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[MRG] Speed-up SeqToHashes() #1938

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merged 2 commits into from
Apr 10, 2022
Merged

[MRG] Speed-up SeqToHashes() #1938

merged 2 commits into from
Apr 10, 2022

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@mr-eyes mr-eyes commented Apr 10, 2022 •
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@mr-eyes mr-eyes added the rust label Apr 10, 2022
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codecov bot commented Apr 10, 2022 •
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Codecov Report

Merging #1938 (3954d5d) into latest (93cbd3a) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           latest    #1938   +/-   ##
=======================================
  Coverage   82.93%   82.93%           
=======================================
  Files         125      125           
  Lines       13755    13755           
  Branches     1877     1877           
=======================================
  Hits        11408    11408           
  Misses       2075     2075           
  Partials      272      272
Flag Coverage Δ
python 90.96% <ø> (ø)
rust 65.13% <100.00%> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/core/src/signature.rs 67.98% <100.00%> (ø)

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@mr-eyes mr-eyes changed the title use VecDeque instead of Vec [MRG] Speedup SeqToHashes() Apr 10, 2022
@mr-eyes mr-eyes changed the title [MRG] Speedup SeqToHashes() [MRG] Speed-up SeqToHashes() Apr 10, 2022
@mr-eyes mr-eyes mentioned this pull request Apr 10, 2022
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mr-eyes commented Apr 10, 2022

Ready for review/merge @sourmash-bio/devs

@mr-eyes mr-eyes requested a review from luizirber April 10, 2022 09:52
ctb
ctb approved these changes Apr 10, 2022
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awesome ;). works for me!

@ctb ctb merged commit d1d8397 into latest Apr 10, 2022
@ctb ctb deleted the mo/speedup_translate branch April 10, 2022 12:45
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This is AMAZING, @mr-eyes!

@luizirber luizirber mentioned this pull request Apr 10, 2022
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luizirber added a commit that referenced this pull request Apr 10, 2022
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Benchmarks for seq_to_hashes in protein mode (#1944)
01119a2 
Add some rust benchmarks for seq_to_hashes in protein mode, 
so we don't regress after the awesome progress in #1938 

Other fixes:
- Default python in `asv` to the one where `asv` is running
  (fixes #1937)
- Make `ComputeParameters` initliazer use explicit keywords
  (and fix `__repr__`)
- make keyword args in ComputeParameters required
@mr-eyes mr-eyes restored the mo/speedup_translate branch April 12, 2022 07:14
@mr-eyes mr-eyes deleted the mo/speedup_translate branch April 12, 2022 07:14
@mr-eyes mr-eyes mentioned this pull request Apr 12, 2022
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@ctb ctb mentioned this pull request Apr 21, 2022
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@ctb ctb ctb approved these changes

@luizirber luizirber Awaiting requested review from luizirber

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is sourmash sketch translate really slow on long sequences?
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@mr-eyes @luizirber @ctb