CoreMS 3.0.0__tar.gz → 3.0.2__tar.gz

{CoreMS-3.0.0 → CoreMS-3.0.2}/CoreMS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 3.0.0
+Version: 3.0.2
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -20,7 +20,7 @@ License-File: LICENSE
 
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
 
@@ -65,7 +65,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.0`
+ `3.0.2`
 
 ***
 
@@ -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 [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
+Version [3.0.2 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.2), archived on Zenodo:  
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![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 (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.2 (Version v3.0.2), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.0 → CoreMS-3.0.2}/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-3.0.0 → CoreMS-3.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: CoreMS
-Version: 3.0.0
+Version: 3.0.2
 Summary: Mass Spectrometry Framework for Small Molecules Analysis
 Home-page: https://github.com/EMSL-Computing/CoreMS
 Author: Corilo, Yuri
@@ -20,7 +20,7 @@ License-File: LICENSE
 
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
 
@@ -65,7 +65,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.0`
+ `3.0.2`
 
 ***
 
@@ -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 [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
+Version [3.0.2 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.2), archived on Zenodo:  
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![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 (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.2 (Version v3.0.2), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.0 → CoreMS-3.0.2}/README.md

@@ -4,7 +4,7 @@
 
 <br>
 <br>
-<a href="https://doi.org/10.5281/zenodo.4641552"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg" alt="CoreMS DOI" style="width:150px"></a>
+<a href="https://doi.org/10.5281/zenodo.14009575"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14009575.svg" alt="DOI"></a>
 <br>
 </div>
 
