make random state argument handling more consistent #166
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ilia-kats
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Aug 14, 2025
ilia-kats
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- always default to non-None random_state (consistent within muon and with scanpy)
- fix condition before setting random state in .tl.leiden (closes random_state=0 does not set seed in muon.tl.leiden, either a bug or unclear documentation #154)
ilan-gold
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Oct 10, 2025
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How is this not a breaking change for reproducibility given that you're changing the default? If you didn't set the random seed by default now in each of these, you're setting it every time now to 0. I think handling random state this way is a separate issue
- always default to non-None random_state (consistent within muon and with scanpy) - fix condition before setting random state in .tl.leiden (closes scverse#154)
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We already weren't reproducible before, unless someone set their global random seed at the very beginning of the analysis, which very few people do. I would think this improves reproducibility. But I guess we can defer that change to muon 0.2 or something, with an explicit warning in the release notes. |
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Up to you! If the goal is to just "fix the issue" I think checking |
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