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qiime2 / q2-diversity-lib

BSD 3-Clause "New" or "Revised" License
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Alpha diversity as sparse or on smaller dense tables #36

Closed wasade closed 2 years ago

wasade commented 3 years ago

Compute alpha metrics either directly from sparse data, or operate on partitions to minimize memory use on dense conversions.

This PR is important as, at present, it takes 40GB to compute observed features on a table that contains 0.2GB of nonzero data.

wasade commented 3 years ago

Sorry about the failures, thought I had run all tests but skipped that rather important step. New commit momentarily

lizgehret commented 2 years ago

Hey @wasade looks like there were some merge conflicts - I went ahead and fixed those, since it was quick and easy. Pending successful CI, this should be in good shape! I'll do a final review after all tests pass.

wasade commented 2 years ago

Thanks!

On Thu, Aug 18, 2022, 16:28 Liz Gehret @.***> wrote:

Hey @wasade https://github.com/wasade looks like there were some merge conflicts - I went ahead and fixed those, since it was quick and easy. Pending successful CI, this should be in good shape! I'll do a final review after all tests pass.

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