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Change variance_threshold default to 0.01 #286

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merged 2 commits into from
Jun 8, 2023

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@shntnu shntnu commented Jun 8, 2023

Description

From: #282

I noticed that variance_threshold always had unique_cut=0.01 as a default, while feature_select later set more strict default unique_cut=0.1, overriding that of variance_threshold.

The threshold of 0.1 is too high; I think we should change the default to 0.01. This might be a breaking change of sorts but this might be the right time to do it (given the upcoming v1.0.0).

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Codecov Report

Merging #286 (ee24fef) into master (182745a) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #286   +/-   ##
=======================================
  Coverage   95.12%   95.12%           
=======================================
  Files          57       57           
  Lines        3057     3057           
=======================================
  Hits         2908     2908           
  Misses        149      149           
Flag Coverage Δ
unittests 95.12% <ø> (ø)

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

Impacted Files Coverage Δ
pycytominer/feature_select.py 94.44% <ø> (ø)
pycytominer/operations/variance_threshold.py 97.05% <ø> (ø)

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@shntnu shntnu marked this pull request as ready for review June 8, 2023 14:10
@shntnu shntnu self-assigned this Jun 8, 2023
@shntnu shntnu requested a review from gwaybio June 8, 2023 14:11
@gwaybio gwaybio merged commit 77d93a3 into master Jun 8, 2023
@gwaybio gwaybio deleted the ss-variance_threshold-default branch June 8, 2023 16:11
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3 participants