masster 0.2.5__py3-none-any.whl → 0.3.1__py3-none-any.whl

masster/logger.py

@@ -1,244 +1,318 @@
-# masster/logger.py
-"""
-Simple logger system for masster Study and Sample instances.
-Uses basic Python logging                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
-                
-                # Loguru-style colors for different log levels
-                level_colors = {
-                    'TRACE': '\x1b[90m',      # bright black (gray)
-                    'DEBUG': '\x1b[36m',      # cyan
-                    'INFO': '\x1b[34m',       # blue
-                    'SUCCESS': '\x1b[32m',    # green
-                    'WARNING': '\x1b[33m',    # yellow
-                    'ERROR': '\x1b[31m',      # red
-                    'CRITICAL': '\x1b[35m',   # magenta
-                }
-                
-                level_str = record.levelname.ljust(8)complex loguru filtering.
-"""
-from __future__ import annotations
-import sys
-import uuid
-import logging
-import datetime
-from typing import Any, Optional
-
-
-class MassterLogger:
-    """Simple logger wrapper for Study/Sample instances.
-    Each instance gets its own Python logger to avoid conflicts.
-    
-    Args:
-        instance_type: Type of instance ("study" or "sample")
-        instance_id: Unique identifier for this instance (auto-generated if None)
-        level: Logging level ("DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL")
-        label: Custom label to include in log messages
-        sink: Output sink (defaults to sys.stdout)
-    """
-    
-    def __init__(
-        self,
-        instance_type: str,
-        instance_id: Optional[str] = None,
-        level: str = "INFO",
-        label: str = "",
-        sink: Optional[Any] = None
-    ):
-        if instance_id is None:
-            instance_id = str(uuid.uuid4())[:8]
-        self.instance_type = instance_type.lower()
-        self.instance_id = instance_id
-        self.level = level.upper()
-        self.label = label
-        
-        # Convert string sink to actual object
-        if sink == "sys.stdout" or sink is None:
-            self.sink = sys.stdout
-        else:
-            self.sink = sink
-        
-        # Create a unique logger name for this instance
-        self.logger_name = f"masster.{self.instance_type}.{self.instance_id}"
-        
-        # Get a Python logger instance
-        self.logger_instance = logging.getLogger(self.logger_name)
-        
-        # Remove any existing handlers to prevent duplicates
-        if self.logger_instance.hasHandlers():
-            self.logger_instance.handlers.clear()
-            
-        self.logger_instance.setLevel(getattr(logging, self.level))
-        
-        # Create a stream handler
-        self.handler = logging.StreamHandler(self.sink)
-        
-        # Create formatter that matches the original masster style
-        class massterFormatter(logging.Formatter):
-            def __init__(self, label):
-                super().__init__()
-                self.label = label
-                
-            def format(self, record):
-                # Create timestamp in the same format as loguru
-                dt = datetime.datetime.fromtimestamp(record.created)
-                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]  # Remove last 3 digits for milliseconds
-                
-                # Loguru-style colors for different log levels
-                level_colors = {
-                    'TRACE': '\x1b[90m',      # bright black (gray)
-                    'DEBUG': '\x1b[36m',      # cyan
-                    'INFO': '\x1b[37m',       # white
-                    'SUCCESS': '\x1b[32m',    # green
-                    'WARNING': '\x1b[33m',    # yellow
-                    'ERROR': '\x1b[31m',      # red
-                    'CRITICAL': '\x1b[35m',   # magenta
-                }
-                
-                level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
-                label_part = self.label if self.label else ""
-                
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <cyan>label</cyan> - <level>message</level>
-                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
-                       f"{level_color}{level_str}\x1b[0m | "  # colored level
-                       f"\x1b[36m{label_part}\x1b[0m"  # cyan label
-                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
-        
-        self.handler.setFormatter(massterFormatter(self.label))
-        self.logger_instance.addHandler(self.handler)
-        
-        # Prevent propagation to avoid duplicate messages
-        self.logger_instance.propagate = False
-    
-    def update_level(self, level: str):
-        """Update the logging level."""
-        if level.upper() in ["TRACE", "DEBUG", "INFO", "SUCCESS", "WARNING", "ERROR", "CRITICAL"]:
-            self.level = level.upper()
-            self.logger_instance.setLevel(getattr(logging, self.level))
-        else:
-            self.warning(f"Invalid logging level '{level}'. Keeping current level: {self.level}")
-    
-    def update_label(self, label: str):
-        """Update the label prefix for log messages."""
