Improve tests

taxonomicallyinformedannotation · Jul 3, 2024 · 8849e80 · 8849e80
1 parent 34998ac
commit 8849e80
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/R/get_params.R b/R/get_params.R
@@ -22,12 +22,12 @@ get_params <- function(step) {
 
  default_path <-
  if (step == "prepare_params") {
- file.path(paths$params$prepare_params)
+ system.file("params/prepare_params.yaml", package = "timaR")
  } else {
  if (step == "prepare_params_advanced") {
- file.path(paths$params$prepare_params_advanced)
+ system.file("params/prepare_params_advanced.yaml", package = "timaR")
  } else {
- file.path(paths$params$default$path, paste0(step, ".yaml"))
+ file.path(system.file("params/default/", package = "timaR"), paste0(step, ".yaml"))
  }
  }
 
@@ -38,10 +38,10 @@ get_params <- function(step) {
  stopifnot("Your step does not exist." = step %in% steps)
 
  doc_path <-
- file.path(paths$inst$scripts$docopt, paste0(step, ".txt"))
+ file.path(system.file("scripts/docopt/", package = "timaR"), paste0(step, ".txt"))
 
  user_path <-
- file.path(paths$params$user$path, paste0(step, ".yaml"))
+ file.path(system.file("params/user/", package = "timaR"), paste0(step, ".yaml"))
 
  doc <- readChar(
  con = doc_path,

diff --git a/codemeta.json b/codemeta.json
@@ -578,7 +578,7 @@
  "SystemRequirements": null
  },
  "keywords": ["metaboliteannotation", "chemotaxonomy", "scoringsystem", "naturalproducts", "computationalmetabolomics", "taxonomicdistance", "specializedmetabolome"],
- "fileSize": "4379.46KB",
+ "fileSize": "4379.43KB",
  "citation": [
  {
  "@type": "ScholarlyArticle",