[GitHub Actions] Style code

chrisholbrook · chrisholbrook · commit 0eca5e97c2df · 2026-04-03T18:27:04.000Z
diff --git a/R/load-read_glatos_workbook.r b/R/load-read_glatos_workbook.r
@@ -143,7 +143,6 @@ read_glatos_workbook <- function(
   wb_version = NULL,
   simplify = TRUE
 ) {
-  
   # See version-specific file specifications
   # internal glatos_workbook_spec in R/sysdata.r
 
@@ -156,7 +155,6 @@ read_glatos_workbook <- function(
 
   #-Workbook v1.3, v1.4--------------------------------------------------------------
   if (wb_version %in% c("1.3", "1.4")) {
-    
     # Get sheet names in external file
     wb_sheets <- readxl::excel_sheets(wb_file)
 
@@ -167,26 +165,38 @@ read_glatos_workbook <- function(
       } else {
         wb_sheets[tolower(wb_sheets) %in% names(glatos_workbook_schema$v1.3)]
       }
-    
+
     # Identify extra (project-specific) sheets
-    extra_sheets <- setdiff(tolower(sheets_to_read), 
-                            names(glatos_workbook_schema$v1.3))
-    
+    extra_sheets <- setdiff(
+      tolower(sheets_to_read),
+      names(glatos_workbook_schema$v1.3)
+    )
+
     # Check that extra sheet names do not match any standard sheet names
-    invalid_sheet_names <- 
-      if(simplify){ intersect(extra_sheets, 
-                                      c("metadata",
-                                        "animals",
-                                        "receivers"))
-      } else { NULL }
-
-    if(length(invalid_sheet_names) > 0) stop("When `read_all = TRUE` and ",
-                                              "`simplify = TRUE`, ",
-                                             "a project specific sheet cannot ",
-                                             "be named 'metadata', 'animals' ",
-                                             "or 'receivers'.", 
-                                             call. = FALSE)
-      
+    invalid_sheet_names <-
+      if (simplify) {
+        intersect(
+          extra_sheets,
+          c(
+            "metadata",
+            "animals",
+            "receivers"
+          )
+        )
+      } else {
+        NULL
+      }
+
+    if (length(invalid_sheet_names) > 0) {
+      stop("When `read_all = TRUE` and ",
+        "`simplify = TRUE`, ",
+        "a project specific sheet cannot ",
+        "be named 'metadata', 'animals' ",
+        "or 'receivers'.",
+        call. = FALSE
+      )
+    }
+
 
     # Preallocate glatos_workbook object
     wb <- stats::setNames(
@@ -205,10 +215,9 @@ read_glatos_workbook <- function(
       value = TRUE,
       invert = TRUE
     )
-    
+
 
     for (i in 1:length(sheets_to_read)) {
-    
       schema_i <- glatos_workbook_schema[["v1.3"]][[tolower(sheets_to_read[i])]]
 
       # Specify first row to read (with headers)
@@ -229,13 +238,17 @@ read_glatos_workbook <- function(
           readxl::read_excel(
             wb_file,
             sheet = sheets_to_read[i],
-            range = if(extra_sheet_i) NULL else readxl::cell_limits(
-              ul = c(xl_first_row, 1),
-              lr = c(NA, xl_last_col)
-            ),
-            col_types = if(extra_sheet_i) NULL else "list", 
+            range = if (extra_sheet_i) {
+              NULL
+            } else {
+              readxl::cell_limits(
+                ul = c(xl_first_row, 1),
+                lr = c(NA, xl_last_col)
+              )
+            },
+            col_types = if (extra_sheet_i) NULL else "list",
             na = c("", "NA"),
-            #n_max = 0,
+            # n_max = 0,
             guess_max = 1048576,
             .name_repair = "minimal"
           ),
@@ -294,30 +307,29 @@ read_glatos_workbook <- function(
           )
       }
 
