more linting

mjskay · Feb 9, 2024 · 727dbe7 · 727dbe7
1 parent cb97af7
commit 727dbe7
Show file tree

Hide file tree

Showing 20 changed files with 189 additions and 134 deletions.
diff --git a/.lintr b/.lintr
@@ -1,13 +1,19 @@
 linters: all_linters(
     assignment_linter = NULL,
-    commas_linter(allow_trailing = TRUE),
+    commas_linter = NULL,
     consecutive_assertion_linter = NULL,
     duplicate_argument_linter(except = c("mutate", "transmute", "c")),
+    expect_identical_linter = NULL,
+    expect_null_linter = NULL,
+    expect_true_false_linter = NULL,
+    function_argument_linter = NULL,
     implicit_integer_linter = NULL,
     infix_spaces_linter(exclude_operators = c("/", "*")),
     keyword_quote_linter = NULL,
     line_length_linter(120L),
-    missing_argument_linter(except = c("alist", "quote", "switch", "pairlist2")),
+    missing_argument_linter(except = c("alist", "quote", "switch", "pairlist2", "lapply")),
+    nested_ifelse_linter = NULL,
+    nonportable_path_linter = NULL,
     numeric_leading_zero_linter = NULL,
     object_length_linter = NULL,
     object_name_linter(
@@ -16,14 +22,17 @@ linters: all_linters(
         misc = "^(F_x|x_1_hat,x_n_hat|R_inv|Amat|Aind)$",
         CamelCase = "^(RankCorr.*|.*Geom.*|.*Stat.*|Scale.*|Position.*|K|Mode.*|.*Pr.*|.*linearGradient.*|\\.Deprecated.*)$",
         dot.case = "^(na\\.rm|na\\.translate|na\\.value|lower\\.tail|log\\.p|width\\.cutoff)$",
-        bandwidth = "^(bandwidth_.*)$"
+        bandwidth = "^(bandwidth_.*)$",
+        breaks = "^breaks_.*$"
       )
     ),
     object_overwrite_linter(
       allow_names = c("dist", "data", "layout", "pdf", "q")
     ),
+    object_usage_linter = NULL,
     quotes_linter = NULL,
     scalar_in_linter = NULL,
+    todo_comment_linter = NULL,
     undesirable_function_linter(modify_defaults(
       defaults = all_undesirable_functions,
       library = NULL,

diff --git a/R/geom_dotsinterval.R b/R/geom_dotsinterval.R
@@ -375,9 +375,7 @@ GeomDotsinterval = ggproto("GeomDotsinterval", GeomSlabinterval,
     aes_docs
   },
 
-  hidden_aes = union(c(
-    "thickness"
-  ), GeomSlabinterval$hidden_aes),
+  hidden_aes = union("thickness", GeomSlabinterval$hidden_aes),
 
   default_aes = defaults(aes(
     family = "",

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -3,8 +3,8 @@
 #
 # Where should you do additional test configuration?
 # Learn more about the roles of various files in:
-# * https://r-pkgs.org/tests.html
-# * https://testthat.r-lib.org/reference/test_package.html#special-files
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
 
 library(testthat)
 library(ggdist)

diff --git a/tests/testthat/test.binning_methods.R b/tests/testthat/test.binning_methods.R
@@ -110,8 +110,8 @@ test_that("bin nudging works", {
     NULL
   )
   expect_equal(
-    nudge_bins(c(1), width = 1),
-    c(1)
+    nudge_bins(1, width = 1),
+    1
   )
   expect_equal(
     nudge_bins(c(1,2), width = 1),

diff --git a/tests/testthat/test.lkj_marginal.R b/tests/testthat/test.lkj_marginal.R
@@ -43,10 +43,10 @@ test_that("lkjcorr_marginal throws an error for invalid K", {
 test_that("marginalize_lkjcorr works", {
   ref = as.data.frame(tibble(
     coef = c("a", "b"),
-    prior = c("lkjcorr(3)", "lkjcorr(3)" ),
+    prior = c("lkjcorr(3)", "lkjcorr(3)"),
     .dist = c("lkjcorr_marginal", "lkjcorr_marginal"),
     .args = list(list(2, 3), list(4, 3)),
-    .dist_obj = dist_wrap(dist = "lkjcorr_marginal", c(2, 4), c(3, 3), package = "ggdist"),
+    .dist_obj = dist_wrap(dist = "lkjcorr_marginal", c(2, 4), c(3, 3), package = "ggdist")
   ))
 
   expect_equal(

diff --git a/tests/testthat/test.rd_lineribbon.R b/tests/testthat/test.rd_lineribbon.R
@@ -23,7 +23,10 @@ test_that("lineribbon aesthetic documention generator works", {
 
