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Maintenance and bugfix release

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@jeromekelleher jeromekelleher released this 03 Feb 15:43
· 9 commits to main since this release

0.1.7 2026-02-03

Bug fixes

  • Fix issue with 0-dimensional arrays (#437)
  • Fix issue with pandas 3.x (required in plink code; #439)

Breaking changes

  • Require NumPy 2 (#426)
  • Require tskit >= 1.0.
  • The default isolated_as_missing behaviour for tskit conversion now follows
    tskit's default (currently True). To get the previous behaviour, create a
    model mapping using ts.map_to_vcf_model(isolated_as_missing=False) and pass
    it via the model_mapping parameter (or use tskit2zarr convert --isolated-as-ancestral).
  • The contig_id and isolated_as_missing parameters to
    bio2zarr.tskit.convert have been removed; set these via
    tskit.TreeSequence.map_to_vcf_model and pass the returned mapping via the
    model_mapping parameter.

Maintenance

  • Add support for Python 3.13