Most tests pass now

VisruthSK · VisruthSK · commit ee70347c56cb · 2025-06-20T20:23:31.000-07:00
diff --git a/tests/testthat/_snaps/loo_predictive_metric.md b/tests/testthat/_snaps/loo_predictive_metric.md
@@ -0,0 +1,60 @@
+# loo_predictive_metric is equal to snapshot
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP+b6DHwJlO4AAAAOAAAAAT+0VQV434B0
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP/c/cc5N6ckAAAAOAAAAAT/C02/w8SU2
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP+r8D5W4BOIAAAAOAAAAAT+07COl+XlU
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP/qvkDt3DvwAAAAOAAAAAT/BcF2FCRTJ
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP+bBWsjIsVUAAAAOAAAAAT/BpKrAKkv4
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABQAZBDZS19iwAAAAOAAAAAT/dFfIrJ59T
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP9gAAAAAAAAAAAAOAAAAAT+16K3SNqWP
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP9QAAAAAAAAAAAAOAAAAAT+0+ea7xOyz
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP9aw32sN9rEAAAAOAAAAAT+uapXy8Hyq
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAITAAAAAgAAAA4AAAABP+AAAAAAAAAAAAAOAAAAAQAAAAAAAAAA
+    AAAEAgAAAAEABAAJAAAABW5hbWVzAAAAEAAAAAIABAAJAAAACGVzdGltYXRlAAQACQAAAAJz
+    ZQAAAP4=
+
diff --git a/tests/testthat/_snaps/loo_subsampling.md b/tests/testthat/_snaps/loo_subsampling.md
@@ -0,0 +1,20 @@
+# loo_compare_subsample
+
+    Code
+      lcss <- loo:::loo_compare.psis_loo_ss_list(x = list(lss1, lss2, lss3))
+    Condition
+      Warning:
+      Different subsamples in 'model3' and 'model2'. Naive diff SE is used.
+      Warning:
+      Different subsamples in 'model3' and 'model1'. Naive diff SE is used.
+
+---
+
+    Code
+      lcssapi <- loo_compare(lss1, lss2, lss3)
+    Condition
+      Warning:
+      Different subsamples in 'model3' and 'model2'. Naive diff SE is used.
+      Warning:
+      Different subsamples in 'model3' and 'model1'. Naive diff SE is used.
+
diff --git a/tests/testthat/_snaps/model_weighting.md b/tests/testthat/_snaps/model_weighting.md
@@ -0,0 +1,8 @@
+# loo_model_weights (stacking and pseudo-BMA) gives expected result
+
+    WAoAAAACAAQFAAACAwAAAAAOAAAAAz/KEXngFjO6P+l7oXTIUDU+YzIi3AAAAA==
+
+---
+
+    WAoAAAACAAQFAAACAwAAAAAOAAAAAz+xA6UGtqDFP+3eFS5zKzY/J2MLYAsc4w==
+
diff --git a/tests/testthat/_snaps/print_plot.md b/tests/testthat/_snaps/print_plot.md
@@ -0,0 +1,4 @@
+# mcse_loo extractor gives correct value
+
+    WAoAAAACAAQFAAACAwAAAAAOAAAAAT+2J8YDcP5s
+
diff --git a/tests/testthat/_snaps/psis.md b/tests/testthat/_snaps/psis.md
diff --git a/tests/testthat/_snaps/psislw.md b/tests/testthat/_snaps/psislw.md
@@ -0,0 +1,14 @@
+# psislw handles special cases, throws appropriate errors/warnings
+
+    Code
+      psis <- psislw(x[, 1], wcp = 0.01)
+    Condition
+      Warning in `psislw()`:
+      'psislw' is deprecated.
+      Use 'psis' instead.
+      See help("Deprecated")
+      Warning:
+      All tail values are the same. Weights are truncated but not smoothed.
+      Warning:
+      Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details.
+
diff --git a/tests/testthat/test_loo_subsampling.R b/tests/testthat/test_loo_subsampling.R
diff --git a/tests/testthat/test_model_weighting.R b/tests/testthat/test_model_weighting.R
@@ -1,7 +1,5 @@
 library(loo)
 