-      
+
       # Check and cast standard columns in standard sheets
-      
-      if(tolower(sheets_to_read[i]) %in% names(glatos_workbook_schema$v1.3)){
 
+      if (tolower(sheets_to_read[i]) %in% names(glatos_workbook_schema$v1.3)) {
         # Preallocate new object for parsed/cast values
         # keep as tibble here to preserve structure
         sheet_i2 <- sheet_i[]
-        
+
         # Add attribute for warnings and errors
         # warnings are warning_cast_to_check
         # errors are error_input_class_skipped and error_cast_failed
-  
+
         attr(sheet_i2, "warning_cast_to_check") <- list()
         attr(sheet_i2, "error_input_class_skipped") <- list()
         attr(sheet_i2, "error_cast_failed") <- list()
-  
-  
+
+
         # Coerce by expected column type
-  
+
         # character
         char_cols <- col_names_i[tolower(col_names_i) %in%
           with(schema_i, name[type == "character"])]
-  
+
         for (j in char_cols) {
           sheet_i2[[j]] <-
             if (nrow(sheet_i) > 0) {
@@ -328,12 +340,12 @@ read_glatos_workbook <- function(
               as.character(sheet_i[[j]])
             }
         }
-  
-  
+
+
         # numeric
         num_cols <- col_names_i[tolower(col_names_i) %in%
           with(schema_i, name[type == "numeric"])]
-  
+
         for (j in num_cols) {
           sheet_i2[[j]] <-
             if (nrow(sheet_i) > 0) {
@@ -344,16 +356,16 @@ read_glatos_workbook <- function(
               as.numeric(sheet_i[[j]])
             }
         }
-  
-  
+
+
         # POSIXct
-  
+
         # Only support POSIXct or character string that parses correctly
         # Do not accept numeric input.
-  
+
         posix_cols <- col_names_i[tolower(col_names_i) %in%
           with(schema_i, name[type == "POSIXct"])]
-  
+
         for (j in posix_cols) {
           # cast existing POSIXct or character to character
           sheet_i2[[j]] <-
@@ -365,26 +377,26 @@ read_glatos_workbook <- function(
             } else {
               as.character(sheet_i[[j]])
             }
-  
-  
+
+
           # cast character to POSIXct, enforce timezone, but return UTC
-  
+
           args_ij <- schema_i$args[schema_i$name == tolower(j)]
-  
+
           # strip spaces (for formatting consistency)
           args_ij <- gsub(" ", "", args_ij)
-  
+
           if (grepl("tz=REFCOL", args_ij)) {
             tz_col <- gsub("tz=REFCOL\\(|\\)", "", args_ij)
-  
+
             tz_ij <- paste0("US/", sheet_i[[grep(tz_col,
               names(sheet_i),
               ignore.case = TRUE
             )]])
           } else {
             tz_ij <- gsub("tz=|tz=\"|\"", "", args_ij)
           }
-  
+
           sheet_i2[[j]] <-
             if (nrow(sheet_i) > 0) {
               cast(sheet_i2[[j]],
@@ -398,19 +410,19 @@ read_glatos_workbook <- function(
             } else {
               as.POSIXct(NA, tz = tz_ij)[0]
             }
-  
+
           attr(sheet_i2[[j]], "tzone") <- "UTC"
         } # end j
-  
-  
+
+
         # Date
-  
+
         # Only support POSIXct or character string that parses correctly
         # Do not accept numeric input.
-  
+
         date_cols <- col_names_i[tolower(col_names_i) %in%
           with(schema_i, name[type == "Date"])]
-  
+
         for (j in date_cols) {
           # cast existing POSIXct or character to character
           sheet_i2[[j]] <-
@@ -423,13 +435,13 @@ read_glatos_workbook <- function(
               as.Date(NA)[0]
             }
         } # end j
-  
-  
+
+
         # Handle 'extra' columns (not in schema)
         # if multiple classes present in a column, cast to "highest-level" class
-  
+
         extra_cols <- col_names_i[!(tolower(col_names_i) %in% schema_i$name)]
-  
+
         if (read_all) {
           supported_classes <- c(
             "POSIXct",
@@ -438,16 +450,16 @@ read_glatos_workbook <- function(
             "character",
             "logical"
           )
-  
+
           for (j in extra_cols) {
             types_ij <- unique(unlist(lapply(sheet_i[[j]], class)))
-  
+
             # expect 'highest-level' observed class
             type_exp <- intersect(supported_classes, types_ij)[1]
-  
+
             # cast to type_exp
             # but if type_exp is POSIXct, cast to character
-  
+
             sheet_i2[[j]] <-
               if (nrow(sheet_i2) > 0) {
                 cast(sheet_i[[j]],
@@ -464,21 +476,17 @@ read_glatos_workbook <- function(
         } else {
           std_names_i <- names(sheet_i2)[tolower(names(sheet_i2)) %in%
             schema_i$name]
-  
+
           sheet_i2 <- sheet_i2[, std_names_i]
         }
 
