Merge pull request #275 from pharmaverse/devel

0.4 release (related to admiral 0.11.0)

Author: zdz2101

.Rprofile

@@ -1,4 +1,14 @@
-if (Sys.getenv("GITHUB_ACTIONS") == "" || (Sys.getenv("GITHUB_ACTIONS") == "true" && getRversion()$major == 3 && getRversion()$minor == 6)) {
+# Set renv profile base on R version.
+if ((Sys.getenv("GITHUB_ACTIONS") == "") && (Sys.getenv("DOCKER_CONTAINER_CONTEXT") == "")) {
+  renv_profile <- paste(R.version$major, substr(R.version$minor, 1, 1), sep = ".")
+  if (file.exists("./renv/profile")) {
+    message("Using renv profile from `renv/profile` file.")
+  } else if (renv_profile %in% c("4.1", "4.2", "4.3")) {
+    message("Set renv profile to `", renv_profile, "`")
+    Sys.setenv("RENV_PROFILE" = renv_profile)
+  } else {
+    message("This repository do not contains the renv profile for your R version.")
+  }
   source("renv/activate.R")
 } else {
   options(repos = c(CRAN = "https://cran.rstudio.com"))

.github/workflows/common.yml

@@ -45,25 +45,25 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/style.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   spellcheck:
     name: Spelling
     uses: pharmaverse/admiralci/.github/workflows/spellcheck.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   readme:
     name: Render README
     uses: pharmaverse/admiralci/.github/workflows/readme-render.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   validation:
     name: Validation
     uses: pharmaverse/admiralci/.github/workflows/r-pkg-validation.yml@main
     if: github.event_name == 'release'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   check:
     name: Check
     uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
@@ -73,7 +73,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/pkgdown.yml@main
     if: github.event_name == 'push'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip multiversion docs
       # Note that if you have multiple versions of docs,
       # your URL links are likely to break due to path changes
@@ -85,7 +85,7 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/lintr.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
   links:
     name: Links
     uses: pharmaverse/admiralci/.github/workflows/links.yml@main
@@ -97,7 +97,7 @@ jobs:
     if: >
       github.event_name == 'push' || github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"
       # Whether to skip code coverage badge creation
       # Setting to 'false' will require you to create
       # an orphan branch called 'badges' in your repository
@@ -107,4 +107,4 @@ jobs:
     uses: pharmaverse/admiralci/.github/workflows/man-pages.yml@main
     if: github.event_name == 'pull_request'
     with:
-      r-version: "4.0"
+      r-version: "4.1"

.lintr

@@ -1,2 +1,11 @@
-linters: with_defaults(line_length_linter(100), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20))
-exclusions: list("R/data.R")
+linters: linters_with_defaults(
+    line_length_linter(100),
+    object_usage_linter=NULL,
+    cyclocomp_linter(complexity_limit = 20),
+    undesirable_function_linter = undesirable_function_linter()
+  )
+exclusions: list(
+    "R/data.R" = Inf,
+    "inst" = list(undesirable_function_linter = Inf),
+    "vignettes" = list(undesirable_function_linter = Inf)
+  )

.lycheeignore

@@ -11,3 +11,6 @@ tj-actions/branch-names@v5.2
 file:///home/runner/work/admiraldev/admiraldev/.github/workflows/pkgdown
 file:///home/runner/work/admiraldev/admiraldev/.github/workflows/style.yml%60
 file:///home/runner/work/admiraldev/admiraldev/.github/workflows/sd-repo
+https://packagemanager.posit.co/cran/2021-05-03/
+https://packagemanager.posit.co/cran/2022-01-03/
+https://packagemanager.posit.co/cran/2023-04-20/

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: admiraldev
 Type: Package
 Title: Utility Functions and Development Tools for the Admiral Package Family
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Ben", "Straub", email = "ben.x.straub@gsk.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),
@@ -22,15 +22,16 @@ Description: Utility functions to check data, variables and conditions for funct
  'admiral' and 'admiral' extension packages.  Additional utility helper functions to assist developers 
  with maintaining documentation, testing and general upkeep of 'admiral' and 'admiral' extension packages.  
 License: Apache License (>= 2)
+BugReports: https://github.com/pharmaverse/admiraldev/issues
 URL: https://pharmaverse.github.io/admiraldev/main/, https://github.com/pharmaverse/admiraldev/
 Encoding: UTF-8
 Language: en-US
 LazyData: false
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: R (>= 3.5)
 Imports:
-    dplyr (>= 0.8.4),
+    dplyr (>= 1.0.5),
     hms (>= 0.5.3),
     lifecycle (>= 0.1.0),
     lubridate (>= 1.7.4),

NAMESPACE

@@ -12,6 +12,7 @@ export(assert_data_frame)
 export(assert_date_var)
 export(assert_date_vector)
 export(assert_expr)
+export(assert_expr_list)
 export(assert_filter_cond)
 export(assert_function)
 export(assert_function_param)
@@ -20,6 +21,7 @@ export(assert_integer_scalar)
 export(assert_list_element)
 export(assert_list_of)
 export(assert_logical_scalar)
+export(assert_named)
 export(assert_named_exprs)
 export(assert_numeric_vector)
 export(assert_one_to_one)

NEWS.md

@@ -1,3 +1,33 @@
+# admiraldev 0.4.0
+
+## New Features
+
+- New function `assert_named()` to check if all elements of an argument are
+named (#241)
+- New function `assert_expr_list()` to check if an argument is a list of
+expressions (#241)
+
+- Added a **Report a bug** link on `admiraldev` website (#257)
+
+## Updates of Existing Functions
+
+## Breaking Changes
+
+- `assert_order_vars()` was deprecated in favor of `assert_expr_list()`. (#241)
+- The following functions have been deprecated from previous admiral versions using the next phase of the deprecation process: (#272)
+
+  - `quo_c()`
+  - `quo_not_missing()`
+  - `replace_symbol_in_quo()`
+- The `quosures` argument was replaced by the `expressions` argument in `replace_values_by_names()`.
+
+## Documentation
+
+- The deprecation strategy was updated regarding unit tests for deprecated
+functions/arguments in phase 1. (#247)
+
+- The programming strategy was updated regarding permitted values and calling functions from package dependencies (#72, #253)
+
 # admiraldev 0.3.0
 
 ## New Features

R/addin_format_testthat.R

@@ -1,4 +1,3 @@
-
 # Returns the call for updating a given test_that test file
 # by adding a function name, a test number, and a section.
 # Call the function either by using RStudio Addin "format_test_that_file" or
@@ -13,7 +12,7 @@ prepare_test_that_file <- function(path) {
   }
 
   # check that testthat is used and testing file is opened
-  uses_test_file <- grepl("tests/testthat/test-", path, fixed = T)
+  uses_test_file <- grepl("tests/testthat/test-", path, fixed = TRUE)
   if (!uses_test_file) {
     stop("This Addin works only on unit test files that follow a testthat structure.")
   }