Improve tests

taxonomicallyinformedannotation · Jul 3, 2024 · 9af7d88 · 9af7d88
1 parent 8849e80
commit 9af7d88
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Showing 2 changed files with 2 additions and 18 deletions.
diff --git a/R/parse_yaml_paths.R b/R/parse_yaml_paths.R
@@ -10,20 +10,6 @@
 #' @export
 #'
 #' @examples NULL
-parse_yaml_paths <- function(file = system.file("extdata",
- "paths.yaml",
- package = "timaR"
- )) {
- ## Read the YAML file containing the paths
- suppressWarnings(
- paths <- yaml::read_yaml(
- file = file
- )
- )
-
- ## Set the working directory to the base directory specified in the YAML file
- setwd(paths$base_dir)
-
- ## Return the list of paths
- return(paths)
+parse_yaml_paths <- function(file = system.file("extdata", "paths.yaml", package = "timaR")) {
+ return(suppressWarnings(yaml::read_yaml(file = file)))
 }
diff --git a/tests/testthat/test-functions.R b/tests/testthat/test-functions.R
@@ -6,8 +6,6 @@ test_that(desc = "Test functions", code = {
  ## Prepare parameters
  paths <- parse_yaml_paths()
  params <- get_params(step = "prepare_params")
- ## Prepare config for a single step only
- prepare_params(step = "weight_annotations")
  ## For all steps
  params$organisms$taxon <- ""
  prepare_params(params_small = params)