Attempt to fix test uncoupling by using namespacing instead of packag…

…e loading (#361)
easystats · Apr 3, 2023 · c5446ea · c5446ea
1 parent 6f38ef5
commit c5446ea
Show file tree

Hide file tree

Showing 14 changed files with 67 additions and 48 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -53,9 +53,9 @@ Imports:
     bayestestR (>= 0.13.0),
     effectsize (> 0.8.2),
     insight (>= 0.19.1),
-    parameters (>= 0.20.0),
-    performance (>= 0.9.2),
-    datawizard (>= 0.6.5),
+    parameters (>= 0.20.2),
+    performance (>= 0.10.2),
+    datawizard (>= 0.7.0),
     stats,
     tools,
     utils

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
diff --git a/tests/testthat/test-format_model.R b/tests/testthat/test-format_model.R
@@ -7,7 +7,7 @@ test_that("format_model", {
 
 
 test_that("format_model", {
-  skip_if_not_or_load_if_installed("lme4")
+  skip_if_not_installed("lme4")
   expect_identical(format_model(lme4::lmer(wt ~ cyl + (1 | gear), data = mtcars)), "linear mixed model")
   expect_identical(
     format_model(lme4::glmer(vs ~ cyl + (1 | gear), data = mtcars, family = "binomial")),
@@ -23,7 +23,7 @@ test_that("format_model", {
 
 
 test_that("format_model", {
-  skip_if_not_or_load_if_installed("rstanarm")
+  skip_if_not_installed("rstanarm")
   expect_identical(
     format_model(suppressWarnings(rstanarm::stan_glm(mpg ~ wt, data = mtcars, refresh = 0, iter = 50))),
     "Bayesian linear model"

diff --git a/tests/testthat/test-report.bayesfactor_models.R b/tests/testthat/test-report.bayesfactor_models.R
@@ -18,8 +18,6 @@ test_that("models", {
   expect_output(print(r), "Compared to the Species model")
 })
 
-
-
 test_that("inclusion", {
   inc_bf <- bayestestR::bayesfactor_inclusion(BFmodels, prior_odds = c(1, 2, 3), match_models = TRUE)
   r <- report(inc_bf)

diff --git a/tests/testthat/test-report.brmsfit.R b/tests/testthat/test-report.brmsfit.R
@@ -1,10 +1,13 @@
-skip_if_not_or_load_if_installed("brms")
+skip_if_not_installed("brms")
 
 test_that("report.brms", {
-  testthat::skip_if_not(packageVersion("rstan") >= "2.26.0")
+  testthat::skip_if_not_installed("rstan", "2.26.0")
 
   set.seed(333)
-  model <- suppressWarnings(brm(mpg ~ qsec + wt, data = mtcars, refresh = 0, iter = 300, seed = 333))
+  model <- suppressMessages(suppressWarnings(brms::brm(
+    mpg ~ qsec + wt,
+    data = mtcars, refresh = 0, iter = 300, seed = 333
+  )))
   r <- report(model, verbose = FALSE)
 
   expect_s3_class(summary(r), "character")

diff --git a/tests/testthat/test-report.data.frame.R b/tests/testthat/test-report.data.frame.R
@@ -1,4 +1,5 @@
-skip_if_not(getRversion() <= "4.2.1")
+# skip_if_not(getRversion() <= "4.2.1")
+# This skip does not seem necessary??
 
 test_that("report.numeric", {
   r <- report(seq(0, 1, length.out = 100))
@@ -43,7 +44,7 @@ test_that("report.factor", {
 })
 
 test_that("report.data.frame", {
-  skip_if_not_or_load_if_installed("dplyr")
+  skip_if_not_installed("dplyr")
 
   r <- report(iris)
   expect_equal(nrow(as.data.frame(r)), 7, tolerance = 0)
@@ -60,26 +61,26 @@ test_that("report.data.frame", {
   expect_equal(nrow(as.data.frame(r)), 7, tolerance = 0)
   expect_equal(mean(as.data.frame(r)$n_Obs), 107, tolerance = 0.01)
 
