Apply suggestions from code review

Co-authored-by: Valeriu Predoi <[email protected]>

bgcval2/bgcval2_make_report.py

@@ -984,10 +984,10 @@ def newImageLocation(fn):
             outlevels = {}
             for i, fn in enumerate(l2Fields):
                 for lv in levels:
-                    if fn.find(lv)>-1:
-                        outlevels[lv]= True
+                    if fn.find(lv) > -1:
+                        outlevels[lv] = True
                     fn = fn.replace(lv, '')
-                outdict[fn]= True
+                outdict[fn] = True
 
             l2Fields = [key for key, v in outdict.items()]
             slices = [key for key, v in outlevels.items()]
@@ -1000,7 +1000,6 @@ def newImageLocation(fn):
         Descriptions = {}
         FileLists = {}
         FileOrder = {}
-        #print(l2Fields, slices)
 
         for key in sorted(l2Fields):
             #if key not in ['Alkalinity','Nitrate']: continue
@@ -1546,8 +1545,6 @@ def newImageLocation(fn):
             if found: continue
             sectionTitle = 'Physics Key Metrics'
             if fn.find(key) > -1:
-#               if key in ['MA_SST', 'MA_SSS', 'MA_Nitrate',] and fn.find('Global_Surface') < 0:
-#                   continue
                 try:
                     categories[sectionTitle].append(fn)
                 except:

bgcval2/functions/circulation.py

@@ -304,18 +304,11 @@ def twentysixnorth025(nc,keys,**kwargs):
             continue
         if not depths[t, z, la, lo] or np.ma.is_masked(depths[t, z, la, lo]):
             continue
-#       if not alttmask_AMOC26N[la, lo]:
-#           continue
-#       if not tmask_AMOC26N[z, la, lo]:
-#           continue
-#       if np.ma.is_masked(zv[0, z, la, lo]):
-#           continue
         atlmoc[z, la] = atlmoc[z, la] - e1v[t, 0, la, lo] * thkcello[t, z, la, lo] * vo[t, z, la, lo] / 1.E06
 
     for z in range(thkcello.shape[1] -2, 1, -1): # add from the bottom up
         atlmoc[z, :] = atlmoc[z+1, :] + atlmoc[z, :]
     print('AMOC:', atlmoc.max())
-    #assert 0
     return atlmoc.max()
 
 

bgcval2/p2p/matchDataAndModel.py

@@ -943,7 +943,6 @@ def loadMesh(self, modelfile=None):
             if not set(ncER.variables.keys()).intersection(set(depthNames)):
                 print('load mesh: no depth field available in ', modelfile)
                 self.depthcc = np.array([0])
-#                assert 0
 
 #        self.depthcc = choose_best_ncvar(ncER, depthNames)[:]
         self.datescc = var_to_datetime(ncER.variables[self.modelcoords['t']])
@@ -1135,7 +1134,7 @@ def var_to_datetime(ncvar):
     if units in ['months since 0000-01-01 00:00:00', ]:
         units = 'months since 2000-01-01 00:00:00'
         return num2date(ncvar[:], 'months since 2000-01-01 00:00:00', calendar='360_day') 
-    elif units.find('months since')>-1:
+    elif units.find('months since') > -1:
         return num2date(ncvar[:], units, calendar='360_day') 
 
     return num2date(ncvar[:], ncvar.units, calendar=calendar)

bgcval2/revert_shelves.py

@@ -13,8 +13,6 @@
 from bgcval2.Paths.paths import paths_setter
 
 
-
-
 def get_paths(
         config_user=None
     ):
@@ -84,12 +82,12 @@ def remove_data(jobID,
 
         # generate a time key from year/month.
         if month:
-            if isinstance(month, str) and len(month) ==1:
+            if isinstance(month, str) and len(month) == 1:
                 month = int(month)
             if isinstance(month, int):
                 month = bvt.mnStr(month)
 
-            time_key = year+month
+            time_key = year + month
         else:
             time_key = year
 
@@ -186,7 +184,7 @@ def get_args():
                         default=['all',],
                         nargs='+',
                         type=str,
-                        help='One or more datasets - default is everything. ',
+                        help='One or more datasets - default is everything (all available keys). ',
                         required=False)
 
     parser.add_argument('-d',