Closes #264, #288 cleanup assertions and continue deprecation process

NAMESPACE

@@ -55,11 +55,8 @@ export(is_order_vars)
 export(is_valid_dtc)
 export(left_join)
 export(process_set_values_to)
-export(quo_c)
-export(quo_not_missing)
 export(remove_tmp_vars)
 export(replace_symbol_in_expr)
-export(replace_symbol_in_quo)
 export(replace_values_by_names)
 export(squote)
 export(suppress_warning)

NEWS.md

@@ -6,6 +6,16 @@
 
 ## Breaking Changes
 
+- The following functions/arguments have been deprecated from previous admiral versions using the next phase of the deprecation process: (#288)
+  - `assert_order_vars()`
+  - `quo_c()`
+  - `quo_not_missing()`
+  - `replace_symbol_in_quo()`
+  - The `quosures` argument was replaced by the `expressions` argument in `replace_values_by_names()`, `get_source_vars()`, and `vars2chr()`. (#288)
+- `assert_function_param()` was deprecated in favor of `assert_function()`. (#264)
+- `assert_named_expr()` was deprecated in favor of `assert_expr_list()`. (#264)
+- `assert_has_variables()` was deprecated in favor of `assert_data_frame()`. (#264)
+
 ## Documentation
 
 - Guidance around issues and merging updated (#286)

R/assertions.R

@@ -545,9 +545,7 @@ assert_vars <- function(arg, expect_names = FALSE, optional = FALSE) {
 assert_order_vars <- function(arg, optional = FALSE) {
   assert_logical_scalar(optional)
 
-  deprecate_warn("0.4.0", "assert_order_vars()", "assert_expr_list()")
-
-  assert_expr_list(arg, optional = optional)
+  deprecate_stop("0.4.0", "assert_order_vars()", "assert_expr_list()")
 }
 
 #' Is an Argument an Integer Scalar?
@@ -871,41 +869,35 @@ assert_named <- function(arg, optional = FALSE) {
 
 #' Assert Argument is a Named List of Expressions
 #'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This function is *deprecated*, please use `assert_expr_list()` instead.
+#'
 #' @inheritParams assert_data_frame
 #'
-#' @keywords assertion
-#' @family assertion
+#' @keywords deprecated
+#' @family deprecated
 #'
 #' @return
 #' The function throws an error if `arg` is not a named `list` of expression or
 #' returns the input invisibly otherwise
 #'
 #' @export
 assert_named_exprs <- function(arg, optional = FALSE) {
-  assert_logical_scalar(optional)
-
-  if (optional && is.null(arg)) {
-    return(invisible(arg))
-  }
-
-  if (!is.list(arg) ||
-    !all(map_lgl(arg, ~ is.language(.x) | is.logical(.x))) ||
-    any(names(arg) == "")) {
-    err_msg <- sprintf(
-      "`%s` must be a named list of expressions created using `rlang::exprs()` but is %s",
-      arg_name(substitute(arg)),
-      what_is_it(arg)
-    )
-    abort(err_msg)
-  }
-
-  invisible(arg)
+  deprecate_warn("0.5.0", "assert_named_exprs()", "assert_expr_list()", always = TRUE)
+  assert_expr_list(arg = arg, named = TRUE)
 }
 
 #' Does a Dataset Contain All Required Variables?
 #'
 #' Checks if a dataset contains all required variables
 #'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' This function is *deprecated*, please use `assert_data_frame()` instead.
+#'
 #' @param dataset A `data.frame`
 #' @param required_vars A `character` vector of variable names
 #'
@@ -915,38 +907,29 @@ assert_named_exprs <- function(arg, optional = FALSE) {
 #'
 #' @export
 #'
-#' @keywords assertion
-#' @family assertion
-#' @examples
-#' library(admiral.test)
-#' data(admiral_dm)
-#'
-#' assert_has_variables(admiral_dm, "STUDYID")
-#'
-#' try(assert_has_variables(admiral_dm, "AVAL"))
+#' @keywords deprecated
+#' @family deprecated
 assert_has_variables <- function(dataset, required_vars) {
-  is_missing <- !required_vars %in% colnames(dataset)
-  if (any(is_missing)) {
-    missing_vars <- required_vars[is_missing]
-    if (length(missing_vars) == 1L) {
-      err_msg <- paste0("Required variable `", missing_vars, "` is missing.")
-    } else {
-      err_msg <- paste0(
-        "Required variables ",
-        enumerate(missing_vars),
-        " are missing."
-      )
-    }
-    abort(err_msg)
-  }
-  invisible(dataset)
+  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)
+    )
+  )
 }
 
 #' 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
@@ -965,8 +948,8 @@ assert_has_variables <- function(dataset, required_vars) {
 #'
 #' @export
 #'
-#' @keywords assertion
-#' @family assertion
+#' @keywords deprecated
+#' @family deprecated
 #' @examples
 #' example_fun <- function(fun) {
 #'   assert_function(fun, params = c("x"))
@@ -1029,32 +1012,9 @@ assert_function <- function(arg, params = NULL, optional = FALSE) {
 #' the function given by `arg`
 #'
 #' @export
-#'
-#' @examples
-#' hello <- function(name) {
-#'   print(sprintf("Hello %s", name))
-#' }
-#'
-#' assert_function_param("hello", "name")
-#'
-#' try(assert_function_param("hello", "surname"))
 assert_function_param <- function(arg, params) {
-  assert_character_scalar(arg)
-  assert_character_vector(params)
-  fun <- match.fun(arg)
-
-  is_param <- params %in% names(formals(fun))
-  if (!all(is_param)) {
-    txt <- if (sum(!is_param) == 1L) {
-      "%s is not an argument of `%s()`"
-    } else {
-      "%s are not arguments of `%s()`"
-    }
-    err_msg <- sprintf(txt, enumerate(params[!is_param]), arg)
-    abort(err_msg)
-  }
-
-  invisible(arg)
+  deprecate_warn("0.5.0", "assert_function_param()", "assert_function()", always = TRUE)
+  assert_function(arg = arg, params = params)
 }
 
