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[ENH] clustering/hierarchical: Use optimal_leaf_ordering from scipy #4288

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ales-erjavec
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Scipy >= 1.0.0 has a compiled optimal_leaf_ordering implementation that can be used instead of the implementation here.

Description of changes
  • Use scipy.cluster.hierarchical.optimal_leaf_ordering instead of the implementation contained here.
  • Remove some scipy <= 0.18 compatibility code.
Includes
  • Code changes
  • Tests
  • Documentation

@ales-erjavec ales-erjavec force-pushed the hierarchical-opt-leaf-order-scipy branch from 55c8bfd to 380fff9 Compare December 20, 2019 12:54
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codecov bot commented Dec 20, 2019

Codecov Report

Merging #4288 into master will increase coverage by 0.02%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #4288      +/-   ##
==========================================
+ Coverage   86.68%   86.71%   +0.02%     
==========================================
  Files         396      396              
  Lines       71510    71393     -117     
==========================================
- Hits        61988    61906      -82     
+ Misses       9522     9487      -35

@janezd janezd merged commit 8db6a3a into biolab:master Jan 6, 2020
@ales-erjavec ales-erjavec deleted the hierarchical-opt-leaf-order-scipy branch March 16, 2020 13:43
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3 participants