From 8d603a9695eeae338f8677611abb4551b8a31337 Mon Sep 17 00:00:00 2001
From: olivroy <olivierroy71@hotmail.com>
Date: Thu, 26 Oct 2023 08:39:27 -0400
Subject: [PATCH] Simplify dependencies and don't use testthat in code (as it
 is suggests, not Imports.)

---
 DESCRIPTION                                   |  4 +-
 R/are_beast2_input_lines.R                    |  2 +-
 R/check_beast2_options.R                      |  6 +--
 R/check_can_create_file.R                     |  4 +-
 R/check_can_create_screenlog_file.R           |  6 +--
 R/check_can_create_tracelog_file.R            |  2 +-
 R/check_can_create_treelog_file.R             |  2 +-
 R/check_rng_seed.R                            |  2 +-
 R/check_true_false.R                          | 43 +++++++++++++++++++
 R/continue_beast2.R                           |  6 +--
 R/create_beast2_continue_cmd_from_options.R   | 12 +++---
 R/create_beast2_screenlog_folder.R            |  4 +-
 R/create_beast2_tracelog_folder.R             |  4 +-
 R/create_beast2_treelog_folder.R              |  4 +-
 R/create_beast2_validate_cmd.R                | 10 ++---
 R/create_beast2_version_cmd.R                 |  6 +--
 R/create_mcbette_beast2_options.R             |  2 +-
 R/create_random_fasta.R                       |  4 +-
 ...creenlog_filename_from_beast2_input_file.R |  4 +-
 ...tracelog_filename_from_beast2_input_file.R |  6 +--
 ..._treelog_filename_from_beast2_input_file.R |  4 +-
 R/get_beast2_example_filenames.R              |  4 +-
 R/get_beast2_version.R                        |  2 +-
 R/get_default_java_path.R                     |  4 +-
 R/is_beast2_input_file.R                      |  6 +--
 R/is_beast2_installed.R                       |  2 +-
 R/remove_file_if_present.R                    |  4 +-
 R/run_beast2_from_options.R                   |  2 +-
 tests/testthat/test-get_beast2_version.R      |  2 +-
 tests/testthat/test-gives_beast2_warning.R    |  2 +-
 tests/testthat/test-is_beast2_input_file.R    |  2 +-
 tests/testthat/test-remove_file_if_present.R  |  8 ++--
 tests/testthat/test-run_beast2.R              |  8 ++--
 tests/testthat/test-run_beast2_from_options.R |  2 +-
 34 files changed, 113 insertions(+), 72 deletions(-)
 create mode 100644 R/check_true_false.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 0f5be58..4d3d89a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,17 +26,15 @@ Imports:
     rappdirs,
     readr,
     rJava,
+    rlang (>= 1.1.0),
     sessioninfo,
     stringr,
     tibble,
     xml2
 Suggests:
-    hunspell,
     knitr,
-    markdown,
     rmarkdown,
     spelling,
-    testit,
     testthat (>= 2.1.0),
     tracerer (>= 2.2.3)
 URL: https://docs.ropensci.org/beastier/ (website)
diff --git a/R/are_beast2_input_lines.R b/R/are_beast2_input_lines.R
index 4cf0a2b..e962bb2 100644
--- a/R/are_beast2_input_lines.R
+++ b/R/are_beast2_input_lines.R
@@ -38,7 +38,7 @@ are_beast2_input_lines <- function(
     file.remove(filename)
     return(is_valid)
   } else {
-    testit::assert(method == "fast")
+    check_true(method == "fast")
     return(
       are_beast2_input_lines_fast(lines) # nolint internal function
     )
diff --git a/R/check_beast2_options.R b/R/check_beast2_options.R
index 32b6a86..0baf732 100644
--- a/R/check_beast2_options.R
+++ b/R/check_beast2_options.R
@@ -67,8 +67,8 @@ check_beast2_options_names <- function( # nolint long function name indeed, whic
 check_beast2_options_data_types <- function( # nolint long function name indeed, which is fine for an internal function
   beast2_options
 ) {
-  testthat::expect_true(beautier::is_one_string(beast2_options$input_filename))
-  testthat::expect_true(beautier::is_one_string(beast2_options$output_state_filename))
+  check_true(beautier::is_one_string(beast2_options$input_filename))
+  check_true(beautier::is_one_string(beast2_options$output_state_filename))
   check_rng_seed(beast2_options$rng_seed)
   check_n_threads(beast2_options$n_threads)
   if (!beautier::is_one_bool(beast2_options$use_beagle)) {
@@ -77,7 +77,7 @@ check_beast2_options_data_types <- function( # nolint long function name indeed,
   if (!beautier::is_one_bool(beast2_options$overwrite)) {
     stop("'overwrite' must be one boolean")
   }
-  testthat::expect_true(beautier::is_one_string(beast2_options$beast2_path))
+  check_true(beautier::is_one_string(beast2_options$beast2_path))
   if (!beautier::is_one_bool(beast2_options$verbose)) {
     stop("'verbose' must be one boolean")
   }
diff --git a/R/check_can_create_file.R b/R/check_can_create_file.R
index b75b369..06d3698 100644
--- a/R/check_can_create_file.R
+++ b/R/check_can_create_file.R
@@ -28,7 +28,7 @@ check_can_create_file <- function(
     } else {
       # Delete the file
       file.remove(filename)
-      testthat::expect_true(
+      check_true(
         !file.exists(filename),
         info = paste0(
           "Cannot delete the file already present at location ", filename
@@ -58,7 +58,7 @@ check_can_create_file <- function(
   }
 
