masster 0.4.3__py3-none-any.whl → 0.4.5__py3-none-any.whl

masster/study/defaults/study_def.py

@@ -33,7 +33,7 @@ class study_defaults:
 
     eic_mz_tol: float = 0.01
     eic_rt_tol: float = 10.0
-    
+
     polarity: str = "positive"
     adducts: list[str] | None = None
     adduct_min_probability: float = 0.04
@@ -54,7 +54,14 @@ class study_defaults:
                 "dtype": str,
                 "description": "Logging level to be set for the logger",
                 "default": "INFO",
-                "allowed_values": ["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
+                "allowed_values": [
+                    "TRACE",
+                    "DEBUG",
+                    "INFO",
+                    "WARNING",
+                    "ERROR",
+                    "CRITICAL",
+                ],
             },
             "log_label": {
                 "dtype": "Optional[str]",
@@ -92,14 +99,19 @@ class study_defaults:
                 "default": ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"],
                 "examples": {
                     "positive": ["H:+:0.8", "Na:+:0.1", "NH4:+:0.1"],
-                    "negative": ["H-1:-:0.95", "Cl:-:0.05", "CH2O2:0:0.2", "H-2-O:0:0.2"]
+                    "negative": [
+                        "H-1:-:0.95",
+                        "Cl:-:0.05",
+                        "CH2O2:0:0.2",
+                        "H-2-O:0:0.2",
+                    ],
                 },
                 "validation_rules": [
                     "Format: element:charge:probability",
                     "Charge must be +, -, or 0 (neutral)",
                     "Probability must be between 0.0 and 1.0",
-                    "Sum of all charged adduct probabilities must equal 1.0"
-                ]
+                    "Sum of all charged adduct probabilities must equal 1.0",
+                ],
             },
             "adduct_min_probability": {
                 "dtype": float,
@@ -116,54 +128,71 @@ class study_defaults:
         """Set polarity-specific defaults for adducts if not explicitly provided."""
         # If adducts is None, set based on polarity
         if self.adducts is None:
-            if self.polarity.lower() in ['positive', 'pos']:
-                self.adducts = ["+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"]
-            elif self.polarity.lower() in ['negative', 'neg']:
-                self.adducts = ["-H:-1:0.9", "+Cl:-1:0.1", "+CH2O2:0:0.15", "-H2O:0:0.15"]
+            if self.polarity.lower() in ["positive", "pos"]:
+                self.adducts = [
+                    "+H:1:0.65",
+                    "+Na:1:0.15",
+                    "+NH4:1:0.15",
+                    "+K:1:0.05",
+                    "-H2O:0:0.15",
+                ]
+            elif self.polarity.lower() in ["negative", "neg"]:
+                self.adducts = [
+                    "-H:-1:0.9",
+                    "+Cl:-1:0.1",
+                    "+CH2O2:0:0.15",
+                    "-H2O:0:0.15",
+                ]
             else:
                 # Default to positive if polarity is not recognized
-                self.adducts = ["+H:1:0.65", "+Na:1:0.15", "+NH4:1:0.15", "+K:1:0.05", "-H2O:0:0.15"]
+                self.adducts = [
+                    "+H:1:0.65",
+                    "+Na:1:0.15",
+                    "+NH4:1:0.15",
+                    "+K:1:0.05",
+                    "-H2O:0:0.15",
+                ]
 
     def _validate_adducts(self, adduct_list: list[str]) -> bool:
         """
         Validate adducts according to OpenMS convention.
-        
+
         Format: element:charge:probability
         - Elements can be molecular formulas (e.g., H, Na, NH4, H-1, CH2O2)
         - Charge must be +, -, or 0 (for neutral)
         - Probability must be a float between 0 and 1
         - Total probability of all charged adducts should sum to 1.0
-        
+
         Args:
             adduct_list: List of adduct strings in OpenMS format
-            
+
         Returns:
             True if all adducts are valid, False otherwise
         """
         if not adduct_list:  # Empty list is valid
             return True
-            
+
         charged_total_prob = 0.0
         neutral_total_prob = 0.0
-        
+
         for adduct in adduct_list:
             if not isinstance(adduct, str):
                 return False
-                
+
             parts = adduct.split(":")
             if len(parts) != 3:
                 return False
-                
+
             element, charge, prob_str = parts
-            
+
             # Validate element (non-empty string)
             if not element:
                 return False
-                
+
             # Validate charge
             if charge not in ["+", "-", "0"]:
                 return False
-                
+
             # Validate probability
             try:
                 probability = float(prob_str)
@@ -171,20 +200,20 @@ class study_defaults:
                     return False
             except (ValueError, TypeError):
                 return False
-                
+
             # Sum probabilities by charge type
             if charge in ["+", "-"]:
                 charged_total_prob += probability
             else:  # charge == "0" (neutral)
                 neutral_total_prob += probability
-        
+
         # Validate probability constraints
         # Charged adducts should sum to 1.0 (within tolerance)
         if charged_total_prob > 0 and abs(charged_total_prob - 1.0) > 1e-6:
             return False
-            
+
         # Neutral adducts can have any total probability (they're optional)
-        
+
         return True
 
     def get_info(self, param_name: str) -> dict[str, Any]:
@@ -316,7 +345,11 @@ class study_defaults:
             expected_dtype = self._param_metadata[param_name]["dtype"]
 
             # Handle optional types
-            if isinstance(expected_dtype, str) and expected_dtype.startswith("Optional") and value is not None:
+            if (
+                isinstance(expected_dtype, str)
+                and expected_dtype.startswith("Optional")
+                and value is not None
+            ):
                 if "int" in expected_dtype and not isinstance(value, int):
                     try:
                         value = int(value)