 test_that("shortcut stat documentation generator works", {
 
-  stat_output = paste0(rd_lineribbon_shortcut_stat("lineribbon", chart_type = "multiple-ribbon", from_name = "slabinterval"), collapse = "\n")
+  stat_output = paste0(
+    rd_lineribbon_shortcut_stat("lineribbon", chart_type = "multiple-ribbon", from_name = "slabinterval"),
+    collapse = "\n"
+  )
   expect_match(stat_output, "@title Multiple-ribbon plot (shortcut stat)", fixed = TRUE)
   expect_match(stat_output, ".width = c(0.5, 0.8, 0.95)", fixed = TRUE)
 

diff --git a/tests/testthat/test.scale_.R b/tests/testthat/test.scale_.R
@@ -38,7 +38,7 @@ test_that("direct scale setting works", {
         slab_linetype = "dotted",
         slab_alpha = .5
       )
-    )
+  )
 })
 
 test_that("mapping custom aesthetics works", {

diff --git a/tests/testthat/test.smooth.R b/tests/testthat/test.smooth.R
@@ -30,18 +30,30 @@ test_that("smooth_discrete works", {
   x = rep(1:4, times = 4:1)
 
   ld = layer_data(ggplot() + geom_dots(aes(x), smooth = "discrete"))
-  ref_x = c(0.760112695656659, 0.920256356040445, 1.08040001642423, 1.24054367680802,  1.78654853188863, 2.00007341240034, 2.21359829291206, 2.83977362126489,  3.16006094203247, 3.99967181376766)
+  ref_x = c(
+    0.760112695656659, 0.920256356040445, 1.08040001642423, 1.24054367680802,
+    1.78654853188863, 2.00007341240034, 2.21359829291206, 2.83977362126489,
+    3.16006094203247, 3.99967181376766
+  )
   expect_equal(ld$x, ref_x, tolerance = 0.001)
 
   ld = layer_data(ggplot() + geom_dots(aes(x), smooth = smooth_discrete(kernel = "ep")))
-  ref_x = c(0.816364320617873, 0.944625373470495, 1.05539072151476, 1.18366670884155,  1.84144365484769, 2.00000507797274, 2.15857922335003, 2.88568947241406,  3.11432520840337, 3.99999280566278)
+  ref_x = c(
+    0.816364320617873, 0.944625373470495, 1.05539072151476, 1.18366670884155,
+    1.84144365484769, 2.00000507797274, 2.15857922335003, 2.88568947241406,
+    3.11432520840337, 3.99999280566278
+  )
   expect_equal(ld$x, ref_x, tolerance = 0.001)
 })
 
 test_that("smooth_bounded works", {
   x = 1:10
 
   ld = layer_data(ggplot() + geom_dots(aes(x), smooth = "bounded"))
-  ref_x = c(0.997794316080475, 1.99639357461413, 2.99631978598422, 3.99740164666058,  4.99908084276668, 6.00091915723332, 7.00259835333942, 8.00368021401578,  9.00360642538587, 10.0022056839195)
+  ref_x = c(
+    0.997794316080475, 1.99639357461413, 2.99631978598422, 3.99740164666058,
+    4.99908084276668, 6.00091915723332, 7.00259835333942, 8.00368021401578,
+    9.00360642538587, 10.0022056839195
+  )
   expect_equal(ld$x, ref_x, tolerance = 0.001)
 })
diff --git a/tests/testthat/test.stat_cdfinterval.R b/tests/testthat/test.stat_cdfinterval.R
@@ -11,7 +11,7 @@ test_that("dodged ccdf barplots work", {
   skip_if_no_vdiffr()
 
 
-  df = data.frame(y = 1:5, x = "a", g = c("g1")) %>%
+  df = data.frame(y = 1:5, x = "a", g = "g1") %>%
     rbind(data.frame(y = rep(1:5, each = 3) + 1:3, x = "b", g = c("g1", "g2", "g3")))
 
   p = ggplot(df, aes(x = x, y = y))

diff --git a/tests/testthat/test.stat_sample_slabinterval.R b/tests/testthat/test.stat_sample_slabinterval.R
@@ -137,12 +137,22 @@ test_that("scale transformation works on halfeye", {
     scale_x_log10(breaks = 10^seq(-1,1))
 
