refactor return signature of load_dbs_and_sigs

src/sourmash/search.py

@@ -29,7 +29,7 @@ def search_databases(query, databases, threshold, do_containment, best_only,
                      ignore_abundance, unload_data=False):
     results = []
     found_md5 = set()
-    for (obj, filename, filetype) in databases:
+    for (obj, filename) in databases:
         search_iter = obj.search(query, threshold=threshold,
                                  do_containment=do_containment,
                                  ignore_abundance=ignore_abundance,
@@ -84,7 +84,7 @@ def _find_best(dblist, query, threshold_bp):
     threshold_bp = int(threshold_bp / query_scaled) * query_scaled
 
     # search across all databases
-    for (obj, filename, filetype) in dblist:
+    for (obj, filename) in dblist:
         for cont, match, fname in obj.gather(query, threshold_bp=threshold_bp):
             assert cont                   # all matches should be nonzero.
 

src/sourmash/sourmash_args.py

@@ -256,6 +256,8 @@ def load_dbs_and_sigs(filenames, query, is_similarity_query, *, cache_size=None)
     Load one or more SBTs, LCAs, and/or signatures.
 
     Check for compatibility with query.
+
+    This is basically a user-focused wrapping of _load_databases.
     """
     query_ksize = query.minhash.ksize
     query_moltype = get_moltype(query)
@@ -281,7 +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, False))
+            databases.append((linear, filename))
 
             n_signatures += len(linear)
 
@@ -291,7 +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, 'SBT'))
+            databases.append((db, filename))
             notify('loaded SBT {}', filename, end='\r')
             n_databases += 1
 
@@ -304,7 +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, 'LCA'))
+            databases.append((db, filename))
 
         # signature file
         elif dbtype == DatabaseType.SIGLIST:
@@ -316,7 +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, 'signature'))
+            databases.append((linear, filename))
 
             notify('loaded {} signatures from {}', len(linear),
                    filename, end='\r')