 #' Asserts That a Parameter is Provided in the Expected Unit

R/dev_utilities.R

@@ -162,12 +162,11 @@ contains_vars <- function(arg) {
 #' vars2chr(exprs(USUBJID, AVAL))
 vars2chr <- function(expressions, quosures) {
   if (!missing(quosures)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.10.0",
       "vars2chr(quosures = )",
       "vars2chr(expressions = )"
     )
-    expressions <- map(quosures, rlang::quo_get_expr)
   }
   rlang::set_names(
     map_chr(expressions, as_string),

R/get.R

@@ -86,12 +86,11 @@ get_duplicates <- function(x) {
 #' @export
 get_source_vars <- function(expressions, quosures) {
   if (!missing(quosures)) {
-    deprecate_warn(
+    deprecate_stop(
       "0.10.0",
       "get_source_vars(quosures = )",
       "get_source_vars(expressions = )"
     )
-    expressions <- map(quosures, rlang::quo_get_expr)
   }
   assert_varval_list(expressions, optional = TRUE)
 

R/quo.R

@@ -1,30 +1,3 @@
-#' Concatenate One or More Quosure(s)
-#'
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `expr_c()` instead.
-#'
-#' @param ... One or more objects of class `quosure` or `quosures`
-#'
-#' @return An object of class `quosures`
-#'
-#'
-#' @keywords deprecated
-#' @family deprecated
-#'
-#' @export
-quo_c <- function(...) {
-  deprecate_stop(
-    "0.3.0",
-    "quo_c()",
-    "expr_c()",
-    details = paste(
-      "Expressions created by `exprs()` must be used",
-      "instead of quosures created by `vars()`."
-    )
-  )
-}
-
 #' Concatenate One or More Expressions
 #'
 #' @param ... One or more expressions or list of expressions
@@ -53,30 +26,6 @@ expr_c <- function(...) {
   inputs[!is_null]
 }
 
-#' Check Whether an Argument Is Not a Quosure of a Missing Argument
-#'
-#' @param x Test object
-#'
-#' @return TRUE or error.
-#'
-#'
-#' @keywords deprecated
-#' @family deprecated
-#'
-#' @export
-quo_not_missing <- function(x) {
-  deprecate_stop(
-    "0.3.0",
-    "quo_not_missing()",
-    details = paste(
-      "Due to changing from `vars()` to `exprs()` the function is no longer required.",
-      "It will be removed in future.",
-      sep = "\n"
-    )
-  )
-}
-
-
 #' Replace Expression Value with Name
 #'
 #' @param expressions A list of expressions
@@ -101,7 +50,6 @@ replace_values_by_names <- function(expressions, quosures) {
       "replace_values_by_names(quosures = )",
       "replace_values_by_names(expressions = )"
     )
-    expressions <- map(quosures, rlang::quo_get_expr)
   }
   if (is.null(names(expressions))) {
     return(expressions)
@@ -114,40 +62,6 @@ replace_values_by_names <- function(expressions, quosures) {
   })
 }
 
-#' Replace Symbols in a Quosure
-#'
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `replace_symbol_in_expr()` instead.
-#'
-#' @param quosure Quosure
-#'
-#' @param target Target symbol
-#'
-#' @param replace Replacing symbol
-#'
-#'
-#' @return The quosure where every occurrence of the symbol `target` is replaced
-#'   by `replace`
-#'
-#' @keywords deprecated
-#' @family deprecated
-#'
-#' @export
-replace_symbol_in_quo <- function(quosure,
-                                  target,
-                                  replace) {
-  deprecate_stop(
-    "0.3.0",
-    "replace_symbol_in_quo()",
-    "replace_symbol_in_expr()",
-    details = paste(
-      "Expressions created by `exprs()` must be used",
-      "instead of quosures created by `vars()`."
-    )
-  )
-}
-
 #' Replace Symbols in an Expression
 #'
 #' Replace symbols in an expression

docs/pkgdown.yml

@@ -1,4 +1,4 @@
-pandoc: 2.11.4
+pandoc: 2.19.2
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -7,10 +7,11 @@ articles:
   git_usage: git_usage.html
   pr_review_guidance: pr_review_guidance.html
   programming_strategy: programming_strategy.html
+  rcmd_issues: rcmd_issues.html
   release_strategy: release_strategy.html
   unit_test_guidance: unit_test_guidance.html
   writing_vignettes: writing_vignettes.html
-last_built: 2023-04-12T17:21Z
+last_built: 2023-06-26T16:08Z
 urls:
   reference: https://pharmaverse.github.io/admiraldev/devel/reference
   article: https://pharmaverse.github.io/admiraldev/devel/articles