Run all tox python3

Add check for overlapping points in neurites #873

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Run time

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Job	Run time
build (3.8)	2m 9s
build (3.9)	1m 58s
build (3.10)	2m 26s
build (3.11)	1m 31s
build (3.12)	1m 32s
	9m 36s