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[ENH] Enable Ward clustering in Hierarchical clustering widget #1515

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merged 4 commits into from
Sep 9, 2016

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ales-erjavec
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  • Enable ward clustering in Hierarchical clustering widget
  • Implement a workaround for scipy's input checking in scipy.cluster.hierarchy.linkage in scipy 0.16 and 0.17 (scipy issue 5220)
  • Adjust limits for clustering in 'Distance map' and 'Heatmap' widgets.

Also add a workaround for erroneous input checking in scipy 0.16
and 0.17 which prevented ward clustering on a precomputed distance
matrix.
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codecov-io commented Aug 23, 2016

Current coverage is 88.43% (diff: 56.25%)

Merging #1515 into master will increase coverage by 0.17%

@@             master      #1515   diff @@
==========================================
  Files            77         77          
  Lines          7624       7635    +11   
  Methods           0          0          
  Messages          0          0          
  Branches          0          0          
==========================================
+ Hits           6729       6752    +23   
+ Misses          895        883    -12   
  Partials          0          0          

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Ensure the return value order is the same when k is equal or larger
then the number of leaves.
@tomazc
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tomazc commented Sep 9, 2016

Looks good. @ales-erjavec, should we include a unit test for the currently untested special handling of Ward linkage in scipy prior to 0.18? If yes, then we need to modify travis so that it will test also with older versions of scipy (current requirement is scipy>=0.11.0).

@tomazc tomazc merged commit b0793ac into biolab:master Sep 9, 2016
@ales-erjavec ales-erjavec deleted the ward branch September 28, 2016 10:29
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3 participants