type checking fixes

lib/module_utils/slurm_utils.py

@@ -1,13 +1,15 @@
 from pathlib import Path
-from typing import Dict
+from typing import Dict, Union
 
 from lib.core_utils.logging_utils import custom_logger
 
 logging = custom_logger(__name__.split(".")[-1])
 
 
 def generate_slurm_script(
-    args_dict: Dict[str, str], template_fpath: str, output_fpath: str
+    args_dict: Dict[str, str],
+    template_fpath: Union[str, Path],
+    output_fpath: Union[str, Path],
 ) -> bool:
     """Generate a Slurm batch script by filling in placeholders in a template.
 
@@ -17,8 +19,8 @@ def generate_slurm_script(
     Args:
         args_dict (Dict[str, str]): A dictionary of arguments and their values to be
             inserted into the template.
-        template_fpath (str): The filepath to the Slurm script template.
-        output_fpath (str): The filepath where the generated Slurm script will be saved.
+        template_fpath (Union[str, Path]): The filepath to the Slurm script template.
+        output_fpath (Union[str, Path]): The filepath where the generated Slurm script will be saved.
 
     Returns:
         bool: True if the script is successfully written, False otherwise.

lib/realms/tenx/lab_sample.py

@@ -1,6 +1,6 @@
 import glob
 from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Mapping, Optional
 
 from lib.core_utils.config_loader import ConfigLoader
 from lib.core_utils.logging_utils import custom_logger
@@ -11,7 +11,7 @@
 class TenXLabSample:
     """Class representing a TenX lab sample."""
 
-    config: Dict[str, Any] = ConfigLoader().load_config("10x_config.json")
+    config: Mapping[str, Any] = ConfigLoader().load_config("10x_config.json")
 
     def __init__(
         self,

lib/realms/tenx/run_sample.py

@@ -1,5 +1,5 @@
 import csv
-from typing import Any, Dict, List, Optional
+from typing import Any, Dict, List, Mapping, Optional
 
 from lib.base.abstract_sample import AbstractSample
 from lib.core_utils.logging_utils import custom_logger
@@ -21,7 +21,7 @@ def __init__(
         sample_id: str,
         lab_samples: List[Any],
         project_info: Dict[str, Any],
-        config: Dict[str, Any],
+        config: Mapping[str, Any],
         yggdrasil_db_manager: Any,
         **kwargs: Any,
     ) -> None:
@@ -31,14 +31,14 @@ def __init__(
             sample_id (str): The run sample ID.
             lab_samples (List[Any]): A list of lab sample instances.
             project_info (Dict[str, Any]): Project-specific information.
-            config (Dict[str, Any]): Configuration data.
+            config (Mapping[str, Any]): Configuration data.
             yggdrasil_db_manager (Any): Yggdrasil database manager instance.
             **kwargs (Any): Additional keyword arguments.
         """
         self.run_sample_id: str = sample_id
         self.lab_samples: List[Any] = lab_samples
         self.project_info: Dict[str, Any] = project_info
-        self.config: Dict[str, Any] = config
+        self.config: Mapping[str, Any] = config
         self.ydm: Any = yggdrasil_db_manager
 
         # self.decision_table = TenXUtils.load_decision_table("10x_decision_table.json")

lib/realms/tenx/tenx_project.py

@@ -1,6 +1,6 @@
 import asyncio
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple
+from typing import Any, Dict, List, Mapping, Optional, Tuple
 
 from lib.base.abstract_project import AbstractProject
 from lib.core_utils.config_loader import ConfigLoader
@@ -16,7 +16,7 @@ class TenXProject(AbstractProject):
     Class representing a TenX project.
     """
 
-    config: Dict[str, Any] = ConfigLoader().load_config("10x_config.json")
+    config: Mapping[str, Any] = ConfigLoader().load_config("10x_config.json")
 
     def __init__(self, doc: Dict[str, Any], yggdrasil_db_manager: Any) -> None:
         """
@@ -425,8 +425,8 @@ async def process(self):
         )
         self.finalize_project()
 
-    def create_slurm_job(self, data: Any) -> None:
-        pass
+    def create_slurm_job(self, data: Any) -> str:
+        return ""
 
     def post_process(self, result: Any) -> None:
         pass