-  r <- report(group_by(iris, Species))
+  r <- report(dplyr::group_by(iris, Species))
   expect_equal(nrow(as.data.frame(r)), 8, tolerance = 0)
   expect_equal(mean(as.data.frame(r)$n_Obs), 50, tolerance = 0)
 
   expect_snapshot(variant = "windows", r)
 })
 
 test_that("report.data.frame - with NAs", {
-  skip_if_not_or_load_if_installed("dplyr")
+  skip_if_not_installed("dplyr")
 
   df <- mtcars
   df[1, 2] <- NA
   df[1, 6] <- NA
 
-  report_grouped_df <- report(group_by(df, cyl))
+  report_grouped_df <- report(dplyr::group_by(df, cyl))
   expect_snapshot(variant = "windows", report_grouped_df)
 })
 
 test_that("report.data.frame - with list columns", {
-  skip_if_not_or_load_if_installed("dplyr")
+  skip_if_not_installed("dplyr")
 
   set.seed(123)
   expect_snapshot(variant = "windows", report(dplyr::starwars))

diff --git a/tests/testthat/test-report.ivreg.R b/tests/testthat/test-report.ivreg.R
@@ -1,12 +1,13 @@
-skip_if_not_or_load_if_installed("ivreg")
+skip_if_not_installed("ivreg")
+
 test_that("report-survreg", {
   data("CigaretteDemand", package = "ivreg")
 
   # model
   set.seed(123)
   ivr <-
-    ivreg(log(packs) ~ log(rprice) + log(rincome) | salestax + log(rincome),
-      data = CigaretteDemand
+    ivreg::ivreg(log(packs) ~ log(rprice) + log(rincome) | salestax + log(rincome),
+      data = ivreg::CigaretteDemand
     )
 
   expect_snapshot(variant = "windows", report(ivr))

diff --git a/tests/testthat/test-report.lavaan.R b/tests/testthat/test-report.lavaan.R
@@ -1,10 +1,11 @@
-skip_if_not_or_load_if_installed("lavaan")
+skip_if_not_installed("lavaan")
+
 structure <- " ind60 =~ x1 + x2 + x3
   dem60 =~ y1 + y2 + y3
   dem60 ~ ind60 "
 
 set.seed(123)
-model <- lavaan::sem(structure, data = PoliticalDemocracy)
+model <- lavaan::sem(structure, data = lavaan::PoliticalDemocracy)
 
 # Specific reports
 test_that("model-lavaan detailed report", {

diff --git a/tests/testthat/test-report.lm.R b/tests/testthat/test-report.lm.R
@@ -1,4 +1,6 @@
 skip_if_not(getRversion() <= "4.2.1")
+# This skip does not seem necessary??
+# Readding back because of a .1 decimal difference in snapshots
 
 test_that("report.lm - lm", {
   # lm -------

diff --git a/tests/testthat/test-report.lmer.R b/tests/testthat/test-report.lmer.R
@@ -1,4 +1,4 @@
-skip_if_not_or_load_if_installed("lme4")
+skip_if_not_installed("lme4")
 
 test_that("report-lmer", {
   df <- lme4::sleepstudy

diff --git a/tests/testthat/test-report.stanreg.R b/tests/testthat/test-report.stanreg.R
@@ -1,6 +1,7 @@
-skip_if_not_or_load_if_installed("rstanarm")
+skip_if_not_installed("rstanarm")
+
 set.seed(123)
-model <- suppressWarnings(stan_glm(mpg ~ qsec + wt, data = mtcars, refresh = 0, iter = 300))
+model <- suppressWarnings(rstanarm::stan_glm(mpg ~ qsec + wt, data = mtcars, refresh = 0, iter = 300))
 
 test_that("model-stanreg", {
   r <- report(model, centrality = "mean")

diff --git a/tests/testthat/test-report.survreg.R b/tests/testthat/test-report.survreg.R
@@ -1,12 +1,19 @@
 test_that("report-survreg", {
-  skip_if_not_or_load_if_installed("survival")
+  skip_if_not_installed("survival")
+  require("survival", quietly = TRUE)
 
