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v0.5.0

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@AADavin AADavin released this 24 Jul 20:35

Added

  • Opt-in parallelism for the unordered-genome and sequence engines (parallel= in Python,
    --parallel on the CLI): a separate, worker-count-invariant engine that evolves independent units
    (gene families, gene trees) across processes. It covers D/T/L/O with uniform/distance transfer;
    a driven or clade-based transfer_to falls back to the serial engine (loudly). Also stream_to=
    to write each family straight to disk for the many-families regime. The serial path is the default
    and is unchanged. (#233)
  • Clades transfer_to rule + the Between kernel — weight horizontal transfers by the donor's
    and the recipient's named clade, so transfer can be steered to run between two clades rather
    than within them (a topological rule, sibling of "distance"). Name a clade by a few of its tips or
    a node id. The trait-driven form is mod.DrivenBy(trait, Between({...})). (#235)

Changed

  • Faster nucleotide sequence runs at lower memory: a run-wide CDF cache and lazy genome assembly,
    plus batched decoding and a streaming FASTA writer. (#234)