Closes #233 #324 #332 admiraldev miscellanous documentation updates #333

zdz2101 · 2023-09-19T20:15:10Z

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.

…ease_tidying@devel Closes #283 update description and news as post-release cleanup tasks

* docs: #286 commit messaging, new r-cmd vignette * chore: #286 spelling * docs: #286 squash and merge blurb * Update vignettes/git_usage.Rmd Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

… keep_source_vars argument; @family tag; compute_ functions (#287) * docs: #271 #213 clarify get_datasets and add keep_source_vars to prog strat * docs: #260 cleanup @family mentions * docs: #240 add blurb about compute functions * docs: #271 #213 #240 #260 add news blurb * adopt suggestion for family/keywords Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * docs #271 adopt get_dataset feedback * docs: #213 #240 adopt recommendations from PR * chore: #240 add BMI to WORDLIST for spellcheck * chore: #271 #213 #260 adopt feedback --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com>

…#289) * feat: #288 cleanup deprecation process * feat: #264 deprecate assert_function * test: #264 cleanup some tests in assert_function, confused how others would go * test: #264 rewrite tests in a more logical way * chore: #264 run styler/lintr * chore: #288 revert back to devel test file * chore: #288 properly fix assert_order_vars again * feat: #264 begin deprecation of redundant assertions * feat: #288 deprecate assert_named_exprs * deprecate assert_has_variables properly #264 * chore: #264 run styler * docs: #264 add blurb in news for the deprecated assertions * chore: #264 fix description version and remove deprecated examples --------- Co-authored-by: Zelos Zhu <zdz2101@github.com>

renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com>

…tation updates (#303) * feat: #22 add documentation to friendly_type_of * feat: #181 add the appropriate URL * feat: #201 #292 add documentation about PR guidance and codeowners * chore: update wordlist for codeowners * chore: add NEWS --------- Co-authored-by: Zelos Zhu <zdz2101@github.com>

…#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md

* #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document

* renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com>

* #295 set up package extension guidance page * #295 fix vignetteindexentry * #295 chore: spellcheck * #295 chore: fix encoding issues in vignettes that prevented package from being built * #295: updates following review * #295 Chore: spellcheck * Update vignettes/package_extensions.Rmd Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com>

* #296 - `missing_value` and `missing_values` added to the table of common arguments. * #296 - add in discussion of when to use singular vs plural arguments to programming strategy. * #296 - run checks required for PR and update NEWS.md. * #296 - Update according to requested changes. * #296 - revert the 'wrapped' changes in the programming strategy vignette * #296 - re-insert the new text into the programming strategy vignette, altered according to changes requested. * #296 - update NEWS.md with changes requested and run the required checks for PR.

* #282: add test_data_guidance.Rmd, copy from admiraldata README devel * #282: update .yml * #282: add link for packages, remove SDTM, add naming conventions for program name * #282 spelling * #282: link to two data packages * #282: updated wordlist * #282: update pharmaverseadam description --------- Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com>

renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <galachad@users.noreply.github.com>

* renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com>

argument descriptions added to table Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

) * feat: #316 remove messaging that includes "-" as year not handled * feat: #316 replace warning message * chore: #316 fix warning message and typos * chore: #316 add news blurb --------- Co-authored-by: Zelos Zhu <zdz2101@github.com>

…pendencies, and function arguments (#323)

Resolves #325

* brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

* feat: #295 add missing news entries * feat: #295 add missing news entries * fixed it * feat: add news entry for #306 * chore: #312 missing reference * chore: fix link that pointed to merged branch and use devel * Update NEWS.md --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com>

github-actions · 2023-09-19T20:19:18Z

Package	Line Rate	Health
admiraldev	96%	✔
Summary	96% (1046 / 1091)	✔

bms63 · 2023-09-20T13:43:06Z

We should have this go to main. Going to purge devel in the great GitHub Flow update of 2023

manciniedoardo

Thanks for working on this @zdz2101!

vignettes/programming_strategy.Rmd

vignettes/writing_vignettes.Rmd

manciniedoardo

Great work!

vignettes/programming_strategy.Rmd

zdz2101 · 2023-09-27T14:30:24Z

R/assertions.R

 }

 #' Is Argument a Function?
 #'
 #' Checks if the argument is a function and if all expected arguments are
 #' provided by the function.
 #'
-#' @description


The roxgyen deprecation stuff was in the wrong place

zdz2101 · 2023-09-27T14:31:42Z

R/assertions.R

 #'
 #' @return
 #' The function throws an error if any elements of `params` is not an argument of
 #' the function given by `arg`
 #'
 #' @export
 assert_function_param <- function(arg, params) {
-  deprecate_warn("0.5.0", "assert_function_param()", "assert_function()", always = TRUE)
-  assert_function(arg = arg, params = params)
+  deprecate_stop("0.5.0", "assert_function_param()", "assert_function()", always = TRUE)


Correct function was deprecated, but the roxygen documentation portion of it was misplaced

zdz2101 · 2023-09-27T14:36:13Z

@bundfussr @manciniedoardo @bms63 added post-release cleanup stuff while I was at it

bundfussr · 2023-09-28T12:08:30Z

.github/pull_request_template.md

@@ -3,16 +3,17 @@ Thank you for your Pull Request! We have developed this task checklist from the
 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)
+- [ ] Increment the development version number by calling `usethis::use_version("dev")`. Ensure on the Pull Request in the `DESCRIPTION` file the development version has moved up by 1, e.g. from `x.x.x.9002` -> `x.x.x.9003`.


