Tom White
Tom White
@benjeffery I can't see what could have caused this. To debug you could print a stacktrace for the unaltered code to see which code path causes that line to run...
Thanks for opening this @benjeffery - I was just about to open the same issue! This is a regression - [started on Friday](https://github.com/pystatgen/sgkit/actions/runs/3246811613). I can reproduce locally and I get...
You're right - I was running the wrong cell - I can reproduce it in the notebook now.
From https://github.com/pydata/xarray/releases/tag/v2022.10.0: "This release brings numerous bugfixes, a change in minimum supported versions, and a new scatter plot method for DataArrays."
It's fine to pin xarray on an older version while we address this (if there's no obvious fix) - that would unblock the other issues.
The underlying issue hasn't been fixed (see #1122), so it might be worth reporting upstream @benjeffery?
This seems like a good idea. Best thing is probably to try it out and see if it triggers any failure in the unit tests.
I just realized that the `""` usage is from the spec, https://github.com/pystatgen/vcf-zarr-spec/blob/main/vcf_zarr_spec.md#missing-and-fill-values, so may be harder to change (and also was in the 0.5.0 release I think). @benjeffery it would...
The information in #840 is relevant here, although I would recommend combining the samples into a single VCF first before using sgkit, if possible.
#293 is related