fix modules db brite table to hierarchy dict method

anvio/kegg.py

@@ -9075,8 +9075,15 @@ def get_brite_table_as_ortholog_dict(self, ortholog_accessions_of_interest=None,
         return ortholog_dict
 
 
-    def get_brite_table_as_hierarchy_dict(self, hierarchy_accessions_of_interest=None, level_cutoff=None, collapse_keys=False, collapse_mixed_branches=True):
-        """Load the BRITE hierarchies table as a dictionary keyed by hierarchy.
+    def get_brite_table_as_hierarchy_dict(
+        self,
+        hierarchy_accessions_of_interest=None,
+        level_cutoff=None,
+        collapse_keys=False,
+        collapse_mixed_branches=True
+    ):
+        """
+        Load the BRITE hierarchies table as a dictionary keyed by hierarchy.
 
         The returned dictionary contains the category structure of the hierarchy and a set of
         orthologs in each categorization.
@@ -9302,22 +9309,25 @@ def get_brite_table_as_hierarchy_dict(self, hierarchy_accessions_of_interest=Non
         # find the maximum depth of each hierarchy
         max_depth_dict = self.get_brite_max_depth_dict(dict_from_brite_table)
 
-        if level_cutoff == 0 or type(level_cutoff) != int:
+        if level_cutoff is not None and (level_cutoff == 0 or type(level_cutoff) != int):
             raise ConfigError("`level_cutoff` must be a nonzero integer.")
 
         # set the level cutoff for each hierarchy
-        if level_cutoff > 0:
+        if level_cutoff is None:
+            topdown_level_cutoff_dict = max_depth_dict
+        elif level_cutoff > 0:
             topdown_level_cutoff_dict = {hierarchy_accession: min(level_cutoff, max_depth) for hierarchy_accession, max_depth in max_depth_dict.items()}
-        elif level_cutoff < 0:
+        else:
             # find the positive level corresponding to the negative level cutoff for each
             # hierarchy, ensuring that at least one category remains per hierarchy
             topdown_level_cutoff_dict = {hierarchy_accession: max(max_depth + level_cutoff, 1) for hierarchy_accession, max_depth in max_depth_dict.items()}
-        else:
-            topdown_level_cutoff_dict = max_depth_dict
 
         # hierarchy level cutoffs can be affected by collapsing subcategories of mixed categories
         if collapse_mixed_branches:
-            topdown_level_cutoff_dict = self.get_brite_topdown_level_cutoff_dict_ignoring_subcategories_of_mixed_categories(topdown_level_cutoff_dict, dict_from_brite_table)
+            topdown_level_cutoff_dict = self.get_brite_depth_dict_ignoring_subcategories_of_mixed_categories(
+                dict_from_brite_table=dict_from_brite_table,
+                input_depth_dict=topdown_level_cutoff_dict
+            )
 
         # create the per-hierarchy dict
         hierarchy_dict = {}