From 98d7023764fd1e2566278b88aebe7fede255f5b8 Mon Sep 17 00:00:00 2001
From: VisruthSK <67435125+VisruthSK@users.noreply.github.com>
Date: Sun, 7 Dec 2025 18:49:15 -0800
Subject: [PATCH 1/6] Gitignored code-oss settings folder

---
 .Rbuildignore | 1 +
 .gitignore    | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 031ffa55..6d67ff72 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,5 +14,6 @@ images/*
 book/*
 docs/*
 Rplots.pdf
+.vscode/*
 ^\.github$
 ^release-prep\.R$
diff --git a/.gitignore b/.gitignore
index 7e658a14..695e6e77 100644
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,6 @@ revdep/*
 CRAN-RELEASE
 CRAN-SUBMISSION
 release-prep.R
+
+# vscode/positron/etc settings
+.vscode/*

From 42c2872e8013b96e20cc0b58bc7989b43e1ca79a Mon Sep 17 00:00:00 2001
From: VisruthSK <67435125+VisruthSK@users.noreply.github.com>
Date: Sun, 7 Dec 2025 18:54:59 -0800
Subject: [PATCH 2/6] Removed context() and library(bayesplot) in tests

---
 DESCRIPTION                                     | 3 ++-
 tests/testthat/test-aesthetics.R                | 4 ----
 tests/testthat/test-available_ppc.R             | 4 ----
 tests/testthat/test-bayesplot_grid.R            | 3 ---
 tests/testthat/test-convenience-functions.R     | 3 ---
 tests/testthat/test-example-draws.R             | 3 ---
 tests/testthat/test-extractors.R                | 3 ---
 tests/testthat/test-helpers-mcmc.R              | 5 -----
 tests/testthat/test-helpers-ppc.R               | 3 ---
 tests/testthat/test-helpers-shared.R            | 3 ---
 tests/testthat/test-mcmc-combo.R                | 3 ---
 tests/testthat/test-mcmc-diagnostics.R          | 3 ---
 tests/testthat/test-mcmc-distributions.R        | 3 ---
 tests/testthat/test-mcmc-intervals.R            | 4 ----
 tests/testthat/test-mcmc-nuts.R                 | 3 ---
 tests/testthat/test-mcmc-recover.R              | 3 ---
 tests/testthat/test-mcmc-scatter-and-parcoord.R | 3 ---
 tests/testthat/test-mcmc-traces.R               | 3 ---
 tests/testthat/test-pp_check.R                  | 3 ---
 tests/testthat/test-ppc-censoring.R             | 3 ---
 tests/testthat/test-ppc-discrete.R              | 2 --
 tests/testthat/test-ppc-distributions.R         | 3 ---
 tests/testthat/test-ppc-errors.R                | 3 ---
 tests/testthat/test-ppc-input-validation.R      | 3 ---
 tests/testthat/test-ppc-intervals.R             | 3 ---
 tests/testthat/test-ppc-loo.R                   | 3 ---
 tests/testthat/test-ppc-scatterplots.R          | 3 ---
 tests/testthat/test-ppc-test-statistics.R       | 3 ---
 28 files changed, 2 insertions(+), 86 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a1a3a5e1..df6b5f7d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -56,9 +56,10 @@ 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
diff --git a/tests/testthat/test-aesthetics.R b/tests/testthat/test-aesthetics.R
index 21b054de..fade8bcf 100644
--- a/tests/testthat/test-aesthetics.R
+++ b/tests/testthat/test-aesthetics.R
@@ -1,7 +1,3 @@
-library(bayesplot)
-context("Aesthetics")
-
-
 # color scheme stuff ------------------------------------------------------
 
 prepare_colors_for_test <- function(scheme) {
diff --git a/tests/testthat/test-available_ppc.R b/tests/testthat/test-available_ppc.R
index 68a6e316..9fe05e31 100644
--- a/tests/testthat/test-available_ppc.R
+++ b/tests/testthat/test-available_ppc.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")
diff --git a/tests/testthat/test-bayesplot_grid.R b/tests/testthat/test-bayesplot_grid.R
index c2146800..ac4373d0 100644
--- a/tests/testthat/test-bayesplot_grid.R
+++ b/tests/testthat/test-bayesplot_grid.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("bayesplot_grid")
-
 skip_if_not_installed("gridExtra")
 
 y <- example_y_data()
diff --git a/tests/testthat/test-convenience-functions.R b/tests/testthat/test-convenience-functions.R
index 068e24a9..3505211d 100644
--- a/tests/testthat/test-convenience-functions.R
+++ b/tests/testthat/test-convenience-functions.R
@@ -1,7 +1,4 @@
-library(bayesplot)
 library(ggplot2)
-context("Convenience functions (for ggplot objects)")
-
 
