Delint and debug

.Rbuildignore

@@ -1,3 +1,4 @@
+.coderabbit.yaml
 .lintr
 .codecov.yaml
 ^Makefile$

.coderabbit.yaml

@@ -0,0 +1,15 @@
+# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json
+language: "en-US"
+early_access: false
+reviews:
+  profile: "chill"
+  request_changes_workflow: false
+  high_level_summary: false
+  poem: false
+  review_status: true
+  collapse_walkthrough: false
+  auto_review:
+    enabled: true
+    drafts: false
+chat:
+  auto_reply: false

.lintr

@@ -1,14 +1,13 @@
-linters: linters_with_defaults(
-    line_length_linter(305),
-    commented_code_linter = NULL,
-    object_name_linter = NULL,
-    indentation_linter = NULL,
-    infix_spaces_linter = NULL,
-    spaces_left_parentheses_linter = NULL,
-    seq_linter = NULL,
-    vector_logic_linter = NULL,
-    function_left_parentheses_linter = NULL,
-    semicolon_linter = NULL,
-    T_and_F_symbol_linter = NULL,
-    object_usage_linter = NULL
+linters: linters_with_tags(
+    tags = c(
+        "default", 
+        "best_practices_linters",
+        "common_mistakes",
+        "correctness",
+        "executing"
+        ),
+    line_length_linter(305),  # TODO — change to 120
+    seq_linter = NULL,  # TODO - small refactor
+    cyclocomp_linter(complexity_limit = 16),  # TODO - small refactor
+    object_name_linter = NULL # Probably never gonna remove this one
   )

Makefile

@@ -1,9 +1,9 @@
 # Makefile for R project
 
-.PHONY: all install document test check-cran lint clean
+.PHONY: all install document update-test-fixtures test check-cran fix-style lint clean
 
 # Default target
-all: install document test test-coverage check check-cran
+all: fix-style install document test check-cran
 
 # Install dependencies
 install:
@@ -15,17 +15,26 @@ install:
 document:
 	Rscript -e "devtools::document()"
 
+# Update test fixtures
+update-test-fixtures:
+	Rscript inst/data-raw/build_test_data.R
+
 # Run unit tests
 test:
-	Rscript -e "devtools::test(stop_on_failure=TRUE)"
+	Rscript -e "Sys.setenv(NOT_CRAN='true'); devtools::test(stop_on_failure=TRUE, stop_on_warning=TRUE)"
 
 # Run R CMD check as CRAN
 check-cran: document
 	Rscript -e "devtools::check(cran=T, remote=T, manual=T, error_on='note')"
 
-# Auto lint the code
-lint:
+# Auto style the code
+fix-style:
 	Rscript -e "styler::style_pkg()"
+	Rscript -e "styler::style_dir('inst/')"
+
+# Check the code for lint
+lint:
+	Rscript -e "lintr::lint_package()"
 
 # Clean up generated files
 clean:

R/S3GenericExtenstions.R

@@ -11,31 +11,32 @@
 #' @export
 #' @examples
 #' \dontrun{
-#'  model_list1 <- caretList(Class ~ .,
-#'   data=Sonar, trControl = ctrl1,
+#' model_list1 <- caretList(Class ~ .,
+#'   data = Sonar, trControl = ctrl1,
 #'   tuneList = list(
-#'                  glm=caretModelSpec(method='glm', family='binomial'),
-#'                  rpart=caretModelSpec(method='rpart')
-#'                  ),
-#'    metric='ROC')
+#'     glm = caretModelSpec(method = "glm", family = "binomial"),
+#'     rpart = caretModelSpec(method = "rpart")
+#'   ),
+#'   metric = "ROC"
+#' )
 #'
 #' model_list2 <- caretList(Class ~ .,
-#'                          data=Sonar,
-#'                          trControl = ctrl1,
-#'                          tuneList = list(
-#'                            glm=caretModelSpec(method='rpart'),
-#'                            rpart=caretModelSpec(method='rf')
-#'                          ),
-#'                          metric='ROC')
+#'   data = Sonar,
+#'   trControl = ctrl1,
+#'   tuneList = list(
+#'     glm = caretModelSpec(method = "rpart"),
+#'     rpart = caretModelSpec(method = "rf")
+#'   ),
+#'   metric = "ROC"
+#' )
 #'
-#'  bigList <- c(model_list1, model_list2)
+#' bigList <- c(model_list1, model_list2)
 #' }
 #'
 c.caretList <- function(...) {
-
   new_model_list <- unlist(lapply(list(...), function(x) {
-    if(! inherits(x, "caretList")) {
-      if(! inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
+    if (!inherits(x, "caretList")) {
+      if (!inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
 
       ## assuming this is a single train object
       x <- list(x)
@@ -66,23 +67,24 @@ c.caretList <- function(...) {
 #' @examples
 #' \dontrun{
 #' rpartTrain <- train(Class ~ .,
-#'                     data=Sonar,
-#'                     trControl = ctrl1,
-#'                     method='rpart')
+#'   data = Sonar,
+#'   trControl = ctrl1,
+#'   method = "rpart"
+#' )
 #'
 #' rfTrain <- train(Class ~ .,
-#'                  data=Sonar,
-#'                  trControl = ctrl1,
-#'                  method='rf')
+#'   data = Sonar,
+#'   trControl = ctrl1,
+#'   method = "rf"
+#' )
 #'
-#'  bigList <- c(model_list1, model_list2)
+#' bigList <- c(model_list1, model_list2)
 #' }
 #'
 c.train <- function(...) {
-
   new_model_list <- unlist(lapply(list(...), function(x) {
-    if(! inherits(x, "caretList")) {
-      if(! inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
+    if (!inherits(x, "caretList")) {
+      if (!inherits(x, "train")) stop("class of modelList1 must be 'caretList' or 'train'")
 
       ## assuming this is a single train object
       x <- list(x)

R/caretEnsemble-package.R

@@ -57,12 +57,15 @@ NULL
 #' @keywords data
 NULL
 
-#Hack to make data.table functions work with devtools::load_all
-#http://stackoverflow.com/questions/23252231/r-data-table-breaks-in-exported-functions
-#http://r.789695.n4.nabble.com/Import-problem-with-data-table-in-packages-td4665958.html
+# Hack to make data.table functions work with devtools::load_all
+# http://stackoverflow.com/questions/23252231/r-data-table-breaks-in-exported-functions
+# http://r.789695.n4.nabble.com/Import-problem-with-data-table-in-packages-td4665958.html
 assign(".datatable.aware", TRUE)
 
-#Avoid false positives in R CMD CHECK:
+# Avoid false positives in R CMD CHECK:
 utils::globalVariables(
-  c(".fitted", ".resid", "method", "id", "yhat",
-    "ymax", "yavg", "ymin", "metric", "metricSD", "n"))
+  c(
+    ".fitted", ".resid", "method", "id", "yhat",
+    "ymax", "yavg", "ymin", "metric", "metricSD", "n"
+  )
+)