MRG: update to code for forthcoming sourmash release #467
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This was referenced Oct 11, 2024
luizirber
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Oct 12, 2024
ctb
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Ready for review! Please let me manage merging tho 😭 . |
…water into update_sourmash_latest
luizirber
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Oct 15, 2024
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…ather` bug around `scaled`. (#3342) This PR does five things: First, it swaps the implementation of `KmerMinHash::downsample_max_hash` with `KmerMinHash::downsample_scaled`, and the same for `KmerMinHashBTree`. Previously a call to `downsample_scaled` calculated the right `max_hash` from `scaled`, then called `downsample_max_hash`, which then converted `max_hash` back to `scaled`. This reverses the logic so that (slightly) less work is done and, more importantly, the code is a bit more straightforward. Second, it changes the `downsample_*` functions so that they do not downsample when no downsampling is needed. As part of this the method signatures are changed to take an object, rather than a reference. This lets the functions return an unmodified `KmerMinHash` when no downsampling is needed. Third, it turns out the `downsample_*` functions didn't check to make sure that the new `scaled` value was larger than the old one, i.e. they didn't prevent upsampling. That check was added and a new error, `CannotUpsampleScaled`, was added to sourmash core. Fourth, this uncovered a bug in `RevIndex::gather` where the query was downsampled to the match, even when the match was lower scaled. This PR rejiggers the code so that downsampling is done appropriately in the `gather` and `calculate_gather_stats`. Since `RevIndex::gather` isn't used in the the sourmash CLI, the bug only presented in the test suite and in the branchwater plugin; see sourmash-bio/sourmash_plugin_branchwater#468 and sourmash-bio/sourmash_plugin_branchwater#467, where a fastmultigather test had to be fixed because of the incorrect scaled values output by `RevIndex::gather`. Fifth, it includes #3348 from @luizirber, which adds a `Signature::try_into()` to `KmerMinHash` to support the elimination of some clones. Because of the method signature change for the `downsample_*` functions, the sourmash-core version needs to be bumped to a new major version, 0.16.0. It's been a fun journey! 😅 Fixes #3343 Some notes on further changes and performance implications: As a consequence of the `RevIndex::gather` changes, redundant downsampling has to be done in `RevIndex::gather` and `calculate_gather_stats`, unless we want to change the method signature of `calculate_gather_stats`. I decided the PR was big enough that I didn't want to do that in addition. It should not affect most use cases where `scaled` is the same, and we will see if it results in any slowdowns over in the branchwater plugin. See #3196 for an issue on all of this. We could also just insist that the query scaled is the one to pay attention to, per #2951. This would simplify the code in Python-land as well. Overall, the performance implications of this PR are not clear. Previously downsampling was being done even when it wasn't needed, so this may speed things up quite a lot for our typical use case! On the other hand, redundant downsampling will happen in cases where there are scaled mismatches. We just need to benchmark it, I think. Some preliminary benchmarking reported in sourmash-bio/sourmash_plugin_branchwater#430 (comment) suggests that fastgather is now much more memory effficient 🎉 so that's good! TODO: - [x] resolve the scaled mismatch stuff. do we return an `Err` or what if the downsampling can't be performed? - [x] update PR description - [x] add more tests for downsampling, and maybe for gather - [x] play with this code over in the branchwater plugin too! sourmash-bio/sourmash_plugin_branchwater#467 --------- Co-authored-by: Luiz Irber <[email protected]>
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This PR is a standing PR to update to the forthcoming sourmash release, probably 0.16.0, which will hopefully include:
HashFunctionssourmash#3344 (not projected to cause any problems ;)KmerMinHash; fixRevIndex::gatherbug aroundscaled. sourmash#3342 (will need changes here ;))Fixes #468
TODO:
KmerMinHash; fixRevIndex::gatherbug aroundscaled. sourmash#3342 and this PR. (It probably won't be, but we could use a test anyway!)KmerMinHash; fixRevIndex::gatherbug aroundscaled. sourmash#3342