[Bot] Update dependencies (#2040) #4461

Job	Run time
Linters (mypy, flake8, etc.)	1m 38s
Get qemu emulated architectures	11s
Test cibuildwheel building pyodide wheels	5m 20s
Test on ubuntu-latest (3.13)	38m 42s
Test on windows-latest (3.13)	44m 28s
Test on macos-13 (3.13)	20m 0s
Test on macos-14 (3.13)	14m 29s
Test on ubuntu-latest (3.8)	38m 46s
Test Linux aarch64 using qemu	25m 38s
Test Linux armv7l using qemu	8m 57s
Test Linux ppc64le using qemu	17m 17s
Test Linux s390x using qemu	18m 43s
	3h 54m 9s

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