[Bot] Update dependencies (#2051) #4474

Job	Run time
Linters (mypy, flake8, etc.)	50s
Test cibuildwheel building pyodide wheels	5m 24s
Get qemu emulated architectures	22s
Test on ubuntu-latest (3.13)	40m 46s
Test on windows-latest (3.13)	44m 55s
Test on macos-13 (3.13)	22m 42s
Test on macos-14 (3.13)	13m 21s
Test on ubuntu-latest (3.8)	44m 31s
Test Linux aarch64 using qemu	27m 14s
Test Linux armv7l using qemu	9m 2s
Test Linux ppc64le using qemu	18m 1s
Test Linux s390x using qemu	19m 33s
	4h 6m 41s

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