 
-  testthat::expect_true(
+  check_true(
     !file.exists(filename),
     info = paste0(
       "Cannot delete the temporary file created at location ", filename
diff --git a/R/check_can_create_screenlog_file.R b/R/check_can_create_screenlog_file.R
index 2ca17b6..1543409 100644
--- a/R/check_can_create_screenlog_file.R
+++ b/R/check_can_create_screenlog_file.R
@@ -11,18 +11,18 @@ check_can_create_screenlog_file <- function( # nolint indeed a long function nam
   beast2_options
 ) {
   # Extract the screenlog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   text <- readr::read_lines(beast2_options$input_filename, progress = FALSE)
   screenlog_line <- stringr::str_subset(
     string = text,
     pattern = "<logger id=\"screenlog\""
   )
-  testthat::expect_equal(length(screenlog_line), 1)
+  check_true(length(screenlog_line) == 1)
   matches <- stringr::str_match(
     string = screenlog_line,
     pattern = "fileName=\\\"([:graph:]+)\\\" "
   )
-  testthat::expect_equal(ncol(matches), 2)
+  check_true(ncol(matches) == 2)
   screenlog_filename <- matches[1, 2]
 
   if (is.na(screenlog_filename)) return()
diff --git a/R/check_can_create_tracelog_file.R b/R/check_can_create_tracelog_file.R
index 6e3e161..92c9aaa 100644
--- a/R/check_can_create_tracelog_file.R
+++ b/R/check_can_create_tracelog_file.R
@@ -13,7 +13,7 @@
 check_can_create_tracelog_file <- function(
   beast2_options
 ) {
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   tracelog_filename <- extract_tracelog_filename_from_beast2_input_file( # nolint indeed a long internal function name
     input_filename = beast2_options$input_filename
   )
diff --git a/R/check_can_create_treelog_file.R b/R/check_can_create_treelog_file.R
index f026916..ba7d4ef 100644
--- a/R/check_can_create_treelog_file.R
+++ b/R/check_can_create_treelog_file.R
@@ -11,7 +11,7 @@ check_can_create_treelog_file <- function(
   beast2_options
 ) {
   # Extract the treelog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   treelog_filename <- extract_treelog_filename_from_beast2_input_file(
     input_filename = beast2_options$input_filename
   )
diff --git a/R/check_rng_seed.R b/R/check_rng_seed.R
index 1ba40b6..ad4115a 100644
--- a/R/check_rng_seed.R
+++ b/R/check_rng_seed.R
@@ -30,7 +30,7 @@ check_rng_seed <- function(rng_seed) {
       "Actual value: ", rng_seed
     )
   }
-  testthat::expect_true(beautier::is_one_int(rng_seed))
+  check_true(beautier::is_one_int(rng_seed))
   if (rng_seed <= 0) {
     stop(
       "'rng_seed' should be one NA or one non-zero positive value.\n",
diff --git a/R/check_true_false.R b/R/check_true_false.R
new file mode 100644
index 0000000..3ece9dd
--- /dev/null
+++ b/R/check_true_false.R
@@ -0,0 +1,43 @@
+# Created by modifying check_bool from import-standalone-type-check.
+check_true <- function(x,
+                       ...,
+                       allow_na = FALSE,
+                       allow_null = FALSE,
+                       arg = caller_arg(x),
+                       call = caller_env()) {
+
+  if (!missing(x) && !isFALSE(x) &&.standalone_types_check_dot_call(ffi_standalone_is_bool_1.0.7, x, allow_na, allow_null)) {
+    return(invisible(NULL))
+  }
+
+  stop_input_type(
+    x,
+    c("`TRUE`"),
+    ...,
+    allow_na = allow_na,
+    allow_null = allow_null,
+    arg = arg,
+    call = call
+  )
+}
+# Adapted from standalone-types-check.R
+check_false <- function(x,
+                        ...,
+                        allow_na = FALSE,
+                        allow_null = FALSE,
+                        arg = caller_arg(x),
+                        call = caller_env()) {
+  if (!missing(x) && !isTRUE(x) && .standalone_types_check_dot_call(ffi_standalone_is_bool_1.0.7, x, allow_na, allow_null)) {
+    return(invisible(NULL))
+  }
+
+  stop_input_type(
+    x,
+    c("`FALSE`"),
+    ...,
+    allow_na = allow_na,
+    allow_null = allow_null,
+    arg = arg,
+    call = call
+  )
+}
diff --git a/R/continue_beast2.R b/R/continue_beast2.R
index d9675a6..ffd1cac 100644
--- a/R/continue_beast2.R
+++ b/R/continue_beast2.R
@@ -65,7 +65,7 @@ continue_beast2 <- function(
   )
   # This assumpion should have been proven to be valid
   # by check_can_create_dir_for_state_output_file
-  testthat::expect_true(dir.exists(output_folder))
+  check_true(dir.exists(output_folder))
 