 # abline_01, vline_ and hline_ ------------------------------------------
 test_that("abline_01 returns the correct object", {
diff --git a/tests/testthat/test-example-draws.R b/tests/testthat/test-example-draws.R
index 399c4281..cc4317aa 100644
--- a/tests/testthat/test-example-draws.R
+++ b/tests/testthat/test-example-draws.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("Example draws")
-
 test_that("example_mcmc_draws throws correct errors", {
   expect_error(example_mcmc_draws(chains = 5), "chains <= 4")
   expect_error(example_mcmc_draws(chains = 0), "chains >= 1")
diff --git a/tests/testthat/test-extractors.R b/tests/testthat/test-extractors.R
index 5cb990ce..236f6704 100644
--- a/tests/testthat/test-extractors.R
+++ b/tests/testthat/test-extractors.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("Extractors")
-
 if (requireNamespace("rstanarm", quietly = TRUE)) {
   ITER <- 1000
   CHAINS <- 3
diff --git a/tests/testthat/test-helpers-mcmc.R b/tests/testthat/test-helpers-mcmc.R
index 3f181426..26fbcdd3 100644
--- a/tests/testthat/test-helpers-mcmc.R
+++ b/tests/testthat/test-helpers-mcmc.R
@@ -1,10 +1,5 @@
-library(bayesplot)
-context("MCMC: misc. functions")
-
 source(test_path("data-for-mcmc-tests.R"))
 
-
-
 # melt_mcmc ----------------------------------------------------------------
 test_that("melt_mcmc does not convert integer parameter names to integers #162", {
   mat2 <- mat[, 1:2]
diff --git a/tests/testthat/test-helpers-ppc.R b/tests/testthat/test-helpers-ppc.R
index 73daf4ae..36f921d3 100644
--- a/tests/testthat/test-helpers-ppc.R
+++ b/tests/testthat/test-helpers-ppc.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: misc. functions")
-
 source(test_path("data-for-ppc-tests.R"))
 source(test_path("data-for-mcmc-tests.R"))
 
diff --git a/tests/testthat/test-helpers-shared.R b/tests/testthat/test-helpers-shared.R
index 9badd2eb..35e1cb2b 100644
--- a/tests/testthat/test-helpers-shared.R
+++ b/tests/testthat/test-helpers-shared.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("Shared: misc. functions")
-
 # suggested packages ------------------------------------------------------
 test_that("suggested_package throws correct errors", {
   expect_error(suggested_package("NOPACKAGE"),
diff --git a/tests/testthat/test-mcmc-combo.R b/tests/testthat/test-mcmc-combo.R
index f657c1a9..bbf18eeb 100644
--- a/tests/testthat/test-mcmc-combo.R
+++ b/tests/testthat/test-mcmc-combo.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: combo")
-
 source(test_path("data-for-mcmc-tests.R"))
 
 test_that("mcmc_combo returns a gtable object", {
diff --git a/tests/testthat/test-mcmc-diagnostics.R b/tests/testthat/test-mcmc-diagnostics.R
index 3ebe0c37..5e95f46b 100644
--- a/tests/testthat/test-mcmc-diagnostics.R
+++ b/tests/testthat/test-mcmc-diagnostics.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: diagnostics")
-
 source(test_path("data-for-mcmc-tests.R"))
 
 test_that("rhat and neff plots return a ggplot object", {
diff --git a/tests/testthat/test-mcmc-distributions.R b/tests/testthat/test-mcmc-distributions.R
index 7b2ae9fa..5a6f670a 100644
--- a/tests/testthat/test-mcmc-distributions.R
+++ b/tests/testthat/test-mcmc-distributions.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: distributions")
-
 source(test_path("data-for-mcmc-tests.R"))
 
 get_palette <- function(ggplot, n) {
diff --git a/tests/testthat/test-mcmc-intervals.R b/tests/testthat/test-mcmc-intervals.R
index ee4a8bc4..88854753 100644
--- a/tests/testthat/test-mcmc-intervals.R
+++ b/tests/testthat/test-mcmc-intervals.R
@@ -1,9 +1,5 @@
-library(bayesplot)
-context("MCMC: intervals")
-
 source(test_path("data-for-mcmc-tests.R"))
 
