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@hyanwong hyanwong released this 30 Mar 15:04
· 11 commits to main since this release
0.2.2
6c8bd3e
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Learn about vigilant mode.

Features

  • An allow_unary flag (False by default) has been added to all methods.

  • A set_metadata flag has been added so that node and mutation metadata can be
    omitted, saved (default), or overwritten even if this requires changing the schema.

  • An environment variable TSDATE_ENABLE_NUMBA_CACHE can be set to cache JIT
    compiled code, speeding up loading time (useful when testing).

  • The time taken for running tsdate is now recorded in the provenance data

  • Historical samples (sample nodes with time > 0) are now allowed in the
    tree sequence.

Documentation

  • Various fixes in documentation, including documenting returned fits.

Breaking changes

  • The return_posteriors argument has been removed and replaced with return_fit.
    An instance of one of two previously internal classes, ExpectationPropagation
    and BeliefPropagation, are now returned when return_fit=True, and posteriors can
    be obtained using fit.node_posteriors().

  • Topology-only dating (setting mutation_rate=None) has been removed for tree sequences
    of more than one tree, as tests have found that span-weighting the conditional coalescent
    causes substantial bias.

  • The trim_telomeres parameter in the tsdate.preprocess_ts() function has been renamed
    to erase_flanks, to match tinfer.preprocess(). The previous name is kept as a
    deprecated alias.

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