masster 0.3.10__tar.gz → 0.3.12__tar.gz

{masster-0.3.10 → masster-0.3.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.3.10
+Version: 0.3.12
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster

{masster-0.3.10 → masster-0.3.12}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.3.10"
+version = "0.3.12"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }

{masster-0.3.10 → masster-0.3.12}/src/masster/logger.py

@@ -86,40 +86,44 @@ class MassterLogger:
 
                 # 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
+                    "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
+                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']:
+                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'
+                    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'
+                        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 (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
-        
+                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)
 
@@ -150,40 +154,44 @@ class MassterLogger:
 
                 # 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
+                    "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
+                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']:
+                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'
+                    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'
+                        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 (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
-        
+                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):
@@ -210,40 +218,44 @@ class MassterLogger:
 
                 # 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
+                    "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
+                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']:
+                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'
+                    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
-                
+                    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
-        
+                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)
 
@@ -252,36 +264,38 @@ class MassterLogger:
         """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 = 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
+            "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
-        
+        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 = 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
+            "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
-        
+        kwargs["extra"] = extra
+
         self.logger_instance.debug(message, *args, **kwargs)
 
     def info(self, message: str, *args, **kwargs):

{masster-0.3.10 → masster-0.3.12}/src/masster/sample/defaults/find_features_def.py

@@ -52,6 +52,10 @@ class find_features_defaults:
         peaks accepted). Typical values range from ~3 (relaxed) to >10
         (stringent). Default: 10.0.
 
+    - isotope_filtering_model (str):
+        Isotope filtering model to use ('metabolites (2% RMS)', 'metabolites (5% RMS)',
+        'peptides', 'none'). Default: 'metabolites (5% RMS)'.
+
     Use these three parameters together to balance sensitivity and
     specificity for your dataset: tune `chrom_fwhm` to match chromatographic
     peak shapes, set `noise` to a conservative background level for your
@@ -62,12 +66,12 @@ class find_features_defaults:
     isotope handling, post-processing and reporting flags). See individual
     parameter metadata (`_param_metadata`) for allowed ranges and types.
     """
-    
+
     # Main params
     noise: float = 200.0
     chrom_fwhm: float = 1.0
     chrom_peak_snr: float = 10.0
-    
+
     # Mass Trace Detection parameters
     tol_ppm: float = 30.0
     reestimate_mt_sd: bool = True
@@ -78,7 +82,7 @@ class find_features_defaults:
 
     min_trace_length: float = 0.5
     min_trace_length_multiplier: float = 0.2
-    max_trace_length: float = -1.0   
+    max_trace_length: float = -1.0
 
     # Elution Peak Detection parameters
     enabled: bool = True
@@ -108,9 +112,9 @@ class find_features_defaults:
     deisotope: bool = True
     deisotope_mz_tol: float = 0.02
     deisotope_rt_tol_factor: float = 0.5  # Will be multiplied by chrom_fwhm
+    isotope_filtering_model: str = "metabolites (5% RMS)"
 
     # chrom extraction parameters
-   
 
     # Parameter metadata for validation and description
     _param_metadata: dict[str, dict[str, Any]] = field(
@@ -202,6 +206,12 @@ class find_features_defaults:
                 "min_value": 0.1,
                 "max_value": 2.0,
             },
+            "isotope_filtering_model": {
+                "dtype": str,
+                "description": "Isotope filtering model",
+                "default": "metabolites (5% RMS)",
+                "allowed_values": ["metabolites (2% RMS)", "metabolites (5% RMS)", "peptides", "none"],
+            },
             "threads": {
                 "dtype": int,
                 "description": "Number of threads to use for parallel processing",
@@ -228,12 +238,12 @@ class find_features_defaults:
                 "min_value": 2,
                 "max_value": 100,
             },
-'''            "min_fwhm": {
+            """            "min_fwhm": {
                 "dtype": float,
                 "description": "Minimum full width at half maximum for peaks (seconds)",
                 "min_value": 0.1,
                 "max_value": 10.0,
-            },'''
+            },"""
             "chrom_fwhm_max": {
                 "dtype": float,
                 "description": "Maximum full width at half maximum for peaks (seconds)",

{masster-0.3.10 → masster-0.3.12}/src/masster/sample/defaults/sample_def.py

@@ -53,7 +53,7 @@ class sample_defaults:
     centroid_prominence: int = -1
     max_points_per_spectrum: int = 50000
     dia_window: float | None = None
-    
+
     eic_mz_tol: float = 0.01
     eic_rt_tol: float = 10.0
 

{masster-0.3.10 → masster-0.3.12}/src/masster/sample/h5.py

@@ -294,13 +294,13 @@ def _load_sample5(self, filename: str, map: bool = True):
         if "metadata" in f:
             metadata_group = f["metadata"]
             self.file_path = decode_metadata_attr(metadata_group.attrs.get("file_path", ""))
-            
+
             # Load file_source if it exists, otherwise set it equal to file_path
             if "file_source" in metadata_group.attrs:
                 self.file_source = decode_metadata_attr(metadata_group.attrs.get("file_source", ""))
             else:
                 self.file_source = self.file_path
-            
+
             self.file_type = decode_metadata_attr(metadata_group.attrs.get("file_type", ""))
             self.label = decode_metadata_attr(metadata_group.attrs.get("label", ""))