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MRG: refactor `calculate_gather_stats` to disallow repeated downsampling #5745

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Run time

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Job	Run time
mamba (ubuntu-latest)	9m 40s
nix (ubuntu-latest)	10m 1s
pixi (ubuntu-latest)	9m 23s
nix (macos-14)	7m 22s
pixi (macos-14)	8m 26s
mamba (macos-14)	7m 33s
	52m 25s