-
 test_that("mcmc_intervals_data computes quantiles", {
   xs <- melt_mcmc(merge_chains(prepare_mcmc_array(arr, pars = "beta[1]")))
   d <- mcmc_intervals_data(arr, pars = "beta[1]",
diff --git a/tests/testthat/test-mcmc-nuts.R b/tests/testthat/test-mcmc-nuts.R
index c9f52a98..841a6bc4 100644
--- a/tests/testthat/test-mcmc-nuts.R
+++ b/tests/testthat/test-mcmc-nuts.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: nuts")
-
 if (requireNamespace("rstanarm", quietly = TRUE)) {
   ITER <- 1000
   CHAINS <- 3
diff --git a/tests/testthat/test-mcmc-recover.R b/tests/testthat/test-mcmc-recover.R
index a545caa8..2c8dd3eb 100644
--- a/tests/testthat/test-mcmc-recover.R
+++ b/tests/testthat/test-mcmc-recover.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: recover")
-
 set.seed(123)
 draws <- matrix(rnorm(4 * 1000), nrow = 1000)
 colnames(draws) <- c("alpha", "beta[1]", "beta[2]", "sigma")
diff --git a/tests/testthat/test-mcmc-scatter-and-parcoord.R b/tests/testthat/test-mcmc-scatter-and-parcoord.R
index b737515d..a0d22358 100644
--- a/tests/testthat/test-mcmc-scatter-and-parcoord.R
+++ b/tests/testthat/test-mcmc-scatter-and-parcoord.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: scatter, hex, and parallel coordinates plots")
-
 source(test_path("data-for-mcmc-tests.R"))
 
 if (requireNamespace("rstanarm", quietly = TRUE)) {
diff --git a/tests/testthat/test-mcmc-traces.R b/tests/testthat/test-mcmc-traces.R
index 2faec4b6..7d02b4ee 100644
--- a/tests/testthat/test-mcmc-traces.R
+++ b/tests/testthat/test-mcmc-traces.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("MCMC: traces")
-
 source(test_path("data-for-mcmc-tests.R"))
 
 test_that("mcmc_trace returns a ggplot object", {
diff --git a/tests/testthat/test-pp_check.R b/tests/testthat/test-pp_check.R
index 0e56574a..b1a8ab81 100644
--- a/tests/testthat/test-pp_check.R
+++ b/tests/testthat/test-pp_check.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: pp_check generic and default method")
-
 test_that("default pp_check method works", {
   y <- example_y_data()
   yrep <- example_yrep_draws()
diff --git a/tests/testthat/test-ppc-censoring.R b/tests/testthat/test-ppc-censoring.R
index d733c0ee..2224df7b 100644
--- a/tests/testthat/test-ppc-censoring.R
+++ b/tests/testthat/test-ppc-censoring.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: censoring")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_km_overlay returns a ggplot object", {
diff --git a/tests/testthat/test-ppc-discrete.R b/tests/testthat/test-ppc-discrete.R
index c8e749a8..4bf788d0 100644
--- a/tests/testthat/test-ppc-discrete.R
+++ b/tests/testthat/test-ppc-discrete.R
@@ -1,6 +1,4 @@
-library(bayesplot)
 # suppressPackageStartupMessages(library(rstanarm))
-context("PPC: discrete")
 
