Simplify dependencies and don't use testthat in code (as it is sugges…

…ts, not Imports.)
ropensci · Oct 26, 2023 · 8d603a9 · 8d603a9
1 parent 2b8f7ca
commit 8d603a9
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Showing 34 changed files with 113 additions and 72 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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:]+)\\\" "