masster 0.4.5__py3-none-any.whl → 0.4.9__py3-none-any.whl

masster/__init__.py

@@ -1,5 +1,5 @@
 """
-master - Mass Spectrometry Analysis Assistant
+masster - Mass Spectrometry Analysis Assistant
 
 A comprehensive Python package for processing and analyzing untargeted metabolomics data,
 supporting both DDA (Data-Dependent Acquisition) and DIA (Data-Independent Acquisition)
@@ -8,14 +8,14 @@ mass spectrometry workflows.
 
 from __future__ import annotations
 
-from master._version import __version__
+from masster._version import __version__
 
-# from master._version import get_version
-from master.chromatogram import Chromatogram
-from master.lib import Lib
-from master.sample.sample import Sample
-from master.spectrum import Spectrum
-from master.study.study import Study
+# from masster._version import get_version
+from masster.chromatogram import Chromatogram
+from masster.lib import Lib
+from masster.sample.sample import Sample
+from masster.spectrum import Spectrum
+from masster.study.study import Study
 
 
 __all__ = [

masster/_version.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 
-__version__ = "0.4.4"
+__version__ = "0.4.8"
 
 
 def get_version():

masster/chromatogram.py

@@ -88,10 +88,10 @@ class Chromatogram:
 
     Example Usage:
         >>> import numpy as np
-        >>> from master import chrom
+        >>> from masster import Chromatogram
         >>> rt = np.linspace(0, 300, 1000)
         >>> intensity = np.random.normal(1000, 100, 1000)
-        >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")
+        >>> chromatogram = Chromatogram(rt=rt, inty=intensity, label="EIC m/z 150")
         >>> chromatogram.find_peaks()
         >>> chromatogram.calculate_area()
 

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
@@ -124,7 +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
@@ -143,7 +143,7 @@ class MasterLogger:
         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
@@ -192,7 +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."""
@@ -207,7 +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
@@ -256,7 +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
@@ -329,4 +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.
 """

masster/sample/adducts.py

@@ -18,7 +18,7 @@ from typing import List, Dict
 from itertools import combinations
 
 # Import defaults class for external use
-from master.sample.defaults.find_adducts_def import find_adducts_defaults
+from masster.sample.defaults.find_adducts_def import find_adducts_defaults
 
 
 def _get_adducts(self, adducts_list: list = None, **kwargs):

masster/sample/h5.py

@@ -7,8 +7,8 @@ import polars as pl
 
 from typing import Any, Dict, List, Optional, Tuple
 
-from master.chromatogram import Chromatogram
-from master.spectrum import Spectrum
+from masster.chromatogram import Chromatogram
+from masster.spectrum import Spectrum
 
 
 def _save_sample5(
@@ -33,7 +33,7 @@ def _save_sample5(
             Set to True if you need to maintain featureXML files for legacy workflows.
 
     Stores:
-        - metadata/format (str): Data format identifier (master-sample-1)
+        - metadata/format (str): Data format identifier (masster-sample-1)
         - metadata/file_path (str): Source file path
         - metadata/file_type (str): Source file type
         - metadata/label (str): Sample label
@@ -85,7 +85,7 @@ def _save_sample5(
         ms1_group = f.create_group("ms1")
 
         # Store metadata
-        metadata_group.attrs["format"] = "master-sample-1"
+        metadata_group.attrs["format"] = "masster-sample-1"
         if self.file_path is not None:
             metadata_group.attrs["file_path"] = str(self.file_path)
         else:
@@ -356,7 +356,7 @@ def _load_sample5(self, filename: str, map: bool = False):
             loaded_data = load_parameters_from_metadata(metadata_group)
 
             # Always create a fresh sample_defaults object
-            from master.sample.defaults.sample_def import sample_defaults
+            from masster.sample.defaults.sample_def import sample_defaults
 
             self.parameters = sample_defaults()
 
@@ -1096,7 +1096,7 @@ def _load_sample5_study(self, filename: str, map: bool = False):
             loaded_data = load_parameters_from_metadata(metadata_group)
 