   ##############################################################################
   # Run BEAST2
@@ -77,7 +77,7 @@ continue_beast2 <- function(
     stderr = TRUE
   )
   # If the output is only 1 line, this will probably be an error message
-  testthat::expect_true(
+  check_true(
     length(output) != 1,
     info = paste0(
       "Command '", paste0(cmd, collapse = " "), "' failed ",
@@ -89,7 +89,7 @@ continue_beast2 <- function(
   # The files as created by BEAST2
   ##############################################################################
   # This is only true if there has been one sampling event in the MCMC
-  testthat::expect_true(
+  check_true(
     file.exists(beast2_options$output_state_filename),
     info = paste0(
       "BEAST2 state file not created after a continued run. \n",
diff --git a/R/create_beast2_continue_cmd_from_options.R b/R/create_beast2_continue_cmd_from_options.R
index 0e00197..19cfd7c 100644
--- a/R/create_beast2_continue_cmd_from_options.R
+++ b/R/create_beast2_continue_cmd_from_options.R
@@ -17,8 +17,8 @@
 #' @export
 create_beast2_continue_cmd_from_options <- function(beast2_options) { # nolint indeed a long function name
   check_beast2_options(beast2_options)
-  testit::assert(file.exists(beast2_options$beast2_path))
-  testit::assert(file.exists(get_default_java_path()))
+  check_true(file.exists(beast2_options$beast2_path))
+  check_true(file.exists(get_default_java_path()))
   cmds <- NULL
   if (is_jar_path(beast2_options$beast2_path)) {
     cmds <- c(
@@ -27,13 +27,13 @@ create_beast2_continue_cmd_from_options <- function(beast2_options) { # nolint i
       add_quotes_if_has_spaces(beast2_options$beast2_path),
       get_beast2_main_class_name()
     )
-    testit::assert(file.exists(cmds[1]))
-    # Cannot do: testit::assert(file.exists(cmds[3]))
+    check_true(file.exists(cmds[1]))
+    # Cannot do: check_true(file.exists(cmds[3]))
     # because that path is quotes
     # and file.exists does not know what to do with that
   } else {
-    testit::assert(is_bin_path(beast2_options$beast2_path))
-    testit::assert(file.exists(beast2_options$beast2_path))
+    check_true(is_bin_path(beast2_options$beast2_path))
+    check_true(file.exists(beast2_options$beast2_path))
     cmds <- add_quotes_if_has_spaces(beast2_options$beast2_path)
   }
   if (!beautier::is_one_na(beast2_options$rng_seed)) {
diff --git a/R/create_beast2_screenlog_folder.R b/R/create_beast2_screenlog_folder.R
index 2de508b..ceb2a74 100644
--- a/R/create_beast2_screenlog_folder.R
+++ b/R/create_beast2_screenlog_folder.R
@@ -6,7 +6,7 @@
 #' @export
 create_beast2_screenlog_folder <- function(beast2_options) {
   # Extract the screenlog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   screenlog_filename <- extract_screenlog_filename_from_beast2_input_file( # nolint indeed a long line
     input_filename = beast2_options$input_filename
   )