-        self.label = label
-        
-        # Update formatter with new label
-        class massterFormatter(logging.Formatter):
-            def __init__(self, label):
-                super().__init__()
-                self.label = label
-                
-            def format(self, record):
-                dt = datetime.datetime.fromtimestamp(record.created)
-                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
-                
-                # Loguru-style colors for different log levels
-                level_colors = {
-                    'TRACE': '\x1b[90m',      # bright black (gray)
-                    'DEBUG': '\x1b[36m',      # cyan
-                    'INFO': '\x1b[37m',       # white
-                    'SUCCESS': '\x1b[32m',    # green
-                    'WARNING': '\x1b[33m',    # yellow
-                    'ERROR': '\x1b[31m',      # red
-                    'CRITICAL': '\x1b[35m',   # magenta
-                }
-                
-                level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
-                label_part = self.label if self.label else ""
-                
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <cyan>label</cyan> - <level>message</level>
-                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
-                       f"{level_color}{level_str}\x1b[0m | "  # colored level
-                       f"\x1b[36m{label_part}\x1b[0m"  # cyan label
-                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
-        
-        self.handler.setFormatter(massterFormatter(self.label))
-    
-    def update_sink(self, sink: Any):
-        """Update the output sink for log messages."""
-        # Convert string sink to actual object
-        if sink == "sys.stdout":
-            self.sink = sys.stdout
-        else:
-            self.sink = sink
-        
-        # Remove old handler and create new one with new sink
-        self.logger_instance.removeHandler(self.handler)
-        self.handler = logging.StreamHandler(self.sink)
-        
-        # Apply formatter
-        class massterFormatter(logging.Formatter):
-            def __init__(self, label):
-                super().__init__()
-                self.label = label
-                
-            def format(self, record):
-                dt = datetime.datetime.fromtimestamp(record.created)
-                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
-                
-                # Loguru-style colors for different log levels
-                level_colors = {
-                    'TRACE': '\x1b[90m',      # bright black (gray)
-                    'DEBUG': '\x1b[36m',      # cyan
-                    'INFO': '\x1b[37m',       # white
-                    'SUCCESS': '\x1b[32m',    # green
-                    'WARNING': '\x1b[33m',    # yellow
-                    'ERROR': '\x1b[31m',      # red
-                    'CRITICAL': '\x1b[35m',   # magenta
-                }
-                
-                level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
-                label_part = self.label if self.label else ""
-                
-                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <cyan>label</cyan> - <level>message</level>
-                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
-                       f"{level_color}{level_str}\x1b[0m | "  # colored level
-                       f"\x1b[36m{label_part}\x1b[0m"  # cyan label
-                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
-        
-        self.handler.setFormatter(massterFormatter(self.label))
-        self.logger_instance.addHandler(self.handler)
-    
-    # Logger method delegates
-    def trace(self, message: str, *args, **kwargs):
-        """Log a TRACE level message (mapped to DEBUG)."""
-        self.debug(message, *args, **kwargs)
-    
-    def debug(self, message: str, *args, **kwargs):
-        """Log a DEBUG level message."""
-        self.logger_instance.debug(message, *args, **kwargs)
-    
-    def info(self, message: str, *args, **kwargs):
-        """Log an INFO level message."""
-        self.logger_instance.info(message, *args, **kwargs)
-    
-    def success(self, message: str, *args, **kwargs):
-        """Log a SUCCESS level message (mapped to INFO)."""
-        self.info(message, *args, **kwargs)
-    
-    def warning(self, message: str, *args, **kwargs):
-        """Log a WARNING level message."""
-        self.logger_instance.warning(message, *args, **kwargs)
-    
-    def error(self, message: str, *args, **kwargs):
-        """Log an ERROR level message."""
-        self.logger_instance.error(message, *args, **kwargs)
-    
-    def critical(self, message: str, *args, **kwargs):
-        """Log a CRITICAL level message."""
-        self.logger_instance.critical(message, *args, **kwargs)
-    
-    def exception(self, message: str, *args, **kwargs):
-        """Log an exception with ERROR level."""
-        self.logger_instance.exception(message, *args, **kwargs)
-    
-    def remove(self):
-        """Remove this logger's handler."""
-        if self.handler:
-            self.logger_instance.removeHandler(self.handler)
-            self.handler = None
-    
-    def __repr__(self):
-        return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
+# masster/logger.py
+"""
+Simple logger system for masster Study and Sample instances.
