feat: setup pre-commit and handle linting errors

.Rbuildignore

@@ -1,19 +1,21 @@
-^whirl\.Rproj$
-^\.Rproj\.user$
 ^LICENSE\.md$
-^_pkgdown\.yml$
-^docs$
-^pkgdown$
 ^README\.Rmd$
-^\.lintr$
+^\.Rproj\.user$
 ^\.github$
-^inst/output$
+^\.lintr$
+^\.pre-commit-config\.yaml$
+^_pkgdown\.yml$
+^dev/
+^docs$
 ^inst/examples/*\\.html$
 ^inst/examples/*_files$
-^dev/
-summary.html
-plot1.png
-^whirl\.Rcheck$
+^inst/output$
+^pkgdown$
+^vignettes/articles$
 ^whirl.*\.tar\.gz$
 ^whirl.*\.tgz$
-^vignettes/articles$
+^whirl\.Rcheck$
+^whirl\.Rproj$
+^înst/WORDLIST$
+plot1.png
+summary.html

.github/workflows/check_and_co.yaml

@@ -7,6 +7,9 @@ on:
     branches:
       - main
       - master
+permissions:
+  contents: write
+  pull-requests: write
 name: All actions
 jobs:
   check-current-version:

.pre-commit-config.yaml

@@ -0,0 +1,90 @@
+# All available hooks: https://pre-commit.com/hooks.html
+# R specific hooks: https://github.com/lorenzwalthert/precommit
+repos:
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.3.9003
+    hooks:
+    # -   id: style-files
+    #     args: [--style_pkg=styler, --style_fun=tidyverse_style]
+    -   id: roxygenize
+        additional_dependencies:
+          - checkmate
+          - dplyr
+          - ggplot2
+          - httr
+          - jsonlite
+          - kableExtra
+          - options
+          - quarto
+          - rmarkdown
+          - sessioninfo
+          - tibble
+          - tidyr
+          - unglue
+          - NovoNordisk-OpenSource/zephyr
+          - reticulate
+    -   id: use-tidy-description
+    -   id: spell-check
+        exclude: >
+          (?x)^(
+          .*\.[rR]|
+          .*\.feather|
+          .*\.jpeg|
+          .*\.pdf|
+          .*\.png|
+          .*\.py|
+          .*\.RData|
+          .*\.rds|
+          .*\.Rds|
+          .*\.Rproj|
+          .*\.sh|
+          (.*/|)\.gitignore|
+          (.*/|)\.gitlab-ci\.yml|
+          (.*/|)\.lintr|
+          (.*/|)\.pre-commit-.*|
+          (.*/|)\.Rbuildignore|
+          (.*/|)\.Renviron|
+          (.*/|)\.Rprofile|
+          (.*/|)\.travis\.yml|
+          (.*/|)appveyor\.yml|
+          (.*/|)NAMESPACE|
+          (.*/|)renv/settings\.dcf|
+          (.*/|)renv\.lock|
+          (.*/|)WORDLIST|
+          \.github/workflows/.*|
+          data/.*|
+          )$
+    # -   id: lintr
+    -   id: readme-rmd-rendered
+    -   id: parsable-R
+    -   id: no-browser-statement
+    # -   id: no-print-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+    -   id: pkgdown
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: check-added-large-files
+        args: ['--maxkb=200']
+    -   id: file-contents-sorter
+        files: '^\.Rbuildignore$'
+    -   id: end-of-file-fixer
+        exclude: '\.Rd'
+-   repo: https://github.com/pre-commit-ci/pre-commit-ci-config
+    rev: v1.6.1
+    hooks:
+    # Only required when https://pre-commit.ci is used for config validation
+    -   id: check-pre-commit-ci-config
+-   repo: local
+    hooks:
+    -   id: forbid-to-commit
+        name: Don't commit common R artifacts
+        entry: Cannot commit .Rhistory, .RData, .Rds or .rds.
+        language: fail
+        files: '\.(Rhistory|RData|Rds|rds)$'
+        # `exclude: <regex>` to allow committing specific files
+
+ci:
+    autoupdate_schedule: monthly
+    skip: [pkgdown]

