fix: fix modulatity inconsistency by using Weighted_Adjacency directly#4113
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fix: fix modulatity inconsistency by using Weighted_Adjacency directly#4113flying-sheep wants to merge 2 commits intomainfrom
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Comparison: https://github.com/scverse/scanpy/compare/6af627e3de1d7ee2468ea717f6b965bc4a492d89..a89d635b78223c14ccb423b20f84115f4da301bc More details: https://github.com/scverse/scanpy/pull/4113/checks?check_run_id=75040758121 |
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OK wild, I didn’t expect this to be slower wtf. Maybe just a fluke? /edit: tried the new Python 3.15 profiler from (for
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As pointed out by @jpintar,
sc._utils.get_igraph_from_adjacency(..., directed=False)created duplicate edges. This version switches to the upstream API directly which doesn’t do that, resulting in extremely small differences in connectivity scores compared to before.If we see some performance gain, I think it’s worth the early breakage. I think scanpy 1.13 will have a few smaller breaking changes anyway …
sc.tl.leidenandsc.metrics.modularityleads to modularity mismatch #4099