apply styler (#13)

* apply styler

* fix working directory when linting in ci

* fix linting issues

.github/workflows/R-packages.yaml

@@ -34,6 +34,7 @@ jobs:
         with:
           extra-packages: any::lintr, local::.
           needs: lint
+          working-directory: packages/r/${{ matrix.package }}
 
       - name: Lint -- run `styler::style_pkg()` if this fails!
         working-directory: packages/r/${{ matrix.package }}

packages/r/openproblems/.Rbuildignore

@@ -1,3 +1,4 @@
 ^LICENSE\.md$
 ^\.gitignore$
-^CHANGELOG\.md$
+^CHANGELOG\.md$
+^\.lintr$

packages/r/openproblems/.lintr

@@ -0,0 +1,3 @@
+linters: linters_with_defaults(
+    line_length_linter(120)
+  )

packages/r/openproblems/CHANGELOG.md

@@ -20,6 +20,8 @@ Initial release
 
 * `find_project_root`: simplify implementation (PR #11).
 
+* Clean up code formatting with `styler::style_pkg()` (PR #13).
+
 ## TESTING
 
 * Add tests for `find_project_root` (PR #11).

packages/r/openproblems/R/deep_merge.R

@@ -1,14 +1,14 @@
 #' Deep merge two lists
-#' 
+#'
 #' This function will merge two lists recursively. If both lists
 #' are named lists, the keys will be merged. If both lists are
 #' lists, they will be appended. Otherwise, the second list will
 #' override the first list.
-#' 
+#'
 #' @param obj1 The first object
 #' @param obj2 The second object
 #' @return The merged list
-#' 
+#'
 #' @noRd
 #' @examples
 #' deep_merge(list(a = 1, b = 2), list(b = 3, c = 4))
@@ -44,4 +44,4 @@ deep_merge <- function(obj1, obj2) {
     # else override list1 with list2
     obj2
   }
-}
+}

packages/r/openproblems/R/find_project_root.R

@@ -24,4 +24,4 @@ find_project_root <- function(path) {
   }
 
   as.character(path)
-}
+}

packages/r/openproblems/R/is_named_list.R

@@ -1,16 +1,16 @@
 #' Check if an object is a named list
-#' 
+#'
 #' @param obj An object
 #' @return TRUE if the object is a named list, FALSE otherwise
-#' 
+#'
 #' @noRd
-#' 
-#' @examples 
-#' is_named_list(list(a = 1, b = 2))    # TRUE
-#' is_named_list(list(1, 2))            # FALSE
-#' is_named_list(NULL)                  # TRUE
-#' is_named_list(list())                # TRUE
-#' is_named_list(c(1, 2, 3))            # FALSE
+#'
+#' @examples
+#' is_named_list(list(a = 1, b = 2)) # TRUE
+#' is_named_list(list(1, 2)) # FALSE
+#' is_named_list(NULL) # TRUE
+#' is_named_list(list()) # TRUE
+#' is_named_list(c(1, 2, 3)) # FALSE
 is_named_list <- function(obj) {
   is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj))))
-}
+}

packages/r/openproblems/R/read_nested_yaml.R

@@ -17,25 +17,28 @@
 #' }
 read_nested_yaml <- function(path, project_path = find_project_root(path)) {
   path <- normalizePath(path, mustWork = FALSE)
-  data <- tryCatch({
-    suppressWarnings(yaml::read_yaml(path))
-  }, error = function(e) {
-    stop("Could not read ", path, ". Error: ", e)
-  })
+  data <- tryCatch(
+    {
+      suppressWarnings(yaml::read_yaml(path))
+    },
+    error = function(e) {
+      stop("Could not read ", path, ". Error: ", e)
+    }
+  )
   process_nested_yaml(data, data, path, project_path)
 }
 
 #' Process the merge keys in a YAML
-#' 
+#'
 #' This function will recursively process the merge keys in a YAML
-#' 
+#'
 #' @param data The YAML data
 #' @param root_data The root YAML data
 #' @param path The path to the current YAML file
 #' @param project_path The path to the root of the Viash project
-#' 
+#'
 #' @noRd
-process_nested_yaml <- function(data, root_data, path, project_path) {
+process_nested_yaml <- function(data, root_data, path, project_path) { # nolint cyclocomp_linter
   if (is_named_list(data)) {
     # check whether children have `__merge__` entries
     processed_data <- lapply(data, function(dat) {
@@ -72,11 +75,14 @@ process_nested_yaml <- function(data, root_data, path, project_path) {
             new_data_path <- normalizePath(new_data_path, mustWork = FALSE)
 
             # read in the new data
-            tryCatch({
-              suppressWarnings(yaml::read_yaml(new_data_path))
-            }, error = function(e) {
-              stop("Could not read ", new_data_path, ". Error: ", e)
-            })
+            tryCatch(
+              {
+                suppressWarnings(yaml::read_yaml(new_data_path))
+              },
+              error = function(e) {
+                stop("Could not read ", new_data_path, ". Error: ", e)
+              }
+            )
           }
         x_root <- x
 

packages/r/openproblems/R/read_viash_config.R

@@ -19,9 +19,8 @@
 #'
 #' @export
 read_viash_config <- function(
-  target_config_path,
-  project_root_dir = find_project_root(target_config_path)
-) {
+    target_config_path,
+    project_root_dir = find_project_root(target_config_path)) {
   # note: if this config was not generated by viash, use `viash config view` first?
   config <- read_nested_yaml(target_config_path)
 

packages/r/openproblems/R/resolve_path.R

@@ -28,4 +28,4 @@ resolve_path <- function(path, project_path, parent_path) {
     paste0(project_path, path),
     fs::path_abs(path, parent_path)
   )
-}
+}

packages/r/openproblems/R/strip_margin.R

@@ -1,4 +1,3 @@
-
 #' Strip margin from a string
 #'
 #' @param text A character vector.
@@ -13,4 +12,4 @@
 #'   |")
 strip_margin <- function(text, symbol = "\\|") {
   gsub(paste0("(^|\n)[ \t]*", symbol), "\\1", text)
-}
+}

packages/r/openproblems/tests/testthat/test-find_project_root.R

@@ -1,4 +1,3 @@
-
 test_that("find_project_root works", {
   # create a temporary directory with a _viash.yaml file
   # project/
@@ -54,4 +53,4 @@ test_that("find_project_root works", {
   expect_null(
     find_project_root(temp_dir)
   )
-})
+})