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Closes #2595 deprecation of previous "superseded" functions #2615

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@bms63 bms63 commented Dec 18, 2024

Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the main branch until you have checked off each task.

  • Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
  • Code is formatted according to the tidyverse style guide. Run styler::style_file() to style R and Rmd files
  • Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See Unit Test Guide
  • If you removed/replaced any function and/or function parameters, did you fully follow the deprecation guidance?
  • Review the Cheat Sheet. Make any required updates to it by editing the file inst/cheatsheet/admiral_cheatsheet.pptx and re-upload a PDF and a PNG version of it to the same folder. (The PNG version can be created by taking a screenshot of the PDF version.)
  • Update to all relevant roxygen headers and examples, including keywords and families. Refer to the categorization of functions to tag appropriate keyword/family.
  • Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
  • Address any updates needed for vignettes and/or templates
  • Update NEWS.md under the header # admiral (development version) if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers). A Developer Notes section is available in NEWS.md for tracking developer-facing issues.
  • Build admiral site pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
  • Address or fix all lintr warnings and errors - lintr::lint_package()
  • Run R CMD check locally and address all errors and warnings - devtools::check()
  • Link the issue in the Development Section on the right hand side.
  • Address all merge conflicts and resolve appropriately
  • Pat yourself on the back for a job well done! Much love to your accomplishment!

@bms63 bms63 requested a review from bundfussr December 18, 2024 23:32
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bms63 commented Dec 18, 2024

@bundfussr Question: How to set it up so I can use the admiraldev branch with the new deprecation function?

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github-actions bot commented Dec 18, 2024

Code Coverage

Package Line Rate Health
admiral 98%
Summary 98% (5251 / 5357)

R/derive_var_dthcaus.R Show resolved Hide resolved
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@bundfussr Question: How to set it up so I can use the admiraldev branch with the new deprecation function?

For the workflows which use staged dependencies it should work with the branch naming you are using. For the snapshot workflows it will not work. We would need to update these workflows to enable it. However, I'm not sure if it is worth the effort.

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bms63 commented Dec 19, 2024

@bundfussr Question: How to set it up so I can use the admiraldev branch with the new deprecation function?

For the workflows which use staged dependencies it should work with the branch naming you are using. For the snapshot workflows it will not work. We would need to update these workflows to enable it. However, I'm not sure if it is worth the effort.

awesome thanks for confirming. wnated to make sure this was set up correctly before i started to update

@bms63 bms63 changed the title chore: #2595 renaming branch and attempt to use branch from admiraldev Closes #2595 deprecation of previous "superseded" functions Dec 19, 2024
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bms63 commented Dec 23, 2024

Alright! Adventure is nearing the end. @ddsjoberg @manciniedoardo @bundfussr hoping you all can review please

Comment on lines +144 to +145
x = "This message will turn into a warning with release of 1.3.0",
i = "https://pharmaverse.github.io/admiral/reference/derive_extreme_event.html"
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I think I may have made this suggestion previously, but I wouldn't promise to the users the precise version when we're going to make deprecation message changes. We have a long deprecation cycle, and who knows if we need to change things in the future, e.g. we release v1.3 earlier than we had previously planned, or we wait longer. I recommend that before each release (and not just after a release), we search for all the deprecation messages in our package and update based on the deprecation calendar.

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You did! ummm.... maybe just "This message will turn into a warning at the next release"

I just want to stress to the user to start looking at updating their code.

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