             # Always create a fresh sample_defaults object
-            from master.sample.defaults.sample_def import sample_defaults
+            from masster.sample.defaults.sample_def import sample_defaults
 
             self.parameters = sample_defaults()
 
@@ -2213,7 +2213,7 @@ def create_h5_metadata_group(
         label: Sample label
     """
     metadata_group = f.create_group("metadata")
-    metadata_group.attrs["format"] = "master-sample5-1"
+    metadata_group.attrs["format"] = "masster-sample5-1"
     metadata_group.attrs["file_path"] = str(file_path) if file_path is not None else ""
     metadata_group.attrs["file_source"] = (
         str(file_source) if file_source is not None else ""

masster/sample/lib.py

@@ -34,7 +34,7 @@ Supported Adducts:
 
 Example Usage:
 ```python
-from master.sample.lib import Lib
+from masster.sample.lib import Lib
 
 # Create library instance
 lib = Lib()
@@ -63,7 +63,7 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.chromatogram import Chromatogram
+from masster.chromatogram import Chromatogram
 # Parameters removed - using hardcoded defaults
 
 

masster/sample/load.py

@@ -47,10 +47,10 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.chromatogram import Chromatogram
+from masster.chromatogram import Chromatogram
 
 # Parameters removed - using hardcoded defaults
-from master.spectrum import Spectrum
+from masster.spectrum import Spectrum
 
 
 def load(
@@ -556,12 +556,12 @@ def _load_wiff(
     filename=None,
 ):
     try:
-        # Use master's own implementation first
-        from master.sample.sciex import SciexWiffData as MasterSciexWiffData
+        # Use masster's own implementation first
+        from masster.sample.sciex import SciexWiffData as MassterSciexWiffData
 
-        SciexWiffDataClass = MasterSciexWiffData
+        SciexWiffDataClass = MassterSciexWiffData
     except ImportError:
-        # Fallback to alpharaw if master implementation fails
+        # Fallback to alpharaw if masster implementation fails
         from alpharaw.sciex import SciexWiffData as AlpharawSciexWiffData
 
         SciexWiffDataClass = AlpharawSciexWiffData
@@ -972,8 +972,8 @@ def index_file(self):
         try:
             from alpharaw.sciex import SciexWiffData
         except ImportError:
-            # Fallback to master's own implementation
-            from master.sample.sciex import SciexWiffData
+            # Fallback to masster's own implementation
+            from masster.sample.sciex import SciexWiffData
 
         raw_data = SciexWiffData(centroided=False)
         raw_data.keep_k_peaks_per_spec = self.parameters.max_points_per_spectrum

masster/sample/parameters.py

@@ -85,7 +85,7 @@ def update_parameters(self, **kwargs):
                  - Individual parameter names and values (see sample_defaults for details)
     """
     # Import here to avoid circular imports
-    from master.sample.defaults.sample_def import (
+    from masster.sample.defaults.sample_def import (
         sample_defaults as SampleDefaults,
     )
 

masster/sample/plot.py

@@ -2073,7 +2073,7 @@ def plot_tic(
         return
 
     # Import helper locally to avoid circular imports
-    from master.study.helpers import get_tic
+    from masster.study.helpers import get_tic
 
     # Delegate TIC computation to study helper which handles ms1_df and scans_df fallbacks
     try:
@@ -2128,7 +2128,7 @@ def plot_bpc(
         return
 
     # Import helper locally to avoid circular imports
-    from master.study.helpers import get_bpc
+    from masster.study.helpers import get_bpc
 
     # Delegate BPC computation to study helper
     try:

masster/sample/processing.py

@@ -8,13 +8,13 @@ import pyopenms as oms
 
 from tqdm import tqdm
 
-from master.spectrum import Spectrum
+from masster.spectrum import Spectrum
 from .defaults.find_features_def import find_features_defaults
 from .defaults.find_ms2_def import find_ms2_defaults
 from .defaults.get_spectrum_def import get_spectrum_defaults
 
 
-from master.chromatogram import Chromatogram
+from masster.chromatogram import Chromatogram
 
 
 def get_spectrum(self, scan, **kwargs):

masster/sample/sample.py

@@ -23,7 +23,7 @@ Classes:
 
 Example Usage:
 ```python
-from master.sample import Sample
+from masster.sample import Sample
 
 sample = Sample(file="example.mzML")
 sample.find_features()
@@ -38,87 +38,87 @@ import sys
 
 import polars as pl
 
-from master._version import get_version
-from master.logger import MasterLogger
+from masster._version import get_version
+from masster.logger import MassterLogger
 
