Expand all use of postgres db in CI CD

Author: kheal

tests/xtest_classification.py tests/test_classification.pytests/xtest_classification.py renamed to tests/test_classification.py

@@ -6,7 +6,7 @@
 
 
 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

…sts/xtest_mass_spectrum_export_import.py tests/test_mass_spectrum_export_import.pytests/xtest_mass_spectrum_export_import.py renamed to tests/test_mass_spectrum_export_import.py tests/xtest_mass_spectrum_export_import.py renamed to 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

tests/xtest_search_mass_list.py tests/test_search_mass_list.pytests/xtest_search_mass_list.py renamed to tests/test_search_mass_list.py

@@ -7,7 +7,7 @@
 
 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

tests/xtest_wf_lipidomics.py tests/test_wf_lipidomics.pytests/xtest_wf_lipidomics.py renamed to 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),