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[MRG] fix lca summarize to support general collections for queries #2107

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merged 6 commits into from
Jul 8, 2022

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ctb
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@ctb ctb commented Jul 7, 2022

This PR:

  • adds a test for lca classify with a query zipfile
  • fixes lca summarize to support any kind of query, not just JSON
  • renames 3 tests in test_lca.py from test_lca_summarize to test_summarize for consistency's sake.

Addresses #1959.

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codecov bot commented Jul 7, 2022

Codecov Report

Merging #2107 (31fcf79) into latest (d212087) will increase coverage by 7.38%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2107      +/-   ##
==========================================
+ Coverage   84.30%   91.69%   +7.38%     
==========================================
  Files         130       99      -31     
  Lines       15280    11004    -4276     
  Branches     2171     2171              
==========================================
- Hits        12882    10090    -2792     
+ Misses       2095      611    -1484     
  Partials      303      303              
Flag Coverage Δ
python 91.69% <100.00%> (ø)
rust ?

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

Impacted Files Coverage Δ
src/sourmash/lca/command_summarize.py 87.82% <100.00%> (ø)
src/core/src/ffi/storage.rs
src/core/src/ffi/index/mod.rs
src/core/src/encodings.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/ffi/mod.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/index/sbt/mod.rs
src/core/src/from.rs
src/core/tests/minhash.rs
... and 22 more

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@bluegenes bluegenes left a comment

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this lgtm!

@ctb ctb merged commit a2da84f into latest Jul 8, 2022
@ctb ctb deleted the fix/lca_query branch July 8, 2022 23:46
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2 participants