Merge pull request #69 from pharmaverse/61-address-lintr-updates

Closes #61: fixed linter config and findings

.lintr

@@ -1,2 +1,2 @@
-linters: with_defaults(line_length_linter(125), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20), object_name_linter(styles = c("snake_case", "symbols", "dotted.case")), single_quotes_linter=NULL)
+linters: linters_with_defaults(line_length_linter(125), object_usage_linter=NULL, cyclocomp_linter(complexity_limit = 20), object_name_linter(styles = c("snake_case", "symbols", "dotted.case")))
 exclusions: list("R/data.R")

R/autos.R

@@ -21,7 +21,7 @@ set_autos <- function(autos, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"))
 
   # Must be named list
   if (!is_named(autos)) {
-    stop("Paths for autos in your envsetup configuration file must be named", call.=FALSE)
+    stop("Paths for autos in your envsetup configuration file must be named", call. = FALSE)
   }
 
   for (i in seq_along(autos)) {
@@ -30,7 +30,7 @@ set_autos <- function(autos, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"))
     if (length(cur_autos) > 1) {
       # Hierarchical paths must be named
       if (!is_named(cur_autos)) {
-        stop("Hierarchical autos paths in your envsetup configuration file must be named", call.=FALSE)
+        stop("Hierarchical autos paths in your envsetup configuration file must be named", call. = FALSE)
       }
 
       # envsetup_environ must be used if using hierarchical paths
@@ -43,7 +43,7 @@ set_autos <- function(autos, envsetup_environ = Sys.getenv("ENVSETUP_ENVIRON"))
     }
 
     if (!is.null(names(cur_autos)) && !envsetup_environ %in% names(cur_autos)
-        && envsetup_environ != ""){
+        && envsetup_environ != "") {
       warning(paste(
         "The", ui_field(names(autos[i])), "autos has named",
         "environments",  ui_field(names(cur_autos)),
@@ -105,7 +105,7 @@ attach_auto <- function(path, name) {
   if (!(dir.exists(path) || file.exists(path))) {
     # Check if the auto actually exists
     warning(sprintf("An autos path specified in your envsetup configuration file does not exist: %s = %s", name, path),
-         call.=FALSE)
+            call. = FALSE)
   } else if (file.exists(path) && !dir.exists(path)) {
     # if file, source it
     sys.source(path, envir = attach(NULL, name = name_with_prefix))
@@ -282,13 +282,13 @@ detach_autos <- function() {
 #' # see autos are still above purrr in the search path
 #' search()
 library <- function(..., pos = NULL) {
-  if(is.null(pos)) {
-      ## we have at least one package loaded (envsetup itself)
-      ## use earliest current package position as place to
-      ## attach all future packages, regardless of what
-      ## envsetup, devtools, or anything else has put
-      ## in front of them
-      pos <- min(grep("^package:", search()))
+  if (is.null(pos)) {
+    ## we have at least one package loaded (envsetup itself)
+    ## use earliest current package position as place to
+    ## attach all future packages, regardless of what
+    ## envsetup, devtools, or anything else has put
+    ## in front of them
+    pos <- min(grep("^package:", search()))
   }
   base::library(..., pos = pos)
-}
+}

R/init.R

@@ -68,15 +68,15 @@ init <- function(project, config_path = NULL, create_paths = NULL) {
         ui_info(
           c("The following paths in your configuration do not exist:",
             paths[missing_directories])
-          )
+        )
 
         # if not, ask if user would like them built
         if (is.null(create_paths)) {
           create_paths <-
             usethis::ui_yeah(
               "Would you like us to create your directories to match your configuration?",
               n_no = 1
-          )
+            )
         }
 
         if (!create_paths) {
@@ -134,7 +134,8 @@ envsetup_write_rprofile <- function(add, file) {
 
   # if there is a call to `rprofile()` in the .Rprofile, assume setup was already done and exit
   if (any(grepl("rprofile\\(", before))) {
-    warning("It looks like your project has already been initialized to use envsetup. Manually adjust your .Rprofile if you need to change the environment setup.",
+    warning("It looks like your project has already been initialized to use envsetup.
+            Manually adjust your .Rprofile if you need to change the environment setup.",
       call. = FALSE
     )
     return(invisible())

R/paths.R

@@ -218,7 +218,7 @@ object_in_path <- function(path, object) {
 
 #' Build directory structure from a configuration file
 #'
-#' @param config configuration object from config::get() containing paths#'
+#' @param config configuration object from config::get() containing paths
 #' @param root root directory to build from.
 #' Leave as NULL if using absolute paths.  Set to working directory if using relative paths.
 #'

R/utils.R

@@ -63,8 +63,6 @@
 #' validate_config(config::get(file = file.path(tmpdir, "no_paths.yml")))
 validate_config <- function(config) {
   validate_paths(config)
-
-  # validate_autos(config)
 }
 
