Removed ConfigPaths dependency external files retrieval

workflow/rules/retrieve.smk

@@ -39,7 +39,8 @@ rule download_external_files:
     message:
         "Downloading external files..."
     params:
-        files = get_external_links()
+        files = get_external_links(),
+        input_data_dir = 'resources/data'
     log:
         log = "results/logs/external_files.log"
     output:

workflow/scripts/osemosys_global/external_files.py

@@ -2,7 +2,6 @@
 logging.basicConfig(format="%(levelname)s:%(message)s", level=logging.INFO)
 
 from pathlib import Path
-from configuration import ConfigPaths
 import os
 import requests
 import sys
@@ -21,14 +20,11 @@ def download_file(file: str, url: Path | str) -> None:
     with open(path, "wb") as f:
         f.write(data.content)
 
-# CONFIGURATION PARAMETERS
-config_paths = ConfigPaths()
-input_data_dir = config_paths.input_data_dir
-
 if __name__ == "__main__":
 
     if "snakemake" in globals():
         external_files = snakemake.params.files
+        input_data_dir = snakemake.params.input_data_dir
     else:
         if len(sys.argv) != 3:
             msg = "Usage: python {} <save_name> <url>"
@@ -38,6 +34,8 @@ def download_file(file: str, url: Path | str) -> None:
             in_file = sys.argv[1]
             in_url = sys.argv[2]
             external_files = {in_file: in_url}
+
+        input_data_dir = 'resources/data'
 
     for file, url in external_files.items():
         path = os.path.join(input_data_dir, file)