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102 patternmarkers all returning empty lists #103

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merged 31 commits into from
Jun 5, 2024

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dimalvovs
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  • add a test that fails on empty patterMarkers
  • make it pass by rewriting the method for threshold='all'

@dimalvovs dimalvovs linked an issue May 2, 2024 that may be closed by this pull request
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@kwoyshner can you review please?

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I tried reinstalling from this branch and was able to get patternMarkers with 'all' now, thank you!

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@kwoyshner do you want to have a look at threshold = 'cut'? I've updated it too. This part of code is poorly documented so I was not sure what that mode should do but there was a dimension mismatch. simplicityGENES function needs to be inspected for functionality.

@dimalvovs dimalvovs marked this pull request as ready for review May 5, 2024 22:50
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I am unqualified to comment on how these changes affect the integrity of the CoGAPS algorithm, but I left a few comments. Hopefully, it helps in some small way!

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@dimalvovs dimalvovs requested a review from genesofeve May 9, 2024 21:30
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please reinstate

@dimalvovs dimalvovs merged commit 45fdd42 into master Jun 5, 2024
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@dimalvovs dimalvovs deleted the 102-patternmarkers-all-returning-empty-lists branch June 5, 2024 19:28
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patternMarkers 'all' returning empty lists
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