+Uses basic Python logging                timestamp = dt.strftime('%Y-%m-%d %H:%M:%S.%f')[:-3]
+
+                # Loguru-style colors for different log levels
+                level_colors = {
+                    'TRACE': '\x1b[34m',      # blue
+                    'DEBUG': '\x1b[36m',      # cyan
+                    'INFO': '\x1b[37m',       # white
+                    'SUCCESS': '\x1b[32m',    # green
+                    'WARNING': '\x1b[33m',    # yellow
+                    'ERROR': '\x1b[31m',      # red
+                    'CRITICAL': '\x1b[35m',   # magenta
+                }
+
+                level_str = record.levelname.ljust(8)complex loguru filtering.
+"""
+
+from __future__ import annotations
+import sys
+import uuid
+import logging
+import datetime
+from typing import Any
+
+
+class MassterLogger:
+    """Simple logger wrapper for Study/Sample instances.
+    Each instance gets its own Python logger to avoid conflicts.
+
+    Args:
+        instance_type: Type of instance ("study" or "sample")
+        instance_id: Unique identifier for this instance (auto-generated if None)
+        level: Logging level ("DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL")
+        label: Custom label to include in log messages
+        sink: Output sink (defaults to sys.stdout)
+    """
+
+    def __init__(
+        self,
+        instance_type: str,
+        instance_id: str | None = None,
+        level: str = "INFO",
+        label: str = "",
+        sink: Any | None = None,
+    ):
+        if instance_id is None:
+            instance_id = str(uuid.uuid4())[:8]
+        self.instance_type = instance_type.lower()
+        self.instance_id = instance_id
+        self.level = level.upper()
+        self.label = label
+
+        # Convert string sink to actual object
+        if sink == "sys.stdout" or sink is None:
+            self.sink = sys.stdout
+        else:
+            self.sink = sink
+
+        # Create a unique logger name for this instance
+        self.logger_name = f"masster.{self.instance_type}.{self.instance_id}"
+
+        # Get a Python logger instance
+        self.logger_instance = logging.getLogger(self.logger_name)
+
+        # Remove any existing handlers to prevent duplicates
+        if self.logger_instance.hasHandlers():
+            self.logger_instance.handlers.clear()
+
+        self.logger_instance.setLevel(getattr(logging, self.level))
+
+        # Create a stream handler
+        self.handler = logging.StreamHandler(self.sink)
+
+        # Create formatter that matches the original masster style
+        class massterFormatter(logging.Formatter):
+            def __init__(self, label):
+                super().__init__()
+                self.label = label
+
+            def format(self, record):
+                # Create timestamp in the same format as loguru
+                dt = datetime.datetime.fromtimestamp(record.created)
+                timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]  # Remove last 3 digits for milliseconds
+
+                # Loguru-style colors for different log levels
+                level_colors = {
+                    'TRACE': '\x1b[34m',      # blue
+                    'DEBUG': '\x1b[36m',      # cyan
+                    'INFO': '\x1b[37m',       # white
+                    'SUCCESS': '\x1b[32m',    # green
+                    'WARNING': '\x1b[33m',    # yellow
+                    'ERROR': '\x1b[31m',      # red
+                    'CRITICAL': '\x1b[35m',   # magenta
+                }
+
+                level_str = record.levelname.ljust(8)
+                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
+                label_part = self.label + " | " if self.label else ""
+                
+                # For DEBUG and TRACE levels, add module/location information
+                location_info = ""
+                if record.levelname in ['TRACE']:
+                    # Use caller information if available (from extra), otherwise fall back to record info
+                    if hasattr(record, 'caller_module'):
+                        module_name = record.caller_module.split('.')[-1] if record.caller_module else 'unknown'
+                        line_no = record.caller_lineno
+                        func_name = record.caller_funcname
+                    else:
+                        module_name = record.module if hasattr(record, 'module') else 'unknown'
+                        line_no = record.lineno
+                        func_name = record.funcName
+                    location_info = f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
+                
+                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                       f"{level_color}{level_str}\x1b[0m | "  # colored level
+                       f"{location_info}"  # location info for DEBUG/TRACE
+                       f"{level_color}{label_part}\x1b[0m"  # colored label
+                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
+        
+        self.handler.setFormatter(massterFormatter(self.label))
+        self.logger_instance.addHandler(self.handler)
+
+        # Prevent propagation to avoid duplicate messages
+        self.logger_instance.propagate = False
+
+    def update_level(self, level: str):
+        """Update the logging level."""