-from master.sample.defaults.sample_def import sample_defaults
-from master.sample.defaults.find_features_def import find_features_defaults
-from master.sample.defaults.find_adducts_def import find_adducts_defaults
-from master.sample.defaults.find_ms2_def import find_ms2_defaults
-from master.sample.defaults.get_spectrum_def import get_spectrum_defaults
+from masster.sample.defaults.sample_def import sample_defaults
+from masster.sample.defaults.find_features_def import find_features_defaults
+from masster.sample.defaults.find_adducts_def import find_adducts_defaults
+from masster.sample.defaults.find_ms2_def import find_ms2_defaults
+from masster.sample.defaults.get_spectrum_def import get_spectrum_defaults
 
 # Sample-specific imports
-from master.sample.h5 import _load_sample5
-from master.sample.h5 import _load_sample5_study
-from master.sample.h5 import _save_sample5
-from master.sample.helpers import _delete_ms2
-from master.sample.helpers import _estimate_memory_usage
-from master.sample.helpers import _get_scan_uids
-from master.sample.helpers import _get_feature_uids
-from master.sample.helpers import _features_sync
-
-# from master.sample.helpers import _parse_adduct_specs
-# from master.sample.helpers import _calculate_adduct_mass_shift
-# from master.sample.helpers import _parse_formula_expression
-# from master.sample.helpers import _calculate_molecular_mass
-# from master.sample.helpers import _parse_legacy_adduct_format
-# from master.sample.helpers import _extract_adduct_probability
-# from master.sample.helpers import _detect_adduct_groups_direct
-# from master.sample.helpers import _check_adduct_relationship
-from master.sample.adducts import _get_adducts
-from master.sample.adducts import find_adducts
-from master.sample.helpers import features_delete
-from master.sample.helpers import features_filter
-from master.sample.helpers import select
-from master.sample.helpers import select_closest_scan
-from master.sample.helpers import get_dda_stats
-from master.sample.helpers import get_feature
-from master.sample.helpers import get_scan
-from master.sample.helpers import get_eic
-from master.sample.helpers import set_source
-from master.sample.helpers import _recreate_feature_map
-from master.sample.helpers import _get_feature_map
-from master.sample.load import _load_featureXML
-from master.sample.load import _load_ms2data
-from master.sample.load import _load_mzML
-from master.sample.load import _load_raw
-from master.sample.load import _load_wiff
-from master.sample.load import chrom_extract
-from master.sample.load import index_file
-from master.sample.load import load
-from master.sample.load import load_noms1
-from master.sample.load import load_study
-from master.sample.load import sanitize
-from master.sample.plot import plot_2d
-from master.sample.plot import plot_2d_oracle
-from master.sample.plot import plot_dda_stats
-from master.sample.plot import plot_chrom
-from master.sample.plot import plot_feature_stats
-from master.sample.plot import plot_ms2_cycle
-from master.sample.plot import plot_ms2_eic
-from master.sample.plot import plot_ms2_q1
-from master.sample.plot import plot_bpc
-from master.sample.plot import plot_tic
-from master.sample.plot import _handle_sample_plot_output
-from master.sample.processing import _clean_features_df
-from master.sample.processing import _features_deisotope
-from master.sample.processing import _get_ztscan_stats
-from master.sample.processing import _spec_to_mat
-from master.sample.processing import analyze_dda
-from master.sample.processing import find_features
-from master.sample.processing import find_ms2
-from master.sample.processing import get_spectrum
-from master.sample.parameters import store_history
-from master.sample.parameters import get_parameters
-from master.sample.parameters import update_parameters
-from master.sample.parameters import get_parameters_property
-from master.sample.parameters import set_parameters_property
