change ConfigManager to abc and add ProteinConfig for issue #5

CodonTransformer/CodonData.py

@@ -26,7 +26,7 @@
     STOP_CODONS,
     STOP_SYMBOL,
     STOP_SYMBOLS,
-    ConfigManager,
+    ProteinConfig,
     find_pattern_in_fasta,
     get_taxonomy_id,
     sort_amino2codon_skeleton,
@@ -175,7 +175,7 @@ def preprocess_protein_sequence(protein: str) -> str:
     )
 
     # Handle ambiguous amino acids based on the specified behavior
-    config = ConfigManager()
+    config = ProteinConfig()
     ambiguous_aminoacid_map_override = config.get('ambiguous_aminoacid_map_override')
     ambiguous_aminoacid_behavior = config.get('ambiguous_aminoacid_behavior')
     ambiguous_aminoacid_map = AMBIGUOUS_AMINOACID_MAP.copy()

CodonTransformer/CodonUtils.py

@@ -8,6 +8,7 @@
 import os
 import pickle
 import re
+from abc import ABC, abstractmethod
 from dataclasses import dataclass
 from typing import Any, Dict, Iterator, List, Optional, Tuple
 
@@ -545,30 +546,12 @@ def __init__(self, data_path: str, train: bool = True, **kwargs):
         self.train = train
 
 
-class ConfigManager:
+class ConfigManager(ABC):
     """
-    A class to manage configuration settings.
-
-    This class ensures that the configuration is a singleton.
-    It provides methods to get, set, and update configuration values.
-
-    Attributes:
-        _instance (Optional[ConfigManager]): The singleton instance of the ConfigManager.
-        _config (Dict[str, Any]): The configuration dictionary.
+    Abstract base class for managing configuration settings.
     """
-    _instance = None
-
-    def __new__(cls):
-        """
-        Create a new instance of the ConfigManager class.
-
-        Returns:
-            ConfigManager: The singleton instance of the ConfigManager.
-        """
-        if cls._instance is None:
-            cls._instance = super(ConfigManager, cls).__new__(cls)
-            cls._instance.reset_config()
-        return cls._instance
+    def __init__(self):
+        self._config: Dict[str, Any] = {}
 
     def __enter__(self):
         return self
@@ -578,6 +561,11 @@ def __exit__(self, exc_type, exc_value, traceback):
             print(f"Exception occurred: {exc_type}, {exc_value}, {traceback}")
         self.reset_config()
 
+    @abstractmethod
+    def reset_config(self) -> None:
+        """Reset the configuration to default values."""
+        pass
+
     def get(self, key: str) -> Any:
         """
         Get the value of a configuration key.
@@ -610,8 +598,37 @@ def update(self, config_dict: dict) -> None:
         """
         for key, value in config_dict.items():
             self.validate_inputs(key, value)
-        for key, value in config_dict.items():
-            self.set(key, value)
+        self._config.update(config_dict)
+
+    @abstractmethod
+    def validate_inputs(self, key: str, value: Any) -> None:
+        """Validate the inputs for the configuration."""
+        pass
+
+class ProteinConfig(ConfigManager):
+    """
+    A class to manage configuration settings for protein sequences.
+
+    This class ensures that the configuration is a singleton.
+    It provides methods to get, set, and update configuration values.
+
+    Attributes:
+        _instance (Optional[ConfigManager]): The singleton instance of the ConfigManager.
+        _config (Dict[str, Any]): The configuration dictionary.
+    """
+    _instance = None
+
+    def __new__(cls):
+        """
+        Create a new instance of the ProteinConfig class.
+
+        Returns:
+            ProteinConfig: The singleton instance of the ProteinConfig.
+        """
+        if cls._instance is None:
+            cls._instance = super(ProteinConfig, cls).__new__(cls)
+            cls._instance.reset_config()
+        return cls._instance
 
     def validate_inputs(self, key: str, value: Any) -> None:
         """
@@ -644,6 +661,7 @@ def validate_inputs(self, key: str, value: Any) -> None:
                     raise ValueError(f"Invalid amino acid in ambiguous_aminoacid_map_override: {ambiguous_aminoacid}")
         else:
             raise ValueError(f"Invalid configuration key: {key}")
+
     def reset_config(self) -> None:
         """
         Reset the configuration to the default values.

tests/test_CodonData.py

@@ -11,11 +11,11 @@
     read_fasta_file,
     preprocess_protein_sequence,
 )
-from CodonTransformer.CodonUtils import ConfigManager
+from CodonTransformer.CodonUtils import ProteinConfig
 
 class TestCodonData(unittest.TestCase):
     def test_preprocess_protein_sequence(self):
-        with ConfigManager() as config:
+        with ProteinConfig() as config:
             protein = "Z_"
             try:
                 preprocess_protein_sequence(protein)

tests/test_CodonUtils.py

@@ -4,7 +4,7 @@
 import unittest
 
 from CodonTransformer.CodonUtils import (
-    ConfigManager,
+    ProteinConfig,
     find_pattern_in_fasta,
     get_organism2id_dict,
     get_taxonomy_id,
@@ -17,7 +17,7 @@
 
 class TestCodonUtils(unittest.TestCase):
     def test_config_manager(self):
-        with ConfigManager() as config:
+        with ProteinConfig() as config:
             config.set(
                 "ambiguous_aminoacid_behavior",
                 "standardize_deterministic"
@@ -51,7 +51,7 @@ def test_config_manager(self):
                 self.fail("Expected ValueError")
             except ValueError:
                 pass
-        with ConfigManager() as config:
+        with ProteinConfig() as config:
             self.assertEqual(
                 config.get("ambiguous_aminoacid_behavior"),
                 "raise_error"