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: whirl
 Title: Logging package
-Version: 0.1.7
+Version: 0.1.7.9000
 Authors@R: c(
     person("Aksel", "Thomsen", , "[email protected]", role = c("aut", "cre")),
     person("Lovemore", "Gakava", , "[email protected]", role = "aut"),
@@ -10,7 +10,7 @@ Authors@R: c(
     person("Vladimir", "Obucina", , email = "[email protected]", role = "aut"),
     person("Novo Nordisk A/S", role = "cph")
   )
-Description: Provides functionalities for running R scripts in batch, while simultanously creating logs for each script execution.
+Description: Provides functionalities for running R scripts in batch, while simultaneously creating logs for each script execution.
 License: Apache License (>= 2)
 URL: https://novonordisk-opensource.github.io/whirl/, https://github.com/novonordisk-opensource/whirl
 Depends: 
@@ -47,7 +47,7 @@ Suggests:
     testthat (>= 3.0.0),
     usethis
 Remotes: 
-    NovoNordisk-OpenSource/zephyr
+    NovoNordisk-OpenSource/zephyr@a4d5163108e2c4042f98bd00f17f1af7353b08c2
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,3 +1,7 @@
+# whirl dev
+* Added pre-commit for developers
+* Fixed linting errors
+
 # whirl 0.1.7 (2024-12-17)
 * Enable redirection of logs through the `log_dir` argument in `run()`.
 * Changed the title on the individual logs to the script name and moved the path to a distinct section within the title-block.

R/approvedpkgs.R

@@ -2,7 +2,7 @@
 #'
 #' An utility function to help you build your approved packages .
 #' @noRd
 check_approved <- function(approved_pkg_folder,
                            approved_pkg_url,
                            session_pkgs,
                            output_file = NULL) {
@@ -34,7 +34,10 @@
         ) |>
         dplyr::select("Package", "Version", "Repository")
       session_pkgs |>
-        dplyr::left_join(src_url, by = c("package" = "Package", "loadedversion" = "Version")) |>
+        dplyr::left_join(
+          y = src_url,
+          by = c("package" = "Package", "loadedversion" = "Version")
+        ) |>
         dplyr::mutate(
           Approved = ifelse(is.na(.data[["Repository"]]), "No", "Yes"),
           "Approved Repository" = url
@@ -56,7 +59,10 @@
         ) |>
         dplyr::select("Package", "Version", "Repository")
       session_pkgs |>
-        dplyr::left_join(src_file, by = c("package" = "Package", "loadedversion" = "Version")) |>
+        dplyr::left_join(
+          y = src_file,
+          by = c("package" = "Package", "loadedversion" = "Version")
+        ) |>
         dplyr::mutate(
           Approved = ifelse(is.na(.data[["Repository"]]), "No", "Yes"),
           "Approved Repository" = folder
@@ -69,17 +75,30 @@
 
   if (is.null(approved_pkg_folder)) {
     approved_dset <- approved_dset_url |>
-      dplyr::select("package", "loadedversion", "date", "source", "Approved", "Approved Repository") |>
+      dplyr::select(
+        "package", "loadedversion", "date", "source", "Approved",
+        "Approved Repository"
+      ) |>
       dplyr::rename("Repository URL" = "Approved Repository") |>
       dplyr::arrange(.data[["Approved"]], .data[["package"]])
   } else if (is.null(approved_pkg_url) || length(approved_pkg_url) == 0) {
     approved_dset <- approved_dset_file |>
-      dplyr::select("package", "loadedversion", "date", "source", "Approved", "Approved Repository") |>
+      dplyr::select(
+        "package", "loadedversion", "date", "source", "Approved",
+        "Approved Repository"
+      ) |>
       dplyr::rename("Repository Folder" = "Approved Repository") |>
       dplyr::arrange(.data[["Approved"]], .data[["package"]])
   } else {
-    approved_dset <- dplyr::full_join(approved_dset_url, approved_dset_file, by = c("package", "loadedversion")) |>
-      dplyr::select("package", "loadedversion", "date.x", "source.x", "Approved.x", "Approved Repository.x", "Approved.y", "Approved Repository.y") |>
+    approved_dset <- dplyr::full_join(
+      x = approved_dset_url,
+      y = approved_dset_file,
+      by = c("package", "loadedversion")
+    ) |>
+      dplyr::select(
+        "package", "loadedversion", "date.x", "source.x", "Approved.x",
+        "Approved Repository.x", "Approved.y", "Approved Repository.y"
+      ) |>
       dplyr::rename(
         "date" = "date.x",
         "source" = "source.x",
@@ -88,7 +107,11 @@
         "Approved in Repository URL" = "Approved.x",
         "Approved in Repository Folder" = "Approved.y"
       ) |>
-      dplyr::arrange(.data[["Approved in Repository URL"]], .data[["Approved in Repository Folder"]], .data[["package"]])
+      dplyr::arrange(
+        .data[["Approved in Repository URL"]],
+        .data[["Approved in Repository Folder"]],
+        .data[["package"]]
+      )
   }
 
   if (is.null(output_file)) {
@@ -103,18 +126,36 @@
 create_approval_plot <- function(data) {
   row.names(data) <- NULL
 
