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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Rename converters #591

Closed thpralas closed 3 days ago

thpralas commented 1 week ago

This PR makes the following naming modifications:

makeTreeSEFromDADA2 --> convertFromDADA2 makeTreeSEFromBIOM --> convertFromBIOM makeTreeSEFromPhyloseq --> convertFromPhyloseq makePhyloseqFromTreeSE --> convertToPhyloseq

and deprecate the following functions: makeTreeSummarizedExperimentFromDADA2 makeTreeSummarizedExperimentFromPhyloseq makeTreeSummarizedExperimentFromBIOM makePhyloseqFromTreeSummarizedExperiment

codecov[bot] commented 1 week ago

Codecov Report

Attention: Patch coverage is 4.54545% with 42 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@c17fa9f). Learn more about missing BASE report.

:exclamation: Current head af2d633 differs from pull request most recent head 2fcf74e

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Files Patch % Lines
R/deprecate.R 0.00% 42 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## devel #591 +/- ## ======================================== Coverage ? 66.92% ======================================== Files ? 41 Lines ? 4964 Branches ? 0 ======================================== Hits ? 3322 Misses ? 1642 Partials ? 0 ```

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TuomasBorman commented 3 days ago

@thpralas Can you check other mia* packages and OMA that they reflect these changes?