Minor fixes for Numpy 2

[timothymillar]

Fixes #1225

This only fixes a couple of small issues for Numpy 2 compatibility. However, many tests are still failing due to Cython-Numpy 2 compatibility issues. See brentp/cyvcf2#307.

[timothymillar]

Tests now failing with cyvcf2 code: ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

[tomwhite]

LGTM thanks @timothymillar

The cyvcf2 fix is not ready yet so should we merge this now, along with a numpy<2 pin?

[timothymillar]

cyvcf2 and cbgen both have new releases for numpy 2 (the latest cbgen pins to numpy >= 2). But the tests against scikit-allel are still failing. Maybe time to add the scikit-allel test data and drop the dependency?

[tomwhite]

Good to merge now

[jeromekelleher]

Agreed, let's pin to numpy < 2 for now and push out a release?

[tomwhite]

But the tests against scikit-allel are still failing. Maybe time to add the scikit-allel test data and drop the dependency?

I wonder if we need the scikit-allel conversion still? We could deprecate read_scikit_allel_vcfzarr. The VCF reading code is going to be replaced by bio2zarr soon anyway.

Thoughts @jeromekelleher?

[jeromekelleher]

I'm wondering the same, it may be best to just drop direct VCF support soon and be done with it.