   vdiffr::expect_doppelganger("halfeyeh log scale tri",
-    p_log + stat_halfeye(point_interval = mode_hdci, n = 20, density = density_unbounded(kernel = "tri"), .width = .5) +
+    p_log +
+      stat_halfeye(
+        point_interval = mode_hdci, n = 20,
+        density = density_unbounded(kernel = "tri"),
+        .width = .5
+      ) +
       geom_point(data = data.frame(x = 10^c(-1, 1)))
   )
 
   vdiffr::expect_doppelganger("halfeyeh log scale tri no trim",
-    p_log + stat_halfeye(point_interval = mode_hdci, n = 20, density = density_unbounded(kernel = "tri"), trim = FALSE, .width = .5) +
+    p_log +
+      stat_halfeye(
+        point_interval = mode_hdci, n = 20,
+        density = density_unbounded(kernel = "tri"), trim = FALSE,
+        .width = .5
+      ) +
       geom_point(data = data.frame(x = 10^c(-1, 1)))
   )
 

diff --git a/tests/testthat/test.student_t.R b/tests/testthat/test.student_t.R
@@ -28,4 +28,3 @@ test_that("student_t functions work", {
   set.seed(1234)
   expect_equal(rstudent_t(10, df, median, scale), r)
 })
-
diff --git a/tests/testthat/test.theme_ggdist.R b/tests/testthat/test.theme_ggdist.R
@@ -16,7 +16,8 @@ test_that("theme helper functions work", {
   p = data.frame(
     x = 1:2,
     y = 0,
-    g = c("aaa","bbb")
+    g = c("aaa","bbb"),
+    stringsAsFactors = FALSE
   ) %>%
     ggplot(aes(x, y)) +
     geom_point() +

diff --git a/tests/testthat/test.weighted_ecdf.R b/tests/testthat/test.weighted_ecdf.R
@@ -12,5 +12,8 @@ test_that("weighted_ecdf works", {
 })
 
 test_that("quantile(<weighted_ecdf>) works", {
-  expect_equal(quantile(weighted_ecdf(c(1, 2, 2, 3), 1:4), ppoints(10)), weighted_quantile(c(1, 2, 2, 3), weights = 1:4, ppoints(10)))
+  expect_equal(
+    quantile(weighted_ecdf(c(1, 2, 2, 3), 1:4), ppoints(10)),
+    weighted_quantile(c(1, 2, 2, 3), weights = 1:4, ppoints(10))
+  )
 })
diff --git a/tests/testthat/test.weighted_hist.R b/tests/testthat/test.weighted_hist.R
@@ -75,10 +75,22 @@ test_that("align functions work", {
   x = c(1,2,3,4,5,6)
   breaks = c(0.25, 2.25, 4.25, 6.25)
 
-  expect_equal(weighted_hist(x, breaks = breaks, align = 0.25), weighted_hist(x, breaks = breaks - 0.25))
-  expect_equal(weighted_hist(x, breaks = breaks, align = align_none()), weighted_hist(x, breaks = breaks))
-  expect_equal(weighted_hist(x, breaks = breaks, align = align_center(at = 2)), weighted_hist(x, breaks = breaks + 0.75))
-  expect_equal(weighted_hist(x, breaks = breaks, align = align_boundary(at = 2)), weighted_hist(x, breaks = breaks - 0.25))
+  expect_equal(
+    weighted_hist(x, breaks = breaks, align = 0.25),
+    weighted_hist(x, breaks = breaks - 0.25)
+  )
+  expect_equal(
+    weighted_hist(x, breaks = breaks, align = align_none()),
+    weighted_hist(x, breaks = breaks)
+  )
+  expect_equal(
+    weighted_hist(x, breaks = breaks, align = align_center(at = 2)),
+    weighted_hist(x, breaks = breaks + 0.75)
+  )
+  expect_equal(
+    weighted_hist(x, breaks = breaks, align = align_boundary(at = 2)),
+    weighted_hist(x, breaks = breaks - 0.25)
+  )
 })
 
 

diff --git a/tests/testthat/test.weighted_quantile.R b/tests/testthat/test.weighted_quantile.R
@@ -15,8 +15,8 @@ test_that("weighted_quantile is equivalent to quantile on non-weighted samples",
 
 test_that("weighted_quantile is equivalent to quantile on weighted samples", {
   x = c(1,1,1,1,2,2,2,3,3,4)
-  xw = c(1:4)
-  w = c(4:1)
+  xw = 1:4
+  w = 4:1
 
   p = ppoints(20, a = 1)
   for (type in 1:9) {
@@ -48,4 +48,3 @@ test_that("0- and 1-length vectors work", {
 
   expect_equal(weighted_quantile(numeric(), c(0, 0.5, 1, NA), names = FALSE), c(NA_real_, NA_real_, NA_real_, NA_real_))
 })
-