Changelog#

Version History#

Split decomposition ([Bandelt and Dress, 1992]) for distance matrices:
- isolation_index() — computes the isolation index of a bipartition with respect to a distance matrix.
- split_decomposition() — canonical decomposition d = d^0 + Σ α_S δ_S, returning a WeightedSplitSystem of all d-splits and the split-prime residual as a DistanceMatrix.
- Both functions are re-exported from phylozoo.core.distance.
New classification functions in phylozoo.core.distance.classifications:
- is_tree_metric() — four-point condition check (Numba-accelerated, \(O(n^4)\)).
- is_totally_decomposable() — checks whether the split-prime residual is zero.
distances_from_splitsystem() ↔ split_decomposition() round-trip tests and tree_from_splitsystem() ↔ induced_splits() round-trip tests.
Documentation: new Split Decomposition section in the distance manual; updated Algorithms section in the split-system manual; new api/core/distance entry for the decomposition module. BibTeX entry Bandelt1992 added to bibliography.bib.

_check_kalmanson_conditions moved from a nested closure inside is_kalmanson() to a module-level @njit function, consistent with the other Numba helpers in the module.

New phylozoo.core.triplet module providing Triplet, TripletProfile, and TripletProfileSet for working with rooted three-taxon trees (characterised by a trivial 1|2 split a|bc or by an unresolved 3-taxon star). All three classes are re-exported from the top-level phylozoo namespace.
New displayed_triplets() derivation on DirectedPhyNetwork, returning a TripletProfileSet aggregated over the displayed trees.
Manual chapter Triplets (overview + per-class pages) and an api/core/triplets API page.
Manual page Parallel Execution and api/utils/parallel API page documenting phylozoo.utils.parallel as the standard interface for parallel execution in PhyloZoo. No functions currently expose a parallel parameter; the module is the intended way to introduce parallelization in future implementations.
New CI GitHub Actions workflow (.github/workflows/ci.yml) running pytest (Python 3.10 and 3.11), ruff, black --check, and mypy on every push to master and every pull request. See the Testing Guide for details. A CI badge has been added to the project README.

ParallelBackend class docstring restructured to plain prose (the enum members are now described inline rather than in a NumPy-style Attributes section) to avoid duplicate Sphinx object descriptions.
Black, Ruff, and Mypy fixes have been made thoughout the codebase.

phylozoo.core.distance.operations (and the entire operations.py file). The Traveling Salesman Problem solvers (optimal_tsp_tour, approximate_tsp_tour) have been removed, together with the corresponding manual section and API entry. Their implementation is now part of the dependent package physquirrel.
phylozoo.core.quartet.qdistance.quartet_distance_with_partition and its documentation in the Quartet Profile Sets manual page.

Fixed newick parsing branch length order: it must be after the hybrid marker, not before.