masster 0.4.0__py3-none-any.whl → 0.4.1__py3-none-any.whl

masster/data/wiff/2025_01_14_VW_7600_LpMx_DBS_CID_2min_TOP15_030msecMS1_005msecReac_CE35_DBS-ON_3.mzML

@@ -3737,7 +3737,7 @@
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
               <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-              <binary>eJxLc8kSdWiMd7jv0xLzySnJ4ZJviuSrjeUOAqceWutcqnA4P61n2WPLOodZoY1nuYPrHASHqhXP</binary>
+              <binary>eJxLc8kSdWiMd7jv0xLzySnJ4ZJviuSrjeUOAqceWutcqnA4P61n2WPLOodZoY1nuYPrHAAHqhXP</binary>
             </binaryDataArray>
             <binaryDataArray encodedLength="80">
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
@@ -59915,7 +59915,7 @@
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>
               <cvParam cvRef="MS" accession="MS:1000574" name="zlib compression" value=""/>
               <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>
-              <binary>eJxTnsnTIfu52MHt1MT0v7uaHAS51weV</binary>
+              <binary>eJxTnsnTIfu52MHt1MT0v7uaHAA51weV</binary>
             </binaryDataArray>
             <binaryDataArray encodedLength="36">
               <cvParam cvRef="MS" accession="MS:1000523" name="64-bit float" value=""/>

masster/logger.py

@@ -1,6 +1,6 @@
 # masster/logger.py
 """
-Simple logger system for master Study and Sample instances.
+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
@@ -25,7 +25,7 @@ import datetime
 from typing import Any
 
 
-class MasterLogger:
+class MassterLogger:
     """Simple logger wrapper for Study/Sample instances.
     Each instance gets its own Python logger to avoid conflicts.
 
@@ -59,7 +59,7 @@ class MasterLogger:
             self.sink = sink
 
         # Create a unique logger name for this instance
-        self.logger_name = f"master.{self.instance_type}.{self.instance_id}"
+        self.logger_name = f"masster.{self.instance_type}.{self.instance_id}"
 
         # Get a Python logger instance
         self.logger_instance = logging.getLogger(self.logger_name)
@@ -73,8 +73,8 @@ class MasterLogger:
         # Create a stream handler
         self.handler = logging.StreamHandler(self.sink)
 
-        # Create formatter that matches the original master style
-        class masterFormatter(logging.Formatter):
+        # Create formatter that matches the original masster style
+        class massterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -82,9 +82,7 @@ class MasterLogger:
             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
+                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 = {
@@ -98,10 +96,7 @@ class MasterLogger:
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(
-                    record.levelname,
-                    "\x1b[37m",
-                )  # default white
+                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
@@ -109,20 +104,16 @@ class MasterLogger:
                 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"
-                        )
+                        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"
-                        )
+                        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
+                    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 (
@@ -133,7 +124,7 @@ class MasterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(masterFormatter(self.label))
+        self.handler.setFormatter(massterFormatter(self.label))
         self.logger_instance.addHandler(self.handler)
 
         # Prevent propagation to avoid duplicate messages
@@ -141,28 +132,18 @@ class MasterLogger:
 
     def update_level(self, level: str):
         """Update the logging level."""
-        if level.upper() in [
-            "TRACE",
-            "DEBUG",
-            "INFO",
-            "SUCCESS",
-            "WARNING",
-            "ERROR",
-            "CRITICAL",
-        ]:
+        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}",
-            )
+            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 masterFormatter(logging.Formatter):
+        class massterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -183,10 +164,7 @@ class MasterLogger:
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(
-                    record.levelname,
-                    "\x1b[37m",
-                )  # default white
+                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
@@ -194,20 +172,16 @@ class MasterLogger:
                 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"
-                        )
+                        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"
-                        )
+                        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
+                    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 (
@@ -218,7 +192,7 @@ class MasterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(masterFormatter(self.label))
+        self.handler.setFormatter(massterFormatter(self.label))
 
     def update_sink(self, sink: Any):
         """Update the output sink for log messages."""
@@ -233,7 +207,7 @@ class MasterLogger:
         self.handler = logging.StreamHandler(self.sink)
 
         # Apply formatter
-        class masterFormatter(logging.Formatter):
+        class massterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -254,10 +228,7 @@ class MasterLogger:
                 }
 
                 level_str = record.levelname.ljust(8)
-                level_color = level_colors.get(
-                    record.levelname,
-                    "\x1b[37m",
-                )  # default white
+                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
@@ -265,18 +236,16 @@ class MasterLogger:
                 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"
-                        )
+                        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
+                    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 (
@@ -287,7 +256,7 @@ class MasterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(masterFormatter(self.label))
+        self.handler.setFormatter(massterFormatter(self.label))
         self.logger_instance.addHandler(self.handler)
 
     # Logger method delegates
@@ -300,14 +269,12 @@ class MasterLogger:
 
         # 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,
-            },
-        )
+        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)
@@ -321,14 +288,12 @@ class MasterLogger:
 
         # 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,
-            },
-        )
+        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)
@@ -364,4 +329,4 @@ class MasterLogger:
             self.handler = None
 
     def __repr__(self):
-        return f"MasterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
+        return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"

masster/sample/__init__.py

@@ -1,5 +1,5 @@
 """
-Sample module for master.
+Sample module for masster.
 
 This module provides the Sample class for handling mass spectrometry data.
 """