 

tests/testthat/ref/envre.R

@@ -2,14 +2,14 @@ test_envre <- list()
 
 test_envre$PDEV <- get_path(
   topdrv, "PDEV", username, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PREPROD <- get_path(
   topdrv, "PREPROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PROD <- get_path(
   topdrv, "PROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 envre_loc <- "pdev"

tests/testthat/ref/envre_preprod.R

@@ -2,14 +2,14 @@ test_envre <- list()
 
 test_envre$PDEV <- get_path(
   topdrv, "PDEV", username, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PREPROD <- get_path(
   topdrv, "PREPROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PROD <- get_path(
   topdrv, "PROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 envre_loc <- "preprod"

tests/testthat/ref/envre_prod.R

@@ -2,14 +2,14 @@ test_envre <- list()
 
 test_envre$PDEV <- get_path(
   topdrv, "PDEV", username, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PREPROD <- get_path(
   topdrv, "PREPROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 test_envre$PROD <- get_path(
   topdrv, "PROD", NA, compound, protocol, dbrelease, rpteff, "analysis"
-  )
+)
 
 envre_loc <- "prod"

tests/testthat/ref/func.R

@@ -1,3 +1,3 @@
 func <- function() {
   print(rlang::env_parent())
-  }
+}

tests/testthat/test-autos.R

@@ -45,13 +45,16 @@ test_that("Autos validation from yml happens correctly", {
 
   # Hierarchical list is named
   expect_error(
-    set_autos(list(project = c("path1", "path2"))), "Hierarchical autos paths in your envsetup configuration file must be named"
+    set_autos(list(project = c("path1", "path2"))),
+    "Hierarchical autos paths in your envsetup configuration file must be named"
   )
 
   # Paths are characters
-  expect_error(set_autos(list(global = 1)), "Paths provided for autos must be directories")
+  expect_error(set_autos(list(global = 1)),
+               "Paths provided for autos must be directories")
 
-  expect_warning(set_autos(list(x = "/bad/path/")), "An autos path specified in your envsetup configuration file does not exist")
+  expect_warning(set_autos(list(x = "/bad/path/")),
+                 "An autos path specified in your envsetup configuration file does not exist")
 })
 
 # Detatch and re-setup for QA now
@@ -108,16 +111,17 @@ test_that("Autos no longer exist when detached", {
 
 test_that("the configuration can be named anything and library will
           reattach the autos correctly", {
-  suppressMessages(rprofile(custom_name))
+    suppressMessages(rprofile(custom_name))
 
-  expect_invisible(suppressPackageStartupMessages(library("purrr")))
+    expect_invisible(suppressPackageStartupMessages(library("purrr")))
 
-  purrr_location <- which(search() == "package:purrr")
-  autos_locatios <- which(grepl("^autos:", search()))
+    purrr_location <- which(search() == "package:purrr")
+    autos_locatios <- which(grepl("^autos:", search()))
 
-  expect_true(all(purrr_location > autos_locatios))
-  detach("package:purrr")
-})
+    expect_true(all(purrr_location > autos_locatios))
+    detach("package:purrr")
+  }
+)
 
 
 test_that("Autos warns user when ENVSETUP_ENVIRON does not match named environments in autos", {

tests/testthat/test-paths.R

@@ -86,11 +86,16 @@ test_that("1.1", {
 #' @editor Aidan Ceney
 #' @editDate 2022-05-12
 test_that("1.2", {
-  expect_error(readr::read_csv(read_path(data,
-    "iris.csv",
-    full.path = TRUE,
-    envsetup_environ = "PROD"
-  )))
+  expect_error(
+    readr::read_csv(
+      read_path(
+        data,
+        "iris.csv",
+        full.path = TRUE,
+        envsetup_environ = "PROD"
+      )
+    )
+  )
 })
 
 #' @editor Aidan Ceney

tests/testthat/test-rprofile.R

@@ -41,7 +41,7 @@ test_that("rprofile stores the configuration", {
   stored_config <- base::get(
     "auto_stored_envsetup_config",
     pos = which(search() == "envsetup:paths")
-    )
+  )
 
   expect_equal(custom_name, stored_config)
 })

vignettes/config.Rmd

@@ -155,11 +155,11 @@ writeLines(
   paste0(
 "default:
   paths:
-    data: !expr list(DEV = '",dir,"/demo/DEV/username/project1/data', PROD = '",dir,"/demo/PROD/project1/data')
-    output: '",dir,"/demo/DEV/username/project1/output'
-    programs: '",dir,"/demo/DEV/username/project1/programs'
+    data: !expr list(DEV = '", dir,"/demo/DEV/username/project1/data', PROD = '", dir, "/demo/PROD/project1/data')
+    output: '", dir, "/demo/DEV/username/project1/output'
+    programs: '", dir, "/demo/DEV/username/project1/programs'
     envsetup_environ: !expr Sys.setenv(ENVSETUP_ENVIRON = 'DEV'); 'DEV'"
-  ), file_conn)
+ ), file_conn)
 close(file_conn)
 ```