appease codecov. modify docs. and refactor run_cargo

DESCRIPTION

@@ -73,3 +73,4 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 SystemRequirements: Rust 'cargo'; the crate 'libR-sys' must compile
     without error
+Config/rextendr/version: 0.3.1.9001

R/clean.R

@@ -31,8 +31,10 @@ clean <- function(path = ".", echo = TRUE) {
 
   if (!dir.exists(target_dir)) {
     cli::cli_abort(
-      "Could not clean binaries.",
-      "Target directory not found at {.path target_dir}.",
+      c(
+        "Could not clean binaries.",
+        "Target directory not found at {.path target_dir}."
+      ),
       call = rlang::caller_call(),
       class = "rextendr_error"
     )
@@ -52,7 +54,6 @@ clean <- function(path = ".", echo = TRUE) {
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo
   )
 

R/license_note.R

@@ -4,8 +4,6 @@
 #' recursive dependencies in Rust crate.
 #'
 #' @param path character scalar, the R package directory
-#' @param echo logical scalar, whether to print cargo command and outputs to the
-#' console (default is `TRUE`)
 #' @param quiet logical scalar, whether to signal successful writing of
 #' LICENSE.note (default is `FALSE`)
 #' @param force logical scalar, whether to regenerate LICENSE.note if
@@ -21,11 +19,9 @@
 #' }
 write_license_note <- function(
     path = ".",
-    echo = TRUE,
     quiet = FALSE,
     force = TRUE) {
   check_string(path, class = "rextendr_error")
-  check_bool(echo, class = "rextendr_error")
   check_bool(quiet, class = "rextendr_error")
   check_bool(force, class = "rextendr_error")
 
@@ -42,8 +38,7 @@ write_license_note <- function(
   metadata <- run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
-    echo = echo,
+    echo = FALSE,
     parse_json = TRUE
   )
 

R/read_cargo_metadata.R

@@ -1,26 +1,27 @@
 #' Retrieve metadata for packages and workspaces
 #'
 #' @param path character scalar, the R package directory
-#' @param dependencies logical scalar, whether to include all recursive
-#' dependencies in stdout (default is FALSE)
-#' @param echo logical scalar, should cargo command and outputs be printed to
-#' console (default is TRUE)
+#' @param dependencies Default `FALSE`. A logical scalar, whether to include
+#' all recursive dependencies in stdout.
+#' @param echo Default `FALSE`. A logical scalar, should cargo command and
+#'  outputs be printed to the console.
 #'
 #' @details
 #' For more details, see
 #' \href{https://doc.rust-lang.org/cargo/commands/cargo-metadata.html}{Cargo docs}
 #' for `cargo-metadata`. See especially "JSON Format" to get a sense of what you
 #' can expect to find in the returned list.
 #'
-#' @return `list`, including the following elements:
-#' - "packages"
-#' - "workspace_members"
-#' - "workspace_default_members"
-#' - "resolve"
-#' - "target_directory"
-#' - "version"
-#' - "workspace_root"
-#' - "metadata"
+#' @returns
+#' A `list` including the following elements:
+#' - `packages`
+#' - `workspace_members`
+#' - `workspace_default_members`
+#' - `resolve`
+#' - `target_directory`
+#' - `version`
+#' - `workspace_root`
+#' - `metadata`
 #'
 #' @export
 #'
@@ -32,7 +33,7 @@
 read_cargo_metadata <- function(
     path = ".",
     dependencies = FALSE,
-    echo = TRUE) {
+    echo = FALSE) {
   check_string(path, class = "rextendr_error")
   check_bool(dependencies, class = "rextendr_error")
   check_bool(echo, class = "rextendr_error")
@@ -53,7 +54,6 @@ read_cargo_metadata <- function(
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo,
     parse_json = TRUE
   )