+        if level.upper() in ["TRACE", "DEBUG", "INFO", "SUCCESS", "WARNING", "ERROR", "CRITICAL"]:
+            self.level = level.upper()
+            self.logger_instance.setLevel(getattr(logging, self.level))
+        else:
+            self.warning(f"Invalid logging level '{level}'. Keeping current level: {self.level}")
+
+    def update_label(self, label: str):
+        """Update the label prefix for log messages."""
+        self.label = label
+
+        # Update formatter with new label
+        class massterFormatter(logging.Formatter):
+            def __init__(self, label):
+                super().__init__()
+                self.label = label
+
+            def format(self, record):
+                dt = datetime.datetime.fromtimestamp(record.created)
+                timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
+
+                # Loguru-style colors for different log levels
+                level_colors = {
+                    'TRACE': '\x1b[34m',      # blue
+                    'DEBUG': '\x1b[36m',      # cyan
+                    'INFO': '\x1b[37m',       # white
+                    'SUCCESS': '\x1b[32m',    # green
+                    'WARNING': '\x1b[33m',    # yellow
+                    'ERROR': '\x1b[31m',      # red
+                    'CRITICAL': '\x1b[35m',   # magenta
+                }
+
+                level_str = record.levelname.ljust(8)
+                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
+                label_part = self.label + " | " if self.label else ""
+                
+                # For DEBUG and TRACE levels, add module/location information
+                location_info = ""
+                if record.levelname in ['TRACE']:
+                    # Use caller information if available (from extra), otherwise fall back to record info
+                    if hasattr(record, 'caller_module'):
+                        module_name = record.caller_module.split('.')[-1] if record.caller_module else 'unknown'
+                        line_no = record.caller_lineno
+                        func_name = record.caller_funcname
+                    else:
+                        module_name = record.module if hasattr(record, 'module') else 'unknown'
+                        line_no = record.lineno
+                        func_name = record.funcName
+                    location_info = f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
+                
+                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                       f"{level_color}{level_str}\x1b[0m | "  # colored level
+                       f"{location_info}"  # location info for DEBUG/TRACE
+                       f"{level_color}{label_part}\x1b[0m"  # colored label
+                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
+        
+        self.handler.setFormatter(massterFormatter(self.label))
+
+    def update_sink(self, sink: Any):
+        """Update the output sink for log messages."""
+        # Convert string sink to actual object
+        if sink == "sys.stdout":
+            self.sink = sys.stdout
+        else:
+            self.sink = sink
+
+        # Remove old handler and create new one with new sink
+        self.logger_instance.removeHandler(self.handler)
+        self.handler = logging.StreamHandler(self.sink)
+
+        # Apply formatter
+        class massterFormatter(logging.Formatter):
+            def __init__(self, label):
+                super().__init__()
+                self.label = label
+
+            def format(self, record):
+                dt = datetime.datetime.fromtimestamp(record.created)
+                timestamp = dt.strftime("%Y-%m-%d %H:%M:%S.%f")[:-3]
+
+                # Loguru-style colors for different log levels
+                level_colors = {
+                    'TRACE': '\x1b[34m',      # blue
+                    'DEBUG': '\x1b[36m',      # cyan
+                    'INFO': '\x1b[37m',       # white
+                    'SUCCESS': '\x1b[32m',    # green
+                    'WARNING': '\x1b[33m',    # yellow
+                    'ERROR': '\x1b[31m',      # red
+                    'CRITICAL': '\x1b[35m',   # magenta
+                }
+
+                level_str = record.levelname.ljust(8)
+                level_color = level_colors.get(record.levelname, '\x1b[37m')  # default white
+                label_part = self.label + " | " if self.label else ""
+                
+                # For DEBUG and TRACE levels, add module/location information
+                location_info = ""
+                if record.levelname in ['TRACE']:
+                    # Use caller information if available (from extra), otherwise fall back to record info
+                    if hasattr(record, 'caller_module'):
+                        module_name = record.caller_module.split('.')[-1] if record.caller_module else 'unknown'
+                        line_no = record.caller_lineno
+                        func_name = record.caller_funcname
+                    else:
+                        module_name = record.module
+                        line_no = record.lineno
+                        func_name = record.funcName
+                    location_info = f"\x1b[90m{module_name}:{func_name}:{line_no}\x1b[0m | "  # dim gray for location info
+                
+                # Loguru-style format: <white>timestamp</white> | <level>LEVEL</level> | <location> | <cyan>label</cyan> - <level>message</level>
+                return (f"\x1b[37m{timestamp}\x1b[0m | "  # white timestamp
+                       f"{level_color}{level_str}\x1b[0m | "  # colored level
+                       f"{location_info}"  # location info for DEBUG/TRACE
+                       f"{level_color}{label_part}\x1b[0m"  # colored label
+                       f"{level_color}{record.getMessage()}\x1b[0m")  # colored message
+        
+        self.handler.setFormatter(massterFormatter(self.label))
+        self.logger_instance.addHandler(self.handler)
+
+    # Logger method delegates
+    def trace(self, message: str, *args, **kwargs):
+        """Log a TRACE level message (mapped to DEBUG)."""
