Skip to content

v0.8.0

Choose a tag to compare

@AADavin AADavin released this 26 Jul 19:33

Changed

  • The genome level's first resolution is now family, not unordered. It is the default
    resolution and the first thing a new user meets, and it was named for the feature it lacks rather
    than for what it is. The other two resolutions keep their names, and the model itself is untouched —
    the three still share one engine, one rate grammar and one event log. This is a breaking rename
    with no deprecation aliases
    :

    was is
    simulate_genomes_unordered(…) simulate_genomes_family(…)
    GenomesResult FamilyGenomesResult
    UnorderedGenome FamilyGenome
    genomes.unordered(…) genomes.family(…)
    zombi2.genomes.unordered zombi2.genomes.family
    --resolution unordered, and the same value in a --params file --resolution family

    Renaming the result class also removes an asymmetry: the first resolution returned the unprefixed
    GenomesResult while its two siblings carried a prefix, which read as a default plus two variants
    rather than three resolutions of one model. The run log's resolution row and the run-completion
    summary now say family; no output filename, directory or column header changes, so nothing that
    reads a run's tables needs updating. Chapter 4 is now Genomes I: gene families. (#245)

  • families= is now family_names=, on simulate_genomes_family, simulate_genomes_ordered and
    genomes.family(…); zombi2 joint --families is likewise now --family-names. The argument takes a
    list of names and always did — the attribute it fills has been result.family_names all along — so
    input and output now agree, and initial_families=100 (a count) no longer reads as a sibling of the
    name list beside it. (#245)