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How to expose the B-Tree MinHash impl to Python? #1056

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luizirber opened this issue Jun 27, 2020 · 3 comments
Open

How to expose the B-Tree MinHash impl to Python? #1056

luizirber opened this issue Jun 27, 2020 · 3 comments
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@luizirber
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#1045 defaults compute to use the B-Tree impl. Also add a flag in the CLI to choose the Vec one?
The Vec one is better in very limited cases (very small datasets), so I think we don't need the CLI flag.

On the Python API, there are some places where we change the MinHash that (maybe?) could also benefit from the B-Tree impl. Check gather (which modifies the query), for example.

(punted from #1045 (comment))

@ctb
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ctb commented Aug 4, 2022

Started digging into this a little bit, just for fun -

  • KmerMinHashBTree doesn't have a few necessary methods, in particular as_hll, update, and remove_from;
  • SourmashNodegraph.matches(mh) expects a KmerMinHash not a KmerMinHashBTree;
  • the revindex implementation doesn't like KmerMinHashBTree either;

@ctb
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ctb commented Sep 23, 2023

@luizirber might be fun to tie this into your recent rust work, if relevant.

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A lot of this happens in #2728

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