Jerome Kelleher

Nice. Do you think it's the long old edges that are causing the problem, or more recent ones that are closely associated with the sweep?

Edge plot is definitely showing it's picking something up re the sweep. When you look closely there's also these odd curves in there, where the ends of edges seem to...

Interesting! Possible explanation for why previous attempts at iteration didn't seem to work?

I like it, let's file it as a1.0 feature?

Good point. We want to follow sgkit, no point in thinking any harder than that.

Would it be simpler to assume that there is *always* an individual and site mask, and just try to preserve the old API with those imposed? From tsinfer's perspective, we...

I think this is a nice pattern we could adopt here for the general iteration: https://github.com/pystatgen/vcf-zarr-publication/blob/a01de00e36d0918a7e47fb2f8c6b3a4fd810eb66/src/zarr_afdist.py#L110 So, for iterating over haplotypes we'd do: ```python # Use zarr arrays to get...

This is surprising - is this because of the pytest fixtures doing something unexpected with the environment? We definitely don't want fixtures based on the installed version. I'm not generally...

I'm sure we have an order preserving iterator lying around the place somewhere - ping me if you start implementing this and I'll dig.

Just a note here that the SgkitSample data is a temporary way to let use use data in sgkit format internally, without breaking too much code. We're not going to...