[Bot] Update dependencies #4628

Job	Run time
Linters (mypy, flake8, etc.)	55s
Get qemu emulated architectures	6s
Test cibuildwheel building Pyodide wheels	5m 45s
Test on ubuntu-latest (3.13)	46m 0s
Test on windows-latest (3.13)	45m 37s
Test on macos-13 (3.13)	21m 16s
Test on macos-14 (3.13)	14m 11s
Test on ubuntu-latest (3.8)	46m 52s
Test Linux aarch64 using qemu	27m 9s
Test Linux armv7l using qemu	16m 42s
Test Linux ppc64le using qemu	17m 15s
Test Linux s390x using qemu	19m 27s
	4h 21m 15s

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