@@ -19,7 +19,7 @@ create_beast2_screenlog_folder <- function(beast2_options) {
     showWarnings = FALSE,
     recursive = TRUE
   )
-  testthat::expect_true(
+  check_true(
     dir.exists(dirname(screenlog_filename))
   )
   invisible(beast2_options)
diff --git a/R/create_beast2_tracelog_folder.R b/R/create_beast2_tracelog_folder.R
index db64981..c26f508 100644
--- a/R/create_beast2_tracelog_folder.R
+++ b/R/create_beast2_tracelog_folder.R
@@ -6,7 +6,7 @@
 #' @export
 create_beast2_tracelog_folder <- function(beast2_options) {
   # Extract the tracelog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   tracelog_filename <- extract_tracelog_filename_from_beast2_input_file( # nolint indeed a long line
     input_filename = beast2_options$input_filename
   )
@@ -15,7 +15,7 @@ create_beast2_tracelog_folder <- function(beast2_options) {
     showWarnings = FALSE,
     recursive = TRUE
   )
-  testthat::expect_true(
+  check_true(
     dir.exists(dirname(tracelog_filename))
   )
   invisible(beast2_options)
diff --git a/R/create_beast2_treelog_folder.R b/R/create_beast2_treelog_folder.R
index e54ea6f..3bb70ea 100644
--- a/R/create_beast2_treelog_folder.R
+++ b/R/create_beast2_treelog_folder.R
@@ -6,7 +6,7 @@
 #' @export
 create_beast2_treelog_folder <- function(beast2_options) {
   # Extract the treelog file
-  testthat::expect_true(file.exists(beast2_options$input_filename))
+  check_true(file.exists(beast2_options$input_filename))
   treelog_filename <- extract_treelog_filename_from_beast2_input_file(
     input_filename = beast2_options$input_filename
   )
@@ -15,7 +15,7 @@ create_beast2_treelog_folder <- function(beast2_options) {
     showWarnings = FALSE,
     recursive = TRUE
   )
-  testthat::expect_true(
+  check_true(
     dir.exists(dirname(treelog_filename))
   )
   invisible(beast2_options)
diff --git a/R/create_beast2_validate_cmd.R b/R/create_beast2_validate_cmd.R
index 8340423..652b19b 100644
--- a/R/create_beast2_validate_cmd.R
+++ b/R/create_beast2_validate_cmd.R
@@ -26,7 +26,7 @@ create_beast2_validate_cmd <- function(
       beast2_jar_path = beast2_path
     )
   } else {
-    testit::assert(is_bin_path(beast2_path))
+    check_true(is_bin_path(beast2_path))
     create_beast2_validate_cmd_bin(
       input_filename = input_filename,
       beast2_bin_path = beast2_path
@@ -58,7 +58,7 @@ create_beast2_validate_cmd_jar <- function(
   beast2_jar_path = get_default_beast2_jar_path()
 ) {
   beautier::check_file_exists(beast2_jar_path, "beast2_jar_path")
-  testit::assert(is_jar_path(beast2_jar_path))
+  check_true(is_jar_path(beast2_jar_path))
   cmds <- c(
     get_default_java_path(),
     "-cp",
@@ -68,7 +68,7 @@ create_beast2_validate_cmd_jar <- function(
     add_quotes_if_has_spaces(input_filename)
   )
   # The executable must be runnable. This means that it should not have quotes
-  testthat::expect_true(file.exists(cmds[1]))
+  check_true(file.exists(cmds[1]))
   cmds
 }
 