+  # TODO: Use namespace when https://github.com/easystats/datawizard/issues/401 is resolved
   set.seed(123)
-  mod_survreg <- survival::survreg(
+  mod_survreg <- survreg(
     formula = Surv(futime, fustat) ~ ecog.ps + rx,
     data = ovarian,
     dist = "logistic"
   )
 
   expect_snapshot(variant = "windows", report(mod_survreg))
+
+  unloadNamespace("rstanarm")
+  unloadNamespace("multcomp")
+  unloadNamespace("TH.data")
+  unloadNamespace("survival")
 })
diff --git a/tests/testthat/test-report_performance.R b/tests/testthat/test-report_performance.R
@@ -27,7 +27,7 @@ test_that("report_performance", {
   )
 
   # Mixed models
-  skip_if_not_or_load_if_installed("lme4")
+  skip_if_not_installed("lme4")
 
   x <- lme4::lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris)
   expect_identical(
@@ -61,11 +61,10 @@ test_that("report_performance", {
     )
   )
 
-
   # Mixed models
-  skip_if_not_or_load_if_installed("lme4")
+  skip_if_not_installed("lme4")
 
-  x <- lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris)
+  x <- lme4::lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris)
   expect_identical(
     as.character(report_performance(x)),
     paste(
@@ -98,9 +97,12 @@ test_that("report_performance", {
   )
 
   # Bayesian
-  skip_if_not_or_load_if_installed("rstanarm")
+  skip_if_not_installed("rstanarm")
 
-  x <- stan_glm(Sepal.Length ~ Species, data = iris, refresh = 0, iter = 1000, seed = 333)
+  x <- rstanarm::stan_glm(
+    Sepal.Length ~ Species,
+    data = iris, refresh = 0, iter = 1000, seed = 333
+  )
   expect_snapshot(
     variant = "windows",
     report_performance(x)
@@ -110,7 +112,10 @@ test_that("report_performance", {
     summary(report_performance(x))
   )
 
-  x <- stan_glm(vs ~ disp, data = mtcars, family = "binomial", refresh = 0, iter = 1000, seed = 333)
+  x <- rstanarm::stan_glm(vs ~ disp,
+    data = mtcars, family = "binomial",
+    refresh = 0, iter = 1000, seed = 333
+  )
   expect_snapshot(
     variant = "windows",
     report_performance(x)
@@ -120,7 +125,19 @@ test_that("report_performance", {
     summary(report_performance(x))
   )
 
-  x <- stan_lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris, refresh = 0, iter = 1000, seed = 333)
+  suppressWarnings(suppressMessages(library(rstanarm)))
+  # Using namespace instead of loading the package throws an error:
+  # could not find function "stan_glmer"
+  # But we don't call "stan_glmer" directly, I suppose it must be called internally
+  # Even defining it manually, however, we get another error:
+  # stan_glmer <- rstanarm::stan_glmer
+  # Unable to refit the model with standardized data.
+  # Try instead to standardize the data (standardize(data)) and refit the
+  # model manually.
+
+  x <- rstanarm::stan_lmer(Sepal.Length ~ Petal.Length + (1 | Species),
+    data = iris, refresh = 0, iter = 1000, seed = 333
+  )
   expect_snapshot(
     variant = "windows",
     report_performance(x)
@@ -129,4 +146,5 @@ test_that("report_performance", {
     variant = "windows",
     summary(report_performance(x))
   )
+  unloadNamespace("rstanarm")
 })
diff --git a/tests/testthat/test-report_sample.R b/tests/testthat/test-report_sample.R
@@ -35,6 +35,7 @@ test_that("report_sample weights, coorect weighted N", {
 })
 
 test_that("report_sample check input", {
+  skip_if(packageVersion("parameters") < "0.20.3")
   data(iris)
   expect_error(report_sample(lm(Sepal.Length ~ Species, data = iris)))
   expect_silent(report_sample(iris$Species))