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tskit-dev / tsinfer

Infer a tree sequence from genetic variation data.
GNU General Public License v3.0
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Upgrade actions, build with numpy2 #936

Closed benjeffery closed 4 months ago

benjeffery commented 4 months ago

We need numpy<2 for tests here due to numba so I think the solution is to build with numpy2, then test with 1.x.

benjeffery commented 4 months ago

Had to add another conda channel to get cbgen on 3.12. This doesn't have windows though, so skipping that test combo.

jeromekelleher commented 4 months ago

channel to get cbgen on 3.12.

Do we need cbgen? We should only need the minimal sgkit install, not any of the IO packages.

benjeffery commented 4 months ago

channel to get cbgen on 3.12.

Do we need cbgen? We should only need the minimal sgkit install, not any of the IO packages.

If we skip sgkit in the conda install and do it by pip that might be possible. I don't see how to skip the IO packages with conda.

jeromekelleher commented 4 months ago

That seems preferable