masster 0.5.22__py3-none-any.whl → 0.5.24__py3-none-any.whl

masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.5.22"
+__version__ = "0.5.24"
 
 
 def get_version():

masster/logger.py

@@ -3,10 +3,11 @@
 Simple logger system for masster Study and Sample instances.
 Uses basic Python logging                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
 
+                # Universal colors compatible with both dark and light themes
                 # Universal colors compatible with both dark and light themes
                 level_colors = {
                     'TRACE': '\x1b[94m',      # bright blue (readable on both dark/light)
-                    'DEBUG': '\x1b[96m',      # bright cyan (readable on both dark/light)  
+                    'DEBUG': '\x1b[96m',      # bright cyan (readable on both dark/light)
                     'INFO': '\x1b[90m',       # bright black/gray (readable on both dark/light)
                     'SUCCESS': '\x1b[92m',    # bright green (readable on both dark/light)
                     'WARNING': '\x1b[93m',    # bright yellow (readable on both dark/light)
@@ -70,7 +71,7 @@ class MassterLogger:
         # Remove any existing handlers to prevent duplicates
         if self.logger_instance.hasHandlers():
             self.logger_instance.handlers.clear()
-        
+
         # Also ensure no duplicate handlers on parent loggers
         parent = self.logger_instance.parent
         while parent:
@@ -102,19 +103,21 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]  # Remove last 3 digits for milliseconds
 
+                # Universal colors compatible with both dark and light themes
                 # Universal colors compatible with both dark and light themes
                 level_colors = {
                     "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
                     "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
-                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "INFO": "\x1b[90m",  # bright black/gray (readable on both dark/light)
                     "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
                     "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
-                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
-                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
+                    "ERROR": "\x1b[91m",  # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m",  # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
                 level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -133,8 +136,10 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
+                # Universal format: timestamp | level | location | label - message
                 # Universal format: timestamp | level | location | label - message
                 return (
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
@@ -147,14 +152,14 @@ class MassterLogger:
 
         # Prevent propagation to avoid duplicate messages
         self.logger_instance.propagate = False
-        
+
         # Additional fix: ensure no duplicate handlers in the entire logging hierarchy
         masster_logger = logging.getLogger("masster")
         if masster_logger.hasHandlers():
             # Keep only one handler per type
             unique_handlers = {}
             for handler in masster_logger.handlers:
-                handler_key = (type(handler).__name__, getattr(handler, 'stream', None))
+                handler_key = (type(handler).__name__, getattr(handler, "stream", None))
                 if handler_key not in unique_handlers:
                     unique_handlers[handler_key] = handler
             masster_logger.handlers = list(unique_handlers.values())
@@ -181,19 +186,21 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
 
+                # Universal colors compatible with both dark and light themes
                 # Universal colors compatible with both dark and light themes
                 level_colors = {
                     "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
                     "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
-                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "INFO": "\x1b[90m",  # bright black/gray (readable on both dark/light)
                     "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
                     "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
-                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
-                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
+                    "ERROR": "\x1b[91m",  # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m",  # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
                 level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -212,8 +219,9 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
-                # Universal format: timestamp | level | location | label - message  
+                # Universal format: timestamp | level | location | label - message
                 return (
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
@@ -245,19 +253,21 @@ class MassterLogger:
                 dt = datetime.datetime.fromtimestamp(record.created)
                 timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
 
+                # Universal colors compatible with both dark and light themes
                 # Universal colors compatible with both dark and light themes
                 level_colors = {
                     "TRACE": "\x1b[94m",  # bright blue (readable on both dark/light)
                     "DEBUG": "\x1b[96m",  # bright cyan (readable on both dark/light)
-                    "INFO": "\x1b[90m",   # bright black/gray (readable on both dark/light)
+                    "INFO": "\x1b[90m",  # bright black/gray (readable on both dark/light)
                     "SUCCESS": "\x1b[92m",  # bright green (readable on both dark/light)
                     "WARNING": "\x1b[93m",  # bright yellow (readable on both dark/light)
-                    "ERROR": "\x1b[91m",    # bright red (readable on both dark/light)
-                    "CRITICAL": "\x1b[95m", # bright magenta (readable on both dark/light)
+                    "ERROR": "\x1b[91m",  # bright red (readable on both dark/light)
+                    "CRITICAL": "\x1b[95m",  # bright magenta (readable on both dark/light)
                 }
 
                 level_str = record.levelname.ljust(8)
                 level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
+                level_color = level_colors.get(record.levelname, "\x1b[90m")  # default to gray instead of white
                 label_part = self.label + " | " if self.label else ""
 