 source(test_path("data-for-ppc-tests.R"))
 load(test_path("data-for-ordinal.rda"))
diff --git a/tests/testthat/test-ppc-distributions.R b/tests/testthat/test-ppc-distributions.R
index 6ab88d6e..c156223b 100644
--- a/tests/testthat/test-ppc-distributions.R
+++ b/tests/testthat/test-ppc-distributions.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: distributions")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_dens_overlay returns a ggplot object", {
diff --git a/tests/testthat/test-ppc-errors.R b/tests/testthat/test-ppc-errors.R
index 1792e7b7..de4322aa 100644
--- a/tests/testthat/test-ppc-errors.R
+++ b/tests/testthat/test-ppc-errors.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: predictive errors")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_error_hist and ppc_error_scatter return ggplot object", {
diff --git a/tests/testthat/test-ppc-input-validation.R b/tests/testthat/test-ppc-input-validation.R
index c0b77955..c32a6cfe 100644
--- a/tests/testthat/test-ppc-input-validation.R
+++ b/tests/testthat/test-ppc-input-validation.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: input validation")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("validate_y works", {
diff --git a/tests/testthat/test-ppc-intervals.R b/tests/testthat/test-ppc-intervals.R
index d1d7aa9d..a1499303 100644
--- a/tests/testthat/test-ppc-intervals.R
+++ b/tests/testthat/test-ppc-intervals.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: intervals & ribbon")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_intervals returns ggplot object", {
diff --git a/tests/testthat/test-ppc-loo.R b/tests/testthat/test-ppc-loo.R
index 6e3f34ca..9381692f 100644
--- a/tests/testthat/test-ppc-loo.R
+++ b/tests/testthat/test-ppc-loo.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: loo")
-
 options(useFancyQuotes = FALSE)
 
 if (requireNamespace("rstanarm", quietly = TRUE) &&
diff --git a/tests/testthat/test-ppc-scatterplots.R b/tests/testthat/test-ppc-scatterplots.R
index 9116b115..02494796 100644
--- a/tests/testthat/test-ppc-scatterplots.R
+++ b/tests/testthat/test-ppc-scatterplots.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: scatterplots")
-
 source(test_path("data-for-ppc-tests.R"))
 
 test_that("ppc_scatter returns ggplot object", {
diff --git a/tests/testthat/test-ppc-test-statistics.R b/tests/testthat/test-ppc-test-statistics.R
index 73acbe79..bc95ccc3 100644
--- a/tests/testthat/test-ppc-test-statistics.R
+++ b/tests/testthat/test-ppc-test-statistics.R
@@ -1,6 +1,3 @@
-library(bayesplot)
-context("PPC: test-statistics")
-
 source(test_path("data-for-ppc-tests.R"))
 
 q25 <- function(x) quantile(x, 0.25)

From a5e97675aedd02b31a2c0465163ee0e7ebb25e28 Mon Sep 17 00:00:00 2001
From: VisruthSK <67435125+VisruthSK@users.noreply.github.com>
Date: Sun, 7 Dec 2025 19:09:20 -0800
Subject: [PATCH 3/6] Used new environment ignoring argument, tolerance instead
 of tol, and expect_equal() with ignore_attr = TRUE instead of equivalent

---
 tests/testthat/test-aesthetics.R               | 18 +++++++++---------
 tests/testthat/test-convenience-functions.R    | 18 +++++++++---------
 tests/testthat/test-example-draws.R            |  2 +-
 tests/testthat/test-extractors.R               |  6 +++---
 tests/testthat/test-helpers-mcmc.R             |  4 ++--
 tests/testthat/test-mcmc-intervals.R           |  4 ++--
 .../testthat/test-mcmc-scatter-and-parcoord.R  | 12 ++++++------
 tests/testthat/test-pp_check.R                 |  4 ++--
 tests/testthat/test-ppc-discrete.R             |  6 +++---
 tests/testthat/test-ppc-input-validation.R     |  2 +-
 10 files changed, 38 insertions(+), 38 deletions(-)

diff --git a/tests/testthat/test-aesthetics.R b/tests/testthat/test-aesthetics.R
index fade8bcf..1ab27c92 100644
--- a/tests/testthat/test-aesthetics.R
+++ b/tests/testthat/test-aesthetics.R
@@ -9,12 +9,12 @@ 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),
+    expect_equal(color_scheme_get(), prepare_colors_for_test(clr, ignore_attr = TRUE),
                       info = clr)
     expect_named(color_scheme_get(), scheme_level_names())
   }
@@ -24,7 +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")
@@ -56,10 +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")
@@ -68,9 +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")
 })
 
