[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

src/sourmash/index/__init__.py

@@ -323,7 +323,7 @@ def counter_gather(self, query, threshold_bp, **kwargs):
             from .revindex import RevIndex
 
             revindex = RevIndex(template=prefetch_query.minhash)
-            #return revindex.CounterGather(prefetch_query, threshold_bp, **kwargs)
+            # return revindex.CounterGather(prefetch_query, threshold_bp, **kwargs)
 
             for result in self.prefetch(prefetch_query, threshold_bp, **kwargs):
                 revindex.insert(result.signature)

src/sourmash/index/revindex.py

@@ -574,9 +574,9 @@ def __init__(self, query, db, threshold_bp, *, allow_insert=False):
         self.allow_insert = allow_insert
         self.locations = dict()
 
-    def add(self, match_ss, *, location=None, require_overlap=True): # @CTB location
+    def add(self, match_ss, *, location=None, require_overlap=True):  # @CTB location
         if self.allow_insert:
-            x = self.db._check_not_init(do_raise=False)
+            self.db._check_not_init(do_raise=False)
             if self.db._check_not_init(do_raise=False):
                 self.db.insert(match_ss)
             else:
@@ -592,13 +592,13 @@ def add(self, match_ss, *, location=None, require_overlap=True): # @CTB location
 
         self.found_mh += intersect_mh
 
-    def peek(self, query_mh, *, threshold_bp=0): # threshold_bp default?? @CTB
+    def peek(self, query_mh, *, threshold_bp=0):  # threshold_bp default?? @CTB
         if not query_mh:
             return []
 
         if query_mh.contained_by(self.orig_query_mh) != 1.0:
             raise ValueError
-        #assert threshold_bp is not None
+        # assert threshold_bp is not None
 
         res = self.db.peek(query_mh, threshold_bp=threshold_bp)
         if not res:
@@ -607,8 +607,7 @@ def peek(self, query_mh, *, threshold_bp=0): # threshold_bp default?? @CTB
         sr, intersect_mh = res
         sr_ss = sr.signature
         sr_score = sr.score
-        new_sr = IndexSearchResult(sr_score, sr_ss,
-                                   self.locations[sr_ss.md5sum()])
+        new_sr = IndexSearchResult(sr_score, sr_ss, self.locations[sr_ss.md5sum()])
         return new_sr, intersect_mh
 
     def consume(self, intersect_mh):

tests/test_index_protocol.py

@@ -703,8 +703,10 @@ def consume(self, intersect_mh):
 
 ## XXX @CTB
 
+
 def build_RevIndex_CounterGather(query):
     from sourmash.index.revindex import RevIndex_CounterGather
+
     ri = RevIndex(template=query.minhash)
     cg = RevIndex_CounterGather(query, ri, 0, allow_insert=True)
     return cg
@@ -715,7 +717,7 @@ def build_RevIndex_CounterGather(query):
         CounterGather,
         CounterGather_LinearIndex,
         CounterGather_LCA,
-        build_RevIndex_CounterGather
+        build_RevIndex_CounterGather,
     ]
 )
 def counter_gather_constructor(request):
@@ -1184,9 +1186,9 @@ def test_counter_gather_add_after_consume(counter_gather_constructor):
     query_ss = SourmashSignature(query_mh, name="query")
 
     # load up the counter
-    print('create')
+    print("create")
     counter = counter_gather_constructor(query_ss)
-    print('insert')
+    print("insert")
     counter.add(query_ss, location="somewhere over the rainbow")
 
     counter.consume(query_ss.minhash)