                 # For DEBUG and TRACE levels, add module/location information
@@ -276,8 +286,9 @@ class MassterLogger:
                         f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
                     )
 
-                # Universal format: timestamp | level | location | label - message  
+                # Universal format: timestamp | level | location | label - message
                 return (
+                    f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"\x1b[90m{timestamp}\x1b[0m | "  # gray timestamp (universal for both themes)
                     f"{level_color}{level_str}\x1b[0m | "  # colored level
                     f"{location_info}"  # location info for DEBUG/TRACE
@@ -335,16 +346,21 @@ class MassterLogger:
         """Log a SUCCESS level message (custom level)."""
         # Create a custom log record with SUCCESS level
         import logging
-        
+
         # Create a LogRecord manually with SUCCESS level
         record = self.logger_instance.makeRecord(
             self.logger_instance.name,
             logging.INFO,  # Use INFO level for Python's filtering
-            "", 0, message, args, None, func="success"
+            "",
+            0,
+            message,
+            args,
+            None,
+            func="success",
         )
         # Override the levelname for display
         record.levelname = "SUCCESS"
-        
+
         # Handle the record directly through our handler
         if self.handler:
             self.handler.handle(record)
@@ -370,7 +386,7 @@ class MassterLogger:
         if self.handler:
             self.logger_instance.removeHandler(self.handler)
             # Close the file handle if it's not stdout
-            if hasattr(self.sink, 'close') and self.sink != sys.stdout:
+            if hasattr(self.sink, "close") and self.sink != sys.stdout:
                 try:
                     self.sink.close()
                 except Exception:

masster/sample/adducts.py

@@ -156,11 +156,9 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
                         {
                             "components": components,
                             "formatted_name": formatted_name,
-                            "total_mass_shift": pos_spec["mass_shift"]
-                            + neut_spec["mass_shift"],
+                            "total_mass_shift": pos_spec["mass_shift"] + neut_spec["mass_shift"],
                             "total_charge": total_charge,
-                            "combined_probability": pos_spec["probability"]
-                            * neut_spec["probability"],
+                            "combined_probability": pos_spec["probability"] * neut_spec["probability"],
                             "complexity": 2,
                         },
                     )
@@ -176,11 +174,9 @@ def _get_adducts(self, adducts_list: list = None, **kwargs):
                         {
                             "components": components,
                             "formatted_name": formatted_name,
-                            "total_mass_shift": combo[0]["mass_shift"]
-                            + combo[1]["mass_shift"],
+                            "total_mass_shift": combo[0]["mass_shift"] + combo[1]["mass_shift"],
                             "total_charge": total_charge,
-                            "combined_probability": combo[0]["probability"]
-                            * combo[1]["probability"],
+                            "combined_probability": combo[0]["probability"] * combo[1]["probability"],
                             "complexity": 2,
                         },
                     )
@@ -380,9 +376,7 @@ def _format_adduct_name(components: List[Dict]) -> str:
     elif abs(total_charge) == 1:
         charge_str = "1+" if total_charge > 0 else "1-"
     else:
-        charge_str = (
-            f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
-        )
+        charge_str = f"{abs(total_charge)}+" if total_charge > 0 else f"{abs(total_charge)}-"
 
     return f"[M{formula}]{charge_str}"
 
@@ -433,12 +427,12 @@ def find_adducts(self, **kwargs):
                 self.logger.warning(f"Unknown parameter {key} ignored")
 
