Recapitation - sim_ancestry(), ploidy

[csmcal]

I had a couple questions on recapitation:

1. In using recapitate(), I attempted to pass an argument dictionary:
   recap_kwargs = {'gene_conversion_rate':gc_rate,'gene_conversion_tract_length':gc_tract_len}
   However, this gave an error message:
   line 465, in recapitate recap = msprime.simulate( TypeError: simulate() got an unexpected keyword argument 'gene_conversion_rate'
   So, recapitate is using simulate() instead of sim_ancestry() - is this intended? Should I try to adapt my own function based on sim_ancestry()?

2. Does specifying ploidy matter in recapitation? sim_ancestry() seems to take a default of 2, but I'm not clear

[jeromekelleher]

I think the plan is to release an updated version of pyslim soon that takes advantage of the new msprime 1.0 APIs @csmcal. Until then, the behaviour will be exactly the same as before, even if you have msprime 1.0 installed.

@petrelharp, is this correct?

[petrelharp]

Yep- I hope to do this in the next few weeks.

[csmcal]

Thanks for the help! Apologies for not following the versions/updates accurately