New features:
- Added ts.individual_parents(), a way to get the IDs of individual's parents
when both of them are present in the tree sequence. :user:@petrelharp
- Added and documented TSK_INDIVIDUAL_RETAINED flag to reflect the additional
of "retained" individuals in SLiM v3.6. :user:@hyanwong, :user:@petrelharp
Bugfix:
- Modified recaptiate to not error with the current msprime 1.0 alpha release.
Bugfix:
- Making .slim_generation derive from the tree sequence's top-level metadata
had the unanticipated consequence that it could not be modified, which some people were doing. This restores the previous behavior, but in the future, modifying .slim_generation on a tree sequence will be deprecated - instead, this should be modified in the metadata of the TableCollection.
Breaking changes:
- "First generation" individuals no longer need to be retained by SLiM to recapitate, thanks to the "keep_input_roots" argument to simplify (new in tskit 0.3.0). The FIRST_GEN flag and .first_generation_individuals() methods are now deprecated, and if you want these to remain in the tree sequence you must explicitly Remember them. (However, their nodes will remain if necessary for recapitation.) If you wish to simplify an un-recapitated tree sequence you now can, but you must pass keep_input_roots=True. This should only cause breakages if you made explicit use of the first generation individuals, without explicitly Remembering them.
- Information about the tree sequence is now stored in top-level metadata, accessible through ts.metadata['SLiM']. Previous interfaces remain: for instance, ts.slim_generation is now redundant with ts.metadata['SLiM']['generation']. This should not cause breakages, but will cause warnings where none were previously: for instance, pyslim.SlimTreeSequence(msprime.mutate(ts)) may throw a warning because msprime.mutate( ) does not preserve top-level metadata, and so SLiM-relevant information is retrieved from provenance (as in previous file versions).
Notable changes:
- Switched to using tskit native encoding/decoding of metadata via schemas.
- added to conda-forge (@winni2k)
New features:
- added samples_only and population arguments to ts.individuals_alive_at()
- added the ts.slim_time() method
- enabled dumping the reference sequence for nucleotide models
- BUGFIX: if a tree had all first generation individuals removed
(e.g., if it had been simplified) then individuals_alive_at( ) failed.
This is a compatibility release, for the tskit 0.3.0 release.
New features:
- added has_individual_parents, a method to find individuals with all parents are also recorded as individuals
- Provenance handling:
- added the .slim_provenances property to return all SLiM provenance entries
- added the slim_provenance_version and parse_provenance methods to tell if
provenance entries come from SLiM and to parse them
- documentation for recapitation with a nonuniform map by :user:@TeresaPegan
Bug fixes:
- fixed differential time offset for tree sequences saved out in early versus late:
prior to this, mutation_at and nucleotides_at would have been sometimes wrong if the tree sequence was saved out during late
- initialises correctly to work with tskit 0.3.0
Bug fixes:
- checks for the ability to simulate with a discrete recombination map
in the available version of msprime, and sets the default flat recombination map in recapitate appropriately
New features:
- updated to take and output SLiM file version 0.4, which only differs from 0.3
in minor aspects of provenance
New features:
- allows passing in of a recombination map to recapitate (
mufernando) - added first_generation_individuals() function
- defined individual ages for WF ages
- added mutation_at() and fixed up nucleotide_at() functions