@@ -96,13 +96,13 @@ create_beast2_validate_cmd_bin <- function(
   beast2_bin_path = get_default_beast2_bin_path()
 ) {
   beautier::check_file_exists(beast2_bin_path, "beast2_bin_path")
-  testit::assert(is_bin_path(beast2_bin_path))
+  check_true(is_bin_path(beast2_bin_path))
   cmds <- c(
     beast2_bin_path,
     "-validate",
     add_quotes_if_has_spaces(input_filename)
   )
   # The executable must be runnable. This means that it should not have quotes
-  testthat::expect_true(file.exists(cmds[1]))
+  check_true(file.exists(cmds[1]))
   cmds
 }
diff --git a/R/create_beast2_version_cmd.R b/R/create_beast2_version_cmd.R
index 161be87..d618397 100644
--- a/R/create_beast2_version_cmd.R
+++ b/R/create_beast2_version_cmd.R
@@ -18,7 +18,7 @@ create_beast2_version_cmd <- function(
       beast2_jar_path = beast2_path
     )
   } else {
-    testit::assert(is_bin_path(beast2_path))
+    check_true(is_bin_path(beast2_path))
     create_beast2_version_cmd_bin(
       beast2_bin_path = beast2_path
     )
@@ -42,7 +42,7 @@ create_beast2_version_cmd_jar <- function(
   beast2_jar_path = get_default_beast2_jar_path()
 ) {
   beautier::check_file_exists(beast2_jar_path, "beast2_jar_path")
-  testit::assert(is_jar_path(beast2_jar_path))
+  check_true(is_jar_path(beast2_jar_path))
   cmds <- c(
     get_default_java_path(),
     "-cp",
@@ -71,7 +71,7 @@ create_beast2_version_cmd_bin <- function(
   beast2_bin_path = get_default_beast2_bin_path()
 ) {
   beautier::check_file_exists(beast2_bin_path, "beast2_bin_path")
-  testit::assert(is_bin_path(beast2_bin_path))
+  check_true(is_bin_path(beast2_bin_path))
   cmds <- c(
     beast2_bin_path,
     "-version"
diff --git a/R/create_mcbette_beast2_options.R b/R/create_mcbette_beast2_options.R
index 9ff1457..2ea9079 100644
--- a/R/create_mcbette_beast2_options.R
+++ b/R/create_mcbette_beast2_options.R
@@ -31,7 +31,7 @@ create_mcbette_beast2_options <- function(
   beast2_bin_path = get_default_beast2_bin_path(),
   verbose = FALSE
 ) {
-  testit::assert(is_bin_path(beast2_bin_path))
+  check_true(is_bin_path(beast2_bin_path))
   create_beast2_options(
     input_filename = input_filename,
     output_state_filename = output_state_filename,
diff --git a/R/create_random_fasta.R b/R/create_random_fasta.R
index 23d5e51..c610494 100644
--- a/R/create_random_fasta.R
+++ b/R/create_random_fasta.R
@@ -29,12 +29,12 @@ create_random_fasta <- function(
   if (sequence_length < 1) {
     stop("'sequence_length' must be one or more")
   }
-  testthat::expect_true(beautier::is_one_string(fasta_filename))
+  check_true(beautier::is_one_string(fasta_filename))
 
