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scverse / scanpy-tutorials

Scanpy Tutorials.
https://scanpy-tutorials.readthedocs.io/
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Switch to leiden #34

Open flying-sheep opened 3 years ago

flying-sheep commented 3 years ago

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This package has been superseded by the leidenalg package and will no longer be maintained.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

LuckyMD commented 3 years ago

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.

flying-sheep commented 3 years ago

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

LuckyMD commented 3 years ago

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.