refactor: converted all examples to yaml and added test for config2. Updated...

refactor: converted all examples to yaml and added test for config2. Updated readme. Fixed but in diff that assumed all csv files in map directory where map files when some where error files if no codes exists, moved error files to errors directory in the map directory to avoid this. Closes #19

acmc/phen.py

@@ -232,7 +232,9 @@ def validate(phen_dir):
     logger.info(f"Validating phenotype: {phen_dir}")
     phen_path = Path(phen_dir)
     if not phen_path.is_dir():
-        raise NotADirectoryError(f"Error: '{str(phen_path.resolve())}' is not a directory")
+        raise NotADirectoryError(
+            f"Error: '{str(phen_path.resolve())}' is not a directory"
+        )
 
     config_path = phen_path / CONFIG_FILE
     if not config_path.is_file():

tests/test_acmc.py

@@ -46,11 +46,13 @@ def test_phen_init_local_specified(tmp_dir, monkeypatch, caplog):
 
 # TODO: This test will need to be refactored so that the expected outputs match the config files
 # right now it just tests that it runs successfully and does not check the contents of the output
-@pytest.mark.parametrize("config_file", [
+@pytest.mark.parametrize(
+    "config_file",
+    [
         ("config1.yaml"),  # config.yaml test case
         ("config2.yaml"),  # config.yaml test case
-    
-])
+    ],
+)
 def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
     print(f"Temporary directory: {tmp_dir}")  # Prints path for debugging