@@ -49,7 +49,7 @@ CoreMS aims to provide
 
 ## Current Version
 
- `3.0.0`
+ `3.0.2`
 
 ***
 
@@ -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 [3.0.0 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.0), archived on Zenodo:  
+Version [3.0.2 Release on GitHub](https://github.com/EMSL-Computing/CoreMS/releases/tag/v3.0.2), archived on Zenodo:  
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4641552.svg)](https://doi.org/10.5281/zenodo.4641552)
+[![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 (2021, March 27). EMSL-Computing/CoreMS: CoreMS 2.0.1 (Version v2.0.1), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.4641552
+Yuri E. Corilo, William R. Kew, Lee Ann McCue, Katherine R . Heal, James C. Carr (2024, October 29). EMSL-Computing/CoreMS: CoreMS 3.0.2 (Version v3.0.2), as developed on Github. Zenodo. http://doi.org/10.5281/zenodo.14009575
 
 ```
 

{CoreMS-3.0.0 → CoreMS-3.0.2}/corems/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Yuri E. Corilo"
-__version__ = "3.0.0"
+__version__ = "3.0.2"
 import time
 import os
 import sys
@@ -8,9 +8,17 @@ import hashlib
 # Get the path to the README file
 readme_path = os.path.join(os.path.dirname(__file__), "..", "README.md")
 
-# Read the contents of the README file
-with open(readme_path, "r", encoding="utf-8") as readme_file:
-    __doc__ = readme_file.read()
+# Read the contents of the README file if it exists
+if os.path.exists(readme_path):
+    try:
+        with open(readme_path, "r", encoding="utf-8") as readme_file:
+            __doc__ = readme_file.read()
+    except Exception as e:
+        __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+        print(f"Warning: Could not read README.md file. Error: {e}")
+else:
+    __doc__ = "CoreMS: A comprehensive mass spectrometry framework for software development and data analysis of small molecules analysis."
+
 
 
 def timeit(method):

{CoreMS-3.0.0 → CoreMS-3.0.2}/setup.py

@@ -14,7 +14,7 @@ with open('requirements.txt') as f:
 # This call to setup() does all the work
 setup(
     name="CoreMS",
-    version="3.0.0",
+    version="3.0.2",
     description="Mass Spectrometry Framework for Small Molecules Analysis",
     long_description=long_description,
     long_description_content_type="text/markdown",

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_calibration.py

@@ -85,7 +85,7 @@ def test_segmentedmzcalibration(mass_spectrum_ftms, ref_file_location):
 def test_old_calibration(mass_spectrum_ftms):
     usedatoms = {"C": (1, 100), "H": (4, 200), "O": (1, 10)}
 
-    mass_spectrum_ftms.molecular_search_settings.url_database = ""
+    mass_spectrum_ftms.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_ftms.molecular_search_settings.error_method = "None"
     mass_spectrum_ftms.molecular_search_settings.min_ppm_error = -5
     mass_spectrum_ftms.molecular_search_settings.max_ppm_error = 5

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_classification.py

@@ -6,7 +6,7 @@ from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFor
 
 
 def test_heteroatoms_classification(mass_spectrum_ftms):
-    mass_spectrum_ftms.molecular_search_settings.url_database = ''
+    mass_spectrum_ftms.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_ftms.molecular_search_settings.error_method = 'None'
     mass_spectrum_ftms.molecular_search_settings.min_ppm_error  = -10
     mass_spectrum_ftms.molecular_search_settings.max_ppm_error = 10

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_mass_spectrum_export_import.py

@@ -23,7 +23,7 @@ def mass_spectrum_silico():
     mass_spectrum_obj.settings.noise_threshold_method = "relative_abundance"
     mass_spectrum_obj.settings.noise_threshold_absolute_abundance = 0
 
-    mass_spectrum_obj.molecular_search_settings.url_database = ""
+    mass_spectrum_obj.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_obj.molecular_search_settings.error_method = "None"
     mass_spectrum_obj.molecular_search_settings.min_ppm_error = -5
     mass_spectrum_obj.molecular_search_settings.max_ppm_error = 5

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_molecular_formula_search.py

@@ -21,7 +21,7 @@ def test_run_molecular_formula_search():
     mass_spectrum_obj.settings.noise_threshold_absolute_abundance = 0
 
     # Set the settings for the molecular search on the mass spectrum object
-    mass_spectrum_obj.molecular_search_settings.url_database = ""
+    mass_spectrum_obj.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_obj.molecular_search_settings.error_method = "None"
     mass_spectrum_obj.molecular_search_settings.min_ppm_error = -5
     mass_spectrum_obj.molecular_search_settings.max_ppm_error = 5
@@ -60,7 +60,7 @@ def test_run_molecular_formula_search_adduct():
     mass_spectrum_obj.settings.noise_threshold_absolute_abundance = 0
 
     # Set the settings for the molecular search on the mass spectrum object
-    mass_spectrum_obj.molecular_search_settings.url_database = ""
+    mass_spectrum_obj.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_obj.molecular_search_settings.error_method = "None"
     mass_spectrum_obj.molecular_search_settings.min_ppm_error = -5
     mass_spectrum_obj.molecular_search_settings.max_ppm_error = 5
@@ -91,7 +91,7 @@ def test_run_molecular_formula_search_adduct():
 
 
 def test_mspeak_search(mass_spectrum_ftms):
-    mass_spectrum_ftms.molecular_search_settings.url_database = ""
+    mass_spectrum_ftms.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_ftms.molecular_search_settings.usedAtoms = {
         "C": (1, 100),
         "H": (4, 200),
@@ -117,7 +117,7 @@ def test_mspeak_search(mass_spectrum_ftms):
 
 
 def test_molecular_formula_search_db(mass_spectrum_ftms):
-    mass_spectrum_ftms.molecular_search_settings.url_database = ""
+    mass_spectrum_ftms.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_ftms.molecular_search_settings.usedAtoms = {
         "C": (1, 100),
         "H": (4, 200),
@@ -149,7 +149,7 @@ def test_molecular_formula_search_db(mass_spectrum_ftms):
 
 
 def test_priorityAssignment(mass_spectrum_ftms):
-    mass_spectrum_ftms.molecular_search_settings.url_database = ""
+    mass_spectrum_ftms.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mass_spectrum_ftms.molecular_search_settings.error_method = "None"
     mass_spectrum_ftms.molecular_search_settings.min_ppm_error = -3
     mass_spectrum_ftms.molecular_search_settings.max_ppm_error = 5

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_search_mass_list.py

@@ -7,7 +7,7 @@ from corems.molecular_id.search.molecularFormulaSearch import SearchMolecularFor
 
 def test_search_imported_ref_files(mass_spectrum_ftms, ref_file_location):
     mass_spectrum_obj = mass_spectrum_ftms
-    mass_spectrum_obj.molecular_search_settings.url_database = ""
+    mass_spectrum_obj.molecular_search_settings.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     mf_references_list = ImportMassListRef(ref_file_location).from_bruker_ref_file()
     assert len(mf_references_list) == 60
     assert round(mf_references_list[0].mz_calc, 2) == 149.06

{CoreMS-3.0.0 → CoreMS-3.0.2}/tests/test_wf_lipidomics.py

@@ -83,7 +83,7 @@ def test_lipidomics_workflow():
     ms1_params.mass_spectrum.noise_min_mz, ms1_params.mass_spectrum.min_picking_mz = 0, 0
     ms1_params.mass_spectrum.noise_max_mz, ms1_params.mass_spectrum.max_picking_mz = np.inf, np.inf
     ms1_params.ms_peak.legacy_resolving_power = False
-    ms1_params.molecular_search.url_database = ""
+    ms1_params.molecular_search.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
     ms1_params.molecular_search.usedAtoms = {
         'C': (10, 30),
         'H': (18, 200),