fix the tests, simplified the setup greatly. monkeypatching sucks

Author: Benedikt Ehinger

.gitignore

@@ -8,7 +8,7 @@ jsonschema
 empty_log_process_temp.py
 
 tests/**/bids/
-tests/testcases/test_main_functionality/data/projects/test-project/sub-100
+tests/test_main_functionality/data/projects/test-project/sub-100
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

lslautobids/config_globals.py

@@ -56,7 +56,8 @@ def parse_yaml_file(yaml_file):
 
 # Determine config paty based on context
 if "pytest" in sys.modules:
-    config_file = os.path.join(os.path.expanduser("~"), ".config/lslautobids/test-autobids_config.yaml")
+    #config_file = os.path.join(os.path.expanduser("~"), ".config/lslautobids/test-autobids_config.yaml")
+    config_file = "tests/pytest-autobids_config.yaml"
 else:
     config_file = os.path.join(os.path.expanduser("~"), ".config/lslautobids/autobids_config.yaml")
 config = parse_yaml_file(config_file)

tests/testcases/test_main_functionality/test_main_functionality.py renamed to tests/conftest.py

@@ -1,22 +1,24 @@
-import os
-import sys
 import pytest
-import yaml
-import shutil
-
-# Compute project root (two levels up from current test.py)
-PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
+import sys,os
+PROJECT_ROOT = os.path.abspath(os.path.dirname(__file__))
 if PROJECT_ROOT not in sys.path:
     sys.path.insert(0, PROJECT_ROOT)
+import yaml
 
-from test_utils.path_config import get_root_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}")
-
+from path_config import get_root_paths
 
 
+# Dummy CLI argument simulation
+class DummyCLIArgs:
+    def __init__(self):
+        self.project_name = "test-project"
+        self.yes = True
+        self.redo_bids_conversion = False 
+        self.redo_other_pc = False   
+        self.push_to_dataverse = False
+    def init(self, args):
+        # you can store the args or ignore
+        pass
 
 @pytest.fixture(scope="function")
 def setup_project(monkeypatch):
@@ -29,13 +31,15 @@ def setup_project(monkeypatch):
     project_name = dummy_cli_args.project_name
 
     # Ensure directory exists
-    os.makedirs(paths["project_root"], exist_ok=True)
+    #os.makedirs(paths["project_root"], exist_ok=True)
 
     from lslautobids.gen_project_config import main as gen_project_config_main
 
     # Create dummy user config for the test
-    config_file_test = os.path.join(os.path.expanduser("~"),'.config/lslautobids/test-autobids_config.yaml')
-    os.makedirs(os.path.dirname(config_file_test), exist_ok=True)
+    #config_file_test = os.path.join(os.path.expanduser("~"),'.config/lslautobids/test-autobids_config.yaml')
+    config_file_test = ("tests/pytest-autobids_config.yaml")
+    
+    #os.makedirs(os.path.dirname(config_file_test), exist_ok=True)
     config_data = {
         "PROJECT_ROOT": paths["project_root"],
         "BIDS_ROOT": paths["bids_root"],
@@ -67,37 +71,7 @@ def setup_project(monkeypatch):
 
     gen_project_config_main()
 
-    return paths, project_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.
-    """
-    paths, project_name = setup_project
-
-    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
-    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
-    from lslautobids.main import main as runlslautobids
-    #with pytest.raises(SystemExit, match="Duplicate file detected. Please check the file manually."):
-    runlslautobids()
-    
-    # add a subject
-    shutil.copytree(os.path.join(paths["project_root"], "copy_later","sub-100"), os.path.join(paths["project_root"], project_name,"sub-100"))
-    
-    runlslautobids()
-
-
+    yield project_name 
 
+    # crashdown
+    #os.remove(config_file_test)

tests/testcases/test_old_suffix/data/projects/test-project/test-project_config.toml renamed to tests/data/projects/test-project/test-project_config.toml

@@ -18,16 +18,3 @@ def get_root_paths(test_file: str):
     }
 
 
-
-
-# Dummy CLI argument simulation
-class DummyCLIArgs:
-    def __init__(self):
-        self.project_name = "test-project"
-        self.yes = True
-        self.redo_bids_conversion = False 
-        self.redo_other_pc = False   
-        self.push_to_dataverse = False
-    def init(self, args):
-        # you can store the args or ignore
-        pass

tests/test_utils/path_config.py renamed to tests/path_config.py

@@ -0,0 +1,3 @@
+BIDS_ROOT: /home/behinger/projects/LSLAutoBIDS/tests/data/bids
+PROJECT_OTHER_ROOT: /home/behinger/projects/LSLAutoBIDS/tests/data/project_other
+PROJECT_ROOT: /home/behinger/projects/LSLAutoBIDS/tests/data/projects