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Change output csv types to tsv #504

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merged 11 commits into from
Apr 16, 2024
Merged

Change output csv types to tsv #504

merged 11 commits into from
Apr 16, 2024

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zargham-ahmad
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updated csv output types for the below tools to tsv and updated test.

  • matchms metadata export
  • RAMClustR abundance table
  • MSMetaEnhancer on tabular data
  • RIAssigner on tabular data
  • matchms scores formatter
  • biotransformer
  • rem_complexes

closes #439

wverastegui
wverastegui requested changes Mar 19, 2024
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Just a minor comment, otherwise it looks good to me.

hechth
hechth reviewed Mar 20, 2024
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So far so good, just some minor comments which would make the things still a bit nicer.

tools/ramclustr/ramclustr_wrapper.R Show resolved Hide resolved
tools/rem_complex/rem_complex.xml Outdated Show resolved Hide resolved
tools/riassigner/riassigner_from_comment.xml Show resolved Hide resolved
tools/riassigner/riassigner_from_comment.xml Show resolved Hide resolved
@zargham-ahmad zargham-ahmad mentioned this pull request Mar 21, 2024
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@zargham-ahmad
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@hechth CI was failing because of the incompatibility between the upload and download action version "Artifacts created with versions v3 and below are not compatible with the v4 actions. Uploads and downloads must use the same major action versions." link. I updated the download-artifact to v4, which resolved the issue

@zargham-ahmad zargham-ahmad mentioned this pull request Mar 26, 2024
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@zargham-ahmad zargham-ahmad mentioned this pull request Apr 8, 2024
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@zargham-ahmad zargham-ahmad mentioned this pull request Apr 15, 2024
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@hechth hechth self-requested a review April 16, 2024 10:42
@hechth hechth requested a review from wverastegui April 16, 2024 10:44
@hechth hechth merged commit 4b8a43b into RECETOX:master Apr 16, 2024
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@hechth hechth hechth approved these changes

@wverastegui wverastegui Awaiting requested review from wverastegui

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Change all output table types to tabular unless they are parquet
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@zargham-ahmad @hechth @wverastegui