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[MRG] fix gather against signatures with abundances #1519

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merged 2 commits into from
May 13, 2021
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@ctb ctb commented May 13, 2021

The refactoring of gather in #1370 introduced a bug where matching signatures were not flattened, which caused gather to exit with a TypeError exception. This PR provides a fix and a test.

Fixes #1518

@taylorreiter ready for review!

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codecov bot commented May 13, 2021

Codecov Report

Merging #1519 (336d336) into latest (1633121) will increase coverage by 5.03%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           latest    #1519      +/-   ##
==========================================
+ Coverage   90.24%   95.27%   +5.03%     
==========================================
  Files         126       99      -27     
  Lines       21104    17409    -3695     
  Branches     1589     1589              
==========================================
- Hits        19046    16587    -2459     
+ Misses       1829      593    -1236     
  Partials      229      229              
Flag Coverage Δ
python 95.27% <100.00%> (+<0.01%) ⬆️
rust ?

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

Impacted Files Coverage Δ
src/sourmash/search.py 96.24% <100.00%> (ø)
tests/test_sourmash.py 99.72% <100.00%> (+<0.01%) ⬆️
src/core/tests/test.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/index/linear.rs
src/core/src/errors.rs
src/core/src/wasm.rs
src/core/src/signature.rs
src/core/src/ffi/mod.rs
src/core/src/index/sbt/mhbt.rs
... and 19 more

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Woo! Thanks, LGTM. Can confirm, works on real signatures that have abundances.

@ctb ctb merged commit 3b8793c into latest May 13, 2021
@ctb ctb deleted the fix/gather_abund branch May 13, 2021 18:55
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Gather prefetch in 4.0.1 returns TypeError: can only intersect flat MinHash objects
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