Update linter (#170)

* Update lint config * Fix object_usage_liner problems - local variable 'classic' assigned but may not be used excel_themes.R Replace tidyverse package with specific packages - no visible global funtion definition for `set_names` - no visible global funtion definition for `flatten_chr` - no visible global funtion definition for `str_subset` libreoffice_palettes.R Replace tidyverse package with specific packages - no visible global funtion definition for `tibble` - local variable 'name' assigned but mau not be used tests/testthat/helper-utils.R Add testthat library explicitly * Ignore examples with dontrun They cause unexpected symbol lint errors. * Update docs * Fix line length lint issues - Set line length to 120 - Ignore or fix remaining cases * Fix infix_spaces_linter warnings Put spaces around all infix operators * Fix indentation issues Style the examples while ignoring those examples with `\dontrun`. * Remove end-of-file-fixer pre-commit It was screwing up .lintr file which requires a newline, and not adding much benefit otherwise. * Remove indentation_linter Indentation formatting is handled by styler. * Fix misc linter * Fix warning * Add lint * Add lint github action * Try to fix unfound symbol warning * Misc updates * Updating * Fixing
jrnold · Feb 9, 2024 · ff59831 · ff59831
1 parent 61fccbe
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -21,3 +21,4 @@
 ^CONTRIBUTING.*$
 ^\.pre-commit-config\.yaml$
 ^CRAN-SUBMISSION$
+^scripts$
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true
diff --git a/.lintr b/.lintr
@@ -1,2 +1,19 @@
-linters: with_defaults(commented_code_linter = NULL, snake_case_linter = NULL, camel_case_linter = NULL, line_length_linter(80L), multiple_dots_linter = NULL)
-exclusions: list("./inst/examples/ex-palette_pander.R", "./inst/examples/ex-theme_economist.R")
+linters: linters_with_defaults(
+    line_length_linter(120),
+    commented_code_linter = NULL,
+    indentation_linter = NULL
+  )
+encoding: "UTF-8"
+exclusions: list(
+    "./inst/exampels/ex-few_shape_pal.R",
+    "./inst/examples/ex-calc_shape_pal.R",
+    "./inst/examples/ex-cleveland_shape_pal.R",
+    "./inst/examples/ex-few_shape_pal.R",
+    "./inst/examples/ex-palette_pander.R",
+    "./inst/examples/ex-scale_shape_stata.R",
+    "./inst/examples/ex-scale_shape_tableau.R",
+    "./inst/examples/ex-tableau_shape_pal.R",
+    "./inst/examples/ex-tableau_shape_pal.R",
+    "./inst/examples/ex-theme_calc.R",
+    "./inst/examples/ex-theme_economist.R"
+  )
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,5 @@ repos:
     rev: 'v4.5.0'
     hooks:
     -   id: check-yaml
-    -   id: end-of-file-fixer
     -   id: 'no-commit-to-branch'
         args: ['--branch', 'main']
diff --git a/Makefile b/Makefile
@@ -23,4 +23,8 @@ data:
 
 .PHONY: style
 style:
-	$(RSCRIPT) -e 'styler::style_pkg(".", style = styler::tidyverse_style, strict = TRUE)'
+	$(RSCRIPT) scripts/style.R
+
+.PHONY: lint
+lint:
+	$(RSCRIPT) -e 'devtools::lint()'
diff --git a/R/banking.R b/R/banking.R
@@ -1,5 +1,5 @@
 ## 45 degrees in radians
-FORTY_FIVE <- base::pi / 4
+FORTY_FIVE <- base::pi / 4 # nolint: object_name_linter
 
 calc_slopes <- function(x, y, cull = FALSE) {
   dx <- abs(diff(x))
@@ -102,9 +102,9 @@ calc_slopes <- function(x, y, cull = FALSE) {
 bank_slopes <- function(x, y, cull = FALSE, weight = NULL,
                         method = c("ms", "as"), ...) {
   method <- match.arg(method)
-  FUN <- bank_slopes_funs[[method]]
+  fun <- bank_slopes_funs[[method]]
   # Heer produces functions with the target alpha = w/h = x/y
-  xyrat <- FUN(calc_slopes(x, y, cull = cull), ...)
+  xyrat <- fun(calc_slopes(x, y, cull = cull), ...)
   # but coord_fixed ratio is the aspect ratio y/x
   1 / xyrat
 }

diff --git a/R/canva.R b/R/canva.R
@@ -1,3 +1,4 @@
+# nolint start
 #' 150 Color Palettes from Canva
 #'
 #' 150 four-color palettes by the
@@ -20,6 +21,7 @@
 #' }
 #' @example inst/examples/ex-canva_pal.R
 "canva_palettes"
+# nolint end
 