R/run_cargo.R

@@ -6,37 +6,36 @@
 #' @param args character vector, the Cargo subcommand and flags to be executed.
 #' @param wd character scalar, location of the Rust crate, (default is
 #' `find_extendr_crate()`).
-#' @param error_on_status, logical scalar, whether to error if `status != 0`,
-#' (default is `TRUE`).
-#' @param echo_cmd logical scalar, whether to print Cargo subcommand and flags
-#' to the console (default is `TRUE`).
-#' @param echo logical scalar, whether to print standard output and error to the
-#' console (default is `TRUE`).
+#' @param error_on_status Default `TRUE`. A logical scalar, whether to error on a non-zero exist status.
+#' @param echo_cmd Default `TRUE`. A logical scalar, whether to print Cargo subcommand and flags
+#' to the console.
+#' @param echo Default `TRUE`. Alogical scalar, whether to print standard output and error to the
+#' console.
 #' @param env character vector, environment variables of the child process.
-#' @param parse_json logical scalar, whether to parse JSON-structured standard
-#' output (default is `FALSE`).
-#' @param error_call call scalar, from rlang docs: "the defused call with which
-#' the function running in the frame was invoked." (default is
-#' `rlang::caller_call()`)
-#'
-#' @return if `parse_json = TRUE`, result of parsing JSON-structured standard
-#' output; otherwise, standard output is returned as a character scalar.
+#' @param parse_json Default `FALSE`. A logical scalar, whether to parse JSON-structured standard
+#' output using [`jsonlite::parse_json()`] with `simplifyDataFrame = TRUE`.
+#' @param error_call Default [`rlang::caller_call()`]. The defused call with which
+#' the function running in the frame was invoked.
+#' @param ... additional arguments passed to [`processx::run()`].
+#' @returns
+#' A list with elements `status`, `stdout`, `stderr`, and `timeout`. See [`processx::run()`]. If `parse_json = TRUE`, result of parsing JSON-structured standard
+#' output.
 #'
 #' @keywords internal
 #' @noRd
 run_cargo <- function(
     args,
     wd = find_extendr_crate(),
     error_on_status = TRUE,
-    echo_cmd = TRUE,
     echo = TRUE,
     env = get_cargo_envvars(),
     parse_json = FALSE,
-    error_call = rlang::caller_call()) {
+    error_call = rlang::caller_call(), 
+    ...
+) {
   check_character(args, call = error_call, class = "rextendr_error")
   check_string(wd, call = error_call, class = "rextendr_error")
   check_bool(error_on_status, call = error_call, class = "rextendr_error")
-  check_bool(echo_cmd, call = error_call, class = "rextendr_error")
   check_bool(echo, call = error_call, class = "rextendr_error")
   check_character(env, call = error_call, class = "rextendr_error")
   check_bool(parse_json, call = error_call, class = "rextendr_error")
@@ -46,9 +45,10 @@ run_cargo <- function(
     args = args,
     error_on_status = error_on_status,
     wd = wd,
-    echo_cmd = echo_cmd,
+    echo_cmd = echo,
     echo = echo,
-    env = env
+    env = env,
+    ...
   )
 
   stdout <- out[["stdout"]]
@@ -62,8 +62,18 @@ run_cargo <- function(
   }
 
   if (parse_json) {
-    stdout <- jsonlite::parse_json(stdout, simplifyDataFrame = TRUE)
+    res <- rlang::try_fetch(
+      jsonlite::parse_json(stdout, simplifyDataFrame = TRUE),
+      error = function(cnd) {
+        cli::cli_abort(
+          c("Failed to {.code stdout} as json:", " " = "{stdout}"),
+          parent = cnd,
+          class = "rextendr_error"
+        )
+      }
+    )
+    return(res)
   }
 
-  stdout
-}
+  out
+}

R/use_crate.R

@@ -99,7 +99,6 @@ use_crate <- function(
   run_cargo(
     args,
     wd = find_extendr_crate(path = path),
-    echo_cmd = echo,
     echo = echo
   )
 

tests/testthat/test-clean.R

@@ -11,8 +11,15 @@ test_that("rextendr::clean() removes cargo target directory & binaries", {
 
   expect_equal(length(dir("src", pattern = "testpkg\\..*")), 1)
   expect_true(dir.exists(file.path("src", "rust", "target")))
+
+  # clean once
   clean()
 
+  # we expect an error the second time
+  expect_error(clean())
+
+  expect_error(clean(1L))
+  expect_error(clean(echo = NULL))
   expect_equal(length(dir("src", pattern = "testpkg\\..*")), 0)
   expect_false(dir.exists(file.path("src", "rust", "target")))
 })

tests/testthat/test-license_note.R

@@ -3,8 +3,15 @@ test_that("LICENSE.note is generated properly", {
   skip_if_cargo_unavailable(c("license", "--help"))
 
   local_package("testPackage")
+
+  # try running write_license_note() when there is nothing present
+  dir.create(file.path("src", "rust"), recursive = TRUE)
+  expect_error(write_license_note())
+
+  # create license note for extendr package 
   use_extendr()
   write_license_note()
-
   expect_snapshot(cat_file("LICENSE.note"))
+  expect_error(write_license_note(path = NULL))
+  expect_error(write_license_note(force = "yup"))
 })

tests/testthat/test-use_crate.R

@@ -15,16 +15,15 @@ test_that("use_crate() adds dependency to package or workspace", {
     path = path
   )
 
-  metadata <- read_cargo_metadata(path)
+  metadata <- read_cargo_metadata(path, echo = FALSE)
 
   dependency <- metadata[["packages"]][["dependencies"]][[1]]
   dependency <- dependency[dependency[["name"]] == "serde", ]
 
   expect_equal(dependency[["name"]], "serde")
-
   expect_equal(dependency[["features"]][[1]], "derive")
-
   expect_equal(dependency[["req"]], "^1.0.1")
+
 })
 
 test_that("use_crate() errors when user passes git and version arguments", {

tests/testthat/test-utils.R

@@ -20,3 +20,16 @@ test_that("`try_exec_cmd()` returns stdout when command is available", {
   echo <- "This is an echo"
   expect_equal(try_exec_cmd("echo", echo), echo)
 })
+
+
+test_that("`replace_na()` respects type", {
+  x <- 1:5
+  x[2] <- NA
+  expect_error(replace_na(x, "L"))
+})
+
+test_that("`replace_na()` replaces with the correct value", {
+  x <- 1:5
+  x[2] <- NA_integer_
+  expect_identical(replace_na(x, -99L), c(1L, -99L, 3L, 4L, 5L))
+})