-context("loo_model_weights")
-
 # generate fake data
 set.seed(123)
 y<-rnorm(50,0,1)
@@ -22,7 +20,7 @@ loo_list <- lapply(1:length(ll_list), function(j) {
   loo(ll_list[[j]], r_eff = r_eff_list[[j]])
 })
 
-tol <- 0.01 # absoulte tolerance of weights
+tol <- 0.01 # absolute tolerance of weights
 
 test_that("loo_model_weights throws correct errors and warnings", {
   expect_error(loo_model_weights(log_lik1), "list of matrices or a list of 'psis_loo' objects")
@@ -79,7 +77,7 @@ test_that("loo_model_weights (stacking and pseudo-BMA) gives expected result", {
   expect_length(w3, 3)
   expect_named(w3, paste0("model"  ,c(1:3)))
   expect_equal(as.numeric(w3), c(5.365279e-05, 9.999436e-01, 2.707028e-06),
-               tolerance  = tol, scale = 1)
+               tolerance  = tol)
   expect_output(print(w3), "Method: pseudo-BMA")
 
   w3_b <- loo_model_weights(loo_list, method = "pseudobma", BB = FALSE)
diff --git a/tests/testthat/test_pointwise.R b/tests/testthat/test_pointwise.R
@@ -1,7 +1,5 @@
 library(loo)
 
-context("pointwise convenience function")
-
 loo1 <- suppressWarnings(loo(example_loglik_matrix()))
 
 test_that("pointwise throws the right errors", {
diff --git a/tests/testthat/test_print_plot.R b/tests/testthat/test_print_plot.R
@@ -1,8 +1,6 @@
 library(loo)
 set.seed(1414)
 
-context("print, plot, diagnostics")
-
 LLarr <- example_loglik_array()
 waic1 <- suppressWarnings(waic(LLarr))
 loo1 <- suppressWarnings(loo(LLarr))
diff --git a/tests/testthat/test_psis.R b/tests/testthat/test_psis.R
@@ -3,8 +3,6 @@ options(mc.cores=1)
 options(loo.cores=NULL)
 set.seed(123)
 
-context("psis")
-
 LLarr <- example_loglik_array()
 LLmat <- example_loglik_matrix()
 LLvec <- LLmat[, 1]
@@ -78,10 +76,7 @@ test_that("psis throws correct errors and warnings", {
   expect_error(psis(-LLarr, r_eff = r_eff_arr), "mix NA and not NA values")
 
   # tail length warnings
-  expect_warning(
-    psis(-LLarr[1:5,, ]),
-    "Not enough tail samples to fit the generalized Pareto distribution"
-  )
+  expect_snapshot(psis(-LLarr[1:5,, ]))
 
   # no NAs or non-finite values allowed
   LLmat[1,1] <- NA
@@ -147,7 +142,7 @@ test_that("psis_n_eff methods works properly", {
 
 test_that("do_psis_i throws warning if all tail values the same", {
   xx <- c(1,2,3,4,4,4,4,4,4,4,4)
-  val <- expect_warning(do_psis_i(xx, tail_len_i = 6), "all tail values are the same")
+  expect_warning(val <- do_psis_i(xx, tail_len_i = 6), "all tail values are the same")
   expect_equal(val$pareto_k, Inf)
 })
 
diff --git a/tests/testthat/test_psis_approximate_posterior.R b/tests/testthat/test_psis_approximate_posterior.R
@@ -1,7 +1,5 @@
 library(loo)
 
