Merge pull request #1 from JamesLAdair/main

Added initial files for minimal test

src/gcms_data_analysis/main.py

@@ -617,7 +617,7 @@ def name_to_properties(
     )
 
     # print(f"{df.loc[comp_name, :]}")
-    # mol_weigth = df.loc[comp_name, "molecular_weight"]
+    # mol_weight = df.loc[comp_name, "molecular_weight"]
 
     for cl in classes:  # get counts and mf of each class in compound
         newdf.loc[comp_name, cl] = fragmentation[cl]  # counts in
@@ -1649,7 +1649,7 @@ class Project:
     ]
     semi_calibration = True
     tanimoto_similarity_threshold = 0.4
-    delta_mol_weigth_threshold = 100
+    delta_mol_weight_threshold = 100
     column_to_sort_values_in_samples = "retention_time"
 
     @classmethod
@@ -1665,7 +1665,7 @@ class attributes related to the project's directory structure,
         cls.shared_path = cls.in_path.parents[0]
 
     @classmethod
-    def set_auto_save_to_excel(cls, new_auto_save_to_excel):
+    def set_auto_save_to_excel(cls, new_auto_save_to_excel: bool):
         """Enable or disable automatic saving of results to Excel (default True).
         This method updates the class attribute that controls whether
         analysis results are automatically saved in an Excel file."""
@@ -1686,11 +1686,11 @@ def set_tanimoto_similarity_threshold(cls, new_tanimoto_similarity_threshold):
         cls.tanimoto_similarity_threshold = new_tanimoto_similarity_threshold
 
     @classmethod
-    def set_delta_mol_weigth_threshold(cls, new_delta_mol_weigth_threshold):
+    def set_delta_mol_weight_threshold(cls, new_delta_mol_weight_threshold):
         """Set the delta molecular weight threshold for compound matching (default 100).
         This method updates the class attribute that specifies the threshold used for
         comparing molecular weights in compound matching."""
-        cls.delta_mol_weigth_threshold = new_delta_mol_weigth_threshold
+        cls.delta_mol_weight_threshold = new_delta_mol_weight_threshold
 
     @classmethod
     def set_plot_grid(cls, new_plot_grid):
@@ -2434,7 +2434,7 @@ def _apply_calib_to_file(self, filename, calibration, df_comps):
                         df_sim.Similarity >= Project.tanimoto_similarity_threshold
                     ]
                     df_sim = df_sim[
-                        df_sim.delta_mw < Project.delta_mol_weigth_threshold
+                        df_sim.delta_mw < Project.delta_mol_weight_threshold
                     ]
                     # if a compound matches the requirements
                     if not df_sim.empty:  # assign the calibration
@@ -2813,7 +2813,7 @@ def create_files_param_aggrrep(self, param="conc_vial_mg_L"):
                 # each compound contributes to the cumulative sum of each
                 # functional group for the based on the mass fraction it has
                 # of that functional group (fg_mf act as weights)
-                # if fg_mf in subrep: multiply signal for weigth and sum
+                # if fg_mf in subrep: multiply signal for weight and sum
                 # to get aggregated
                 weights = fg_mf_all.loc[list_iupac, fg_mf].astype(signal.dtype)
 
@@ -2964,7 +2964,7 @@ def create_samples_param_aggrrep(self, param: str = "conc_vial_mg_L"):
     #             # each compound contributes to the cumulative sum of each
     #             # functional group for the based on the mass fraction it has
     #             # of that functional group (fg_mf act as weights)
-    #             # if fg_mf in subrep: multiply signal for weigth and sum
+    #             # if fg_mf in subrep: multiply signal for weight and sum
     #             # to get aggregated
     #             weights = fg_mf_all.loc[list_iupac, fg_mf].astype(signal.dtype)
 

