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Maintenance and minor feature release

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@jeromekelleher jeromekelleher released this 30 Oct 16:42
· 3 commits to main since this release

Maintenance

  • Add support and wheels for Python 3.15
  • Require Python >= 3.12

Features

  • CLI commands that load a tree sequence now read from stdin when the input path argument is omitted.
  • The returned object from variant.counts() and variant.frequencies() now stores alleles in the order defined in variant.alleles.
  • If top-level metadata is large, then repeatedly accessing it can be costly, so now it throws a warning if the metadata is more than 200Kb and it is accessed more than 20 times alerting the user to this possibility (both constants are modifiable, however).
  • TreeSequences and TableCollections now have a metadata_size property, returning their size in bytes.

Bugfixes

  • Update to kastore C version 2.1.3 to include file security fix
  • TableCollection.delete_older now checks table integrity first, raising an error for invalid node or mutation references instead of reading out of bounds