-context("psis_approximate_posterior")
-
 load(test_path("data-for-tests/test_data_psis_approximate_posterior.rda"))
 
 test_that("Laplace approximation, independent posterior", {
diff --git a/tests/testthat/test_psislw.R b/tests/testthat/test_psislw.R
@@ -1,8 +1,6 @@
 library(loo)
 SW <- suppressWarnings
 
-context("psislw")
-
 set.seed(123)
 x <- matrix(rnorm(5000), 100, 50)
 
@@ -16,18 +14,9 @@ test_that("psislw throws deprecation warning", {
 
 
 test_that("psislw handles special cases, throws appropriate errors/warnings", {
-  expect_warning(
-    psis <- psislw(x[, 1], wcp = 0.01),
-    regexp = "All tail values are the same. Weights are truncated but not smoothed"
-  )
+  expect_snapshot(psis <- psislw(x[, 1], wcp = 0.01))
   expect_true(is.infinite(psis$pareto_k))
 
-  expect_warning(
-    psislw(x[, 1], wcp = 0.01),
-    regexp = "Some Pareto k diagnostic values are too high. See help('pareto-k-diagnostic') for details",
-    fixed = TRUE
-  )
-
   expect_error(
     expect_deprecated(psislw(wcp = 0.2)),
     regexp = "'lw' or 'llfun' and 'llargs' must be specified"
diff --git a/tests/testthat/test_tisis.R b/tests/testthat/test_tisis.R
@@ -3,8 +3,6 @@ options(mc.cores=1)
 options(loo.cores=NULL)
 set.seed(123)
 
-context("tis and is")
-
 LLarr <- example_loglik_array()
 LLmat <- example_loglik_matrix()
 LLvec <- LLmat[, 1]
@@ -143,20 +141,20 @@ test_that("explict test of values for 'sis' and 'tis'", {
   lw <- 1:16
   expect_silent(tis_true <- tis(log_ratios = lw, r_eff = NA))
   expect_equal(as.vector(weights(tis_true, log = TRUE, normalize = FALSE)),
-               c(-14.0723, -13.0723, -12.0723, -11.0723, -10.0723, -9.0723, -8.0723, -7.0723, -6.0723, -5.0723, -4.0723, -3.0723, -2.0723, -1.0723, -0.0723, 0.) + 15.07238, tol = 0.001)
+               c(-14.0723, -13.0723, -12.0723, -11.0723, -10.0723, -9.0723, -8.0723, -7.0723, -6.0723, -5.0723, -4.0723, -3.0723, -2.0723, -1.0723, -0.0723, 0.) + 15.07238, tolerance = 0.001)
   expect_silent(is_true <- sis(log_ratios = lw, r_eff = NA))
   expect_equal(as.vector(weights(is_true, log = TRUE, normalize = FALSE)),
-               lw, tol = 0.00001)
+               lw, tolerance = 0.00001)
 
   lw <- c(0.7609420, 1.3894140, 0.4158346, 2.5307927, 4.3379119, 2.4159240, 2.2462172, 0.8057697, 0.9333107, 1.5599302)
 
   expect_silent(tis_true <- tis(log_ratios = lw, r_eff = NA))
   expect_equal(as.vector(weights(tis_true, log = TRUE, normalize = FALSE)),
                c(-2.931, -2.303, -3.276, -1.161,  0, -1.276, -1.446, -2.886, -2.759, -2.132) + 3.692668,
-               tol = 0.001)
+               tolerance = 0.001)
   expect_silent(is_true <- sis(log_ratios = lw, r_eff = NA))
   expect_equal(as.vector(weights(is_true, log = TRUE, normalize = FALSE)),
-               lw, tol = 0.00001)
+               lw, tolerance = 0.00001)
 })
 
 

-Original file line number
+Diff line change
@@ @@ -0,0 +1,4 @@ @@
 +# mcse_loo extractor gives correct value
++
 +    WAoAAAACAAQFAAACAwAAAAAOAAAAAT+2J8YDcP5s
++