     # Auto-set adducts based on sample polarity if not explicitly provided
-    if params.adducts is None and hasattr(self, 'polarity') and self.polarity is not None:
-        if self.polarity.lower() in ['positive', 'pos']:
-            params.set('adducts', 'positive', validate=True)
+    if params.adducts is None and hasattr(self, "polarity") and self.polarity is not None:
+        if self.polarity.lower() in ["positive", "pos"]:
+            params.set("adducts", "positive", validate=True)
             self.logger.debug(f"Auto-set adducts to 'positive' based on sample polarity: {self.polarity}")
-        elif self.polarity.lower() in ['negative', 'neg']:
-            params.set('adducts', 'negative', validate=True)
+        elif self.polarity.lower() in ["negative", "neg"]:
+            params.set("adducts", "negative", validate=True)
             self.logger.debug(f"Auto-set adducts to 'negative' based on sample polarity: {self.polarity}")
         else:
             self.logger.debug(f"Unknown sample polarity '{self.polarity}', using default adducts")
@@ -488,7 +482,7 @@ def find_adducts(self, **kwargs):
     self.logger.debug(f"Min probability threshold: {min_probability}")
 
     # Generate comprehensive adduct specifications using the Sample method
-    adducts_df = self._get_adducts( 
+    adducts_df = self._get_adducts(
         adducts_list=adducts_list,
         charge_min=charge_min,
         charge_max=charge_max,
@@ -572,9 +566,7 @@ def find_adducts(self, **kwargs):
                     tol2 = mass_max_diff * mz2 * 1e-6
                     combined_tolerance = tol1 + tol2
                 else:  # Da
-                    combined_tolerance = (
-                        2 * mass_max_diff
-                    )  # Combined tolerance for both features
+                    combined_tolerance = 2 * mass_max_diff  # Combined tolerance for both features
 
                 # Check both directions of mass relationship
                 if charge != 0:
@@ -678,9 +670,7 @@ def find_adducts(self, **kwargs):
 
         # Calculate neutral mass for base ion
         base_mz_measured = feature_mzs[base_feature_idx]
-        neutral_mass_assignments[base_feature_idx] = (
-            base_mz_measured * abs(base_charge) - base_mass_shift
-        )
+        neutral_mass_assignments[base_feature_idx] = base_mz_measured * abs(base_charge) - base_mass_shift
 
         # Assign other features based on their relationships to base
         for feature_idx in component:
@@ -726,9 +716,7 @@ def find_adducts(self, **kwargs):
             mass_shift_assignments[feature_idx] = best_mass_shift
 
             # Calculate neutral mass
-            neutral_mass_assignments[feature_idx] = (
-                feature_mz * abs(best_charge) - best_mass_shift
-            )
+            neutral_mass_assignments[feature_idx] = feature_mz * abs(best_charge) - best_mass_shift
 
     # Assign fallback adduct for features not processed in connected components (isolated features)
     for i in range(n_features):
@@ -743,9 +731,7 @@ def find_adducts(self, **kwargs):
 
             # Calculate neutral mass for isolated features
             feature_mz = feature_mzs[i]
-            neutral_mass_assignments[i] = (
-                feature_mz * abs(fallback_charge) - fallback_mass_shift
-            )
+            neutral_mass_assignments[i] = feature_mz * abs(fallback_charge) - fallback_mass_shift
 
     # Map back to original feature order using stored positions
     original_indices = features_sorted.select("original_position").to_numpy().flatten()

masster/sample/defaults/find_adducts_def.py

@@ -58,9 +58,7 @@ class find_adducts_defaults:
     retention_max_diff_local: float = 1.0  # 1 second - precise RT grouping
 
     # Mass tolerance constraints
-    mass_max_diff: float = (
-        0.01  # 0.01 Da - strict mass tolerance for chemical specificity
-    )
+    mass_max_diff: float = 0.01  # 0.01 Da - strict mass tolerance for chemical specificity
     unit: str = "Da"  # Mass tolerance unit: "Da" or "ppm"
 
     # Probability filtering

masster/sample/defaults/sample_def.py

@@ -46,12 +46,12 @@ class sample_defaults:
     # file and data handling settings
     type: str = "dda"
     polarity: str | None = None
-    
+
     # chromatographic settings
-    #chrom_fwhm: float = 1.0
+    # chrom_fwhm: float = 1.0
     eic_mz_tol: float = 0.01
     eic_rt_tol: float = 10.0
-    
+
     # mz tolerances
     mz_tol_ms1_da: float = 0.002
     mz_tol_ms2_da: float = 0.005
@@ -65,7 +65,7 @@ class sample_defaults:
     centroid_smooth: int = 5
     centroid_refine: bool = True
     centroid_prominence: int = -1
-    
+
     # data retrieval settings
     max_points_per_spectrum: int = 50000