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Bump tolerance for skeletonization test #1658

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Run time

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Job	Run time
Documentation	2m 55s
Mypy	2m 55s
Pylint	3m 4s
Examples	12m 20s
Pytest Linux	44m 32s
Pytest with SymEngine	46m 22s
Pytest Mac	28m 38s
Ruff	4s
Typos	6s
	2h 20m 56s