v4.3.0

What's Changed

• Add filtering by reversions to naive sequence, generalize ranking strategy by @willdumm in #130
  • adds new --ranking_strategy argument, which takes a string consisting of a comma-separated list or linear combination of ranking criterion identifiers.
  • deprecates inference arguments --branching_process_ranking_coeff, --ranking_coeffs, and --use_old_mut_parsimony in favor of the new --ranking_strategy argument. These old options will still work but will throw warnings.
  • adds counts of reversions to the naive sequence as a new ranking criterion
  • adds --show_nucleotide_mutations argument, to specify that rendered tree should have nt mut annotations.
  • modifies all ranking criteria so that smaller values are better. Log likelihoods are negated, and referred to as log loss.

Full Changelog: v4.2.2...v4.3.0

v4.2.2

What's Changed

• Handle truncated dnapars outfiles correctly by @willdumm in #129

Full Changelog: v4.2.1...v4.2.2

v4.2.1

What's Changed

• Fix single ranking criterion bug by @willdumm in #128

Full Changelog: v4.2.0...v4.2.1

v4.2.0

What's Changed

• Poisson context likelihood and better cli flexibility by @willdumm in #126

Full Changelog: v4.1.4...v4.2.0

v4.1.4

What's Changed

• Fix ufunc attribute error from numpy.log by @willdumm in #125

Full Changelog: v4.1.3...v4.1.4

v4.1.3

The purpose of this release is to correct the historydag dependency version number. It also updates versioneer.

What's Changed

• Dependency and warning fix and compatibility with Scipy 1.12 by @willdumm in #122

Full Changelog: v4.1.2...v4.1.3

v4.1.2

What's Changed

• fix gap character ambiguity bug by @willdumm in #118

Full Changelog: v4.1.1...v4.1.2

v4.1.1

What's Changed

• Python 3.10, and macOS integration testing by @wsdewitt in #115

Full Changelog: v4.1.0...v4.1.1

v4.1.0

What's Changed

• Colormap enhancements by @wsdewitt in #102
• jumble parameter in mkconfig by @wsdewitt in #103
• Remove S5F contents and mark experimental features by @willdumm in #110
• rename master to main by @willdumm in #112

Full Changelog: v4.0.4...v4.1.0

v4.0.4

Patch release to fix a deprecation error in a historydag API call.

What's Changed

• Add full inference test and remove deprecated mutation model ignore_ualabel call by @willdumm in #97

Full Changelog: v4.0.3...v4.0.4