-  data$grpvar <- ifelse(rowSums(as.matrix(data[, grepl("^Approved", colnames(data))]) == "No") == ncol(as.matrix(data[, grepl("^Approved", colnames(data))])), "No", "Yes")
+  data$grpvar <- ifelse(
+    rowSums(as.matrix(data[, grepl("^Approved", colnames(data))]) == "No") ==
+      ncol(as.matrix(data[, grepl("^Approved", colnames(data))])),
+    "No", "Yes"
+  )
 
   data |>
     dplyr::count(.data[["grpvar"]]) |>
     dplyr::mutate(
       pct = prop.table(.data[["n"]]),
       status = "grpvar",
-      lbl = paste0(.data[["grpvar"]], ": ", .data[["n"]], "/", sum(.data[["n"]]), " (", scale_to_percent(.data[["pct"]]), ")")
+      lbl = paste0(
+        .data[["grpvar"]], ": ",
+        .data[["n"]], "/",
+        sum(.data[["n"]]), " (",
+        scale_to_percent(.data[["pct"]]), ")"
+      )
     ) |>
-    ggplot2::ggplot(ggplot2::aes(x = .data[["pct"]], y = .data[["status"]], fill = .data[["grpvar"]], label = .data[["lbl"]])) +
+    ggplot2::ggplot(
+      mapping = ggplot2::aes(
+        x = .data[["pct"]],
+        y = .data[["status"]],
+        fill = .data[["grpvar"]],
+        label = .data[["lbl"]]
+      )
+    ) +
     ggplot2::geom_bar(position = "fill", stat = "identity") +
-    ggplot2::geom_text(position = ggplot2::position_stack(vjust = 0.5, reverse = FALSE)) +
+    ggplot2::geom_text(
+      position = ggplot2::position_stack(vjust = 0.5, reverse = FALSE)
+    ) +
     ggplot2::theme_void() +
     ggplot2::theme(
       legend.position = "none",

R/custom_logging.R

@@ -3,14 +3,15 @@
 #' Useful for e.g. read and write operations on databases etc.
 #' that are not automatically captured.
 #'
-#' The default environment variable `WHIRL_LOG_MSG` is set in the session used to log scripts, and input
-#' is automatically captured in the resulting log.
+#' The default environment variable `WHIRL_LOG_MSG` is set in the session used
+#' to log scripts, and input is automatically captured in the resulting log.
 #'
-#' If run outside of whirl, meaning when the above environment variable is unset, the operations
-#' are streamed to `stdout()`. By default the console.
+#' If run outside of whirl, meaning when the above environment variable is
+#' unset, the operations are streamed to `stdout()`. By default the console.
 #'
 #' @name custom_logging
-#' @param file [character()] description of the file that was read, written or deleted.
+#' @param file [character()] description of the file that was read, written or
+#' deleted.
 #' @param log [character()] path to the log file.
 NULL
 
@@ -37,17 +38,15 @@ write_to_log <- function(
     file,
     type = c("read", "write", "delete"),
     log = Sys.getenv("WHIRL_LOG_MSG")) {
-
   type <- rlang::arg_match(type)
   checkmate::assert_string(type)
   checkmate::assert_string(file)
   checkmate::assert_string(log)
-  time <- Sys.time()
 
   x <- log_df(
     type = type,
     file = file
-    )
+  )
 
   if (log == "") {
     jsonlite::stream_out(x = x, verbose = FALSE)
@@ -60,7 +59,6 @@ write_to_log <- function(
 
 #' @noRd
 read_from_log <- function(log = Sys.getenv("WHIRL_LOG_MSG")) {
-
   if (log == "" || !file.exists(log)) {
     return(log_df())
   }
@@ -83,7 +81,6 @@ log_df <- function(type = character(), file = character()) {
 
 #' @noRd
 split_log <- function(log_df, types = c("read", "write", "delete")) {
-
   class(log_df) <- c("whirl_log_info", class(log_df))
 
   # Split in a tibble for each type of output
@@ -108,7 +105,7 @@ split_log <- function(log_df, types = c("read", "write", "delete")) {
 }
 
 #' @noRd
-knit_print.whirl_log_info <- function(x, ...) {
+knit_print.whirl_log_info <- function(x, ...) { # nolint
   x |>
     knitr::kable(
       row.names = FALSE