ploidy being set as 1

[mufernando]

see cc6c9cd

because we can have more than one subpopulation per tree sequence and we want to calculate some stats to each subpop individually, I need to subset my genotype matrix.
it is possible to get the indices belonging to a population for each haploid genome using tskit with ts.samples(population=i), but not for diploid genomes. If I were to treat the genotype matrix with ploidy=2, I wouldn't be able to do the subsetting this way.

ploidy should not matter for the stats we are using so far (pi and dxy), but could be an issue with other stats.

[petrelharp]

Well, let's see:

ind_pops = np.array([i.population for i in ts.individuals()])

gives you the population for each individual - is that what you need?

[mufernando]

solved. see commit 3800681