[Bot] Update dependencies #4440

Job	Run time
Linters (mypy, flake8, etc.)	51s
Test cibuildwheel building pyodide wheels	5m 22s
Get qemu emulated architectures	11s
Test on ubuntu-latest (3.13)	39m 21s
Test on windows-latest (3.13)	43m 29s
Test on macos-13 (3.13)	22m 38s
Test on macos-14 (3.13)	16m 30s
Test on ubuntu-latest (3.8)	41m 50s
Test Linux aarch64 using qemu	25m 41s
Test Linux armv7l using qemu	8m 55s
Test Linux ppc64le using qemu	17m 25s
Test Linux s390x using qemu	19m 12s
	4h 1m 25s

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