set taxon id index on h3 df

we query on this repeatedly. produces 20x speedups.

generate_thresholds.py

@@ -102,7 +102,7 @@ def main(args):
     })
     presence_absence = presence_absence.fillna(0)
 
-    print("...looping through taxa")
+    print("loading taxonomy...")
     output = []
     taxa = pd.read_csv(
         args.taxonomy,
@@ -117,6 +117,12 @@ def main(args):
         taxon_ids = taxon_ids[0:args.stop_after]
     resolution = args.h3_resolution
     area = h3.hex_area(resolution)
+
+    # we want the taxon id to be the index since we'll be selecting on it
+    train_df_h3.reset_index(inplace=True)
+    train_df_h3.set_index("taxon_id", inplace=True)    
+
+    print("...looping through taxa")
     for taxon_id in tqdm(taxon_ids):
         try:
             class_of_interest = mtd.df.loc[taxon_id]["leaf_class_id"]
@@ -130,7 +136,7 @@ def main(args):
 
         # make presence absence dataset
         target_spatial_grid_counts = \
-            train_df_h3[train_df_h3.taxon_id == taxon_id].index.value_counts()
+            train_df_h3[train_df_h3.index == taxon_id].h3_04.value_counts()
         presences = gdfk.loc[target_spatial_grid_counts.index]["pred"]
         if len(presences) == 0:
             print("not present")