Refactor/update dots

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 1.0.9
+Version: 1.0.9.9000
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

NAMESPACE

@@ -263,6 +263,7 @@ importFrom(rlang,is_named)
 importFrom(rlang,quo_name)
 importFrom(rlang,quos)
 importFrom(rlang,syms)
+importFrom(rlang,warn)
 importFrom(stats,as.formula)
 importFrom(stats,rnorm)
 importFrom(stats,setNames)

NEWS.md

@@ -1,3 +1,5 @@
+# mrgsolve (development version)
+
 # mrgsolve 1.0.9
 
 - Fix signatures for `compiled.mrgmod()` and `as_tibble.mrgsims()` based on new

R/Aaaa.R

@@ -29,7 +29,7 @@
 #' @importFrom magrittr %>%
 #' @importFrom tibble tibble as_tibble
 #' @importFrom rlang quos enquo enquos quo_name syms !!! !! eval_tidy as_label
-#' @importFrom rlang is_named .data abort
+#' @importFrom rlang is_named .data abort warn
 #' @importFrom lifecycle deprecate_soft deprecate_warn
 #' @importFrom glue glue
 #' @importFrom Rcpp evalCpp

R/package.R

@@ -31,8 +31,8 @@
 #' - `mrgolve.project`: sets the default project director ([mread()])
 #' - `mrgsolve.soloc`: sets the default package build directory ([mread()])
 #' - `mrgsolve_mread_quiet`: don't print messages during [mread()]
-#' - `mrgsolve.update.strict`: if `TRUE`, print warning when trying to update 
-#'   an item in the model object that doesn't exist
+#' - `mrgsolve.update.strict`: this option has been deprecated; use the `strict`
+#'   argument to [mrgsolve::update()] instead
 #' 
 #' 
 #' @description

R/update.R

@@ -30,18 +30,18 @@ all_updatable <- c(sval,other_val)
 #'
 #' After the model object is created, update various attributes.
 #'
-#' @param object a model object
-#' @param ... named items to update
+#' @param object a model object.
+#' @param ... named items to update.
 #' @param merge logical indicating to merge (rather than replace) 
-#' new and existing attributes
+#' new and existing attributes.
 #' @param open logical; used only when merge is \code{TRUE} and 
 #' parameter list or initial conditions
 #' list is being updated; if \code{FALSE}, no new items will be 
 #' added; if \code{TRUE}, the parameter list may expand.
 #' @param data a list of items to update; this list is combined 
-#' with any items passed in via \code{...}
-#' @param strict if \code{TRUE}, then an error will be generated if there is 
-#' attempt to update a non-existent item
+#' with any items passed in via \code{...}.
+#' @param strict if \code{TRUE}, a warning will be issued when there is an
+#' attempt to update a non-existent item.
 #' 
 #' @return The updated model object is returned.
 #' 
@@ -79,19 +79,22 @@ all_updatable <- c(sval,other_val)
 #' 
 #' @examples
 #' \dontrun{
-#'  mod <- mrgsolve::house()
+#'  mod <- house()
 ##'
-#'  mod <- update(mod, end=120, delta=4, param=list(CL=19.1))
+#'  mod <- update(mod, end = 120, delta = 4, param = list(CL = 19.1))
 #' }
 #'  
 #' @seealso \code{\link{update}}, \code{\link{mrgmod-class}}, 
 #' \code{\link{within}}
 #'  
 #' @export
-#'  
 setMethod("update", "mrgmod", function(object, ..., merge=TRUE, open=FALSE, 
                                        data=NULL, strict=TRUE) {
-
+  # TODO: get rid of the strict argument to `update()`
+  # TODO: get rid of the merge argument to `update()`
+  # TODO: get rid of the open argument to `update()`
+  # TODO: longer term ... error when bad arguments are passed
+
   args <- list(...)
 
   if(!is.null(data)) {
@@ -104,17 +107,30 @@ setMethod("update", "mrgmod", function(object, ..., merge=TRUE, open=FALSE,
 
   a <- names(args)
 
-  m <- charmatch(a,all_updatable)
+  m <- charmatch(a, all_updatable)
 
-  if(strict && anyNA(m)) {
-    if(getOption("mrgsolve.update.strict", FALSE)) {
-      bad <- a[is.na(m)]
-      for(b in bad) {
-        mesg <- paste0("invalid item for model object update: ", b)
-        warning(mesg, call.=FALSE, immediate.=TRUE) 
-      }
+  if(anyNA(m) && isTRUE(strict)) {
+    if(!is.null(getOption("mrgsolve.update.strict"))) {
+      msg <- c("The `mrgsolve.update.strict` option has been deprecated;", 
+               "please use the `strict` argument to `mrgsolve::update()`",
+               "instead.")
+      warn(paste0(msg, collapse = " "))  
     }
+    bad <- a[is.na(m)]
+    names(bad) <- rep("x", length(bad))
+    if(length(bad) > 1) {
+      msg <- c("The following arguments were passed to `mrgsolve::update()`,",
+               "they are either invalid names (check your spelling?) or not", 
+               "eligible attributes for update:")
+    } else {
+      msg <- c("The following argument was passed to `mrgsolve::update()`, but",
+               "it is either an invalid name (check your spelling?) or not an",
+               "eligible attribute for update:")
+    }
+    msg <- c(msg, bad)
+    warn(msg, call = NULL)
   }
+
   valid <- !is.na(m)
   a[valid] <- all_updatable[m[valid]]
   names(args) <- a
@@ -326,7 +342,7 @@ setMethod("update", "parameter_list", function(object, .y, ...) {
       wstop("[param-update] parameters must be single numeric values.")  
     }
   }
-
+  
   object@data <- update_list(
     object@data, 
     .y, 

tests/testthat/test-cache.R

@@ -39,9 +39,11 @@ test_that("model caches via mread_cache", {
 
   saveRDS(mo,cache_file)  
 
-  mod2 <- mread_cache("pk1", modlib(),compile=FALSE)
+  mod2 <- mread_cache("pk1", modlib(), compile = FALSE)
 
-  expect_equal(mod2@args$foo,mo@args$foo)
+  expect_equal(mod2@args$foo, mo@args$foo)
+
+  unlink(cache_file)
 })
 
 test_that("model caches via mcode_cache", {

tests/testthat/test-update.R

@@ -115,9 +115,23 @@ test_that("Solver setting rtol updates", {
 })
 
 test_that("bad update gives warning", {
-  options(mrgsolve.update.strict=TRUE)  
-  expect_warning(update(mod, kyle = 1), "invalid item for model object update")
-  options(mrgsolve.update.strict=FALSE)
+  expect_warning(
+    update(mod, kyle = 1), 
+    "The following argument was passed"
+  )
+  expect_warning(
+    update(mod, kyle = 1, baron = 2), 
+    "The following arguments were passed"
+  )
+})
+
+test_that("the mrgsolve.update.strict option is deprecated", {
+  options(mrgsolve.update.strict = TRUE)
+  expect_warning(
+    update(house(), foo = 2), 
+    regexp="mrgsolve\\.update\\.strict", 
+  )
+  options(mrgsolve.update.strict = NULL)
 })
 
 test_that("update outvars issue-483", {