Do we really want to do this? Most likely this will cause a lot of merge conflicts. What is the benefit of having a different version number for each feature?

I would keep it simple and just call use_version("dev") once directly after the release.

Just going to undo this based on feedback from other PR in admiral

bundfussr · 2023-09-28T13:46:46Z

.github/pull_request_template.md

- [ ] 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](https://pharmaverse.github.io/admiraldev/devel/reference/index.html)" page. 
+- [ ] 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](https://pharmaverse.github.io/admiral/cran-release/reference/index.html)" page. 


The link does not make much sense because the new function will not appear on the referenced page until the new version of the package is released.

bad copy/paste job

Zelos Zhu and others added 25 commits June 12, 2023 19:44

docs: #283 update description and news

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Merge branch 'main' into 283_news_description_postrelease_tidying@devel

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Merge pull request #284 from pharmaverse/283_news_description_postrel…

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…ease_tidying@devel Closes #283 update description and news as post-release cleanup tasks

Propagate renv.lock from pharmaverse/admiralci (#294)

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renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com>

Closes #302 Adding Snapshot testing guidance to unit testing vignette (…

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…#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md

Closes #301: (#307)

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* #301: edoardo added as author, and author/contributor distinction implemented as in core admiral package * #301 chore: document

Propagate renv.lock from pharmaverse/admiralci (#310)

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* renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@gmail.com>

Propagate renv.lock from pharmaverse/admiralci (#314)

3e96248

renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <galachad@users.noreply.github.com>

Propagate renv.lock from pharmaverse/admiralci (#315)

503ffcd

* renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com>

Closes #306 argument descriptions added to table (#320)

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argument descriptions added to table Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

Closes #318 #321 Documentation updates around admiral.test, staged de…

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…pendencies, and function arguments (#323)

Fix hardcoded URL (#326)

390dc59

Resolves #325

Closes #312 breakup wall of text (#319)

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* brick in the wall * remove special characters from image name * remove special characters from image name * replaced iframe with png * fixed image reference --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

feat: #233 documentation for quoting

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feat: #324 add footnotes blurb

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feat: #332 add blurb for roxygen standardization

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zdz2101 linked an issue Sep 19, 2023 that may be closed by this pull request

Documentation: Describe how quoting is used in admiral #233

Closed

zdz2101 changed the title ~~Closes #233 324 332 admiraldev miscellanous documentation updates~~ Closes #233 #324 #332 admiraldev miscellanous documentation updates Sep 19, 2023

zdz2101 changed the base branch from devel to main September 20, 2023 14:02

zdz2101 requested review from bundfussr, bms63 and manciniedoardo and removed request for bundfussr September 25, 2023 14:10

manciniedoardo requested changes Sep 26, 2023

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Zelos Zhu added 3 commits September 26, 2023 14:32

feat: #233 #324 #332 adopt feedback

55bca15

italicize phrase

a699c7d

skip line to make markdown look correct

fbb3f88

zdz2101 requested review from manciniedoardo and bundfussr September 26, 2023 17:33

manciniedoardo approved these changes Sep 27, 2023

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Zelos Zhu added 3 commits September 27, 2023 14:14

chore: run use_verion("dev")

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feat: adding post-release cleanup stuff too

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forgot line

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zdz2101 commented Sep 27, 2023

View reviewed changes

accidental push

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Zelos Zhu added 3 commits September 27, 2023 14:58

chore: fix tests

d1816ef

always is only a deprecate_warn() argument

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.github folder updates

4004eff

zdz2101 requested a review from cicdguy as a code owner September 27, 2023 15:25

yaml syntax

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bundfussr reviewed Sep 28, 2023

View reviewed changes

fix link

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zdz2101 mentioned this pull request Oct 11, 2023

Closes #339 enhances assert_function() and starts pkgdown dev mode #340

Merged

14 tasks

zdz2101 merged commit aafdf33 into main Oct 11, 2023
19 checks passed

zdz2101 deleted the 233_324_332_admiraldev_misc_doc_updates branch October 11, 2023 16:08

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Closes #233 #324 #332 admiraldev miscellanous documentation updates #333

Closes #233 #324 #332 admiraldev miscellanous documentation updates #333

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Closes #233 #324 #332 admiraldev miscellanous documentation updates #333

Closes #233 #324 #332 admiraldev miscellanous documentation updates #333

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