-from master.sample.save import _save_featureXML
-from master.sample.save import export_chrom
-from master.sample.save import export_dda_stats
-from master.sample.save import export_features
-from master.sample.save import export_mgf
-from master.sample.save import save
+from masster.sample.h5 import _load_sample5
+from masster.sample.h5 import _load_sample5_study
+from masster.sample.h5 import _save_sample5
+from masster.sample.helpers import _delete_ms2
+from masster.sample.helpers import _estimate_memory_usage
+from masster.sample.helpers import _get_scan_uids
+from masster.sample.helpers import _get_feature_uids
+from masster.sample.helpers import _features_sync
+
+# from masster.sample.helpers import _parse_adduct_specs
+# from masster.sample.helpers import _calculate_adduct_mass_shift
+# from masster.sample.helpers import _parse_formula_expression
+# from masster.sample.helpers import _calculate_molecular_mass
+# from masster.sample.helpers import _parse_legacy_adduct_format
+# from masster.sample.helpers import _extract_adduct_probability
+# from masster.sample.helpers import _detect_adduct_groups_direct
+# from masster.sample.helpers import _check_adduct_relationship
+from masster.sample.adducts import _get_adducts
+from masster.sample.adducts import find_adducts
+from masster.sample.helpers import features_delete
+from masster.sample.helpers import features_filter
+from masster.sample.helpers import select
+from masster.sample.helpers import select_closest_scan
+from masster.sample.helpers import get_dda_stats
+from masster.sample.helpers import get_feature
+from masster.sample.helpers import get_scan
+from masster.sample.helpers import get_eic
+from masster.sample.helpers import set_source
+from masster.sample.helpers import _recreate_feature_map
+from masster.sample.helpers import _get_feature_map
+from masster.sample.load import _load_featureXML
+from masster.sample.load import _load_ms2data
+from masster.sample.load import _load_mzML
+from masster.sample.load import _load_raw
+from masster.sample.load import _load_wiff
+from masster.sample.load import chrom_extract
+from masster.sample.load import index_file
+from masster.sample.load import load
+from masster.sample.load import load_noms1
+from masster.sample.load import load_study
+from masster.sample.load import sanitize
+from masster.sample.plot import plot_2d
+from masster.sample.plot import plot_2d_oracle
+from masster.sample.plot import plot_dda_stats
+from masster.sample.plot import plot_chrom
+from masster.sample.plot import plot_feature_stats
+from masster.sample.plot import plot_ms2_cycle
+from masster.sample.plot import plot_ms2_eic
+from masster.sample.plot import plot_ms2_q1
+from masster.sample.plot import plot_bpc
+from masster.sample.plot import plot_tic
+from masster.sample.plot import _handle_sample_plot_output
+from masster.sample.processing import _clean_features_df
+from masster.sample.processing import _features_deisotope
+from masster.sample.processing import _get_ztscan_stats
+from masster.sample.processing import _spec_to_mat
+from masster.sample.processing import analyze_dda
+from masster.sample.processing import find_features
+from masster.sample.processing import find_ms2
+from masster.sample.processing import get_spectrum
+from masster.sample.parameters import store_history
+from masster.sample.parameters import get_parameters
+from masster.sample.parameters import update_parameters
+from masster.sample.parameters import get_parameters_property
+from masster.sample.parameters import set_parameters_property
+from masster.sample.save import _save_featureXML
+from masster.sample.save import export_chrom
+from masster.sample.save import export_dda_stats
+from masster.sample.save import export_features
+from masster.sample.save import export_mgf
+from masster.sample.save import save
 
 
 class Sample:
@@ -180,7 +180,7 @@ class Sample:
         self.log_sink = params.log_sink
 
