added more context and description of PhyloX to the JOSS paper. (#52)
• More robust Newick parser: allow empty properties. (#55)
• Add docstrings for LGT generator and for from_cherry_picking_sequence. (#60)
• Fix and test Newick input for HybridizationProblem. (#61)
• Fix bug in HybridizationProblem with lengths due to caching and degree-2 roots. (#62)

[1.0.3] - (2024-01-20)

Changed

• ReadTheDocs requirements, so that it builds again.

[1.0.2] - (2024-01-20)

Changed

• Github action for pypi release

[1.0.1] - (2024-01-20)

Changed

• Version number, for first official release

[0.0.7] - (2024-01-20)

Added

• Heustics for rearrangement move sequence calculations. (#35)
• Exact methods for rearrangement distance computation. (#37)
• JOSS article. (#39)

Changed

• Release action that also creates a github release, but only when a tag is added to the commit. (#41)

[0.0.6] - (2023-08-09)

Added

• Parsers to and from newick. (#30)
• Random methods with seed. (#34, #16)

Changed

• Licence to BSD-3-Clause to align with networkx. (#32)

[0.0.5] - (2023-07-24)

Fixed

• Automatic pypi release when pushing to release FIX.

[0.0.4] - (2023-07-24)

Fixed

• Automatic pypi release when pushing to release.

[0.0.3] - (2023-07-22)

Added

• Network properties methods: b2_balance, count_cherries_and_reticulated_cherries and blob_properties. (#11)
• Tree-child-sequence functions. (#12)
• Usage of NetworkX referenced in README. (#14)
• Cherry picking hybridization workflow works again, including tests. (#15)
• Start documentation using sphinx. (#18)
• ReadtheDocs config. (#21)
• CI/CD release. (#22)

Changed

• Cleaned up generators: beta-splitting trees, add_edges, caterpillar, balanced tree, lgt, zods, random tree-child sequence. (#14)
• Add lots of docstrings for sphinx autosummary. (#18)

Fixed

• Invalid horizontal moves generated by Move.random_move. (#18)
• Bug in Move.is_type: all moves are of type MoveType.ALL. (#18)
• Implementation of apply_move for VMIN and VPLU, change the _reticulation_number, also fixes the mcmc network generator. (#18)

[0.0.2] - (2023-06-19)

Added

• Release and version tag explanation. (#3)
• Automated tests. (#4)

Changed

• Run black and isort. (#4)

[0.0.1] - (2023-06-18)

Changed

• cleaned up DiNetwork class.
• cleaned up basic rearrangement methods.
• cleaned up isomorphism testing.
• cleand up checking for classes, including some cherry-picking methods.

Added

• Migrated messy old code to this repo.
• Automorphism count: count_automorphisms.
• tests for DiNetwork, network classes, rearrangement moves, isomorphism checking, mcmc network generation.
• configuration of pytest with --cov.