masster 0.4.4__tar.gz → 0.4.5__tar.gz

{masster-0.4.4/src/masster.egg-info → masster-0.4.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.4
+Version: 0.4.5
 Summary: Mass spectrometry data analysis package
 Author: Zamboni Lab
 License-Expression: AGPL-3.0-only
@@ -41,6 +41,8 @@ Requires-Dist: tqdm>=4.65.0
 Requires-Dist: openpyxl>=3.1.5
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: altair>=5.5.0
+Requires-Dist: scikit-learn>=1.7.1
+Requires-Dist: ipython>=9.4.0
 Provides-Extra: dev
 Requires-Dist: pytest>=7.0.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0.0; extra == "dev"

{masster-0.4.4 → masster-0.4.5}/pyproject.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "masster"
-version = "0.4.4"
+version = "0.4.5"
 description = "Mass spectrometry data analysis package"
 authors = [
     { name = "Zamboni Lab" }
@@ -48,6 +48,8 @@ dependencies = [
     "openpyxl>=3.1.5",
     "cmap>=0.6.2",
     "altair>=5.5.0",
+    "scikit-learn>=1.7.1",
+    "ipython>=9.4.0",
 ]
 
 [project.optional-dependencies]

{masster-0.4.4 → masster-0.4.5}/src/masster/__init__.py

@@ -1,5 +1,5 @@
 """
-masster - Mass Spectrometry Analysis Assistant
+master - 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 masster._version import __version__
+from master._version import __version__
 
-# 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
+# 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
 
 
 __all__ = [

{masster-0.4.4 → masster-0.4.5}/src/masster/chromatogram.py

@@ -88,7 +88,7 @@ class Chromatogram:
 
     Example Usage:
         >>> import numpy as np
-        >>> from masster import chrom
+        >>> from master import chrom
         >>> rt = np.linspace(0, 300, 1000)
         >>> intensity = np.random.normal(1000, 100, 1000)
         >>> chromatogram = chrom(rt=rt, inty=intensity, label="EIC m/z 150")

{masster-0.4.4 → masster-0.4.5}/src/masster/data/libs/urine.csv

@@ -927,7 +927,7 @@ Lead,[Pb++],RVPVRDXYQKGNMQ-UHFFFAOYSA-N,Pb,CID:122121,pubchem
 O-Desmethylangolensin,CC(C(=O)C1=C(O)C=C(O)C=C1)C1=CC=C(O)C=C1,JDJPNKPFDDUBFV-UHFFFAOYSA-N,C15H14O4,CID:89472,pubchem
 8-Isoprostane,[H][C@@]1(CCCCCCC)CCC[C@]1([H])CCCCCCCC,UKVVPDHLUHAJNZ-UXHICEINSA-N,C20H40,CID:107873,pubchem
 "MG(0:0/20:4(5Z,8Z,11Z,14Z)/0:0)",[H]C(CO)(CO)OC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCCCC,RCRCTBLIHCHWDZ-DOFZRALJSA-N,C23H38O4,CID:5282280,pubchem
-13-HODE,CCCCC[C@H](O)\C=C\C=C/CCCCCCCC(O)=O,HNICUWMFWZBIFP-IRQZEAMPSA-N,C18H32O3,CID:6443013,pubchem
+13-NODE,CCCCC[C@H](O)\C=C\C=C/CCCCCCCC(O)=O,HNICUWMFWZBIFP-IRQZEAMPSA-N,C18H32O3,CID:6443013,pubchem
 7C-aglycone,C\C(CCC(O)=O)=C\CC1=C(C)C(=O)C2=C(C=CC=C2)C1=O,BCNIZSHMXASUGF-XFFZJAGNSA-N,C18H18O4,CID:20348793,pubchem
 5C-aglycone,CC(CCC1=C(C)C(=O)C2=C(C=CC=C2)C1=O)C(O)=O,ALLYVKRLOHDVKI-UHFFFAOYSA-N,C16H16O4,CID:3082405,pubchem
 "2,4-Dichlorophenol",OC1=CC=C(Cl)C=C1Cl,HFZWRUODUSTPEG-UHFFFAOYSA-N,C6H4Cl2O,CID:8449,pubchem
@@ -1848,7 +1848,7 @@ Urolithin B,OC1=CC2=C(C=C1)C1=C(C=CC=C1)C(=O)O2,WXUQMTRHPNOXBV-UHFFFAOYSA-N,C13H
 6-Methylnicotinamide,[H]N([H])C(=O)C1=C(N=C([H])C([H])=C1[H])C([H])([H])C([H])([H])[H],GOIWNSRZUNIIRY-UHFFFAOYSA-N,C8H10N2O,CID:14393052,pubchem
 Lanthanum,[La],FZLIPJUXYLNCLC-UHFFFAOYSA-N,La,CID:23926,pubchem
 N-Acetyltryptophan,CC(=O)N[C@@H](CC1=CNC2=C1C=CC=C2)C(O)=O,DZTHIGRZJZPRDV-LBPRGKRZSA-N,C13H14N2O3,CID:700653,pubchem
-Neodymium,[Nd],QEFYFXOXNSNQGX-UHFFFAOYSA-N,Nd,CID:23934,pubchem
+Neodymium,[And],QEFYFXOXNSNQGX-UHFFFAOYSA-N,And,CID:23934,pubchem
 Norvaline,CCC[C@@H](N)C(O)=O,SNDPXSYFESPGGJ-SCSAIBSYSA-N,C5H11NO2,CID:439575,pubchem
 Rhenium,[Re],WUAPFZMCVAUBPE-UHFFFAOYSA-N,Re,CID:23947,pubchem
 Thallium,Cl[Tl],GBECUEIQVRDUKB-UHFFFAOYSA-M,ClTl,CID:24642,pubchem
@@ -4512,7 +4512,7 @@ Urolithin C 3-glucuronide,O[C@@H]1[C@@H](O)[C@H](OC2=CC3=C(C=C2)C2=C(C=C(O)C(O)=
 "2,6-Di-tert-butyl-4-hydroxy-4-methyl-2,5-cyclohexadienone",CC(C)(C)C1=CC(C)(O)C=C(C1=O)C(C)(C)C,DQBHJILNHNRDTM-UHFFFAOYSA-N,C15H24O2,CID:146102,pubchem
 3-Methylbut-3-enoic acid,CC(=C)CC(O)=O,IGRURXZWJCSNKU-UHFFFAOYSA-N,C5H8O2,CID:417575,pubchem
 D-chiro-Inositol,O[C@H]1[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O,CDAISMWEOUEBRE-LKPKBOIGSA-N,C6H12O6,,
-allo-Inositol,O[C@H]1[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O,CDAISMWEOUEBRE-OQYPVSDDSA-N,C6H12O6,,
+allow-Inositol,O[C@H]1[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O,CDAISMWEOUEBRE-OQYPVSDDSA-N,C6H12O6,,
 Dimethylguanidino valeric acid,CN(C)C(=N)NCCCC(=O)C(O)=O,GLWRPXRMUUZNMD-UHFFFAOYSA-N,C8H15N3O3,CID:101535539,pubchem
 N-Acetyltaurine,CC(=O)NCCS(O)(=O)=O,CXJAAWRLVGAKDV-UHFFFAOYSA-N,C4H9NO4S,CID:159864,pubchem
 Creatine riboside,CN(CC(O)=O)C(=N)N[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O,BGJFEKXALPJEGN-XVFCMESISA-N,C9H17N3O6,CID:91885405,pubchem

