pyslim 1.1.0 released

[Peter Ralph]

Hello, all - I've just released version 1.1.0 of pyslim, which is provided to go along with SLiM v5.0 (sorry for the delay). It's now available to be installed via pip, conda-forge, etcetera. You'll need to use this version with SLiM v5 because of the changes to the metadata in the tree sequence. Of particular note are the following:

If you're doing simulations of a chromosome in which not everyone has the same ploidy, then you'll need to be aware of the "vacant" nodes: tldr; you'll want to "remove" them for downstream analysis. This is similar to the previous problem that recapitation would wrongly try to simulate back from null genomes (and produce an error).

There is now a method, set_slim_state, that will "reset the time" so that you can load the tree sequence into SLiM at some previous time (with a given set of individuals alive).

​And, individual_parents is now deprecated, as it's better to get this information from the parents attribute of the individuals directly. (I've not yet written example documentation of how to do this, if you'd like to give that a try, let me know!)

See the CHANGELOG for additional details: https://github.com/tskit-dev/pyslim/blob/main/CHANGELOG.rst

If you run into any issues, let me know, as always.

Happy slimulating,

  Peter