make list of sites from station_config, switched print to logger.info

Author: BaptisteVandecrux

src/pypromice/process/L0toL1.py

@@ -248,7 +248,7 @@ def getPressDepth(z_pt, p, pt_antifreeze, pt_z_factor, pt_z_coef, pt_z_p_coef):
         rho_af = 1145
     else:
         rho_af = np.nan
-        print('ERROR: Incorrect metadata: "pt_antifreeze" = ' +
+        logger.info('ERROR: Incorrect metadata: "pt_antifreeze" = ' +
               f'{pt_antifreeze}. Antifreeze mix only supported at 50% or 100%')
         # assert(False)
 

src/pypromice/process/join_l2.py

@@ -43,13 +43,17 @@ def loadArr(infile):
     if 'number_of_booms' in ds.attrs.keys():
         ds.attrs['number_of_booms'] = int(ds.attrs['number_of_booms'])
 
-    print(f'{name} array loaded from {infile}')
+    logger.info(f'{name} array loaded from {infile}')
     return ds, name
 
 
 def join_l2():
     args = parse_arguments_join()
-
+    logging.basicConfig(
+        format="%(asctime)s; %(levelname)s; %(name)s; %(message)s",
+        level=logging.INFO,
+        stream=sys.stdout,
+    )
     # Check files
     if os.path.isfile(args.file1) and os.path.isfile(args.file2): 
 
@@ -61,7 +65,7 @@ def join_l2():
         if n1.lower() == n2.lower():
 
         	# Merge arrays
-            print(f'Combining {args.file1} with {args.file2}...')
+            logger.info(f'Combining {args.file1} with {args.file2}...')
             name = n1
             all_ds = ds1.combine_first(ds2)
 
@@ -75,28 +79,28 @@ def join_l2():
                     all_ds['precip_l_cor'],  _ = correctPrecip(all_ds['precip_l'], 
                                                                 all_ds['wspd_l'])                    
         else:
-            print(f'Mismatched station names {n1}, {n2}')
+            logger.info(f'Mismatched station names {n1}, {n2}')
             exit()            
 
     elif os.path.isfile(args.file1):  
         ds1, name = loadArr(args.file1)
-        print(f'Only one file found {args.file1}...')
+        logger.info(f'Only one file found {args.file1}...')
         all_ds = ds1  
 
     elif os.path.isfile(args.file2):
         ds2, name = loadArr(args.file2)
-        print(f'Only one file found {args.file2}...')
+        logger.info(f'Only one file found {args.file2}...')
         all_ds = ds2  
 
     else:
-        print(f'Invalid files {args.file1}, {args.file2}')
+        logger.info(f'Invalid files {args.file1}, {args.file2}')
         exit()
 
 
     # Resample to hourly, daily and monthly datasets and write to file
     prepare_and_write(all_ds, args.outpath, args.variables, args.metadata, resample = False)
 
-    print(f'Files saved to {os.path.join(args.outpath, name)}...')
+    logger.info(f'Files saved to {os.path.join(args.outpath, name)}...')
 
 if __name__ == "__main__":  
     join_l2()

src/pypromice/process/join_l3.py

@@ -160,18 +160,43 @@ def gcnet_postprocessing(l3):
     #         df_in.loc[[df_in.z_surf_combined.first_valid_index()],:].index.astype('int64')[0]
     #     )  +  df_in.loc[df_in.z_surf_combined.first_valid_index(), 'z_surf_combined']
     # return l3m
-
+    
+def build_station_dict(config_folder):
+    station_dict = {}
+    
+    # Iterate through all files in the given folder
+    for filename in os.listdir(config_folder):
+        if filename.endswith(".toml"):
+            # Construct full file path
+            file_path = os.path.join(config_folder, filename)
+            
+            # Load TOML file
+            with open(file_path, 'r') as file:
+                data = toml.load(file)
+                station_key = next(iter(data))
+                station_data = data[station_key]
+               
+                if station_data["station_site"] in station_dict:
+                    station_dict[station_data["station_site"]].append(station_key)
+                else:
+                    station_dict[station_data["station_site"]] = [station_key]
+    
+    return station_dict
+    
 def join_l3():
     args = parse_arguments_joinl3()
-                  
-                      
-    config_file = os.path.join(args.config_folder, args.site+'.toml')
-    conf = toml.load(config_file)
+    logging.basicConfig(
+        format="%(asctime)s; %(levelname)s; %(name)s; %(message)s",
+        level=logging.INFO,
+        stream=sys.stdout,
+    )
+    
+    station_dict = build_station_dict(args.config_folder)
 
     l3m = xr.Dataset()
     l3m.attrs['level'] = 'L3'
-    for stid in conf['stations']:
-        print(stid)
+    for stid in  station_dict[args.site]:
+        logger.info(stid)
 
         is_promice = False
         is_gcnet = False
@@ -183,7 +208,7 @@ def join_l3():
             if os.path.isfile(filepath):
                 is_gcnet = True
         if not is_promice and not is_gcnet:            
-            print(stid, 'not found either in', args.folder_l3, 'or', args.folder_gcnet)
+            logger.info(stid, 'not found either in', args.folder_l3, 'or', args.folder_gcnet)
             continue
 
         l3, _ = loadArr(filepath)
@@ -213,14 +238,15 @@ def join_l3():
 
             # if l3 (older data) has variables that does not have l3m (newer data)
             # then they are removed from l3
-            print('dropping')
+            list_dropped = []
             for v in l3.data_vars:
                 if v not in l3m.data_vars:
                     if v != 'z_stake':
-                       print(v)
+                       list_dropped.append(v)
                        l3 = l3.drop(v)
                     else:
                        l3m[v] = ('time', l3m.t_u.data*np.nan)
+            logger.info('Unused variables in older dataset:',list_dropped)
 
             # saving attributes of station under an attribute called $stid
             l3m = l3m.assign_attrs({stid : l3.attrs.copy()})
@@ -241,7 +267,7 @@ def join_l3():
 
     # Assign site id
     l3m.attrs['site_id'] = args.site
-    l3m.attrs['stations'] = conf['stations']
+    l3m.attrs['stations'] = station_dict[args.site]
 
     if args.outpath is not None:
         prepare_and_write(l3m, args.outpath, args.variables, args.metadata, '60min')