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scverse / scanpy-tutorials

Scanpy Tutorials.
https://scanpy-tutorials.readthedocs.io/
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(feat): dask tutorial #92

Closed ilan-gold closed 8 months ago

ilan-gold commented 8 months ago

Ran into a little issue of exactly how to display this functionality because i/o from disk starting from a sparse representation is non-trivial (hence the various hacks) and also the scanpy data is stored in a very old format so this does not lend itself well to writing a helpful/usable tutorial whose behavior people can mimic.....

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ivirshup commented 8 months ago

@ilan-gold, did you ever end up trying the slurm schedueler? I'm not sure I want to recommend it if it's something we haven't tried.

ilan-gold commented 8 months ago

@ivirshup Fair point, we can remove it then.

ilan-gold commented 8 months ago

@ivirshup Why skip filtering now that the obsp is not being read in?

ivirshup commented 8 months ago

Why skip filtering now that the obsp is not being read in?

It doesn't really need it mainly. Can try it.

I'm realizing we should probably prioritize dask support in sc.get.aggregate and then use that in the sc.tl.rank_genes_groups, as well as the dot-plot and heat map functions.

noqa comment added because of: https://github.com/astral-sh/ruff/issues/10357

ilan-gold commented 8 months ago

I will fix some spelling and such as well.