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Closes #2309 Bypass undesirable_function_linter and indentation_linter checks, as … #2322

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merged 1 commit into from
Feb 5, 2024

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…a temporary solution to failing CI checks.

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 version of it to the same folder.
  • 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)
  • 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()
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  • 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!

@esimms999-gsk esimms999-gsk self-assigned this Feb 5, 2024
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github-actions bot commented Feb 5, 2024

Code Coverage

Package Line Rate Health
admiral 98%
Summary 98% (4719 / 4807)

@bms63
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bms63 commented Feb 5, 2024

Hi Eric - no need to assign project board to PRs. We only do that for Issues. It gets confusing in meetings with Issues and PRs linked on the board.

Thanks for putting in a temporary fix. @gg106046 still lots to look into and decide.

@bms63 bms63 merged commit 18ab7a5 into main Feb 5, 2024
17 checks passed
@bms63 bms63 deleted the 2309_Lintr_CI_check branch February 5, 2024 16:23
esimms999-gsk added a commit that referenced this pull request Feb 5, 2024
* Closes #2309 Bypass undesirable_function_linter and indentation_linter checks, as … (#2322)

Bypass undesirable_function_linter and indentation_linter checks, as a temporary solution to failing CI checks.

* [skip actions] Bump version to 1.0.0.9005

* admiral v1.0.1 - Hotfix for derive_vars_query (#2311) (#2320)

* Closes #2311 attend to `derive_vars_query()` bug (#2313)

* new branch here

* fix typo in news

* 2311 updated unit test to have mixed case

* missing the toupper part

* add more detail to news

* fix links

* add documentation on case insensitivity

---------

Co-authored-by: Gordon Miller <gordon.miller@roche.com>

* chore: #2311 remove renv to get website to build

* [actions skip] Add/Update README.md for patch

* Trigger Build

---------

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Gordon Miller <gordon.miller@roche.com>
Co-authored-by: GitHub Actions <action@github.com>

---------

Co-authored-by: bms63 <bms63@users.noreply.github.com>
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Gordon Miller <gordon.miller@roche.com>
Co-authored-by: GitHub Actions <action@github.com>
bms63 added a commit that referenced this pull request Feb 5, 2024
* Remove test about deprecation of na_val argument. Update comment in code.

* Update 2316 branch with latest main. (#2323)

* Closes #2309 Bypass undesirable_function_linter and indentation_linter checks, as … (#2322)

Bypass undesirable_function_linter and indentation_linter checks, as a temporary solution to failing CI checks.

* [skip actions] Bump version to 1.0.0.9005

* admiral v1.0.1 - Hotfix for derive_vars_query (#2311) (#2320)

* Closes #2311 attend to `derive_vars_query()` bug (#2313)

* new branch here

* fix typo in news

* 2311 updated unit test to have mixed case

* missing the toupper part

* add more detail to news

* fix links

* add documentation on case insensitivity

---------

Co-authored-by: Gordon Miller <gordon.miller@roche.com>

* chore: #2311 remove renv to get website to build

* [actions skip] Add/Update README.md for patch

* Trigger Build

---------

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Gordon Miller <gordon.miller@roche.com>
Co-authored-by: GitHub Actions <action@github.com>

---------

Co-authored-by: bms63 <bms63@users.noreply.github.com>
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Gordon Miller <gordon.miller@roche.com>
Co-authored-by: GitHub Actions <action@github.com>

---------

Co-authored-by: bms63 <bms63@users.noreply.github.com>
Co-authored-by: Ben Straub <ben.x.straub@gsk.com>
Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Gordon Miller <gordon.miller@roche.com>
Co-authored-by: GitHub Actions <action@github.com>
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