EOD

tests/testthat/test-babette_issue_108.R

@@ -26,6 +26,7 @@ test_that("tipdates file must be used in the created file", {
   fasta_filename <- get_beautier_path("babette_issue_108.fasta")
   output_filename <- get_beautier_tempfilename()
   tipdates_filename <- get_beautier_path("babette_issue_108_tipdates.txt")
+  expected_output_filename <- get_beautier_path("babette_issue_108_expected.xml")
   tipdates_table <- readr::read_tsv(
     tipdates_filename,
     col_names = c("A", "year"),
@@ -38,13 +39,18 @@ test_that("tipdates file must be used in the created file", {
       tipdates_filename = tipdates_filename,
       clock_model = create_rln_clock_model(),
       site_model = create_gtr_site_model(),
-      mcmc = create_mcmc(chain_length = 1000),
+      mcmc = create_mcmc(chain_length = 10000000),
       tree_prior = create_cbs_tree_prior(),
-      beauti_options = create_beauti_options_v2_6()
+      beauti_options = create_beauti_options_v2_6(nucleotides_uppercase = TRUE)
     )
   )
   expect_true(file.exists(output_filename))
   beast2_xml_lines <- readr::read_lines(output_filename)
+  expected_beast2_xml_lines <- readr::read_lines(expected_output_filename)
+
+  readr::write_lines(beast2_xml_lines, "~/created.xml")
+  readr::write_lines(expected_beast2_xml_lines, "~/expected.xml")
+
   expect_true(
     length(
       stringr::str_subset(
@@ -54,6 +60,7 @@ test_that("tipdates file must be used in the created file", {
     ) > 0
   )
 
-
+  # If this passes, the issue is solved
+  expect_equal(beast2_xml_lines, expected_beast2_xml_lines)
   remove_beautier_folder()
 })