+        # Get caller frame information (skip this method and go to actual caller)
+        import inspect
+        frame = inspect.currentframe().f_back
+        
+        # Add caller information as extra parameters
+        extra = kwargs.get('extra', {})
+        extra.update({
+            'caller_module': frame.f_globals.get('__name__', 'unknown'),
+            'caller_filename': frame.f_code.co_filename,
+            'caller_lineno': frame.f_lineno,
+            'caller_funcname': frame.f_code.co_name
+        })
+        kwargs['extra'] = extra
+        
+        self.logger_instance.debug(message, *args, **kwargs)
+
+    def debug(self, message: str, *args, **kwargs):
+        """Log a DEBUG level message."""
+        # Get caller frame information (skip this method and go to actual caller)
+        import inspect
+        frame = inspect.currentframe().f_back
+        
+        # Add caller information as extra parameters
+        extra = kwargs.get('extra', {})
+        extra.update({
+            'caller_module': frame.f_globals.get('__name__', 'unknown'),
+            'caller_filename': frame.f_code.co_filename,
+            'caller_lineno': frame.f_lineno,
+            'caller_funcname': frame.f_code.co_name
+        })
+        kwargs['extra'] = extra
+        
+        self.logger_instance.debug(message, *args, **kwargs)
+
+    def info(self, message: str, *args, **kwargs):
+        """Log an INFO level message."""
+        self.logger_instance.info(message, *args, **kwargs)
+
+    def success(self, message: str, *args, **kwargs):
+        """Log a SUCCESS level message (mapped to INFO)."""
+        self.info(message, *args, **kwargs)
+
+    def warning(self, message: str, *args, **kwargs):
+        """Log a WARNING level message."""
+        self.logger_instance.warning(message, *args, **kwargs)
+
+    def error(self, message: str, *args, **kwargs):
+        """Log an ERROR level message."""
+        self.logger_instance.error(message, *args, **kwargs)
+
+    def critical(self, message: str, *args, **kwargs):
+        """Log a CRITICAL level message."""
+        self.logger_instance.critical(message, *args, **kwargs)
+
+    def exception(self, message: str, *args, **kwargs):
+        """Log an exception with ERROR level."""
+        self.logger_instance.exception(message, *args, **kwargs)
+
+    def remove(self):
+        """Remove this logger's handler."""
+        if self.handler:
+            self.logger_instance.removeHandler(self.handler)
+            self.handler = None
+
+    def __repr__(self):
+        return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"

masster/sample/__init__.py

@@ -1,9 +1,9 @@
-"""
-Sample module for masster.
-
-This module provides the Sample class for handling mass spectrometry data.
-"""
-
-from .sample import Sample
-
-__all__ = ["Sample"]
+"""
+Sample module for masster.
+
+This module provides the Sample class for handling mass spectrometry data.
+"""
+
+from .sample import Sample
+
+__all__ = ["Sample"]

masster/sample/defaults/__init__.py

@@ -1,15 +1,15 @@
-"""Sample defaults initialization."""
-
-from .find_adducts_def import find_adducts_defaults
-from .find_features_def import find_features_defaults
-from .find_ms2_def import find_ms2_defaults
-from .get_spectrum_def import get_spectrum_defaults
-from .sample_def import sample_defaults
-
-__all__ = [
-    "find_adducts_defaults",
-    "find_features_defaults",
-    "find_ms2_defaults",
-    "get_spectrum_defaults",
-    "sample_defaults",
-]
+"""Sample defaults initialization."""
+
+from .find_adducts_def import find_adducts_defaults
+from .find_features_def import find_features_defaults
+from .find_ms2_def import find_ms2_defaults
+from .get_spectrum_def import get_spectrum_defaults
+from .sample_def import sample_defaults
+
+__all__ = [
+    "find_adducts_defaults",
+    "find_features_defaults",
+    "find_ms2_defaults",
+    "get_spectrum_defaults",
+    "sample_defaults",
+]