   if (fasta_filename == "") {
     stop("'fasta_filename' must have at least one character")
   }
-  testthat::expect_true(beautier::is_one_string(taxa_name_ext))
+  check_true(beautier::is_one_string(taxa_name_ext))
   alignments <- create_random_alignment(
     n_taxa,
     sequence_length,
diff --git a/R/extract_screenlog_filename_from_beast2_input_file.R b/R/extract_screenlog_filename_from_beast2_input_file.R
index 2f4f595..a930615 100644
--- a/R/extract_screenlog_filename_from_beast2_input_file.R
+++ b/R/extract_screenlog_filename_from_beast2_input_file.R
@@ -8,13 +8,13 @@
 extract_screenlog_filename_from_beast2_input_file <- function( # nolint indeed a long function name
   input_filename
 ) {
-  testthat::expect_true(file.exists(input_filename))
+  check_true(file.exists(input_filename))
   text <- readr::read_lines(input_filename, progress = FALSE)
   screenlog_line <- stringr::str_subset(
     string = text,
     pattern = "<logger id=\"screenlog"
   )
-  testthat::expect_equal(length(screenlog_line), 1)
+  check_true(length(screenlog_line) == 1)
   screenlog_filename <- stringr::str_match(
     string = screenlog_line,
     pattern = "fileName=\\\"([:graph:]+)\\\" "
diff --git a/R/extract_tracelog_filename_from_beast2_input_file.R b/R/extract_tracelog_filename_from_beast2_input_file.R
index ee0eb5c..ff01a00 100644
--- a/R/extract_tracelog_filename_from_beast2_input_file.R
+++ b/R/extract_tracelog_filename_from_beast2_input_file.R
@@ -33,18 +33,18 @@ extract_tracelog_filename_from_beast2_input_file <- function( # nolint indeed a
   input_filename
 ) {
   # Extract the tracelog file
-  testthat::expect_true(file.exists(input_filename))
+  check_true(file.exists(input_filename))
   text <- readr::read_lines(input_filename, progress = FALSE)
   tracelog_line <- stringr::str_subset(
     string = text,
     pattern = "<logger id=\"tracelog\""
   )
-  testthat::expect_equal(length(tracelog_line), 1)
+  check_true(length(tracelog_line) == 1)
   matches <- stringr::str_match(
     string = tracelog_line,
     pattern = "fileName=\\\"([:graph:]+)\\\" "
   )
-  testthat::expect_equal(ncol(matches), 2)
+  check_true(ncol(matches) == 2)
   tracelog_filename <- matches[1, 2]
   tracelog_filename
 }
diff --git a/R/extract_treelog_filename_from_beast2_input_file.R b/R/extract_treelog_filename_from_beast2_input_file.R
index 66f075b..3acbbb2 100644
--- a/R/extract_treelog_filename_from_beast2_input_file.R
+++ b/R/extract_treelog_filename_from_beast2_input_file.R
@@ -24,13 +24,13 @@
 extract_treelog_filename_from_beast2_input_file <- function( # nolint indeed a long function name
   input_filename
 ) {
-  testthat::expect_true(file.exists(input_filename))
+  check_true(file.exists(input_filename))
   text <- readr::read_lines(input_filename, progress = FALSE)
   treelog_line <- stringr::str_subset(
     string = text,
     pattern = "<logger id=\"treelog.t:"
   )
-  testthat::expect_equal(length(treelog_line), 1)
+  check_true(length(treelog_line) == 1)
   treelog_filename <- stringr::str_match(
     string = treelog_line,
     pattern = "fileName=\\\"([:graph:]+)\\\" "
diff --git a/R/get_beast2_example_filenames.R b/R/get_beast2_example_filenames.R
index 237fae7..3ad3bb5 100644
--- a/R/get_beast2_example_filenames.R
+++ b/R/get_beast2_example_filenames.R
@@ -19,9 +19,9 @@ get_beast2_example_filenames <- function(
     )
   }
   beast2_subfolder <- file.path(beast2_folder, "beast")
-  testit::assert(dir.exists(beast2_subfolder))
+  check_true(dir.exists(beast2_subfolder))
   examples_folder <- file.path(beast2_subfolder, "examples")
-  testit::assert(dir.exists(examples_folder))
+  check_true(dir.exists(examples_folder))
   list.files(
     path = examples_folder,
     full.names = TRUE,
diff --git a/R/get_beast2_version.R b/R/get_beast2_version.R
index f3de221..0f0aa9e 100644
--- a/R/get_beast2_version.R
+++ b/R/get_beast2_version.R
@@ -26,7 +26,7 @@ get_beast2_version <- function(
   }
 
   # Create the command
-  testit::assert(length(beast2_path) == 1)
+  check_true(length(beast2_path) == 1)
   cmds <- create_beast2_version_cmd(beast2_path)
   beautier::check_file_exists(cmds[1], "cmds[1]")
   output <- NA
diff --git a/R/get_default_java_path.R b/R/get_default_java_path.R
index 15482a5..7c88256 100644
--- a/R/get_default_java_path.R
+++ b/R/get_default_java_path.R
@@ -11,11 +11,11 @@ get_default_java_path <- function(
   java_folder <- rJava::.jcall(
     "java/lang/System", "S", "getProperty", "java.home"
   )
-  testit::assert(dir.exists(java_folder))
+  check_true(dir.exists(java_folder))
   java_path <- file.path(java_folder, "bin", "java.exe")
   if (os != "win") {
     java_path <- file.path(java_folder, "bin", "java")
   }
-  testit::assert(file.exists(java_path))
+  check_true(file.exists(java_path))
   normalizePath(java_path, mustWork = TRUE)
 }
diff --git a/R/is_beast2_input_file.R b/R/is_beast2_input_file.R
index 18b670f..3e50568 100644
--- a/R/is_beast2_input_file.R
+++ b/R/is_beast2_input_file.R
@@ -44,15 +44,15 @@ is_beast2_input_file <- function(
   }
 
