fix: support uv 0.4.10+ on Linux and update dependencies #4375

Job	Run time
Linters (mypy, flake8, etc.)	52s
Get qemu emulated architectures	10s
Test cibuildwheel building pyodide wheels	5m 22s
Test on ubuntu-latest (3.12)	40m 44s
Test on windows-latest (3.12)	45m 20s
Test on macos-13 (3.12)	21m 56s
Test on macos-14 (3.12)	13m 50s
Test on ubuntu-latest (3.8)	39m 14s
Test Linux aarch64 using qemu	25m 22s
Test Linux ppc64le using qemu	17m 48s
Test Linux s390x using qemu	19m 18s
	3h 49m 56s

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