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WIP: Import taxpasta #574

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merged 38 commits into from
Jul 6, 2024
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Midnighter
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@Midnighter Midnighter commented Jun 8, 2024

To do:

  • expand documentation
  • I need to import some biomformat internals, which I can only do with biomformat:::. I see no way around this at the moment.

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Looks good, let me know if you need help with the documentation

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Thank you for the detailed review @TuomasBorman! I have some open questions from your comments and will appreciate your assistance with the documentation. It's not clear to me why to break up the docstring like that for a single function and how to direct importTaxpasta's docstring to the general file.

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Hi @TuomasBorman,

Starting next week, I will have more time again and could try to complete this PR. I would need some advice and decisions from your side, though, please. If you can take another look, I will be grateful.

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Hi @TuomasBorman,

Starting next week, I will have more time again and could try to complete this PR. I would need some advice and decisions from your side, though, please. If you can take another look, I will be grateful.

Alright, sounds good. I have also been busy, but I will check during this week.

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Looks good already

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@Midnighter Midnighter marked this pull request as ready for review July 4, 2024 20:52
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Midnighter commented Jul 4, 2024

@TuomasBorman, I believe, I have addressed all of your comments. Please have another look and let me know if there's something else to be addressed.

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Looks good!

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codecov bot commented Jul 6, 2024

Codecov Report

Attention: Patch coverage is 96.22642% with 2 lines in your changes missing coverage. Please review.

Please upload report for BASE (devel@a340211). Learn more about missing BASE report.

Files Patch % Lines
R/importTaxpasta.R 96.22% 2 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff            @@
##             devel     #574   +/-   ##
========================================
  Coverage         ?   68.04%           
========================================
  Files            ?       43           
  Lines            ?     5194           
  Branches         ?        0           
========================================
  Hits             ?     3534           
  Misses           ?     1660           
  Partials         ?        0           

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@TuomasBorman TuomasBorman merged commit f58207f into microbiome:devel Jul 6, 2024
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@Midnighter Midnighter deleted the import-taxpasta branch July 9, 2024 14:06
@antagomir antagomir mentioned this pull request Jul 9, 2024
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3 participants