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Closes #2098 Post-release cleanup #2100

Merged
merged 27 commits into from
Oct 6, 2023
Merged

Closes #2098 Post-release cleanup #2100

merged 27 commits into from
Oct 6, 2023

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zdz2101
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@zdz2101 zdz2101 commented Sep 12, 2023 •
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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 devel 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?
  • 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 if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
  • 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!

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github-actions bot commented Sep 12, 2023 •
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Code Coverage

Package Line Rate Health
admiral 99% ✔
Summary 99% (4390 / 4451) ✔

@zdz2101 zdz2101 requested review from bms63 and bundfussr September 12, 2023 17:46
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zdz2101 commented Sep 12, 2023

@bms63 how does our new branching strategy work? Is it straight to main ?

@zdz2101 zdz2101 linked an issue Sep 12, 2023 that may be closed by this pull request
General Issue: Post-release cleanup #2098
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@zdz2101 zdz2101 marked this pull request as ready for review September 12, 2023 19:55
@zdz2101 zdz2101 requested a review from jeffreyad as a code owner September 12, 2023 19:55
bundfussr
bundfussr requested changes Sep 13, 2023
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Are we ready to merge this to main? The extension packages and company specific admiral packages have not been released yet. Do we need to update their CI/CD workflows first such that they are using the released admiral version and not the main version for the merge to main?

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bms63 commented Sep 13, 2023 •
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Are we ready to merge this to main? The extension packages and company specific admiral packages have not been released yet. Do we need to update their CI/CD workflows first such that they are using the released admiral version and not the main version for the merge to main?

I think we need to pause on this PR and others for a bit and let company and extension packages catch up. @ddsjoberg, @dgrassellyb and @cicdguy have listed out some of the impacts to website/workflows which could be a bit of headache.

image

Just FYI @pharmaverse/admiral please feel free to get PRs ready, but we probably will not merge into main till the sky is done falling.

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zdz2101 commented Sep 13, 2023 •
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I'll adopt @bundfussr recs in the meantime, okay with holding off on the PR

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@bms63 bms63 mentioned this pull request Sep 19, 2023
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bms63 commented Sep 19, 2023

Is our only hold up this R CMD check issue? Once pharmaverse/admiralci#146 is done can this be merged or do we have more concerns?

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Is our only hold up this R CMD check issue? Once pharmaverse/admiralci#146 is done can this be merged or do we have more concerns?

I think we should wait until admiralroche is released (end of this month) or until the workflows for admiralroche are updated.
Is there a pending release for admiralgsk?

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bms63 commented Sep 19, 2023

Is our only hold up this R CMD check issue? Once pharmaverse/admiralci#146 is done can this be merged or do we have more concerns?

I think we should wait until admiralroche is released (end of this month) or until the workflows for admiralroche are updated. Is there a pending release for admiralgsk?

Sounds good.

no issues for admiralgsk

zdz2101
zdz2101 commented Sep 22, 2023
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Update NEWS.md
e0e3c29 
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
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bms63 commented Sep 25, 2023

@bundfussr are we still waiting on admiralroche ?

ddsjoberg
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@@ -1,3 +1,36 @@
# admiral 0.12.0.9000
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Update NEWS.md under the header # admiral (development version)

The news file doesn't use the dev version numbers: just keep it as # admiral (development version)

ddsjoberg
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R/compute_kidney.R Outdated
@@ -137,7 +137,7 @@
compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
### BEGIN DEPRECATION
if (!missing(wt)) {
deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
deprecate_stop("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
# old_param is given using exprs()
weight <- wt
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not a big deal, but this line can never be run. we can delete it because the line above throws an error

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this applies to a number of other features gone from deprecate warn to stop

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I think we actually want to return an error to coerce/push the user to use the new argument, as the next step of the deprecation would be to get rid of the old argument all together

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I agree, I am just saying that because the line 140 returns an error, lines 141 and 142 will never be run. @zdz2101

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Ahh yes thats a good point, I'll remove

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@bundfussr are we still waiting on admiralroche ?

Yes, it is not released yet. I think it should be this week or next week. @millerg23 , do we a release date for admiralroche?

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bms63 commented Sep 26, 2023

@bundfussr are we still waiting on admiralroche ?

Yes, it is not released yet. I think it should be this week or next week. @millerg23 , do we a release date for admiralroche?

The 0.12.1 tar.gz is available in release. CAn you all use that or do you use main. We will need to merge in patch into main if so.

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@bundfussr are we still waiting on admiralroche ?

Yes, it is not released yet. I think it should be this week or next week. @millerg23 , do we a release date for admiralroche?

The 0.12.1 tar.gz is available in release. CAn you all use that or do you use main. We will need to merge in patch into main if so.

I think the workflows for admiralroche are not updated yet, i.e., they use main.

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@bundfussr are we still waiting on admiralroche ?

Yes, it is not released yet. I think it should be this week or next week. @millerg23 , do we a release date for admiralroche?

Looking to release this Friday, all going well.

@bms63 bms63 merged commit b449a33 into main Oct 6, 2023
@bms63 bms63 deleted the 2098_post_release_cleanup branch October 6, 2023 15:29
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@ddsjoberg ddsjoberg ddsjoberg left review comments

@bundfussr bundfussr bundfussr requested changes

@bms63 bms63 bms63 approved these changes

@jeffreyad jeffreyad Awaiting requested review from jeffreyad jeffreyad is a code owner

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General Issue: Post-release cleanup
5 participants
@zdz2101 @bms63 @bundfussr @millerg23 @ddsjoberg