         # Initialize independent logger
-        self.logger = MasterLogger(
+        self.logger = MassterLogger(
             instance_type="sample",
             level=params.log_level.upper(),
             label=params.log_label if params.log_label else "",
@@ -329,20 +329,20 @@ class Sample:
 
     def _reload(self):
         """
-        Reloads all master modules to pick up any changes to their source code,
+        Reloads all masster modules to pick up any changes to their source code,
         and updates the instance's class reference to the newly reloaded class version.
         This ensures that the instance uses the latest implementation without restarting the interpreter.
         """
         # Reset logger configuration flags to allow proper reconfiguration after reload
         try:
-            import master.logger as logger_module
+            import masster.logger as logger_module
 
             if hasattr(logger_module, "_SAMPLE_LOGGER_CONFIGURED"):
                 logger_module._SAMPLE_LOGGER_CONFIGURED = False
         except Exception:
             pass
 
-        # Get the base module name (master)
+        # Get the base module name (masster)
         base_modname = self.__class__.__module__.split(".")[0]
         current_module = self.__class__.__module__
 
@@ -358,7 +358,7 @@ class Sample:
             ):
                 sample_modules.append(module_name)
 
-        # Add core master modules
+        # Add core masster modules
         core_modules = [
             f"{base_modname}._version",
             f"{base_modname}.chromatogram",
@@ -437,9 +437,9 @@ class Sample:
 
     def __str__(self):
         if self.features_df is None:
-            str = f"master Sample, source: {os.path.basename(self.file_path)}, features: 0"
+            str = f"masster Sample, source: {os.path.basename(self.file_path)}, features: 0"
         else:
-            str = f"master Sample, source: {os.path.basename(self.file_path)}, features: {len(self.features_df)}"
+            str = f"masster Sample, source: {os.path.basename(self.file_path)}, features: {len(self.features_df)}"
         return str
 
 

masster/sample/save.py

@@ -67,7 +67,7 @@ import pyopenms as oms
 from tqdm import tqdm
 
 # Parameters removed - using hardcoded defaults
-from master.spectrum import combine_peaks
+from masster.spectrum import combine_peaks
 
 
 def save(self, filename=None):

masster/spectrum.py

@@ -138,10 +138,10 @@ class Spectrum:
 
     Example Usage:
         >>> import numpy as np
-        >>> from master import spec
+        >>> from masster import Spectrum
         >>> mz = np.array([100.0, 150.0, 200.0, 250.0])
         >>> intensity = np.array([1000, 5000, 3000, 800])
-        >>> spectrum = spec(mz=mz, inty=intensity, ms_level=1)
+        >>> spectrum = Spectrum(mz=mz, inty=intensity, ms_level=1)
         >>> spectrum.find_peaks()
         >>> spectrum.plot()
 

masster/study/__init__.py

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

masster/study/export.py

@@ -10,9 +10,9 @@ import polars as pl
 
 from tqdm import tqdm
 
-from master.spectrum import combine_peaks
-from master.study.defaults import export_mgf_defaults
-from master._version import get_version
+from masster.spectrum import combine_peaks
+from masster.study.defaults import export_mgf_defaults
+from masster._version import get_version
 
 
 def _get_mgf_df(self, **kwargs):
@@ -444,7 +444,7 @@ def export_mztab(self, filename: str = None, include_mgf=True, **kwargs) -> None
     full_id_data = None
     try:
         # Import here to avoid circular imports
-        from master.study.id import get_id
+        from masster.study.id import get_id
 
         # Get full enriched identification data for SOME section
         full_id_data = get_id(self)
@@ -1157,7 +1157,7 @@ def export_xlsx(self, filename: str = None) -> None:
 
     # 3. Identification results
     try:
-        from master.study.id import get_id
+        from masster.study.id import get_id
 
         id_df = get_id(self)
         if id_df is not None and not id_df.is_empty():
@@ -1171,7 +1171,7 @@ def export_xlsx(self, filename: str = None) -> None:
                 "get_id() returned empty data, skipping identification worksheet",
             )
     except Exception as e:
-        self.logger.warning(
+        self.logger.debug(
             f"Error getting identification data: {e}. Skipping identification worksheet.",
         )
 
@@ -1272,7 +1272,7 @@ def export_parquet(self, basename: str = None) -> None:
 
     # 3. Identification results
     try:
-        from master.study.id import get_id
+        from masster.study.id import get_id
 
         id_df = get_id(self)
         if id_df is not None and not id_df.is_empty():