cleaned up tests a bit

Author: Benedikt Ehinger

tests/path_config.py

@@ -18,3 +18,18 @@ def get_root_paths(test_file: str):
     }
 
 
+
+def monkeypatch_paths(monkeypatch,paths):
+    monkeypatch.setattr("lslautobids.config_globals.project_root", paths["project_root"])
+    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.project_root", paths["project_root"])
+    monkeypatch.setattr("lslautobids.generate_dataset_json.project_root", paths["project_root"])
+    monkeypatch.setattr("lslautobids.main.project_root", paths["project_root"])
+    monkeypatch.setattr("lslautobids.processing_new_files.project_root", paths["project_root"])
+
+    monkeypatch.setattr("lslautobids.config_globals.bids_root", paths["bids_root"])
+    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.bids_root", paths["bids_root"])
+    monkeypatch.setattr("lslautobids.main.bids_root", paths["bids_root"])
+    
+    monkeypatch.setattr("lslautobids.config_logger.bids_root", paths["bids_root"])
+    monkeypatch.setattr("lslautobids.config_globals.project_other_root", paths["project_other_root"])
+    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.project_other_root", paths["project_other_root"])

tests/test_main_functionality/test_main_functionality.py

@@ -12,7 +12,7 @@
     sys.path.insert(0, PROJECT_ROOT)
 
 
-from path_config import get_root_paths
+from path_config import get_root_paths,monkeypatch_paths
 #from test_utils.path_config import DummyCLIArgs
 # Print test file name for traceability
 test_file_name = os.path.basename(__file__)
@@ -26,50 +26,22 @@ def test_process_main_functionality(setup_project, monkeypatch):
     """
     Expect the main pipeline to raise RuntimeError when duplicate files are found.
     """
-    project_name = setup_project
+    project_name = setup_project # fixture via pytest
     paths = get_root_paths(__file__)
-    print("ZZZ - main functionality")
 
-    print(paths)
-
-
-    #importlib.reload(lslautobids.config_globals)
-    #importlib.reload(lslautobids.main)
-
-    monkeypatch.setattr("lslautobids.config_globals.project_root", paths["project_root"])
-    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.project_root", paths["project_root"])
-    monkeypatch.setattr("lslautobids.generate_dataset_json.project_root", paths["project_root"])
-    monkeypatch.setattr("lslautobids.main.project_root", paths["project_root"])
-    monkeypatch.setattr("lslautobids.processing_new_files.project_root", paths["project_root"])
-
-    monkeypatch.setattr("lslautobids.config_globals.bids_root", paths["bids_root"])
-    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.bids_root", paths["bids_root"])
-    monkeypatch.setattr("lslautobids.main.bids_root", paths["bids_root"])
+    monkeypatch_paths(monkeypatch,paths)
 
-    monkeypatch.setattr("lslautobids.config_logger.bids_root", paths["bids_root"])
-    monkeypatch.setattr("lslautobids.config_globals.project_other_root", paths["project_other_root"])
-    monkeypatch.setattr("lslautobids.convert_to_bids_and_upload.project_other_root", paths["project_other_root"])
 
-    #lslautobids.config_globals.project_root = paths["project_root"]
-    #lslautobids.config_globals.bids_root = paths["bids_root"]
-    #lslautobids.config_globals.project_other_root = paths["project_other_root"]
-    #project_toml_path = os.path.join(paths["project_root"], project_name, f"{project_name}_config.toml")
-
     # Reset sys.argv to something that lslautobids.main.main() expects
+    # this effectively removes the -c from setup_project
     sys.argv = [
         "lslautobids.main",
         "-p", project_name,
         # other args expected by lslautobids.main.main
     ]
-
-#    dummy_cli_args = DummyCLIArgs()
-#    monkeypatch.setattr("lslautobids.config_globals.cli_args", dummy_cli_args)
-
-    # Import and run main pipeline, expect a RuntimeError
 
+    # run once
     import lslautobids.main
-
-    #with pytest.raises(SystemExit, match="Duplicate file detected. Please check the file manually."):
     lslautobids.main.main()
 
     # add a subject

tests/test_old_suffix/test_aold_suffix.py

@@ -0,0 +1,47 @@
+import os
+import sys
+import pytest
+import yaml
+
+
+import importlib
+# Compute project root (two levels up from current test.py)
+PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
+if PROJECT_ROOT not in sys.path:
+    sys.path.insert(0, PROJECT_ROOT)
+
+from path_config import get_root_paths,monkeypatch_paths
+#from test_utils.path_config import DummyCLIArgs
+
+# Print test file name for traceability
+test_file_name = os.path.basename(__file__)
+print(f" Running tests in {test_file_name}")
+
+
+
+@pytest.mark.filterwarnings("ignore::DeprecationWarning")
+def test_process_new_files_with_old_suffix(setup_project, monkeypatch):
+    """
+    Expect the main pipeline to raise RuntimeError when duplicate files are found.
+    """
+    project_name = setup_project
+    paths = get_root_paths(__file__)
+
+    monkeypatch_paths(monkeypatch,paths)
+
+    # Reset sys.argv to something that lslautobids.main.main() expects
+    sys.argv = [
+        "lslautobids.main",
+        "-p", project_name,
+        # other args expected by lslautobids.main.main
+    ]
+
+    
+    import lslautobids.main
+    
+    # Import and run main pipeline, expect a RuntimeError
+    with pytest.raises(SystemExit, match="Duplicate file detected. Please check the file manually."):
+        lslautobids.main.main()
+
+
+