{masster-0.4.4 → masster-0.4.5}/src/masster/logger.py

@@ -1,6 +1,6 @@
 # masster/logger.py
 """
-Simple logger system for masster Study and Sample instances.
+Simple logger system for master 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 MassterLogger:
+class MasterLogger:
     """Simple logger wrapper for Study/Sample instances.
     Each instance gets its own Python logger to avoid conflicts.
 
@@ -59,7 +59,7 @@ class MassterLogger:
             self.sink = sink
 
         # Create a unique logger name for this instance
-        self.logger_name = f"masster.{self.instance_type}.{self.instance_id}"
+        self.logger_name = f"master.{self.instance_type}.{self.instance_id}"
 
         # Get a Python logger instance
         self.logger_instance = logging.getLogger(self.logger_name)
@@ -73,8 +73,8 @@ class MassterLogger:
         # Create a stream handler
         self.handler = logging.StreamHandler(self.sink)
 
-        # Create formatter that matches the original masster style
-        class massterFormatter(logging.Formatter):
+        # Create formatter that matches the original master style
+        class masterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -124,7 +124,7 @@ class MassterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(massterFormatter(self.label))
+        self.handler.setFormatter(masterFormatter(self.label))
         self.logger_instance.addHandler(self.handler)
 
         # Prevent propagation to avoid duplicate messages
@@ -143,7 +143,7 @@ class MassterLogger:
         self.label = label
 
         # Update formatter with new label
-        class massterFormatter(logging.Formatter):
+        class masterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -192,7 +192,7 @@ class MassterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(massterFormatter(self.label))
+        self.handler.setFormatter(masterFormatter(self.label))
 
     def update_sink(self, sink: Any):
         """Update the output sink for log messages."""
@@ -207,7 +207,7 @@ class MassterLogger:
         self.handler = logging.StreamHandler(self.sink)
 
         # Apply formatter
-        class massterFormatter(logging.Formatter):
+        class masterFormatter(logging.Formatter):
             def __init__(self, label):
                 super().__init__()
                 self.label = label
@@ -256,7 +256,7 @@ class MassterLogger:
                     f"{level_color}{record.getMessage()}\x1b[0m"
                 )  # colored message
 
-        self.handler.setFormatter(massterFormatter(self.label))
+        self.handler.setFormatter(masterFormatter(self.label))
         self.logger_instance.addHandler(self.handler)
 
     # Logger method delegates
@@ -329,4 +329,4 @@ class MassterLogger:
             self.handler = None
 
     def __repr__(self):
-        return f"MassterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"
+        return f"MasterLogger(type={self.instance_type}, id={self.instance_id}, level={self.level})"

{masster-0.4.4 → masster-0.4.5}/src/masster/sample/__init__.py

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