Merge pull request #404 from stan-dev/master

Update branch

Author: VisruthSK

.Rbuildignore

@@ -14,5 +14,7 @@ images/*
 book/*
 docs/*
 Rplots.pdf
+.vscode/*
 ^\.github$
 ^release-prep\.R$
+release-prep.R

.gitignore

@@ -13,3 +13,6 @@ revdep/*
 CRAN-RELEASE
 CRAN-SUBMISSION
 release-prep.R
+
+# vscode/positron/etc settings
+.vscode/*

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bayesplot
 Type: Package
 Title: Plotting for Bayesian Models
-Version: 1.14.0.9000
-Date: 2025-08-31
+Version: 1.15.0.9000
+Date: 2025-12-11
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "jgabry@gmail.com"),
              person("Tristan", "Mahr", role = "aut", comment = c(ORCID = "0000-0002-8890-5116")),
              person("Paul-Christian", "Bürkner", role = "ctb"),
@@ -12,7 +12,8 @@ Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"), email = "jgabry@gm
              person("Eduardo", "Coronado Sroka", role = "ctb"),
              person("Teemu", "Sailynoja", role = "ctb"),
              person("Aki", "Vehtari", role = "ctb"), 
-             person("Behram", "Ulukır", role = "ctb"))
+             person("Behram", "Ulukır", role = "ctb"), 
+             person("Visruth", "Srimath Kandali", role = "ctb"))
 Maintainer: Jonah Gabry <jgabry@gmail.com>
 Description: Plotting functions for posterior analysis, MCMC diagnostics,
     prior and posterior predictive checks, and other visualizations
@@ -56,9 +57,10 @@ Suggests:
     scales,
     shinystan (>= 2.3.0),
     survival,
-    testthat (>= 2.0.0),
+    testthat (>= 3.0.0),
     vdiffr (>= 1.0.2)
 RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+Config/testthat/edition: 3

NEWS.md

@@ -1,7 +1,16 @@
 # bayesplot (development version)
 
-* Add `shape` argument to `mcmc_scatter()` by @behramulukir (#375)
-* Restore pre ggplot2 v4.0 behavior of bayesplot theme setting (#385)
+# bayesplot 1.15.0
+
+* Add `shape` argument to `mcmc_scatter` by @behramulukir (#375)
+* Restore pre ggplot2 v4.0 behavior of bayesplot theme setting by @jgabry (#385)
+* New pkgdown theme by @VisruthSK in (#378)
+* Testthat 3e by @VisruthSK (#397)
+* Update loo PIT visual tests by @jgabry (#374)
+* Update SVGs for visual tests for ggplot2 v4.0  by @jgabry (#379)
+* Bumped roxygen and fixed linking note by @VisruthSK (#382)
+* Fix height/width attributes in Rd files for CRAN by @jgabry (#387)
+
 
 # bayesplot 1.14.0
 

R/bayesplot-package.R

@@ -104,7 +104,6 @@
 # release reminders (for devtools)
 release_questions <- function() {
   c(
-    "Have you reduced the size of the vignettes for CRAN?",
     "Have you tested with '^tests/testthat/_snaps$' removed from .Rbuildignore?",
     "Have you put '^tests/testthat/_snaps$' back in .Rbuildignore? before submitting?"
   )

man/bayesplot-package.Rd

@@ -1,7 +1,3 @@
-library(bayesplot)
-context("Aesthetics")
-
-
 # color scheme stuff ------------------------------------------------------
 
 prepare_colors_for_test <- function(scheme) {
@@ -13,13 +9,13 @@ prepare_colors_for_test <- function(scheme) {
 
 test_that("getting and setting the color scheme works", {
   color_scheme_set("red")
-  expect_equivalent(color_scheme_get(), prepare_colors_for_test("red"))
+  expect_equal(color_scheme_get(), prepare_colors_for_test("red"), ignore_attr = TRUE)
   expect_named(prepare_colors_for_test("blue"), scheme_level_names())
   expect_named(color_scheme_get(), scheme_level_names())
   for (clr in names(master_color_list)) {
     color_scheme_set(clr)
-    expect_equivalent(color_scheme_get(), prepare_colors_for_test(clr),
-                      info = clr)
+    expect_equal(color_scheme_get(), prepare_colors_for_test(clr),
+                      info = clr, ignore_attr = TRUE)
     expect_named(color_scheme_get(), scheme_level_names())
   }
 
@@ -28,7 +24,7 @@ test_that("getting and setting the color scheme works", {
   expect_gg(plot(color_scheme_get("mix-blue-green")))
 
   color_scheme_set("blue")
-  expect_equivalent(color_scheme_get("teal"), prepare_colors_for_test("teal"))
+  expect_equal(color_scheme_get("teal"), prepare_colors_for_test("teal"), ignore_attr = TRUE)
 
   # error if not character
   expect_error(color_scheme_set(7), "'scheme' should be a character vector of length 1 or 6")
@@ -60,10 +56,10 @@ test_that("color_scheme_get with i argument works", {
 
 test_that("setting mixed scheme works", {
   color_scheme_set("mix-gray-blue")
-  expect_equivalent(color_scheme_get(), mixed_scheme("gray", "blue"))
+  expect_equal(color_scheme_get(), mixed_scheme("gray", "blue"), ignore_attr = TRUE)
 
   color_scheme_set("mix-blue-gray")
-  expect_equivalent(color_scheme_get(), mixed_scheme("blue", "gray"))
+  expect_equal(color_scheme_get(), mixed_scheme("blue", "gray"), ignore_attr = TRUE)
 
