[0.2.0] - 2022-11-01
Major feature release adding many new species and models, as well as support for simulating selection via SLiM.
Samples are now specified via population/individual pairs, using species/chromosome ploidy. The old API for specifying haploid samples via population index has been retained, but is deprecated and will be removed at some point (@nspope, #1361).
New genetic maps:
Various improvements and fixes to the documentation and error messaging.
Additions to CLI:
Sample specification has switched from positional and haploid (e.g.
stdpopsim HomSap -d OutOfAfrica_3G09 6 0 10) to named with species-specific ploidy (equivalent to
stdpopsim HomSap -d OutOfAfrica_3G09 YRI:3 CEU:0 CHB:5). Positional sample specification is still supported but will raise a deprecation warning.
Catalog maintenance infrastructure:
[0.1.2] - 2020-05-29
Important bugfix and feature release, recommended for all users.
Significant errors in the HomSap/OutOfAfrica_3G09 and HomSap/OutOfAfrica_2T12 models have been fixed. We recommend repeating any analyses performed using these models. See here for more details on the error in the three population Out of Africa model and analysis of the differences from the correct model.
The recombination rate for AraTha was also off by a factor of 10. We recommend repeating any analyses performed using this species.
Various documentation and citation improvements.
[0.1.1] - 2020-01-02
Bugfix release. Fixes some distribution issues and temporarily removes the PonPyg species.
Temporarily remove the PonPyg species from the catalog to provide time to fix issues with genomes and multi-species models (#365).
[0.1.0] - 2019-12-18