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sgkit-dev / sgkit

Scalable genetics toolkit
https://sgkit-dev.github.io/sgkit
Apache License 2.0
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Minor fixes for Numpy 2 #1228

Closed timothymillar closed 5 months ago

timothymillar commented 5 months ago

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 https://github.com/brentp/cyvcf2/issues/307.

timothymillar commented 5 months ago

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

timothymillar commented 5 months ago

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?

jeromekelleher commented 5 months ago

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

tomwhite commented 5 months ago

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 commented 5 months ago

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