   expect_error(color_scheme_set("mix-green-reds"), "should be one of")
   expect_error(color_scheme_set("mix-greens-red"), "should be one of")
@@ -72,9 +68,9 @@ test_that("setting mixed scheme works", {
 test_that("setting brewer scheme works", {
   skip_if_not_installed("RColorBrewer")
   color_scheme_set("brewer-Blues")
-  expect_equivalent(unlist(color_scheme_get()), RColorBrewer::brewer.pal(6, "Blues"))
+  expect_equal(unlist(color_scheme_get()), RColorBrewer::brewer.pal(6, "Blues"), ignore_attr = TRUE)
   color_scheme_set("brewer-Spectral")
-  expect_equivalent(unlist(color_scheme_get()), RColorBrewer::brewer.pal(6, "Spectral"))
+  expect_equal(unlist(color_scheme_get()), RColorBrewer::brewer.pal(6, "Spectral"), ignore_attr = TRUE)
   expect_error(color_scheme_set("brewer-FAKE"), "FAKE is not a valid palette")
 })
 
@@ -106,11 +102,11 @@ test_that("mixed_scheme internal function doesn't error", {
 test_that("custom color schemes work", {
   color_scheme_set(orange_scheme_ok)
   expect_named(color_scheme_get())
-  expect_equivalent(unlist(color_scheme_get()), orange_scheme_ok)
+  expect_equal(unlist(color_scheme_get()), orange_scheme_ok, ignore_attr = TRUE)
 
   random_scheme <- colors()[sample(length(colors()), 6)]
   color_scheme_set(random_scheme)
-  expect_equivalent(unlist(color_scheme_get()), random_scheme)
+  expect_equal(unlist(color_scheme_get()), random_scheme, ignore_attr = TRUE)
 })
 
 test_that("get_color returns correct color values", {

tests/testthat/test-aesthetics.R

@@ -1,7 +1,3 @@
-library(bayesplot)
-context("available_mcmc and available_ppc")
-
-
 test_that("available_mcmc works", {
   a <- available_mcmc()
   expect_s3_class(a, "bayesplot_function_list")

tests/testthat/test-available_ppc.R

@@ -1,6 +1,3 @@
-library(bayesplot)
-context("bayesplot_grid")
-
 skip_if_not_installed("gridExtra")
 
 y <- example_y_data()

tests/testthat/test-bayesplot_grid.R

@@ -1,42 +1,39 @@
-library(bayesplot)
 library(ggplot2)
-context("Convenience functions (for ggplot objects)")
-
 
 # abline_01, vline_ and hline_ ------------------------------------------
 test_that("abline_01 returns the correct object", {
   a <- abline_01(color = "green", linetype = 2)
   b <- geom_abline(intercept = 0, slope = 1, color = "green", linetype = 2, na.rm = TRUE)
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 })
 test_that("vline_* and hline_* return correct objects", {
   a <- vline_0(color = "red")
   b <- geom_vline(xintercept = 0, color = "red", na.rm = TRUE)
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 
   a <- hline_0(linewidth = 2, linetype = 3)
   b <- geom_hline(yintercept = 0, linewidth = 2, linetype = 3, na.rm = TRUE)
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 
   a <- vline_at(c(3,4), na.rm = FALSE)
   b <- geom_vline(xintercept = c(3,4))
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 
   a <- hline_at(c(3,4), na.rm = FALSE)
   b <- geom_hline(yintercept = c(3,4))
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 })
 test_that("vline_at with 'fun' works", {
   x <- example_mcmc_draws(chains = 1)
   a <- vline_at(x, colMeans)
   b <- geom_vline(xintercept = colMeans(x), na.rm = TRUE)
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 })
 test_that("calc_v (internal function) works", {
   a <- 1:4
@@ -99,20 +96,21 @@ test_that("facet_bg returns correct theme object", {
 test_that("legend_none returns correct theme object", {
   none <- legend_none()
   expect_s3_class(none, "theme")
-  expect_equivalent(none, list(legend.position = "none"))
+  expect_equal(none$legend.position, "none", ignore_attr = TRUE)
   expect_false(attr(none, "complete"))
 })
 test_that("legend_move returns correct theme object", {
   left <- legend_move("left")
   expect_s3_class(left, "theme")
-  expect_equivalent(left, list(legend.position = "left"))
+  expect_equal(left$legend.position, "left", ignore_attr = TRUE)
   expect_false(attr(left, "complete"))
 
   pos <- legend_move(c(0.25, 0.5))
   expect_s3_class(pos, "theme")
-  expect_equivalent(
+  expect_equal(
     pos$legend.position.inside %||% pos$legend.position,
-    c(0.25, 0.5)
+    c(0.25, 0.5),
+    ignore_attr = TRUE
   )
   expect_false(attr(pos, "complete"))
 })
@@ -133,9 +131,10 @@ test_that("xaxis_text returns correct theme object", {
 })
 test_that("yaxis_text returns correct theme object", {
   expect_identical(yaxis_text(FALSE), theme(axis.text.y = element_blank()))
-  expect_equivalent(
+  expect_equal(
     yaxis_text(face = "bold", angle = 30),
-    theme(axis.text.y = element_text(face = "bold", angle = 30))
+    theme(axis.text.y = element_text(face = "bold", angle = 30)),
+    ignore_attr = TRUE
   )
 })
 test_that("facet_text returns correct theme object", {
@@ -185,7 +184,7 @@ test_that("overlay_function returns the correct object", {
   a <- overlay_function(fun = "dnorm")
   b <- stat_function(fun = "dnorm", inherit.aes = FALSE)
   a$constructor <- b$constructor <- NULL
-  expect_equal(a, b, check.environment = FALSE)
+  expect_equal(a, b, ignore_function_env = TRUE)
 })