@@ -102,11 +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", {
diff --git a/tests/testthat/test-convenience-functions.R b/tests/testthat/test-convenience-functions.R
index 3505211d..3b6fe9f6 100644
--- a/tests/testthat/test-convenience-functions.R
+++ b/tests/testthat/test-convenience-functions.R
@@ -5,35 +5,35 @@ 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
@@ -96,13 +96,13 @@ 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, list(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, list(legend.position = "left"), ignore_attr = TRUE)
   expect_false(attr(left, "complete"))
 
   pos <- legend_move(c(0.25, 0.5))
@@ -182,7 +182,7 @@ 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)
 })
 
 
diff --git a/tests/testthat/test-example-draws.R b/tests/testthat/test-example-draws.R
index cc4317aa..c36e82af 100644
--- a/tests/testthat/test-example-draws.R
+++ b/tests/testthat/test-example-draws.R
@@ -23,7 +23,7 @@ test_that("example ppc data works", {
 
   yrep <- example_yrep_draws()
   expect_type(yrep, "double")
-  expect_is(yrep, "matrix")
+  expect_true(is.matrix(yrep))
   expect_equal(ncol(yrep), length(y))
 
   group <- example_group_data()
diff --git a/tests/testthat/test-extractors.R b/tests/testthat/test-extractors.R
index 236f6704..53e9862c 100644
--- a/tests/testthat/test-extractors.R
+++ b/tests/testthat/test-extractors.R
@@ -81,7 +81,7 @@ test_that("neff_ratio.stanreg returns correct structure", {
   ratio <- neff_ratio(fit)
   expect_named(ratio)
   ans <- summary(fit)[1:length(ratio), "n_eff"] / (floor(ITER / 2) * CHAINS)
-  expect_equal(ratio, ans, tol = 0.001)
+  expect_equal(ratio, ans, tolerance = 0.001)
 })
 
 test_that("rhat.stanfit returns correct structure", {
@@ -104,12 +104,12 @@ test_that("neff_ratio.stanreg returns correct structure", {
   ratio <- neff_ratio(fit$stanfit)
   expect_named(ratio)
   ans <- summary(fit)[, "n_eff"] / denom
-  expect_equal(ratio, ans, tol = 0.001)
+  expect_equal(ratio, ans, tolerance = 0.001)
 
   ratio2 <- neff_ratio(fit$stanfit, pars = c("wt", "sigma"))
   expect_named(ratio2)
   ans2 <- summary(fit, pars = c("wt", "sigma"))[, "n_eff"] / denom
-  expect_equal(ratio2, ans2, tol = 0.001)
+  expect_equal(ratio2, ans2, tolerance = 0.001)
 })
 
 test_that("cmdstanr methods work", {
diff --git a/tests/testthat/test-helpers-mcmc.R b/tests/testthat/test-helpers-mcmc.R
index 26fbcdd3..04f1aee4 100644
--- a/tests/testthat/test-helpers-mcmc.R
+++ b/tests/testthat/test-helpers-mcmc.R
@@ -298,7 +298,7 @@ test_that("diagnostic_factor.rhat works", {
                       high = 1.2, high = 1.7))
 
   r <- diagnostic_factor(unname(rhats))
-  expect_equivalent(r, as.factor(names(rhats)))
+  expect_equal(r, as.factor(names(rhats)), ignore_attr = TRUE)
   expect_identical(levels(r), c("low", "ok", "high"))
 })
 test_that("diagnostic_factor.neff_ratio works", {
@@ -307,7 +307,7 @@ test_that("diagnostic_factor.neff_ratio works", {
                              high = 0.51, high = 0.99, high = 1))
 
   r <- diagnostic_factor(unname(ratios))
-  expect_equivalent(r, as.factor(names(ratios)))
+  expect_equal(r, as.factor(names(ratios)), ignore_attr = TRUE)
   expect_identical(levels(r), c("low", "ok", "high"))
 })
 
diff --git a/tests/testthat/test-mcmc-intervals.R b/tests/testthat/test-mcmc-intervals.R
index 88854753..907d8997 100644
--- a/tests/testthat/test-mcmc-intervals.R
+++ b/tests/testthat/test-mcmc-intervals.R
@@ -7,7 +7,7 @@ test_that("mcmc_intervals_data computes quantiles", {
 