tests/minimal_set/S_1.txt

@@ -0,0 +1,12 @@
+[Header]
+Data File Name	C:\Users\user\Documents\jla278\T1.qgd
+Output Date	3/18/2024
+Output Time	11:00:20 AM
+
+[MC Peak Table]
+# of Peaks	3
+Mass	TIC
+Peak#	Ret.Time	Proc.From	Proc.To	Mass	Area	Height	A/H	Conc.	Mark	Name	Ret. Index	Area%	Height%	SI	CAS #
+1	13.703	13.580	13.900	TIC	20	20	1	0	 V 	Phenol		2.59	3.01	97	108-95-2
+2	20.942	20.767	21.020	TIC	200	200	1	0	 V 	Naphthalene		8.11	9.20	98	91-20-3
+3	21.426	21.373	21.500	TIC	2000	2000	1	0	 V 	Dodecane		0.36	0.57	96	112-40-3

tests/minimal_set/S_2.txt

@@ -0,0 +1,12 @@
+[Header]
+Data File Name	C:\Users\user\Documents\jla278\T1.qgd
+Output Date	3/18/2024
+Output Time	11:00:20 AM
+
+[MC Peak Table]
+# of Peaks	3
+Mass	TIC
+Peak#	Ret.Time	Proc.From	Proc.To	Mass	Area	Height	A/H	Conc.	Mark	Name	Ret. Index	Area%	Height%	SI	CAS #
+1	13.703	13.580	13.900	TIC	40	40	1	0	 V 	Phenol		2.59	3.01	97	108-95-2
+2	20.942	20.767	21.020	TIC	400	400	1	0	 V 	Naphthalene		8.11	9.20	98	91-20-3
+3	21.426	21.373	21.500	TIC	4000	4000	1	0	 V 	Dodecane		0.36	0.57	96	112-40-3

tests/minimal_set/T_1.txt

@@ -0,0 +1,12 @@
+[Header]
+Data File Name	C:\Users\user\Documents\jla278\T1.qgd
+Output Date	3/18/2024
+Output Time	11:00:20 AM
+
+[MC Peak Table]
+# of Peaks	3
+Mass	TIC
+Peak#	Ret.Time	Proc.From	Proc.To	Mass	Area	Height	A/H	Conc.	Mark	Name	Ret. Index	Area%	Height%	SI	CAS #
+1	13.703	13.580	13.900	TIC	20	20	1	0	 V 	Phenol		2.59	3.01	97	108-95-2
+2	20.942	20.767	21.020	TIC	50	50	1	0	 V 	Naphthalene		8.11	9.20	98	91-20-3
+3	21.426	21.373	21.500	TIC	500	500	1	0	 V 	Dodecane		0.36	0.57	96	112-40-3

tests/minimal_set/T_2.txt

@@ -0,0 +1,12 @@
+[Header]
+Data File Name	C:\Users\user\Documents\jla278\T2.qgd
+Output Date	3/18/2024
+Output Time	11:00:20 AM
+
+[MC Peak Table]
+# of Peaks	3
+Mass	TIC
+Peak#	Ret.Time	Proc.From	Proc.To	Mass	Area	Height	A/H	Conc.	Mark	Name	Ret. Index	Area%	Height%	SI	CAS #
+1	13.703	13.580	13.900	TIC	10	10	1	0	 V 	Phenol		2.59	3.01	97	108-95-2
+2	20.942	20.767	21.020	TIC	100	1000	1	0	 V 	Naphthalene		8.11	9.20	98	91-20-3
+3	21.426	21.373	21.500	TIC	1000	1000	1	0	 V 	Dodecane		0.36	0.57	96	112-40-3

tests/minimal_set/T_3.txt

@@ -0,0 +1,12 @@
+[Header]
+Data File Name	C:\Users\user\Documents\jla278\T3.qgd
+Output Date	3/18/2024
+Output Time	11:00:20 AM
+
+[MC Peak Table]
+# of Peaks	3
+Mass	TIC
+Peak#	Ret.Time	Proc.From	Proc.To	Mass	Area	Height	A/H	Conc.	Mark	Name	Ret. Index	Area%	Height%	SI	CAS #
+1	13.703	13.580	13.900	TIC	0	0	1	0	 V 	Phenol		2.59	3.01	97	108-95-2
+2	20.942	20.767	21.020	TIC	150	150	1	0	 V 	Naphthalene		8.11	9.20	98	91-20-3
+3	21.426	21.373	21.500	TIC	1500	1500	1	0	 V 	Dodecane		0.36	0.57	96	112-40-3