Changelog

Changelog#

[1.1.12] - 2025-05-26#

  • Made cyvcf2 an optional dependency via fastdfe[vcf]

  • Improved x-axis labels for discretized DFE plots

  • Added support for introducing ancestral misidentification in Spectrum

  • Added unnormalized Watterson’s theta property

[1.1.11] - 2025-03-30#

  • Support for passing alternative optimizer to BaseInference and JointInference.

[1.1.10] - 2025-03-25#

  • Allow for probabilistic polarization when parsing SFS by looking at ancestral allele probability VCF info tag

  • Allow the transition/transversion ratio in the K2SubstitutionModel to be fixed to the value observed in the data

  • Adjust LRTs to account for parameters near boundaries. The resulting p-values are similar but tend to be somewhat lower

  • Extend ExistingOutgroupFiltration so that number of missing outgroups can be specified

  • Add RandomStratification and ContigFiltration classes

[1.1.9] - 2025-01-01#

  • Add simulation class for simulating SFS data with known DFE

[1.1.8] - 2024-08-14#

  • Update cyvcf2 dependency to fix broken wheel for Mac ARM (see issue)

  • Fix minor problem with remote files when disabling file caching

[1.1.7] - 2024-05-31#

  • Implement serialization of maximum likelihood ancestral annotation to allow for later inspection of results

  • Improved ancestral allele info tag information for site where annotation was not possible

[1.1.6] - 2024-04-20#

  • Lazy-load some modules to allow faster initial loading

[1.1.5] - 2024-03-12#

  • Support for Python 3.12

  • Exclude large files from distribution to speed up installation in R

[1.1.4] - 2024-03-05#

  • Lazy-load some modules to allow faster initial loading

[1.1.3] - 2023-12-27#

  • Implement probabilistic subsampling for ancestral allele annotation

[1.1.2] - 2023-11-27#

  • Improved bootstrapping

  • Set allow_divergence flag to false by default which as it has the potential to bias the SFS

[1.1.1] - 2023-11-21#

  • Probabilistic parsing of SFS

  • Functionality to subsample already existing SFS to lower sample size

  • Support for number of target sites for ancestral allele annotation

  • Improved parallelization when bootstrapping

  • New plotting functionalities

  • Improved logging

[1.1.0] - 2023-10-10#

  • Improved parsing utilities

  • Ancestral allele annotation with outgroups

[1.0.0] - 2023-08-12#

  • First stable release

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