finish removing filename

src/sourmash/search.py

@@ -29,8 +29,8 @@ def search_databases(query, databases, threshold, do_containment, best_only,
                      ignore_abundance, unload_data=False):
     results = []
     found_md5 = set()
-    for (obj, _) in databases:
-        search_iter = obj.search(query, threshold=threshold,
+    for db in databases:
+        search_iter = db.search(query, threshold=threshold,
                                  do_containment=do_containment,
                                  ignore_abundance=ignore_abundance,
                                  best_only=best_only,
@@ -85,8 +85,8 @@ def _find_best(dblist, query, threshold_bp):
     threshold_bp = int(threshold_bp / query_scaled) * query_scaled
 
     # search across all databases
-    for (obj, _) in dblist:
-        for cont, match, fname in obj.gather(query, threshold_bp=threshold_bp):
+    for db in dblist:
+        for cont, match, fname in db.gather(query, threshold_bp=threshold_bp):
             assert cont                   # all matches should be nonzero.
 
             # note, break ties based on name, to ensure consistent order.

src/sourmash/sourmash_args.py

@@ -283,7 +283,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
             siglist = _select_sigs(db, moltype=query_moltype, ksize=query_ksize)
             siglist = filter_compatible_signatures(query, siglist, 1)
             linear = LinearIndex(siglist, filename=filename)
-            databases.append((linear, filename))
+            databases.append(linear)
 
             n_signatures += len(linear)
 
@@ -293,7 +293,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
                                             is_similarity_query):
                 sys.exit(-1)
 
-            databases.append((db, filename))
+            databases.append(db)
             notify('loaded SBT {}', filename, end='\r')
             n_databases += 1
 
@@ -306,7 +306,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
             notify('loaded LCA {}', filename, end='\r')
             n_databases += 1
 
-            databases.append((db, filename))
+            databases.append(db)
 
         # signature file
         elif dbtype == DatabaseType.SIGLIST:
@@ -318,7 +318,7 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
                 sys.exit(-1)
 
             linear = LinearIndex(siglist, filename=filename)
-            databases.append((linear, filename))
+            databases.append(linear)
 
             notify('loaded {} signatures from {}', len(linear),
                    filename, end='\r')