Merge pull request #36 from s-ccs/unit-tests

Unit tests addition

Author: ReboreExplore

.gitignore

@@ -1,4 +1,4 @@
-data/
+/data/
 config/
 pyxdf
 pydataverse

lslautobids/config_globals.py

@@ -1,5 +1,6 @@
 import os
 import yaml
+import sys
 
 class CLIArgs:
     _instance = None
@@ -52,13 +53,20 @@ def parse_yaml_file(yaml_file):
             return None
 
 
-config_file = os.path.join(os.path.expanduser("~"),'.config/lslautobids/autobids_config.yaml')
+# Determine config path based on context
+if "pytest" in sys.modules:
+    config_file = os.path.join(os.path.expanduser("~"), ".config/lslautobids/test-autobids_config.yaml")
+else:
+    config_file = os.path.join(os.path.expanduser("~"), ".config/lslautobids/autobids_config.yaml")
 config = parse_yaml_file(config_file)
 
-project_root = os.path.join(os.path.expanduser("~"),config['PROJECT_ROOT'])
-bids_root = os.path.join(os.path.expanduser("~"),config['BIDS_ROOT'])
-project_stim_root = os.path.join(os.path.expanduser("~"),config['PROJECT_STIM_ROOT'])
-api_key = config['API_KEY']
-dataverse_base_url = config['BASE_URL']
-parent_dataverse_name = config['PARENT_DATAVERSE_NAME']
+if config:
+    project_root = os.path.join(os.path.expanduser("~"), config["PROJECT_ROOT"])
+    bids_root = os.path.join(os.path.expanduser("~"), config["BIDS_ROOT"])
+    project_stim_root = os.path.join(os.path.expanduser("~"), config["PROJECT_STIM_ROOT"])
+    api_key = config.get("API_KEY", "")
+    dataverse_base_url = config.get("BASE_URL", "")
+    parent_dataverse_name = config.get("PARENT_DATAVERSE_NAME", "")
+else:
+    project_root = bids_root = project_stim_root = api_key = dataverse_base_url = parent_dataverse_name = None
 

lslautobids/gen_project_config.py

@@ -72,8 +72,14 @@ def main():
   argparser = argparse.ArgumentParser(description='Get the project name')
   argparser.add_argument('-p','--project_name', type=str, help='Enter the project name')
   argparser.add_argument('-s','--standalone_toml', type=str, default='no', help= 'To enable the standalone toml file creation')
+  argparser.add_argument('-c','--config_file', type=str, default=None, help='Optional path to a custom YAML config file')
   args = argparser.parse_args()
 
+  print(f"ARGS: {args}")
+
+  # Replace hardcoded path
+  config_file = args.config_file or os.path.join(os.path.expanduser("~"),'.config/lslautobids/autobids_config.yaml')
+
   # get the project name and check if the project exists
   project_name = args.project_name
   standalone_toml = args.standalone_toml
@@ -86,9 +92,6 @@ def main():
       print('Creating standalone TOML file')
       file_path = file_name
   else:
-
-    # get the config file and parse it
-    config_file = os.path.join(os.path.expanduser("~"),'.config/lslautobids/autobids_config.yaml')
     config = parse_yaml_file(config_file)
     project_root = config['PROJECT_ROOT']
     # Define the path to the folder where you want to save the TOML file

lslautobids/processing_new_files.py

@@ -27,7 +27,7 @@ def process_new_files(file_status: List[str],logger) -> None:
             file_name_no_ext, ext = os.path.splitext(file_name)
             if re.search(r'_old\d*$', file_name_no_ext):
                 logger.error(f"File '{file_name}' appears to be a duplicate. It ends with an '_old' suffix. Please manually check the file.")
-                raise RuntimeError("Duplicate file detected. Please check the file manually.")
+                raise SystemExit("Duplicate file detected. Please check the file manually.")
 
             processed_files.append(file_name_no_ext + ext)
 

tests/__init__.py

@@ -0,0 +1,29 @@
+import os
+import subprocess
+import sys
+
+# --- Setup ---
+BASE_DIR = os.path.dirname(__file__) # base tests directory
+TESTCASES_DIR = os.path.join(BASE_DIR, "testcases")
+TEST_UTILS_DIR = os.path.join(BASE_DIR, "test_utils")
+
+# Make both testcases and test_utils importable
+sys.path.insert(0, TESTCASES_DIR)
+sys.path.insert(0, TEST_UTILS_DIR)
+
+
+print("Searching for test directories...\n")
+
+for folder in os.listdir(TESTCASES_DIR):
+    folder_path = os.path.join(TESTCASES_DIR, folder)
+
+    if (
+        folder.startswith("test_")
+        and os.path.isdir(folder_path)
+        and any(f.endswith(".py") for f in os.listdir(folder_path))
+        and os.path.exists(os.path.join(folder_path, "data"))
+    ):
+        print(f"Running tests in: {folder} which has folder path {folder_path}")
+        subprocess.run(["pytest", folder_path])
+    else:
+        print(f"Skipping: {folder} (no tests or data)\n")

tests/run_all_tests.py

@@ -0,0 +1,20 @@
+import os
+
+def get_root_paths(test_file: str):
+    """
+    Given a test file (__file__), return relevant test root paths.
+    """
+    # Use the test_file argument, not __file__ from path_config.py
+    test_folder = os.path.basename(os.path.dirname(test_file))
+
+    # Go up to the test folder's path and into its `data/` directory
+    base_dir = os.path.abspath(os.path.join(os.path.dirname(test_file), "data"))
+
+    print(f'The base dir in the get_roots_path function is "{base_dir}"')
+    return {
+        "project_root": os.path.join(base_dir, "projects"),
+        "bids_root": os.path.join(base_dir, "bids"),
+        "project_stim_root": os.path.join(base_dir, "project_stimulus"),
+    }
+
+

tests/test_utils/path_config.py

@@ -0,0 +1,4 @@
+time	event	what
+00:00 	cap size selection	
+00:00	camera working y/n	
+

tests/testcases/test_old_suffix/__init__.py

@@ -0,0 +1 @@
+id	age	gender	handedness	dom_eye	no_preex_conditions	visual_acuity_test	remarks