Update dependencies #4431

Job	Run time
Linters (mypy, flake8, etc.)	50s
Test cibuildwheel building pyodide wheels	5m 26s
Get qemu emulated architectures	10s
Test on ubuntu-latest (3.12)	38m 26s
Test on windows-latest (3.12)	42m 12s
Test on macos-13 (3.12)	20m 6s
Test on macos-14 (3.12)	15m 57s
Test on ubuntu-latest (3.8)	40m 17s
Test Linux aarch64 using qemu	25m 29s
Test Linux armv7l using qemu	9m 7s
Test Linux ppc64le using qemu	17m 17s
Test Linux s390x using qemu	19m 26s
	3h 54m 43s

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