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Use Python 3 compatible stderr logging in Cython #663

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Run time

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Job	Run time
py-3.9 lib-7.1 macos-14	5m 31s
style	23s
py-3.12 lib-7.1 ubuntu-24.04	8m 22s
py-pypy3.10 lib-7.1 ubuntu-24.04	8m 2s
py-3.9 lib-7.1 windows-latest	4m 12s
	26m 30s