Solved the issues related to charge warnings and future warnings in old Pandas versions, additionally added proper handling of the pd.NA objects

src/picor/isotope_correction.py

@@ -96,7 +96,8 @@ def calc_isotopologue_correction(
     )
     if res_corr_info.do_correction:
         rc.warn_direct_overlap(subset, res_corr_info)
-    data = correct_data(raw_data, subset, res_corr_info)
+    clean_data = raw_data.fillna(0)
+    data = correct_data(clean_data, subset, res_corr_info)
     return data
 
 
@@ -119,7 +120,9 @@ def correct_data(uncorrected_data, subset, res_corr_info):
                 data[label2.as_string] - trans_prob * data[label1.as_string]
             )
             # Ensure no negative values after correction, but preserve dtype and avoid inplace modification issues
-            data[label2.as_string] = data[label2.as_string].clip(lower=0)
+            col_name = label2.as_string
+            data.loc[:, col_name] = data[col_name].clip(lower=0)
+            #data[label2.as_string] = data[label2.as_string].clip(lower=0)
             _logger.info(
                 f"Transition prob {label1.as_string} -> {label2.as_string}: {trans_prob}"
             )

src/picor/metabolites.csv

@@ -1,31 +1,29 @@
 name	formula	charge
-Suc	C4H4O3	-1
-Fum	C4H3O4	-1
-Mal	C4H5O5	-1
-Cit	C6H7O7	-1
-aKG	C5H5O5	-1
-OA	C4H3O5	-1
-Asp	C4H6NO4	-1
-Aco	C6HO3	-1
-2/3PG	C3H6O3	-1
-G3P	C3H7O3	-1
-PEP	C3H4O3	-1
-E4P	C4H8O4	-1
-R1P	C5H8O4	-1
-R5P	C5H8O4	-1
-G1P	C6H10O5	-1
-G6P	C6H10O5	-1
-F1P	C6H10O5	-1
-F6P	C6H10O5	-1
-M6P	C6H10O5	-1
-6PG	C6H10O6	-1
-S7P	C7H11O6	-1
-FBP	C6H11O8P	-1
-AMP	C10H14N5O4	-1
-ADP	C10H14N5O4	-1
-ATP	C10H16N5O10	-1
-CDP	C9H15N3O7P	-1
+AcetylCoA	C23H38N7O17P3S	+1
+AcCoA	C23H38N7O17P3S	+1
+ADP	C10H15N5O10P2	+1
+AMP	C10H14N5O7P	+1
+ATP	C10H16N5O13P3	+1
 NAD	C21H28N7O14P2	+1
+AMP	C10H14N5O7P	+1
+NADP	C21H29N7O17P3	+1
+NADPH	C21H30N7O17P3	+1
+NMN	C11H15N2O8P	+1
+CoA	C21H36N7O16P3S	+1
+FMN	C17H21N4O9P	+1
+cFMN	C17H19N4O8P	+1
+NADH	C21H29N7O14P2	+1
+FAD	C27H33N9O15P2	+1
+ADPr	C15H23N5O14P2	+1
+NAM	C6H6N2O	+1
+PRPP	C5H13O14P3	+1
+Pantothenic_acid	O5N1H17C9	+1
+SAH	S1O5N6H20C14	+1
+SAM	S1O5N6H22C15	+1
+NMNH	P1O8N2H16C11	+1
+Pantetheine	C11H22N2O4S	+1
+DephosphoCoA	C21H35N7O13P2S	+1
+
 NADH	C21H29N7O14P2	+1
 NAM	C6H6N2O	+1
 NA	C6H5NO2	+1

src/picor/resolution_correction.py

@@ -81,6 +81,8 @@ def calc_min_mass_diff(mass, charge, mz_cal, resolution):
         """
         if mass < 0:
             raise ValueError("'mass' must be positive.")
+        if charge == 0:
+            raise ValueError("'charge' cannot be 0, change in metabolites.csv file is required.")
         mz = abs(mass / charge)
         return (
             1.66 * abs(charge) * ResolutionCorrectionInfo.fwhm(mz_cal, mz, resolution)