   # Create the command to let BEAST2 validate the created XML file
-  testit::assert(length(filename) == 1)
-  testit::assert(length(beast2_path) == 1)
+  check_true(length(filename) == 1)
+  check_true(length(beast2_path) == 1)
   beautier::check_file_exists(filename, "filename")
   cmds <- create_beast2_validate_cmd(
     input_filename = filename,
     beast2_path = beast2_path
   )
   # The executable must be runnable. This means that it should not have quotes
-  testthat::expect_true(file.exists(cmds[1]))
+  check_true(file.exists(cmds[1]))
   output <- NA
   if (show_warnings == TRUE) {
     output <- system2(
diff --git a/R/is_beast2_installed.R b/R/is_beast2_installed.R
index 70ca463..69303c9 100644
--- a/R/is_beast2_installed.R
+++ b/R/is_beast2_installed.R
@@ -33,6 +33,6 @@ is_beast2_installed <- function(
 
   bin_exists <- file.exists(bin_file_path)
   jar_exists <- file.exists(jar_file_path)
-  testit::assert(bin_exists == jar_exists)
+  check_true(bin_exists == jar_exists)
   jar_exists
 }
diff --git a/R/remove_file_if_present.R b/R/remove_file_if_present.R
index c9ec0b4..f5f4372 100644
--- a/R/remove_file_if_present.R
+++ b/R/remove_file_if_present.R
@@ -11,8 +11,8 @@
 #' @author Richèl J.C. Bilderbeek
 #' @export
 remove_file_if_present <- function(filename) {
-  testthat::expect_true(beautier::is_one_string(filename))
-  testit::assert(length(filename) == 1)
+  check_true(beautier::is_one_string(filename))
+  check_true(length(filename) == 1)
   if (file.exists(filename)) {
     file.remove(filename)
   }
diff --git a/R/run_beast2_from_options.R b/R/run_beast2_from_options.R
index 933ece7..895f379 100644
--- a/R/run_beast2_from_options.R
+++ b/R/run_beast2_from_options.R
@@ -91,7 +91,7 @@ run_beast2_from_options <- function(
   )
   # This assumpion should have been proven to be valid
   # by check_can_create_dir_for_state_output_file
-  testthat::expect_true(dir.exists(output_folder))
+  check_true(dir.exists(output_folder))
 
 
   ##############################################################################
diff --git a/tests/testthat/test-get_beast2_version.R b/tests/testthat/test-get_beast2_version.R
index ea020a1..0860b8c 100644
--- a/tests/testthat/test-get_beast2_version.R
+++ b/tests/testthat/test-get_beast2_version.R
@@ -29,7 +29,7 @@ test_that("cannot ", {
   if (!is_beast2_installed()) return()
 
   win_bin_path <- "BEAST.exe"
-  testit::assert(is_win_bin_path(win_bin_path))
+  expect_true(is_win_bin_path(win_bin_path))
   expect_error(
     get_beast2_version(
       beast2_path = win_bin_path
diff --git a/tests/testthat/test-gives_beast2_warning.R b/tests/testthat/test-gives_beast2_warning.R
index 1b46503..98287c2 100644
--- a/tests/testthat/test-gives_beast2_warning.R
+++ b/tests/testthat/test-gives_beast2_warning.R
@@ -2,7 +2,7 @@ test_that("use, bin", {
   expect_equal(1 + 1, 2) # nolint to prevent 'Reason: empty test'
   if (!is_beast2_installed()) return()
 
-  testit::assert(is_beast2_installed())
+  expect_true(is_beast2_installed())
 