   qs <- unlist(d[, c("ll", "l", "m", "h", "hh")])
   by_hand <- quantile(xs$Value, c(.25, .35, .5, .65, .75))
-  expect_equivalent(qs, by_hand)
+  expect_equal(qs, by_hand, ignore_attr = TRUE)
 
   expect_equal(d$parameter, factor("beta[1]"))
   expect_equal(d$outer_width, .5)
@@ -26,7 +26,7 @@ test_that("mcmc_intervals_data computes point estimates", {
   d <- mcmc_intervals_data(arr, pars = "beta[2]",
                            prob = .3, prob_outer = .5, point_est = "mean")
 
-  expect_equivalent(d$m, mean(xs$Value))
+  expect_equal(d$m, mean(xs$Value), ignore_attr = TRUE)
   expect_equal(d$parameter, factor("beta[2]"))
   expect_equal(d$point_est, "mean")
 
diff --git a/tests/testthat/test-mcmc-scatter-and-parcoord.R b/tests/testthat/test-mcmc-scatter-and-parcoord.R
index a0d22358..570e06e8 100644
--- a/tests/testthat/test-mcmc-scatter-and-parcoord.R
+++ b/tests/testthat/test-mcmc-scatter-and-parcoord.R
@@ -210,40 +210,40 @@ test_that("pairs_condition returns correct structure", {
   # default
   cond0 <- pairs_condition()
   expect_s3_class(cond0, "pairs_condition")
-  expect_equivalent(unclass(cond0), list())
+  expect_equal(unclass(cond0), list(), ignore_attr = TRUE)
   expect_equal(attr(cond0, "type"), "default")
 
   # chains
   cond1 <- pairs_condition(chains = 1:4)
   expect_s3_class(cond1, "integer")
   expect_s3_class(cond1, "pairs_condition")
-  expect_equivalent(unclass(cond1), 1:4)
+  expect_equal(unclass(cond1), 1:4, ignore_attr = TRUE)
   expect_equal(attr(cond1, "type"), "chain_vector")
 
   cond2 <- pairs_condition(chains = list(1:4, 5:6))
   expect_s3_class(cond2, "list")
   expect_s3_class(cond2, "pairs_condition")
-  expect_equivalent(unclass(cond2), list(upper=1:4, lower=5:6))
+  expect_equal(unclass(cond2), list(upper=1:4, lower=5:6), ignore_attr = TRUE)
   expect_equal(attr(cond2, "type"), "chain_list")
 
   # draws
   cond3 <- pairs_condition(draws = 0.7)
   expect_s3_class(cond3, "numeric")
   expect_s3_class(cond3, "pairs_condition")
-  expect_equivalent(unclass(cond3), 0.7)
+  expect_equal(unclass(cond3), 0.7, ignore_attr = TRUE)
   expect_equal(attr(cond3, "type"), "draws_proportion")
 
   cond4 <- pairs_condition(draws = c(T, F, T))
   expect_s3_class(cond4, "logical")
   expect_s3_class(cond4, "pairs_condition")
-  expect_equivalent(unclass(cond4), c(T, F, T))
+  expect_equal(unclass(cond4), c(T, F, T), ignore_attr = TRUE)
   expect_equal(attr(cond4, "type"), "draws_selection")
 
   # nuts
   cond5 <- pairs_condition(nuts = "lp__")
   expect_s3_class(cond5, "character")
   expect_s3_class(cond5, "pairs_condition")
-  expect_equivalent(unclass(cond5), "lp__")
+  expect_equal(unclass(cond5), "lp__", ignore_attr = TRUE)
   expect_equal(attr(cond5, "type"), "nuts")
 })
 
diff --git a/tests/testthat/test-pp_check.R b/tests/testthat/test-pp_check.R
index b1a8ab81..d4bcb598 100644
--- a/tests/testthat/test-pp_check.R
+++ b/tests/testthat/test-pp_check.R
@@ -6,12 +6,12 @@ test_that("default pp_check method works", {
   expect_equal(
     pp_check(y, yrep[1:50, ], ppc_dens_overlay),
     ppc_dens_overlay(y, yrep[1:50, ]),
-    check.environment = FALSE
+    ignore_function_env = TRUE
   )
   expect_equal(
     pp_check(y, yrep, fun = "stat_grouped", group = g, stat = "median"),
     ppc_stat_grouped(y, yrep, group = g, stat = "median"),
-    check.environment = FALSE
+    ignore_function_env = TRUE
   )
 })
 
