Closes #233 #324 #332 admiraldev miscellanous documentation updates (#…

…333) * docs: #283 update description and news * closes #286 commit messaging, new r-cmd vignette (#291) * 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 <[email protected]> * chore: #286 news update --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #271, #213, #260, #240 Documentation Update of get_datasets(); 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #264, #288 cleanup assertions and continue deprecation process (#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 <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#294) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Closes #22 #181 #201 #292 #298 Variety of small-scale general documentation 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 <[email protected]> * Closes #302 Adding Snapshot testing guidance to unit testing vignette (#308) * Update unit_test_guidance.Rmd * Update NEWS.md * Update NEWS.md * Closes #301: (#307) * #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) * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #295 template documentation@devel (#300) * #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 <[email protected]> * #295 update to refer to admiraldev devel site * #295 Chore: spellcheck --------- Co-authored-by: Ross Farrugia <[email protected]> * Closes #296 document_missing_value_s@devel (#311) * #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. * Closes #282: Test Data Guidance vignette (#293) * #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 <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#314) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#315) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * Closes #306 argument descriptions added to table (#320) argument descriptions added to table Co-authored-by: Zelos Zhu <[email protected]> * Closes #316 remove messaging that includes "-" as year not handled (#317) * 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 <[email protected]> * Closes #318 #321 Documentation updates around admiral.test, staged dependencies, and function arguments (#323) * Fix hardcoded URL (#326) Resolves #325 * Closes #312 breakup wall of text (#319) * 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 <[email protected]> * Closes #328 add missing news entries (#329) * 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 <[email protected]> Co-authored-by: Ben Straub <[email protected]> * feat: #233 documentation for quoting * feat: #324 add footnotes blurb * feat: #332 add blurb for roxygen standardization * feat: #233 #324 #332 adopt feedback * italicize phrase * skip line to make markdown look correct * chore: run use_verion("dev") * feat: adding post-release cleanup stuff too * forgot line * accidental push * chore: fix tests * always is only a `deprecate_warn()` argument * .github folder updates * yaml syntax * fix link --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: cicdguy <[email protected]>
pharmaverse · Oct 11, 2023 · aafdf33 · aafdf33
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -9,10 +9,10 @@ Please check off each taskbox as an acknowledgment that you completed the task o
 - [ ] Update to all relevant roxygen headers and examples, including keywords and families. Refer to the [categorization of functions](https://pharmaverse.github.io/admiraldev/devel/articles/programming_strategy.html#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)
+- [ ] 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/admiraldev/devel/reference/index.html)" 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 
+- [ ] Address all merge conflicts and resolve appropriately
 - [ ] Pat yourself on the back for a job well done! Much love to your accomplishment!
diff --git a/.github/workflows/common.yml b/.github/workflows/common.yml
@@ -67,6 +67,8 @@ jobs:
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
+    with:
+      error-on: warning # TODO: find a way to ignore specific notes
     if: github.event_name == 'pull_request'
   docs:
     name: Documentation

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: admiraldev
 Type: Package
 Title: Utility Functions and Development Tools for the Admiral Package Family
-Version: 0.5.0
+Version: 0.5.0.9000
 Authors@R: c(
     person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -25,7 +25,6 @@ export(assert_named)
 export(assert_named_exprs)
 export(assert_numeric_vector)
 export(assert_one_to_one)
-export(assert_order_vars)
 export(assert_param_does_not_exist)
 export(assert_s3_class)
 export(assert_same_type)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,23 @@
+# admiraldev (development version)
+
+## New Features
+
+## Updates of Existing Functions
+
+## Breaking Changes
+
+- The following functions have been deprecated from previous admiral versions using the next phase of the deprecation process
+  - `assert_function_param()`
+  - `assert_named_expr()`
+  - `assert_has_variables()`
+
+## Documentation
+
+- New documentation in programming strategy around quoting/expressions and standardizing roxygen texts (#233, #332)
+- New documentation on how to use footnotes when writing vignettes (#324)
+
+## Various
+
 # admiraldev 0.5.0
 
 ## New Features

diff --git a/R/assertions.R b/R/assertions.R
@@ -518,36 +518,6 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) {
   assert_list_of(arg, "symbol", named = expect_names, optional = optional)
 }
 
