From 8849e80060f7f3331d4114212a27ab4021b77d9b Mon Sep 17 00:00:00 2001
From: Adriano Rutz <adriano.rutz@hotmail.com>
Date: Wed, 3 Jul 2024 10:14:49 +0200
Subject: [PATCH] Improve tests

---
 R/get_params.R | 10 +++++-----
 codemeta.json  |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/get_params.R b/R/get_params.R
index eb11a06d6..bd8239e36 100644
--- 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
index e773841fd..af12414f5 100644
--- 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",