From 73f77c20a1fbf1b9e476950f0f0688c73fae1a09 Mon Sep 17 00:00:00 2001
From: Tom Rix <tom.rix@dkfz-heidelberg.de>
Date: Fri, 12 Jul 2024 13:49:39 +0200
Subject: [PATCH] Put environment variables on second place, fixes #307

---
 simpa/utils/path_manager.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/simpa/utils/path_manager.py b/simpa/utils/path_manager.py
index 2e7ba1ed..74f41f5d 100644
--- a/simpa/utils/path_manager.py
+++ b/simpa/utils/path_manager.py
@@ -20,9 +20,10 @@ class PathManager:
     one we provided in the `simpa_examples`) in the following places in this order:
 
         1. The optional path you give the PathManager
-        2. Your $HOME$ directory
-        3. The current working directory
-        4. The SIMPA home directory path
+        2. Your set environment variables
+        3. Your $HOME$ directory
+        4. The current working directory
+        5. The SIMPA home directory path
     """
 
     def __init__(self, environment_path=None):
@@ -32,6 +33,7 @@ def __init__(self, environment_path=None):
         """
         self.logger = Logger()
         self.path_config_file_name = 'path_config.env'
+        override = False
         if environment_path is None:
             environment_path = os.path.join(str(Path.home()), self.path_config_file_name)
             self.logger.debug(f"Using $HOME$ path to search for config file: {environment_path}")
@@ -44,13 +46,14 @@ def __init__(self, environment_path=None):
                                   f"for {self.path_config_file_name}")
                 environment_path = os.path.join(environment_path, self.path_config_file_name)
             self.logger.debug(f"Using supplied path to search for config file: {environment_path}")
+            override = True
 
         if environment_path is None or not os.path.exists(environment_path) or not os.path.isfile(environment_path):
             error_message = f"Did not find a { self.path_config_file_name} file in any of the standard directories..."
             self.logger.warning(error_message)
 
         self.environment_path = environment_path
-        load_dotenv(environment_path, override=True)
+        load_dotenv(environment_path, override=override)
 
     def detect_local_path_config(self):
         """