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tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
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MacOS ARM wheels packages broken #2285

Closed jeromekelleher closed 2 months ago

jeromekelleher commented 4 months ago

Getting this error when I run on ARM mac in upstream CI:

Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/__init__.py:28: in <module>
27
    from msprime._msprime import (
28
E   ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/msprime/_msprime.cpython-311-darwin.so, 0x0002): symbol not found in flat namespace '_gsl_rng_default'

It looks like this is basically a duplicate of https://github.com/brentp/cyvcf2/issues/305

We should probably push out a release with the numpy < 2 version out ASAP anyway, so good to get this sorted.

I guess the question is whether we should try to tag the current code, or we do a quick maintenance release from a branch which backports the minimal packaging changes to the last release? I feel like there's a good few changes under the hood after happening, and it's a bit premature to release the smc_k code (even as undocumented). What do you think @GertjanBisschop?

GertjanBisschop commented 4 months ago

Agreed @jeromekelleher. It would be good to give the smc_k code some more time for any potential bugs to pop up.

The binary wheels action has been broken since #2277. Error due to delocate package not being able to deal with different parameter values for different architectures (arm64, x86_64). Are these two separate issues?

jeromekelleher commented 4 months ago

I think it's probably the same issue. Should be an easy fix with new macos-14 runner.

jeromekelleher commented 2 months ago

Assuming this is fixed in recent release