 #' Canva.com color palettes
 #'

diff --git a/R/few.R b/R/few.R
@@ -1,3 +1,4 @@
+# nolint start
 #' Color Palettes Few "Show Me the Numbers"
 #'
 #' Qualitative color palettes from Stephen Few (2012)
@@ -23,6 +24,7 @@
 #' @param palette One of \Sexpr[results=rd]{names(ggthemes:::rd_optlist(ggthemes::ggthemes_data$few$colors))}
 #' @family colour few
 #' @example inst/examples/ex-few_pal.R
+# nolint end
 few_pal <- function(palette = "Medium") {
   palette <- ggthemes::ggthemes_data$few$colors[[palette]]
   if (is.null(palette)) {

diff --git a/R/geom-rangeframe.R b/R/geom-rangeframe.R
@@ -31,9 +31,10 @@ geom_rangeframe <- function(mapping = NULL,
                             position = "identity",
                             ...,
                             sides = "bl",
-                            na.rm = FALSE,
-                            show.legend = NA,
-                            inherit.aes = TRUE) {
+                            na.rm = FALSE, # nolint: object_name_linter
+                            show.legend = NA, # nolint: object_name_linter
+                            inherit.aes = TRUE # nolint: object_name_linter
+) {
   layer(
     data = data,
     mapping = mapping,
@@ -56,7 +57,8 @@ geom_rangeframe <- function(mapping = NULL,
 #' @export
 #' @importFrom ggplot2 Geom
 #' @importFrom scales alpha
-GeomRangeFrame <- ggplot2::ggproto("GeomRangeFrame", ggplot2::Geom,
+GeomRangeFrame <- ggplot2::ggproto("GeomRangeFrame", # nolint: object_name_linter
+  ggplot2::Geom,
   optional_aes = c("x", "y"),
   draw_panel = function(data, panel_scales, coord, sides = "bl") {
     rugs <- list()

diff --git a/R/geom-tufteboxplot.R b/R/geom-tufteboxplot.R
@@ -69,17 +69,17 @@ geom_tufteboxplot <-
            data = NULL,
            stat = "fivenumber",
            position = "dodge",
-           outlier.colour = "black",
-           outlier.shape = 19,
-           outlier.size = 1.5,
-           outlier.stroke = 0.5,
+           outlier.colour = "black", # nolint: object_name_linter
+           outlier.shape = 19, # nolint: object_name_linter
+           outlier.size = 1.5, # nolint: object_name_linter
+           outlier.stroke = 0.5, # nolint: object_name_linter
            voffset = 0.01,
            hoffset = 0.005,
-           na.rm = FALSE,
-           show.legend = NA,
-           inherit.aes = TRUE,
-           median.type = "point",
-           whisker.type = "line",
+           na.rm = FALSE, # nolint: object_name_linter
+           show.legend = NA, # nolint: object_name_linter
+           inherit.aes = TRUE, # nolint: object_name_linter
+           median.type = "point", # nolint: object_name_linter
+           whisker.type = "line", # nolint: object_name_linter
            ...) {
     layer(
       data = data,
@@ -111,7 +111,7 @@ geom_tufteboxplot <-
 #' @importFrom ggplot2 draw_key_pointrange ggproto_parent GeomBoxplot GeomSegment GeomPoint
 #' @importFrom scales alpha
 #' @importFrom grid grobTree
-GeomTufteboxplot <-
+GeomTufteboxplot <- # nolint: object_name_linter
   ggplot2::ggproto("GeomTufteboxplot",
     ggplot2::GeomBoxplot,
     setup_data = function(self, data, params) {
@@ -123,15 +123,17 @@ GeomTufteboxplot <-
       data
     },
     draw_group = function(data, panel_scales, coord, fatten = 2,
-                          outlier.colour = "black", outlier.shape = 19,
-                          outlier.size = 1.5, outlier.stroke = 0.5,
+                          outlier.colour = "black", # nolint: object_name_linter
+                          outlier.shape = 19, # nolint: object_name_linter
+                          outlier.size = 1.5, # nolint: object_name_linter
+                          outlier.stroke = 0.5, # nolint: object_name_linter
                           varwidth = FALSE,
-                          median.type = c("point", "line"),
-                          whisker.type = c("line", "point"),
+                          median.type = c("point", "line"), # nolint: object_name_linter
+                          whisker.type = c("line", "point"), # nolint: object_name_linter
                           hoffset = 0.01,
                           voffset = 0.01) {
-      median.type <- match.arg(median.type)
-      whisker.type <- match.arg(whisker.type)
+      median.type <- match.arg(median.type) # nolint: object_name_linter
+      whisker.type <- match.arg(whisker.type) # nolint: object_name_linter
 