   # Binary works under Unix, fails under Windows (see 'abuse' section below)
   if (rappdirs::app_dir()$os == "unix") {
diff --git a/tests/testthat/test-is_beast2_input_file.R b/tests/testthat/test-is_beast2_input_file.R
index ef08eb2..7acd121 100644
--- a/tests/testthat/test-is_beast2_input_file.R
+++ b/tests/testthat/test-is_beast2_input_file.R
@@ -45,7 +45,7 @@ test_that("anthus_2_4.xml is valid, from bin", {
   check_empty_beaustier_folders()
 
   filename <- get_beastier_path("anthus_2_4.xml")
-  testit::assert(file.exists(filename))
+  expect_true(file.exists(filename))
   expect_true(
     beastier::is_beast2_input_file(
       filename,
diff --git a/tests/testthat/test-remove_file_if_present.R b/tests/testthat/test-remove_file_if_present.R
index 5a2d785..19101b8 100644
--- a/tests/testthat/test-remove_file_if_present.R
+++ b/tests/testthat/test-remove_file_if_present.R
@@ -2,9 +2,9 @@ test_that("use, no file present", {
   check_empty_beaustier_folders()
 
   filename <- "abs.ent"
-  testit::assert(!file.exists(filename))
+  expect_true(!file.exists(filename))
   expect_silent(remove_file_if_present(filename))
-  testit::assert(!file.exists(filename))
+  expect_true(!file.exists(filename))
 
   check_empty_beaustier_folders()
 })
@@ -15,9 +15,9 @@ test_that("use, file present", {
   filename <- get_beastier_tempfilename()
   dir.create(dirname(filename), recursive = TRUE, showWarnings = FALSE)
   writeLines(text = "some irrelevant text", con = filename)
-  testit::assert(file.exists(filename))
+  expect_true(file.exists(filename))
   expect_silent(remove_file_if_present(filename))
-  testit::assert(!file.exists(filename))
+  expect_true(!file.exists(filename))
 
   remove_beaustier_folders()
   check_empty_beaustier_folders()
diff --git a/tests/testthat/test-run_beast2.R b/tests/testthat/test-run_beast2.R
index 483c993..9b90222 100644
--- a/tests/testthat/test-run_beast2.R
+++ b/tests/testthat/test-run_beast2.R
@@ -41,7 +41,7 @@ test_that("single alignment, equal RNG seed equal results", {
     output_state_filename_1,
     output_state_filename_2
   )
-  testit::assert(!all(file.exists(output_files)))
+  expect_true(!all(file.exists(output_files)))
 
   rng_seed <- 42
   stdout_1 <- run_beast2(
@@ -112,7 +112,7 @@ test_that("BEAST2 does not overwrite the .xml.state file specified by user", {
     dirname(output_state_filename), recursive = TRUE, showWarnings = FALSE
   )
   write(x = "state", file = output_state_filename)
-  testit::assert(all(readLines(output_state_filename, warn = FALSE) == "state"))
+  expect_true(all(readLines(output_state_filename, warn = FALSE) == "state"))
 
   # Delete the log file iff it is present,
   # only needed when running these tests locally for multiple times
@@ -146,7 +146,7 @@ test_that("BEAST2 overwrites state file", {
   )
   write(x = "state", file = output_state_filename)
 
-  testit::assert(all(readLines(output_state_filename) == "state"))
+  expect_true(all(readLines(output_state_filename) == "state"))
 
   # Cannot use 'expect_silent' as an empty line is produced in the output
   run_beast2(
@@ -207,7 +207,7 @@ test_that("run BEAST2 from binary path", {
       get_beastier_tempfilename(),
       "BEAST2.exe"
     )
-    testit::assert(is_bin_path(fake_windows_exe_filename))
+    expect_true(is_bin_path(fake_windows_exe_filename))
     dir.create(
       dirname(fake_windows_exe_filename),
       recursive = TRUE, showWarnings = FALSE
diff --git a/tests/testthat/test-run_beast2_from_options.R b/tests/testthat/test-run_beast2_from_options.R
index 035fa2b..8110983 100644
--- a/tests/testthat/test-run_beast2_from_options.R
+++ b/tests/testthat/test-run_beast2_from_options.R
@@ -247,7 +247,7 @@ test_that("BEAST2 freezes when treelog file already exists", {
       )
     )
   )
-  testit::assert(file.exists(beast2_xml_filename))
+  expect_true(file.exists(beast2_xml_filename))
 
   # First run works fine, takes approx 1 sec on my computer
   beastier::run_beast2_from_options(