v2.6.1

Author: richelbilderbeek

NEWS.md

@@ -2,7 +2,7 @@
 
 Newest versions at top.
 
-## beautier 2.6.1 (unreleased)
+## beautier 2.6.1 (2021-07-23)
 
 ### NEW FEATURES
 

R/indent.R

@@ -13,10 +13,7 @@ indent <- function(
   if (n_spaces < 0) {
     stop("'n_spaces' must be a positive integer")
   }
-  if (is.null(text)) {
-    stop("Am I really needed? If not, delete my if statement")
-    return(NULL)
-  }
+  testthat::expect_false(is.null(text))
   for (i in seq_along(text)) {
     if (text[i] == "") next
     spaces <- paste(rep(" ", n_spaces), collapse = "")

tests/testthat/test-check_empty_beautier_folder.R

@@ -0,0 +1,38 @@
+test_that("non-existing folder", {
+  expect_silent(
+    check_empty_beautier_folder(beautier_folder = tempfile())
+  )
+})
+
+test_that("empty folder", {
+  beautier_folder <- tempfile()
+  dir.create(beautier_folder)
+  expect_silent(
+    check_empty_beautier_folder(beautier_folder = beautier_folder)
+  )
+  unlink(beautier_folder, recursive = TRUE)
+})
+
+test_that("folder with subfolder", {
+  beautier_folder <- tempfile()
+  dir.create(beautier_folder)
+  dir.create(file.path(beautier_folder, "subfolder"))
+
+  expect_error(
+    check_empty_beautier_folder(beautier_folder = beautier_folder),
+    "Folders found in beautier folder"
+  )
+  unlink(beautier_folder, recursive = TRUE)
+})
+
+test_that("folder with file", {
+  beautier_folder <- tempfile()
+  dir.create(beautier_folder)
+  file.create(file.path(beautier_folder, "file.txt"))
+
+  expect_error(
+    check_empty_beautier_folder(beautier_folder = beautier_folder),
+    "Files found in beautier folder"
+  )
+  unlink(beautier_folder, recursive = TRUE)
+})

tests/testthat/test-clock_models_to_xml_operators.R

@@ -0,0 +1,3 @@
+test_that("deprecated", {
+  expect_error(clock_models_to_xml_operators(), "deprecated")
+})

tests/testthat/test-clock_models_to_xml_prior_distr.R

@@ -0,0 +1,3 @@
+test_that("deprecated", {
+  expect_error(clock_models_to_xml_prior_distr(), "deprecated")
+})

tests/testthat/test-clock_models_to_xml_state.R

@@ -0,0 +1,3 @@
+test_that("deprecated", {
+  expect_error(clock_models_to_xml_state(), "Deprecated")
+})

tests/testthat/test-clock_models_to_xml_tracelog.R

@@ -0,0 +1,3 @@
+test_that("multiplication deprecated", {
+  expect_error(clock_models_to_xml_tracelog(), "deprecated")
+})

tests/testthat/test-create_beast2_input_by_reproducing_files_simple.R

@@ -1446,8 +1446,6 @@ test_that("Tip dating, v2.5", {
 })
 
 test_that("Tip dating, v2.6", {
-
-  skip("WIP Tipdating")
   inference_model <- create_inference_model(
     tree_prior = create_yule_tree_prior(
       birth_rate_distr = create_uniform_distr(id = 1)

tests/testthat/test-parameter_to_xml_clock_rate.R

@@ -0,0 +1,3 @@
+test_that("deprecated", {
+  expect_error(parameter_to_xml_clock_rate(), "deprecated")
+})

tests/testthat/test-parameter_to_xml_m.R

@@ -0,0 +1,3 @@
+test_that("deprecated", {
+  expect_error(parameter_to_xml_m(), "deprecated")
+})