[Bot] Update dependencies #4515

Job	Run time
Linters (mypy, flake8, etc.)	1m 4s
Test cibuildwheel building pyodide wheels	5m 23s
Get qemu emulated architectures	12s
Test on ubuntu-latest (3.13)	44m 10s
Test on windows-latest (3.13)	45m 16s
Test on macos-13 (3.13)	23m 32s
Test on macos-14 (3.13)	12m 0s
Test on ubuntu-latest (3.8)	42m 31s
Test Linux aarch64 using qemu	27m 26s
Test Linux armv7l using qemu	9m 20s
Test Linux ppc64le using qemu	18m 3s
Test Linux s390x using qemu	19m 33s
	4h 8m 30s

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