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[MRG] update gather implementations for LCA and SBT to use thresholding #843

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merged 10 commits into from Jan 14, 2020

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ctb commented Jan 14, 2020

This is for optimization/performance improvement purposes; ref #838.

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@ctb ctb changed the title [WIP] update gather implementations for LCA and SBT to use thresholding [MRG] update gather implementations for LCA and SBT to use thresholding Jan 14, 2020
ctb added 4 commits Jan 14, 2020
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ctb commented Jan 14, 2020

My main comment after this experience is that we need some tests to check that threshold_bp is being passed in properly to both LCA and SBT gather... or maybe generically for Index objects...

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Codecov Report

❗️ No coverage uploaded for pull request base (master@654bf42). Click here to learn what that means.
The diff coverage is 100%.

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@@            Coverage Diff            @@
##             master     #843   +/-   ##
=========================================
  Coverage          ?   79.34%           
=========================================
  Files             ?       83           
  Lines             ?     7026           
  Branches          ?      469           
=========================================
  Hits              ?     5575           
  Misses            ?     1151           
  Partials          ?      300
Flag Coverage Δ
#pytests 89.91% <100%> (?)
#rusttests 48.71% <ø> (?)
Impacted Files Coverage Δ
sourmash/lca/lca_utils.py 96.61% <100%> (ø)

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sourmash/lca/lca_utils.py Outdated Show resolved Hide resolved
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luizirber commented Jan 14, 2020

Big improvements for LCA search and gather, not much difference for SBTs... (This PR is the gather on the X-axis)

LCA:
image
image

SBT:
image
image

ctb added 2 commits Jan 14, 2020
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ctb commented Jan 14, 2020

I think I've addressed all the review issues?

@luizirber luizirber merged commit 4bd286b into master Jan 14, 2020
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@luizirber luizirber deleted the optimize/gather branch Jan 14, 2020
@luizirber luizirber added this to the 3.1 milestone Jan 14, 2020
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