         # Append to wb
         wb[[tolower(sheets_to_read[i])]] <- as.data.frame(sheet_i2)
-        
-        
       } else {
-        
         # Append to wb
         wb[[tolower(sheets_to_read[i])]] <- as.data.frame(sheet_i)
-        
       }
-      
+
 
       if (simplify) {
         # Change names of all standard columns to lowercase
diff --git a/tests/testthat/test-crw_in_polygon.r b/tests/testthat/test-crw_in_polygon.r
@@ -160,7 +160,7 @@ test_that("sf input, sf output gives expected result", {
 
 test_that("sf input, sf output gives expected result with non-default init_pos and missing cartesianCRS (issue 277)", {
   set.seed(30)
-  
+
   expect_s3_class(
     sfin_sfout <- crw_in_polygon(
       polyg = sf::st_transform(great_lakes_polygon, crs = 3175),
@@ -173,9 +173,9 @@ test_that("sf input, sf output gives expected result with non-default init_pos a
     ),
     "sf"
   )
-  
+
   expect_equal(dim(sfin_sfout), c(6, 1))
-  
+
   expect_snapshot(
     sfin_sfout
   )
diff --git a/tests/testthat/test-read_glatos_workbook.r b/tests/testthat/test-read_glatos_workbook.r
@@ -40,7 +40,7 @@ test_that("receivers element gives expected result; v1.3 (read_all = TRUE)", {
   # Check if standard part of workbook is correct
   # RECEIVER is 32nd column
   expect_equal(wb13a[["receivers"]][, -32], walleye_workbook[["receivers"]])
-  
+
   # Check if project-specific sheet is present
   expect_true("my_receivers" %in% names(wb13a))
 })
@@ -92,7 +92,7 @@ test_that("animals gives expected result; v1.4", {
 })
 
 
-# optional arg. read_all = TRUE 
+# optional arg. read_all = TRUE
 wb14a <- read_glatos_workbook(wb14_file, read_all = TRUE)
 
 test_that("receivers element gives expected result; v1.4 (read_all = TRUE)", {
@@ -105,10 +105,9 @@ test_that("receivers element gives expected result; v1.4 (read_all = TRUE)", {
   # Check if standard part of workbook is correct
   # RECEIVER is 32nd column
   expect_equal(wb14a[["receivers"]][, -32], walleye_workbook[["receivers"]])
-  
+
   # Check if project-specific sheet is present
   expect_true("my_receivers" %in% names(wb14a))
-  
 })
 
 test_that("animals gives expected result; v1.4 (read_all = TRUE)", {
@@ -122,4 +121,3 @@ test_that("animals gives expected result; v1.4 (read_all = TRUE)", {
   # Check if standard part of workbook is correct
   expect_equal(wb14a[["animals"]][, 1:55], walleye_workbook[["animals"]])
 })
-
