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Deprecate read10xVisium() #155

Merged
merged 6 commits into from
Jun 24, 2024
Merged

Deprecate read10xVisium() #155

merged 6 commits into from
Jun 24, 2024

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HelenaLC
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@HelenaLC HelenaLC commented Jun 21, 2024

  • We have been using example(read10xVisium) throughout function docs & unit tests; this has been changed to example(SpatialExperiment), which now includes an example using VisiumIO to read in the example data in inst/extdata.
  • Also added two NEWS entires; we have been behind versions 1.11 through 1.15 - it would be great if we can keep things more up to date in the future, even if it's just to add an entry saying "Bioc release 3.nm" prior to the next release when there haven't been any changes in the meantime.
  • Also updated my personal email address & added ORCID iDs in the DESCRIPTION (could not find @Nick-Eagles; happy to add if you have one?)

@HelenaLC HelenaLC changed the title Deprecate read10x visium Deprecate read10xVisium() Jun 21, 2024
@lmweber
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lmweber commented Jun 22, 2024

Updated my email address too. Thanks for adding ORCID IDs and NEWS updates also. I haven't usually been updating NEWS to mention Bioc releases if there are no other updates, but happy to start adding that in the future.

@HelenaLC
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I don't either, just meant it there are 0 changes in a release cycle, it might be worth adding a single entry just to we don't have 3 version-long gaps; but also don't have a strong opinion -- still need someone to accept before I can merge though :)

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@drighelli drighelli left a comment

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I would suggest to not add a new dependency, but instead leaving a message about abandoning read10xVisium in favor of the VisiumIO package

@HelenaLC HelenaLC merged commit 0e6fcad into devel Jun 24, 2024
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@HelenaLC HelenaLC deleted the deprecate_read10xVisium branch June 24, 2024 10:53
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4 participants