diff --git a/tests/testthat/test-ppc-discrete.R b/tests/testthat/test-ppc-discrete.R
index 4bf788d0..005fdc94 100644
--- a/tests/testthat/test-ppc-discrete.R
+++ b/tests/testthat/test-ppc-discrete.R
@@ -72,9 +72,9 @@ test_that("ppc_bars_data includes all levels", {
   d3 <- ppc_bars_data(y_ord, yrep_ord2)
   expect_equal(d3$x, 1:4)
   expect_equal(d3$y_obs, tab)
-  expect_equivalent(d3$l[2], 0)
-  expect_equivalent(d3$m[2], 0)
-  expect_equivalent(d3$h[2], 0)
+  expect_equal(d3$l[2], 0, ignore_attr = TRUE)
+  expect_equal(d3$m[2], 0, ignore_attr = TRUE)
+  expect_equal(d3$h[2], 0, ignore_attr = TRUE)
 })
 
 
diff --git a/tests/testthat/test-ppc-input-validation.R b/tests/testthat/test-ppc-input-validation.R
index c32a6cfe..d9740976 100644
--- a/tests/testthat/test-ppc-input-validation.R
+++ b/tests/testthat/test-ppc-input-validation.R
@@ -20,7 +20,7 @@ test_that("validate_predictions works", {
   expect_equal(validate_predictions(yrep2, length(y2)), yrep2)
 
   colnames(yrep) <- paste0("yrep", 1:ncol(yrep))
-  expect_equivalent(validate_predictions(yrep, length(y)), unname(yrep))
+  expect_equal(validate_predictions(yrep, length(y)), unname(yrep), ignore_attr = TRUE)
 })
 test_that("validate_predictions throws errors", {
   expect_error(validate_predictions(as.matrix(LETTERS), length(y)), "numeric")

From 12efa67a85fbe74dd269fb3269c3ac0c16f58262 Mon Sep 17 00:00:00 2001
From: VisruthSK <67435125+VisruthSK@users.noreply.github.com>
Date: Sun, 7 Dec 2025 19:24:04 -0800
Subject: [PATCH 4/6] Straggler replacements and fixed some tests for compat
 with ggplot 4

---
 tests/testthat/test-aesthetics.R            |  4 ++--
 tests/testthat/test-convenience-functions.R | 14 ++++++++------
 tests/testthat/test-helpers-mcmc.R          | 12 ++++++++++--
 tests/testthat/test-mcmc-intervals.R        |  4 ++--
 tests/testthat/test-ppc-distributions.R     |  2 +-
 5 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/tests/testthat/test-aesthetics.R b/tests/testthat/test-aesthetics.R
index 1ab27c92..067d44c0 100644
--- a/tests/testthat/test-aesthetics.R
+++ b/tests/testthat/test-aesthetics.R
@@ -14,8 +14,8 @@ test_that("getting and setting the color scheme works", {
   expect_named(color_scheme_get(), scheme_level_names())
   for (clr in names(master_color_list)) {
     color_scheme_set(clr)
-    expect_equal(color_scheme_get(), prepare_colors_for_test(clr, ignore_attr = TRUE),
-                      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())
   }
 
diff --git a/tests/testthat/test-convenience-functions.R b/tests/testthat/test-convenience-functions.R
index 3b6fe9f6..7b197f27 100644
--- a/tests/testthat/test-convenience-functions.R
+++ b/tests/testthat/test-convenience-functions.R
@@ -96,20 +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_equal(none, list(legend.position = "none"), ignore_attr = TRUE)
+  expect_equal(none$legend.position, "none", ignore_attr = TRUE)
   expect_false(attr(none, "complete"))
 })
 test_that("legend_move returns correct theme object", {
   left <- legend_move("left")
   expect_s3_class(left, "theme")
-  expect_equal(left, list(legend.position = "left"), ignore_attr = TRUE)
+  expect_equal(left$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"))
 })
@@ -130,9 +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", {
diff --git a/tests/testthat/test-helpers-mcmc.R b/tests/testthat/test-helpers-mcmc.R
index 04f1aee4..63a532f3 100644
--- a/tests/testthat/test-helpers-mcmc.R
+++ b/tests/testthat/test-helpers-mcmc.R
@@ -298,7 +298,11 @@ test_that("diagnostic_factor.rhat works", {
                       high = 1.2, high = 1.7))
 
