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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Rename cluster to addCluster #502

Closed thpralas closed 2 months ago

thpralas commented 4 months ago

Rename cluster to addCluster. Fix indentation in calculateDMM and cluster files following Bioconductor best practices (indentation must be a multiple of 4 spaces). Move deprecated functions from the calculateDMM file to deprecate file.

antagomir commented 3 months ago

There are unresolved comments, and one conflict. If those are resolved then this seems good to me at least?

codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 1.38889% with 71 lines in your changes are missing coverage. Please review.

Project coverage is 72.90%. Comparing base (32d85c6) to head (6d978f5).

Files Patch % Lines
R/calculateDMM.R 0.00% 62 Missing :warning:
R/deprecate.R 0.00% 9 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #502 +/- ## ========================================== - Coverage 73.11% 72.90% -0.21% ========================================== Files 40 40 Lines 4630 4643 +13 ========================================== Hits 3385 3385 - Misses 1245 1258 +13 ```

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