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Update supported python versions and bring CI back to green #448

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Run time

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Job	Run time
others (binder)	42s
Python 3.13	3m 1s
others (manifest)	11s
Python 3.11	2m 5s
others (docs)	44s
Python 3.10	2m 6s
Python 3.12	2m 1s
	10m 50s