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[MRG] Fix selection w/abund and manifest column type conversions #1645

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merged 7 commits into from
Jul 1, 2021

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ctb
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@ctb ctb commented Jun 28, 2021

This PR fixes three issues -

  • signature selection with abundances didn't work for several reasons - select_signatures(...) didn't take an abund keyword arg, and manifest selection didn't either;
  • neither selection technique handled abund, of course!
  • on manifest loading from CSV, the columns were not properly converted to integer/bool appropriately; this was instead done on selection!

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codecov bot commented Jun 28, 2021

Codecov Report

Merging #1645 (a862125) into latest (dcfd973) will increase coverage by 0.00%.
The diff coverage is 87.50%.

Impacted file tree graph

@@           Coverage Diff           @@
##           latest    #1645   +/-   ##
=======================================
  Coverage   81.91%   81.92%           
=======================================
  Files         112      112           
  Lines       11447    11462   +15     
  Branches     1432     1440    +8     
=======================================
+ Hits         9377     9390   +13     
- Misses       1813     1814    +1     
- Partials      257      258    +1     
Flag Coverage Δ
python 89.32% <87.50%> (-0.01%) ⬇️
rust 66.43% <ø> (ø)

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Impacted Files Coverage Δ
src/sourmash/index.py 95.31% <33.33%> (-0.42%) ⬇️
src/sourmash/lca/lca_db.py 91.29% <100.00%> (+0.05%) ⬆️
src/sourmash/manifest.py 90.26% <100.00%> (+0.74%) ⬆️
src/sourmash/sbt.py 82.05% <100.00%> (+0.04%) ⬆️

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ctb commented Jun 28, 2021

Ready for review and merge @sourmash-bio/devs

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lgtm!

@ctb ctb merged commit 21f5e63 into latest Jul 1, 2021
@ctb ctb deleted the fix/manifest_types_and_abund branch July 1, 2021 12:40
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3 participants