Tsdate

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.