v0.8.0
Changed
-
The genome level's first resolution is now
family, notunordered. 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(…)GenomesResultFamilyGenomesResultUnorderedGenomeFamilyGenomegenomes.unordered(…)genomes.family(…)zombi2.genomes.unorderedzombi2.genomes.family--resolution unordered, and the same value in a--paramsfile--resolution familyRenaming the result class also removes an asymmetry: the first resolution returned the unprefixed
GenomesResultwhile its two siblings carried a prefix, which read as a default plus two variants
rather than three resolutions of one model. The run log'sresolutionrow and the run-completion
summary now sayfamily; 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 nowfamily_names=, onsimulate_genomes_family,simulate_genomes_orderedand
genomes.family(…);zombi2 joint --familiesis likewise now--family-names. The argument takes a
list of names and always did — the attribute it fills has beenresult.family_namesall along — so
input and output now agree, andinitial_families=100(a count) no longer reads as a sibling of the
name list beside it. (#245)