Update phykit requirement from >=2.0.1 to >=2.1.5

[dependabot]

Updates the requirements on phykit to permit the latest version.

Changelog

Sourced from phykit's changelog.

PhyKIT 2.1.0 Release Notes

Overview

This release focuses on significant performance improvements across PhyKIT's computationally intensive functions, along with important bug fixes for tree operations.

Key Performance Improvements

Multiprocessing Support

The following functions now utilize multiprocessing for dramatic speedups on multi-core systems:

• Patristic distances: Up to 8x faster for large trees
• Pairwise identity: 5-10x faster with NumPy vectorization
• Polytomy test: Parallel tree processing
• LB Score: Efficient parallel processing for large datasets
• Bipartition support statistics: Concurrent bipartition processing
• Sum of pairs score: Vectorized calculations
• Saturation analysis: Parallel distance calculations
• Hidden paralogy check: Parallel clade processing
• Covarying evolutionary rates: Parallel tree pair analysis

Caching and Memory Optimizations

• Tree reading with LRU cache avoids re-parsing the same files
• Distance matrix caching in patristic distances
• Tree pruning cache in polytomy test
• Streaming file I/O for concatenation operations (reduced memory usage)
• Efficient set operations using frozensets

Additional Optimizations

• Pickle-based fast tree copying for NNI operations (6x faster)
• NumPy vectorization for alignment operations
• Batch processing for large datasets
• Progress indicators (tqdm) for long-running operations

Important Bug Fixes

• Tree caching side effects: Fixed issue where tree modifications would persist across function calls
• Spurious sequence detection: Corrected to use only terminal branches for median calculation
• DNA threader: Fixed NumPy array broadcasting issues
• Tree operations: Fixed branch_length_multiplier, collapse_branches, and other functions that were modifying cached trees
• Test infrastructure: Fixed missing sys.argv patches and standardized exit codes

Installation

pip install --upgrade phykit==2.1.0

Compatibility

• Fully backward compatible with PhyKIT 2.0.x
• Expanded Python support: Now supports Python 3.9, 3.10, 3.11, 3.12, and 3.13
• All existing scripts and pipelines will continue to work
• Tested on macOS, Linux, and Windows

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