Merge pull request #32 from NovoNordisk-OpenSource/feat/cran-prep

feat: prep for CRAN

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: zephyr
-Title: Tools for Informing Users and Control Options
-Version: 0.0.4.9001
+Title: Structured Messages and Options
+Version: 0.0.5
 Authors@R: c(
     person("Aksel", "Thomsen", , "[email protected]", role = c("aut", "cre")),
     person("Mathias Lerbech", "Jeppesen", , "[email protected]", role = "aut"),
@@ -11,23 +11,25 @@ Authors@R: c(
     person("Vladimir", "Obucina", , "[email protected]", role = "aut"),
     person("Novo Nordisk A/S", role = "cph")
   )
-Description: Tools for helping developers of R packages to create consistent
-  messages for their users and enables a streamlined control of options
-  in their packages.
+Description: Provides a structured framework for consistent user
+    communication and configuration management for package developers.
 License: Apache License (>= 2)
 URL: https://novonordisk-opensource.github.io/zephyr/,
-    https://github.com/NovoNordisk-OpenSource/zephyr
+    https://github.com/novonordisk-opensource/zephyr
+BugReports: https://github.com/novonordisk-opensource/zephyr/issues
+Depends: 
+    R (>= 4.1)
 Imports: 
     cli,
     glue,
-    rlang
+    rlang (>= 1.0.0)
 Suggests: 
     callr,
     checkmate,
     devtools,
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0),
+    testthat (>= 3.1.5),
     usethis,
     withr
 Config/testthat/edition: 3

LICENSE.md

@@ -179,7 +179,7 @@ recommend that a file or class name and description of purpose be included on
 the same “printed page” as the copyright notice for easier identification within
 third-party archives.
 
-    Copyright 2024 Novo Nordisk A/S, Danish company registration no. 24256790
+    Copyright 2025 Novo Nordisk A/S, Danish company registration no. 24256790
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.

R/checkmate.R

@@ -13,6 +13,7 @@
 #' if any assertions failed
 #' @param .envir The `[environment]` to use for the error message.
 #' Default `parent.frame()` will be sufficient for most use cases.
+#' @returns `invisible(TRUE)`
 #' @examples
 #' add_numbers <- function(a, b) {
 #'   collection <- checkmate::makeAssertCollection()

R/msg.R

@@ -36,7 +36,7 @@
 #' Default `parent.frame()` will be sufficient for most use cases. Parsed on to
 #' `msg_fun()`.
 #'
-#' @return Return from `msg_fun()`
+#' @returns Return from `msg_fun()`
 #'
 #' @examples
 #' msg("General message")

R/options.R

@@ -144,6 +144,7 @@ get_option <- function(name, .envir = sys.function(which = -1)) {
 #' each option.
 #' @param .envir Environment in which the options are defined.
 #' Default is suitable for use inside your package.
+#' @returns `list` or `character` depending on `as`
 #' @examples
 #' # List all options in zephyr
 #' x <- list_options(.envir = "zephyr")

R/use_zephyr.R

@@ -9,6 +9,10 @@
 #' This code also creates an package specific `verbosity_level` option,
 #' enabling you to control the verbosity of your package functions using
 #' the [msg] functions.
+#' @returns `invisible(TRUE)`
+#' @examplesIf FALSE
+#' use_zephyr()
+#'
 #' @export
 use_zephyr <- function() {
   cli::cli_h1("Setting up {.pkg zephyr}")

README.Rmd

@@ -39,6 +39,15 @@ For packages outside our ecosystem, we recommend using the
 [options](https://cran.r-project.org/package=options) package  
 instead for a more complete implementation of package options.
 
+## Installation
+
+```{r, eval=FALSE}
+# Install the released version from CRAN:
+install.packages("zephyr")
+# Install the development version from GitHub:
+pak::pak("NovoNordisk-OpenSource/zephyr")
+```
+
 ## Use zephyr
 
 The easiest way to use zephyr in your package is to set it up with the 

README.md

@@ -25,6 +25,15 @@ For packages outside our ecosystem, we recommend using the
 [options](https://cran.r-project.org/package=options) package  
 instead for a more complete implementation of package options.
 
+## Installation
+
+``` r
+# Install the released version from CRAN:
+install.packages("zephyr")
+# Install the development version from GitHub:
+pak::pak("NovoNordisk-OpenSource/zephyr")
+```
+
 ## Use zephyr
 
 The easiest way to use zephyr in your package is to set it up with the

cran-comments.md

@@ -1,15 +1,5 @@
-## Overview
-* This is a new lightweight package that provide a wrapper around the cli package as a useful way of providing messages for both users and developers when developing new functions
-
-* The messages can be turned on/off by utilizing environmental options which is a convenient way of controlling the level of messages for both users and developers.  
-
-## Test Environment
-* Ubuntu 18.04 LTS (on github actions), devel, release, oldrel-1
-* Windows Server 2019 (on github actions), release
-* macOS (on github actions), release
-
-
 ## R CMD check results
-0 errors | 0 warnings | 1 note
 
-* This is the first submission.
+0 errors | 0 warnings | 0 note
+
+* This is a new release.

