CoreMS 3.0.1__tar.gz → 3.1.0__tar.gz

{CoreMS-3.0.1 → CoreMS-3.1.0}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 3.0.1
+Version: 3.1.0
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -65,7 +65,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.1`
+ `3.1.0`
 
 ***
 
@@ -351,11 +351,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:  
+Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/CoreMS.egg-info/SOURCES.txt

@@ -30,13 +30,11 @@ corems/mass_spectra/__init__.py
 corems/mass_spectra/calc/GC_Calc.py
 corems/mass_spectra/calc/GC_Deconvolution.py
 corems/mass_spectra/calc/GC_RI_Calibration.py
-corems/mass_spectra/calc/LC_Calc.py
 corems/mass_spectra/calc/MZSearch.py
 corems/mass_spectra/calc/SignalProcessing.py
 corems/mass_spectra/calc/__init__.py
 corems/mass_spectra/calc/lc_calc.py
 corems/mass_spectra/factory/GC_Class.py
-corems/mass_spectra/factory/LC_Class.py
 corems/mass_spectra/factory/__init__.py
 corems/mass_spectra/factory/chromat_data.py
 corems/mass_spectra/factory/lc_class.py

{CoreMS-3.0.1 → CoreMS-3.1.0}/CoreMS.egg-info/requires.txt

@@ -5,7 +5,7 @@ IsoSpecPy~=2.2.2
 lmfit~=1.1.0
 lxml~=4.9.3
 matplotlib~=3.7.0
-ms-entropy~=1.1.2
+ms-entropy~=1.2.2
 netCDF4~=1.6.3
 numpy~=1.24.2
 openpyxl~=3.1.1
@@ -14,7 +14,7 @@ pyswarm~=0.6
 pythonnet~=3.0.1
 pymzml~=2.5.2
 requests~=2.31.0
-ripser==0.6.4
+ripser~=0.6.4
 s3path~=0.4.1
 scikit_learn~=1.2.2
 scipy~=1.10.1

{CoreMS-3.0.1 → CoreMS-3.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 3.0.1
+Version: 3.1.0
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -65,7 +65,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.1`
+ `3.1.0`
 
 ***
 
@@ -351,11 +351,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:  
+Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/README.md

@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.1`
+ `3.1.0`
 
 ***
 
@@ -335,11 +335,11 @@ UML (unified modeling language) diagrams for Direct Infusion FT-MS and GC-MS cla
 
 If you use CoreMS in your work, please use the following citation:
 
-Version [3.0.1 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.1), archived on Zenodo:  
+Version [3.1.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.1.0), archived on Zenodo:  
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg)](https://doi.org/10.5281/zenodo.14009575)
 
-Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.1 (Version v3.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.1.0 (Version v3.1.0), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.0.1"
+__version__ = "3.1.0"
 import time
 import os
 import sys

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/mass_spectra/input/massList.py

@@ -3,7 +3,6 @@ __date__ = "Jun 12, 2019"
 
 import sys
 
-sys.path.append(".")  # Why?
 from pathlib import Path
 from threading import Thread
 import warnings

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/mass_spectra/input/rawFileReader.py

@@ -14,6 +14,8 @@ import sys
 import site
 from pathlib import Path
 import datetime
+import importlib.util
+import os
 
 import clr
 import pandas as pd
@@ -31,9 +33,9 @@ from corems.mass_spectrum.factory.MassSpectrumClasses import (
 from corems.encapsulation.factory.parameters import LCMSParameters, default_parameters
 from corems.mass_spectra.input.parserbase import SpectraParserInterface
 
-# do not change the order from the imports statements and reference ThermoFisher below
-sys.path.append(site.getsitepackages()[0] + "/ext_lib/dotnet/")
-sys.path.append("ext_lib/dotnet/")
+# Add the path of the Thermo .NET libraries to the system path
+spec = importlib.util.find_spec("corems")
+sys.path.append(str(Path(os.path.dirname(spec.origin)).parent) + "/ext_lib/dotnet/")
 
 clr.AddReference("ThermoFisher.CommonCore.RawFileReader")
 clr.AddReference("ThermoFisher.CommonCore.Data")

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/molecular_formula/input/masslist_ref.py