       common <- data.frame(
         colour = data$colour,

diff --git a/R/pander.R b/R/pander.R
@@ -1,7 +1,8 @@
 #' A ggplot theme originated from the pander package
 #'
 #' The \pkg{pander} ships with a default theme when the 'unify plots' option is
-#' enabled via \code{panderOptions}, which is now also available outside of \pkg{pander} internals, like \code{evals}, \code{eval.msgs} or \code{Pandoc.brew}.
+#' enabled via \code{panderOptions}, which is now also available outside of \pkg{pander} internals, like \code{evals},
+#' \code{eval.msgs} or \code{Pandoc.brew}.
 #' @inheritParams ggplot2::theme_bw
 #' @param nomargin suppress the white space around the plot (boolean)
 #' @param ff font family, like \code{sans}. Deprecated: use \code{base_family} instead.
@@ -18,13 +19,13 @@
 #' @param axis axis angle as defined in \code{par(les)}
 #' @export
 #' @example inst/examples/ex-theme_pander.R
-theme_pander <- function(base_size = 12,
+theme_pander <- function(base_size = 12,  # nolint: cyclocomp_linter
                          base_family = "sans",
                          nomargin = TRUE,
                          ff = NULL,
                          fc = "black",
                          fs = NULL,
-                         gM = TRUE,
+                         gM = TRUE, # nolint: object_name_linter
                          gm = TRUE,
                          gc = "grey",
                          gl = "dashed",
@@ -57,7 +58,7 @@ theme_pander <- function(base_size = 12,
       base_size <- pander::panderOptions("graph.fontsize")
     }
     if (missing(gM)) {
-      gM <- pander::panderOptions("graph.grid")
+      gM <- pander::panderOptions("graph.grid")  # nolint: object_name_linter
     }
     if (missing(gm)) {
       gm <- pander::panderOptions("graph.grid.minor")

diff --git a/R/scales.R b/R/scales.R
@@ -1,5 +1,5 @@
 # Much of this code is copied from the labeling package.
-.simplicity <- function(q, Q, j, lmin, lmax, lstep) {
+.simplicity <- function(q, Q, j, lmin, lmax, lstep) {  # nolint: object_name_linter
   eps <- .Machine$double.eps * 100
 
   n <- length(Q)
@@ -10,7 +10,7 @@
   1 - (i - 1) / (n - 1) - j + v
 }
 
-.simplicity.max <- function(q, Q, j) {
+.simplicity_max <- function(q, Q, j) {  # nolint: object_name_linter
   n <- length(Q)
   i <- match(q, Q)[1]
   v <- 1
@@ -22,7 +22,7 @@
   1 - 0.5 * ((dmax - lmax)^2 + (dmin - lmin)^2) / ((0.1 * range)^2)
 }
 
-.coverage.max <- function(dmin, dmax, span) {
+.coverage_max <- function(dmin, dmax, span) {
   range <- dmax - dmin
   if (span > range) {
     half <- (span - range) / 2
@@ -38,7 +38,7 @@
   2 - max(r / rt, rt / r)
 }
 
-.density.max <- function(k, m) {
+.density_max <- function(k, m) {
   if (k >= m) {
     2 - (k - 1) / (m - 1)
   } else {
@@ -52,9 +52,11 @@
 