-#' Is an Argument a List of Order Variables?
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `assert_expr_list()` instead.
-#'
-#' Checks if an argument is a valid list of order variables/expressions created
-#' using `exprs()`
-#'
-#' @param arg A function argument to be checked
-#' @param optional Is the checked argument optional? If set to `FALSE` and `arg`
-#' is `NULL` then an error is thrown
-#'
-#'
-#' @return
-#' The function throws an error if `arg` is not a list of variables or
-#' expressions created using `exprs()` and returns the input invisibly
-#' otherwise.
-#'
-#' @export
-#'
-#' @keywords deprecated
-#' @family deprecated
-assert_order_vars <- function(arg, optional = FALSE) {
-  assert_logical_scalar(optional)
-
-  deprecate_stop("0.4.0", "assert_order_vars()", "assert_expr_list()")
-}
-
 #' Is an Argument an Integer Scalar?
 #'
 #' Checks if an argument is an integer scalar
@@ -885,8 +855,7 @@ assert_named <- function(arg, optional = FALSE) {
 #'
 #' @export
 assert_named_exprs <- function(arg, optional = FALSE) {
-  deprecate_warn("0.5.0", "assert_named_exprs()", "assert_expr_list()", always = TRUE)
-  assert_expr_list(arg = arg, named = TRUE)
+  deprecate_stop("0.5.0", "assert_named_exprs()", "assert_expr_list()")
 }
 
 #' Does a Dataset Contain All Required Variables?
@@ -910,26 +879,14 @@ assert_named_exprs <- function(arg, optional = FALSE) {
 #' @keywords deprecated
 #' @family deprecated
 assert_has_variables <- function(dataset, required_vars) {
-  deprecate_warn("0.5.0", "assert_has_variables()", "assert_data_frame()")
-  assert_data_frame(
-    arg = dataset,
-    required_vars = set_names(
-      exprs(!!!syms(required_vars)),
-      names(required_vars)
-    )
-  )
+  deprecate_stop("0.5.0", "assert_has_variables()", "assert_data_frame()")
 }
 
 #' Is Argument a Function?
 #'
 #' Checks if the argument is a function and if all expected arguments are
 #' provided by the function.
 #'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `assert_function_param()` instead.
-#'
 #' @param arg A function argument to be checked
 #'
 #' @param params A character vector of expected argument names
@@ -948,8 +905,9 @@ assert_has_variables <- function(dataset, required_vars) {
 #'
 #' @export
 #'
-#' @keywords deprecated
-#' @family deprecated
+#' @keywords assertion
+#' @family assertion
+#'
 #' @examples
 #' example_fun <- function(fun) {
 #'   assert_function(fun, params = c("x"))
@@ -1001,20 +959,24 @@ assert_function <- function(arg, params = NULL, optional = FALSE) {
 
 #' Assert Argument is a Parameter of a Function
 #'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This function is *deprecated*, please use `assert_function()` instead.
+#'
 #' @param arg The name of a function passed as a string
 #' @param params A character vector of function parameters
 #'
-#' @keywords assertion
-#' @family assertion
+#' @keywords deprecated
+#' @family deprecated
 #'
 #' @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()")
 }
 
 #' Asserts That a Parameter is Provided in the Expected Unit

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -13,7 +13,7 @@ articles:
   test_data_guidance: test_data_guidance.html
   unit_test_guidance: unit_test_guidance.html
   writing_vignettes: writing_vignettes.html
-last_built: 2023-08-24T20:45Z
+last_built: 2023-09-22T17:42Z
 urls:
   reference: https://pharmaverse.github.io/admiraldev/devel/reference
   article: https://pharmaverse.github.io/admiraldev/devel/articles

diff --git a/man/assert_atomic_vector.Rd b/man/assert_atomic_vector.Rd
diff --git a/man/assert_character_scalar.Rd b/man/assert_character_scalar.Rd
diff --git a/man/assert_character_vector.Rd b/man/assert_character_vector.Rd
diff --git a/man/assert_data_frame.Rd b/man/assert_data_frame.Rd
diff --git a/man/assert_date_vector.Rd b/man/assert_date_vector.Rd
diff --git a/man/assert_expr.Rd b/man/assert_expr.Rd
diff --git a/man/assert_expr_list.Rd b/man/assert_expr_list.Rd
diff --git a/man/assert_filter_cond.Rd b/man/assert_filter_cond.Rd
diff --git a/man/assert_function.Rd b/man/assert_function.Rd
diff --git a/man/assert_function_param.Rd b/man/assert_function_param.Rd
diff --git a/man/assert_has_variables.Rd b/man/assert_has_variables.Rd
diff --git a/man/assert_integer_scalar.Rd b/man/assert_integer_scalar.Rd
diff --git a/man/assert_list_element.Rd b/man/assert_list_element.Rd
diff --git a/man/assert_list_of.Rd b/man/assert_list_of.Rd
diff --git a/man/assert_logical_scalar.Rd b/man/assert_logical_scalar.Rd