refactor remove unnecessary tests

looper/cli_pydantic.py

@@ -40,7 +40,7 @@
 from .utils import (
     dotfile_path,
     enrich_args_via_cfg,
-    is_registry_path,
+    is_pephub_registry_path,
     read_looper_config_file,
     read_looper_dotfile,
     initiate_looper_config,
@@ -195,7 +195,7 @@ def run_looper(args: TopLevelParser, parser: ArgumentParser, test_args=None):
         except yaml.parser.ParserError as e:
             _LOGGER.error(f"Project config parse failed -- {e}")
             sys.exit(1)
-    elif is_registry_path(subcommand_args.config_file):
+    elif is_pephub_registry_path(subcommand_args.config_file):
         if vars(subcommand_args)[SAMPLE_PL_ARG]:
             p = Project(
                 amendments=subcommand_args.amend,

looper/utils.py

@@ -472,7 +472,7 @@ def initiate_looper_config(
         return False
 
     if pep_path:
-        if is_registry_path(pep_path):
+        if is_pephub_registry_path(pep_path):
             pass
         else:
             pep_path = expandpath(pep_path)
@@ -562,10 +562,20 @@ def read_looper_config_file(looper_config_path: str) -> dict:
     for k, v in return_dict.items():
         if isinstance(v, str):
             v = expandpath(v)
-            if not os.path.isabs(v) and not is_registry_path(v):
-                return_dict[k] = os.path.join(config_dir_path, v)
-            else:
+            # TODO this is messy because is_pephub_registry needs to fail on anything NOT a pephub registry path
+            # https://github.com/pepkit/ubiquerg/issues/43
+            if is_PEP_file_type(v):
+                if not os.path.isabs(v):
+                    return_dict[k] = os.path.join(config_dir_path, v)
+                else:
+                    return_dict[k] = v
+            elif is_pephub_registry_path(v):
                 return_dict[k] = v
+            else:
+                if not os.path.isabs(v):
+                    return_dict[k] = os.path.join(config_dir_path, v)
+                else:
+                    return_dict[k] = v
 
     return return_dict
 
@@ -609,19 +619,12 @@ def is_PEP_file_type(input_string: str) -> bool:
     return res
 
 
-def is_registry_path(input_string: str) -> bool:
+def is_pephub_registry_path(input_string: str) -> bool:
     """
     Check if input is a registry path to pephub
     :param str input_string: path to the PEP (or registry path)
     :return bool: True if input is a registry path
     """
-    try:
-        if input_string.endswith(".yaml") or input_string.endswith(".csv"):
-            return False
-    except AttributeError:
-        raise RegistryPathException(
-            msg=f"Malformed registry path. Unable to parse {input_string} as a registry path."
-        )
     try:
         registry_path = RegistryPath(**parse_registry_path(input_string))
     except (ValidationError, TypeError):

tests/smoketests/test_run.py

@@ -594,20 +594,7 @@ class TestLooperPEPhub:
         ],
     )
     def test_pephub_registry_path_recognition(self, pep_path):
-        assert is_registry_path(pep_path) is True
-
-    @pytest.mark.parametrize(
-        "pep_path",
-        [
-            "some/path/to/pep.yaml",
-            "different/path.yaml",
-            "default/path/to/file/without/yaml",
-            "file_in_folder.yaml",
-            "not_yaml_file",
-        ],
-    )
-    def test_config_recognition(self, pep_path):
-        assert is_registry_path(pep_path) is False
+        assert is_pephub_registry_path(pep_path) is True
 
     def test_init_project_using_dict(self, prep_temp_config_with_pep):
         """Verify looper runs using pephub in a basic case and return code is 0"""