Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closes #2521 remove lifecycle deprecation code for get summary records #2568

Merged

Conversation

jimrothstein
Copy link
Collaborator

@jimrothstein jimrothstein commented Nov 17, 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!

#2521  Remove lifecycle deprecation code for get_summary_records().

#2521  BUT,  test #4 in test-get_summary_records.R  shows that user gets no error when using the now deprecated formal argument `analysis_var`
Do I have this right??

Once removed, nothing stops user from using deprecated formal argument (such as `analysis_var`)   SEE test-get_summary_records.R   test #4
@jimrothstein
Copy link
Collaborator Author

jimrothstein commented Nov 17, 2024

#2521 - First attempt:

Removing lifecycle deprecation code for get_summary_records() now allows user to use deprecated formal arguments, which don't think you intended.

Could you clarify, please?

Copy link

github-actions bot commented Nov 17, 2024

Code Coverage

Package Line Rate Health
admiral 97%
Summary 97% (5063 / 5217)

@bms63
Copy link
Collaborator

bms63 commented Nov 17, 2024

Please remove argument from function and related code.

also good to check tests for the argument to see if those need to be excised.

I don’t think this function gets called by user but always good to check vignettes and templates

oh and the documentation - should be cleaned up as well

thanks!!

@bms63 bms63 requested review from bundfussr and bms63 November 19, 2024 22:08
Copy link
Collaborator

@bms63 bms63 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

And many thanks for jumping in here!! we try to follow tidyverse deprecation guidelines, but we are more conservative. New deprecation timelines are coming that are multi-year!! eeckkk!!

  `derive_param_exposure.R` documentation
mentions now deprecated (and gone) variables

`analysis_var`
`summary_fun`
@jimrothstein
Copy link
Collaborator Author

Removed unneeded test... understood!

derive_param_exposure.R

  • I need to adjust this function's documentation. (It references the two vanished variables)

locally, test admiral throwing errors

  • will investigage

Copy link
Collaborator

@bundfussr bundfussr left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Please add an item to NEWS.md

@bundfussr
Copy link
Collaborator

derive_param_exposure.R

  • I need to adjust this function's documentation. (It references the two vanished variables)

Good catch! It seems that we missed it before.

NEWS.md Outdated Show resolved Hide resolved
@bms63
Copy link
Collaborator

bms63 commented Nov 21, 2024

We are close!! I scan for the deprecated arguments in the repo and think we might need to look at derive_param_exposure

image

@jimrothstein
Copy link
Collaborator Author

Suggestion (for now or future)

Replace

@return The input dataset with a new record added for each group (with respect to the variables
#' specified for the by_vars parameter).

With
@return The input dataset with a new record added for each group (as defined by by_vars parameter).

@jimrothstein
Copy link
Collaborator Author

@bms63

Something I did ? (I use linux)

image

@bms63
Copy link
Collaborator

bms63 commented Nov 24, 2024

@bms63

Something I did ? (I use linux)

image

Seems to be a larger issue https://forum.posit.co/t/r-cmd-check-fails-on-macos-latest-release-r-lib-actions-setup-r-v2/195084/3

@bms63
Copy link
Collaborator

bms63 commented Nov 25, 2024

Removed unneeded test... understood!

derive_param_exposure.R

  • I need to adjust this function's documentation. (It references the two vanished variables)

locally, test admiral throwing errors

  • will investigage

Hi @jimrothstein happy to see this update if you still want to make it. After that this is good to go!

@bms63
Copy link
Collaborator

bms63 commented Dec 1, 2024

Suggestion (for now or future)

Replace

@return The input dataset with a new record added for each group (with respect to the variables #' specified for the by_vars parameter).

With @return The input dataset with a new record added for each group (as defined by by_vars parameter).

Hi @jimrothstein is this completed? Love to get this merged in!

bms63 and others added 3 commits December 1, 2024 11:57
…records' of github.com:pharmaverse/admiral into 2521_remove_lifecycle_deprecation_code_for_get_summary_records
@jimrothstein
Copy link
Collaborator Author

@bms63

Same phrase is used about 1/2 dozen times in Admiral, change each ??

Suggestion (for now or future)
Replace
@return The input dataset with a new record added for each group (with respect to the variables #' specified for the by_vars parameter).
With @return The input dataset with a new record added for each group (as defined by by_vars parameter).

@bms63
Copy link
Collaborator

bms63 commented Dec 2, 2024

@bms63

Same phrase is used about 1/2 dozen times in Admiral, change each ??

Suggestion (for now or future)
Replace
@return The input dataset with a new record added for each group (with respect to the variables #' specified for the by_vars parameter).
With @return The input dataset with a new record added for each group (as defined by by_vars parameter).

So lets stay focus on the issue at hand which is the deprecation updates. If not, then our PRs will never be completed! :)

Can you create a new issue for this documentation update. If you already did the minor update for this function here then that is fine! no need to revert, but if not already completed lets add that one to the new documentation issue.

@bms63
Copy link
Collaborator

bms63 commented Dec 2, 2024

@jimrothstein I see it was updated here for the one function! Thanks! Please make an issue for the other documentation updates that you found.

@bms63 bms63 merged commit dd775bc into main Dec 2, 2024
18 of 19 checks passed
@bms63 bms63 deleted the 2521_remove_lifecycle_deprecation_code_for_get_summary_records branch December 2, 2024 01:15
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants