Fix hanging CI due to old dependencies and numpy 2.0 #4107

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Run time

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Job	Run time
lint and style checks	1m 19s
test (windows-latest, 3.9, false)	26m 35s
test (windows-latest, 3.10, false)	38m 55s
test (windows-latest, 3.11, false)	31m 23s
test (ubuntu-latest, 3.9, false)	22m 11s
test (ubuntu-latest, 3.10, false)	15m 36s
test (ubuntu-latest, 3.11, false)	17m 23s
test (macos-latest, 3.9, false)	30m 10s
test (macos-latest, 3.10, false)	32m 25s
test (macos-latest, 3.11, false)	31m 54s
test (3.11, ubuntu-latest, true)	25m 51s
coveralls	13s
	4h 33m 55s