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Switch to leiden

Open flying-sheep opened this issue 5 years ago • 3 comments

see https://github.com/theislab/scanpy/issues/1283#issuecomment-645269898

@LuckyMD we should change the tutorials instead of going back, because louvain is deprecated:

This package has been superseded by the leidenalg package and will no longer be maintained. Please upgrade to the leidenalg package.

flying-sheep avatar Dec 04 '20 10:12 flying-sheep

I don't mind changing the defaults in the tutorials, but I think there's also a louvain function in the leidenalg package if you don't want to change defaults just yet, but just package reliance.

LuckyMD avatar Dec 04 '20 12:12 LuckyMD

Hmm, if we’re going to change something anyway, shouldn’t we just go with the better option?

flying-sheep avatar Dec 04 '20 18:12 flying-sheep

I think that's fine... we could however still wrap sc.tl.louvain to use the leidenalg implementation so that people's code still works.

LuckyMD avatar Dec 04 '20 18:12 LuckyMD