   r <- diagnostic_factor(unname(rhats))
-  expect_equal(r, as.factor(names(rhats)), ignore_attr = TRUE)
+  expect_equal(
+    r,
+    factor(names(rhats), levels = c("low", "ok", "high")),
+    ignore_attr = TRUE
+  )
   expect_identical(levels(r), c("low", "ok", "high"))
 })
 test_that("diagnostic_factor.neff_ratio works", {
@@ -307,7 +311,11 @@ test_that("diagnostic_factor.neff_ratio works", {
                              high = 0.51, high = 0.99, high = 1))
 
   r <- diagnostic_factor(unname(ratios))
-  expect_equal(r, as.factor(names(ratios)), ignore_attr = TRUE)
+  expect_equal(
+    r,
+    factor(names(ratios), levels = c("low", "ok", "high")),
+    ignore_attr = TRUE
+  )
   expect_identical(levels(r), c("low", "ok", "high"))
 })
 
diff --git a/tests/testthat/test-mcmc-intervals.R b/tests/testthat/test-mcmc-intervals.R
index 907d8997..e1794bf0 100644
--- a/tests/testthat/test-mcmc-intervals.R
+++ b/tests/testthat/test-mcmc-intervals.R
@@ -130,8 +130,8 @@ test_that("mcmc_areas_data computes density", {
   densities <- lapply(raw_values, do_dens, 1, 1024)
 
   for (name in names(by_parameter)) {
-    expect_equivalent(by_parameter[[name]][["density"]],
-                      densities[[name]][["y"]])
+    expect_equal(by_parameter[[name]][["density"]],
+                      densities[[name]][["y"]], ignore_attr = TRUE)
   }
 })
 
diff --git a/tests/testthat/test-ppc-distributions.R b/tests/testthat/test-ppc-distributions.R
index c156223b..5f7293c8 100644
--- a/tests/testthat/test-ppc-distributions.R
+++ b/tests/testthat/test-ppc-distributions.R
@@ -36,7 +36,7 @@ test_that("ppc_dens,pp_hist,ppc_freqpoly,ppc_boxplot return ggplot objects", {
   expect_gg(p <- ppc_hist(y, yrep[1:8, ], binwidth = 3))
   if (utils::packageVersion("ggplot2") >= "3.0.0") {
     facet_var <- vars(rep_label)
-    expect_equal(p$facet$params$facets[[1]], facet_var[[1]])
+    expect_equal(p$facet$params$facets[[1]], facet_var[[1]], ignore_function_env = TRUE, ignore_formula_env = TRUE)
   }
 
   # ppd versions

From fa244b92ac090332eebe4f433e7bdc7536616ae6 Mon Sep 17 00:00:00 2001
From: VisruthSK <67435125+VisruthSK@users.noreply.github.com>
Date: Sun, 7 Dec 2025 20:07:19 -0800
Subject: [PATCH 5/6] Setup parallel testing and selected some slow tests to
 run first

---
 DESCRIPTION | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index df6b5f7d..31f240d4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,3 +63,5 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
+Config/testthat/parallel: true
+Config/testthat/start-first: mcmc-scatter-and-parcoord, ppc-distributions, mcmc-intervals, extractors

From 1da4d233eef1067da8086a6d2eaca65b0e957e9f Mon Sep 17 00:00:00 2001
From: jgabry <jgabry@gmail.com>
Date: Mon, 8 Dec 2025 11:28:09 -0700
Subject: [PATCH 6/6] see if disabling parallel tests fixes GHA issue

---
 DESCRIPTION | 2 --
 1 file changed, 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 31f240d4..df6b5f7d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,5 +63,3 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
-Config/testthat/parallel: true
-Config/testthat/start-first: mcmc-scatter-and-parcoord, ppc-distributions, mcmc-intervals, extractors