 #' Pretty axis breaks inclusive of extreme values
 #'
-#' This function returns pretty axis breaks that always include the extreme  values of the data.
-#' This works by calling the extended Wilkinson algorithm (Talbot et. al, 2010), constrained to solutions interior to the data range.
-#' Then, the minimum and maximum labels are moved to the minimum and maximum of the data range.
+#' This function returns pretty axis breaks that always include the extreme values of the data.
+#' This works by calling the extended Wilkinson algorithm (Talbot et al., 2010), constrained to solutions
+#' interior to the data range.
+#' Then, the minimum and maximum labels are moved to the minimum and maximum of the data
+#' range.
 #'
 #' \code{extended_range_breaks} implements the algorithm and returns the break values.
 #' \code{scales_extended_range_breaks} uses the conventions of the \pkg{scales} package, and returns a function.
@@ -65,14 +67,16 @@
 #' @param Q set of nice numbers
 #' @param w weights applied to the four optimization components (simplicity, coverage, density, and legibility)
 #' @return For \code{extended_range_breaks}, the vector of axis label locations.
-#' For \code{scales_extended_range_breaks}, a function which takes a single argument, a vector of data, and returns the vector of axis label locations.
+#' For \code{scales_extended_range_breaks}, a function which takes a single argument, a vector of data, and returns
+#'   the vector of axis label locations.
 #' @references
-#' Talbot, J., Lin, S., Hanrahan, P. (2010) An Extension of Wilkinson's Algorithm for Positioning Tick Labels on Axes, InfoVis 2010.
+#' Talbot, J., Lin, S., Hanrahan, P. (2010) An Extension of Wilkinson's Algorithm
+#'   for Positioning Tick Labels on Axes, InfoVis 2010.
 #' @author Justin Talbot \email{jtalbot@@stanford.edu}, Jeffrey B. Arnold, Baptiste Auguie
 #' @rdname range_breaks
 #' @export
-extended_range_breaks_ <- function(dmin, dmax, n = 5,
-                                   Q = c(1, 5, 2, 2.5, 4, 3),
+extended_range_breaks_ <- function(dmin, dmax, n = 5, # nolint: cyclocomp_linter
+                                   Q = c(1, 5, 2, 2.5, 4, 3), # nolint: object_name_linter
                                    w = c(0.25, 0.2, 0.5, 0.05)) {
   eps <- .Machine$double.eps * 100
 
@@ -96,7 +100,7 @@ extended_range_breaks_ <- function(dmin, dmax, n = 5,
   j <- 1
   while (j < Inf) {
     for (q in Q) {
-      sm <- .simplicity.max(q, Q, j)
+      sm <- .simplicity_max(q, Q, j)
 
       if ((w[1] * sm + w[2] + w[3] + w[4]) < best$score) {
         j <- Inf
@@ -105,7 +109,7 @@ extended_range_breaks_ <- function(dmin, dmax, n = 5,
 
       k <- 2
       while (k < Inf) {
-        dm <- .density.max(k, n)
+        dm <- .density_max(k, n)
         if ((w[1] * sm + w[2] + w[3] * dm + w[4]) < best$score) {
           break
         }
@@ -116,7 +120,7 @@ extended_range_breaks_ <- function(dmin, dmax, n = 5,
         while (z < Inf) {
           step <- j * q * 10^z
 
-          cm <- .coverage.max(dmin, dmax, step * (k - 1))
+          cm <- .coverage_max(dmin, dmax, step * (k - 1))
 
           if ((w[1] * sm + w[2] * cm + w[3] * dm + w[4]) < best$score) {
             break
@@ -213,6 +217,7 @@ precision <- function(x) {
   10^floor(log10(span))
 }
 
+# nolint start
 #' Format numbers with automatic number of digits
 #'
 #' @param x A numeric vector to format
@@ -227,6 +232,7 @@ precision <- function(x) {
 #'
 #' @rdname smart_digits
 #' @export
+# nolint end
 smart_digits <- function(x, ...) {
   if (length(x) == 0) {
     return(character())

diff --git a/R/shapes.R b/R/shapes.R
@@ -1,3 +1,4 @@
+# nolint start
 #' Shape palette from Cleveland "Elements of Graphing Data" (discrete).
 #'
 #' Shape palettes for overlapping and non-overlapping points.
@@ -32,6 +33,7 @@
 #'
 #' @family shapes
 #' @export
+# nolint end
 cleveland_shape_pal <- function(overlap = TRUE) {
   shapes <- if (overlap[[1]]) {
     ggthemes::ggthemes_data$shapes$cleveland$overlap$pch

diff --git a/R/show.R b/R/show.R
@@ -16,7 +16,7 @@ show_shapes <- function(shapes, labels = TRUE) {
   nrow <- ceiling(n / ncol)
   x <- c(shapes, rep(NA, nrow * ncol - length(shapes)))
   x <- matrix(x, ncol = ncol, byrow = TRUE)
-  x <- x[nrow(x):1, ]
+  x <- x[rev(seq_len(nrow(x))), ]
   plot(0, 0,
     xlim = c(1, ncol(x)), ylim = c(1, nrow(x)), type = "n",
     xlab = "", ylab = "", axes = FALSE