@@ -9,8 +9,6 @@ from typing import Dict, List
 
 import pandas as pd
 
-sys.path.append(".")
-
 from corems.encapsulation.constant import Atoms, Labels
 from corems.molecular_formula.factory.MolecularFormulaFactory import (
     LCMSLibRefMolecularFormula,

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/molecular_id/factory/molecularSQL.py

@@ -1,6 +1,5 @@
 import sys
 
-sys.path.append(".")
 import json
 import os
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/corems/molecular_id/search/priorityAssignment.py

@@ -1,7 +1,6 @@
 import os
 import sys
 
-sys.path.append(".")
 from copy import deepcopy
 from threading import Thread
 from itertools import product

{CoreMS-3.0.1 → CoreMS-3.1.0}/requirements.txt

@@ -5,7 +5,7 @@ IsoSpecPy~=2.2.2
 lmfit~=1.1.0
 lxml~=4.9.3
 matplotlib~=3.7.0
-ms-entropy~=1.1.2
+ms-entropy~=1.2.2
 netCDF4~=1.6.3
 numpy~=1.24.2
 openpyxl~=3.1.1
@@ -14,7 +14,7 @@ pyswarm~=0.6
 pythonnet~=3.0.1
 pymzml~=2.5.2
 requests~=2.31.0
-ripser==0.6.4
+ripser~=0.6.4
 s3path~=0.4.1
 scikit_learn~=1.2.2
 scipy~=1.10.1

{CoreMS-3.0.1 → CoreMS-3.1.0}/setup.py

@@ -14,7 +14,7 @@ with open('requirements.txt') as f:
 # This call to setup() does all the work
 setup(
     name="CoreMS",
-    version="3.0.1",
+    version="3.1.0",
     description="Mass Spectrometry Framework for Small Molecules Analysis",
     long_description=long_description,
     long_description_content_type="text/markdown",

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_calibration.py

@@ -2,8 +2,6 @@ import sys
 from pathlib import Path
 import pytest
 
-sys.path.append(".")
-
 from corems.mass_spectrum.calc.AutoRecalibration import HighResRecalibration
 from corems.mass_spectrum.calc.Calibration import MzDomainCalibration
 from corems.mass_spectrum.calc.CalibrationCalc import FreqDomain_Calibration

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_classification.py

@@ -1,5 +1,4 @@
 import sys
-sys.path.append('.')
 
 from corems.molecular_id.factory.classification import  HeteroatomsClassification, Labels
 from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_gcms.py

@@ -5,7 +5,6 @@ import warnings
 warnings.filterwarnings("ignore")
 
 import sys
-sys.path.append(".")
 
 import pytest
 from pathlib import Path

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_input.py

@@ -4,7 +4,6 @@ __date__ = "Jul 02, 2019"
 
 import sys
 
-sys.path.append(".")
 from pathlib import Path
 
 from corems.encapsulation.constant import Labels

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_molecular_formula.py

@@ -3,8 +3,6 @@ __date__ = "Jul 22, 2019"
 
 import sys
 
-sys.path.append(".")
-
 from corems.molecular_formula.factory.MolecularFormulaFactory import MolecularFormula
 from corems.encapsulation.constant import Labels
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_mspeak.py

@@ -1,6 +1,5 @@
 import sys
 
-sys.path.append(".")
 from corems.ms_peak.factory.MSPeakClasses import ICRMassPeak
 
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_output.py

@@ -1,5 +1,4 @@
 import sys
-sys.path.append(".")
 import os
 
 from corems.mass_spectrum.output.export import HighResMassSpecExport

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_search_mass_list.py

@@ -1,7 +1,5 @@
 import sys
 
-sys.path.append(".")
-
 from corems.molecular_formula.input.masslist_ref import ImportMassListRef
 from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFormulas
 

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_setting_settings.py

@@ -1,6 +1,5 @@
 import sys
 import os
-sys.path.append(".")
 
 from corems.encapsulation.output import parameter_to_json, parameter_to_dict
 from corems.encapsulation.factory.processingSetting  import MolecularLookupDictSettings

{CoreMS-3.0.1 → CoreMS-3.1.0}/tests/test_wf_lipidomics.py

@@ -1,7 +1,6 @@
 # %% Import libs
 import sys
 
-sys.path.append("./")
 from pathlib import Path
 
 import shutil