[python] Partition sparse matrix reads in tiledbsoma.io.to_anndata
#3328
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johnkerl
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tiledbsoma.io.to_anndata
johnkerl
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Nov 17, 2024
johnkerl
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Nov 17, 2024
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Thanks @bkmartinjr -- this is a tour de force.
Looks good to me 👀 -wise; also, I ran to_anndata on local disk, S3, and cloud-hosted, comparing main to this branch, on EC2 Ubuntu m5.4xlarge, as well as on my M1 Mac. (Several variables there, all test-driven.) (Re Mac: I have a general feeling, more from the R side than the Python side admittedly, that 'threads are a little different' on MacOS so this was worth some interactive/hands-on/eyes-on experimenting.) I saw a speedup at a solid 2X at 100K cells, with all storage backends. I'll try 300K runs later; I won't report back here unless I see something surprising (which I don't expect.)
cc @nguyenv for another pair of eyes.
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Partition reads to sparse matrices in the
soma.io.to_anndatacode path. This change is solely for performance, and has no functional impact.#3345 [sc-59595]