coverage: 98.286% (+0.07%) from 98.212%
when pulling bf317ff on jeromekelleher:finalise-tskit
into 6eb88ed on sgkit-dev:main.

I think this is nearly ready to go. There's some details about how we deal with coordinate systems between tskit and VCZ which I'm going to punt on, but I think we should be able to handle the vast majority of inputs well with this.

I've added an initial framework for the Python API, just documenting a single function bio2zarr.tskit.convert. I think this is a good start (and will add the same for vcf when I get a chance). I had to skip some of the intersphinx linking for now, as the latest version of the docs don't seem to be live for tskit.

Can .convert() (or perhaps another function) return a handle to the vcz object, for use in tsinfer? So that we can do

tsinfer.infer(tsinfer.VariantData(returned_handle, ancestral_state="ancestral_allele"))

No, that's out of scope because would greatly complicate the semantics (should the returned object be a Zarr hierarchy, or an Xarray dataset? Should it be in read-only mode?). Bio2zarr just deals with the on-disk formats, not providing python APIs for working with them. Bio2zarr will always create an on-disk representation, so returning a handle would just be abstracting the details of where the temporary files are kept.

I think tsinfer should probably write a wrapper which creates a temporary directory and does the conversion so that you can use it like this:

with tsinfer.VariantData.from_tree_sequence(ts) as data:
    tsinfer.infer(data)

That'll take care of a lot of the messiness.

Ah, OK. I had gathered that bio2zarr might also create in-memory representations, which I use quite a lot. But yes, a wrapper would be fine, I guess, assuming temporary directories etc are available.