inst/WORDLIST

@@ -1,4 +1,5 @@
 Aksel
+BugReports
 CMD
 Cervan
 Compats

tests/testthat/test-checkmate.R

@@ -1,4 +1,6 @@
 test_that("report assertions", {
+  skip_if_not_installed("checkmate")
+
   add_numbers <- function(a, b) {
     collection <- checkmate::makeAssertCollection()
     checkmate::assert_numeric(x = a, add = collection)

tests/testthat/test-integration.R

@@ -1,6 +1,12 @@
-run_output <- function(func, extra_lib) {
+run_output <- function(func, extra_lib, args = list()) {
   libpath <- c(extra_lib, .libPaths())
-  callr::r(func = func, show = TRUE, libpath = libpath, spinner = FALSE)
+  callr::r(
+    func = func,
+    args = args,
+    show = TRUE,
+    libpath = libpath,
+    spinner = FALSE
+  )
 }
 
 run_output_project <- function(func, extra_lib, project) {
@@ -21,6 +27,9 @@ libpath <- withr::local_tempdir()
 test_that("integration in new package", {
   skip_on_cran()
   skip_on_covr()
+  skip_if_not_installed("withr")
+  skip_if_not_installed("usethis")
+  skip_if_not_installed("devtools")
 
   # Settings
 
@@ -42,8 +51,24 @@ test_that("integration in new package", {
   )
 
   # Install zephyr in tmp libpath
+  pkg <- file.path(test_path(), "../..")
+  if (file.exists(file.path(pkg, "DESCRIPTION"))) {
+    pkg <- "."
+  } else {
+    skip_on_os("windows")
+    pkg <- file.path(pkg, "zephyr") |>
+      normalizePath()
+  }
 
-  run_output(\() devtools::install(quiet = TRUE), libpath) |>
+  run_output(
+    \(p) devtools::install( # nolint: brace_linter
+      pkg = p,
+      quiet = TRUE,
+      quick = TRUE
+    ),
+    libpath,
+    list(p = pkg)
+  ) |>
     expect_true()
 
   # Use in new package
@@ -69,6 +94,14 @@ test_that("integration in new package", {
 test_that("use in new package", {
   skip_on_cran()
   skip_on_covr()
+  skip_if_not_installed("withr")
+  skip_if_not_installed("usethis")
+  skip_if_not_installed("devtools")
+  skip_if_not_installed("callr")
+  skip_if(
+    condition = !file.exists(file.path(libpath, "testpkg")),
+    message = "testpkg not installed - expected if test above has been skipped"
+  )
 
   run_output(\() testpkg::greet("there"), libpath) |>
     expect_output("hello there")

tests/testthat/test-msg.R

@@ -22,6 +22,7 @@ test_that("Default verbosity work as intended", {
 })
 
 test_that("Minimal verbosity has the expected behavior", {
+  skip_if_not_installed("withr")
   withr::local_options(list(zephyr.verbosity_level = "minimal"))
 
   msg("This gives a message for everything except quiet") |>
@@ -47,6 +48,7 @@ test_that("Minimal verbosity has the expected behavior", {
 })
 
 test_that("Quiet gives no messages", {
+  skip_if_not_installed("withr")
   withr::local_options(list(zephyr.verbosity_level = "quiet"))
 
   msg("This gives a message for everything except quiet") |>

tests/testthat/test-options.R

@@ -29,6 +29,8 @@ test_that("get_option", {
   get_option("test_option", .envir = testenv) |>
     expect_equal(42, info = "Should return default when no option is set")
 
+  skip_if_not_installed("withr")
+
   withr::local_envvar(list(R_TESTENV_TEST_OPTION = "200"))
 
   get_option("test_option", .envir = testenv) |>

tests/testthat/test-use_zephyr.R

@@ -1,4 +1,7 @@
 test_that("use_zephyr", {
+  skip_if_not_installed("withr")
+  skip_if_not_installed("usethis")
+
   rlang::local_interactive(FALSE)
   withr::local_options(usethis.quiet = TRUE)
 

tests/testthat/test-utils.R

@@ -10,6 +10,8 @@ test_that("sys_getenv", {
   sys_getenv("fake_env") |>
     expect_null()
 
+  skip_if_not_installed("withr")
+
   withr::with_envvar(
     new = list(myenv = "myvalue"),
     code = {

tests/testthat/test-verbosity_level.R

@@ -2,6 +2,8 @@ test_that("simple verbosity level", {
   get_verbosity_level() |>
     expect_equal("verbose")
 
+  skip_if_not_installed("withr")
+
   withr::with_options(
     list(zephyr.verbosity_level = "invalid"),
     {
@@ -49,6 +51,8 @@ test_that("verbosity level respects priority hierarchy when used in package", {
   expect_equal(get_verbosity_level(test_env), "verbose")
 
   # Test 2: Package-specific option (highest priority)
+  skip_if_not_installed("withr")
+
   withr::with_options(list(testpkg.verbosity_level = "debug"), {
     expect_equal(get_verbosity_level(test_env), "debug")
   })
@@ -112,6 +116,8 @@ test_that("get_all_verbosity_levels", {
   get_all_verbosity_levels() |>
     expect_equal(c(zephyr = "verbose"))
 
+  skip_if_not_installed("withr")
+
   withr::with_namespace(c("cli", "glue"), {
     withr::local_options(list(
       zephyr.verbosity_level = "quiet",