[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/commands.py

@@ -946,6 +946,7 @@ def gather(args):
         # @CTB foo revindex
         from sourmash.index.revindex import RevIndex
         from sourmash.index import ZipFileLinearIndex
+
         xx = []
         for db in databases:
             if isinstance(db, ZipFileLinearIndex):

src/sourmash/index/__init__.py

@@ -311,7 +311,7 @@ def counter_gather(self, query, threshold_bp, **kwargs):
         with query.update() as prefetch_query:
             prefetch_query.minhash = prefetch_query.minhash.flatten()
 
-        if 0: # @CTB
+        if 0:  # @CTB
             # find all matches and construct a CounterGather object.
             counter = CounterGather(prefetch_query)
             for result in self.prefetch(prefetch_query, threshold_bp, **kwargs):
@@ -321,6 +321,7 @@ def counter_gather(self, query, threshold_bp, **kwargs):
             return counter
         else:
             from .revindex import RevIndex
+
             revindex = RevIndex(template=prefetch_query.minhash)
 
             for result in self.prefetch(prefetch_query, threshold_bp, **kwargs):

src/sourmash/index/revindex.py

@@ -15,7 +15,7 @@
 from sourmash.manifest import CollectionManifest
 
 
-class RevIndex(RustObject): #, Index):
+class RevIndex(RustObject):  # , Index):
     __dealloc_func__ = lib.revindex_free
     manifest = None
     is_database = True
@@ -171,7 +171,8 @@ def select(
         abund=None,
         containment=None,
         picklist=None,
-        **kwargs):
+        **kwargs,
+    ):
         _check_select_parameters(
             ksize=ksize,
             moltype=moltype,
@@ -246,7 +247,9 @@ def search(self, query, *args, **kwargs):
         for i in range(size):
             match = SearchResult._from_objptr(results_ptr[i])
             if match.score >= threshold:
-                results.append(IndexSearchResult(match.score, match.signature, match.location))
+                results.append(
+                    IndexSearchResult(match.score, match.signature, match.location)
+                )
 
         return results
 
@@ -297,8 +300,7 @@ def best_containment(self, query_ss, *, threshold_bp=0, **kwargs):
         if not query_mh:
             raise ValueError("empty query")
         threshold = threshold_bp / query_mh.scaled / len(query_mh)
-        results = self.search(query_ss, threshold=threshold,
-                              do_containment=True)
+        results = self.search(query_ss, threshold=threshold, do_containment=True)
 
         if results:
             results.sort(key=lambda x: -x.score)
@@ -459,7 +461,7 @@ def select(
                 raise ValueError(f"revindex ksize is {my_ksize}, not {ksize}")
         if scaled is not None and scaled < my_scaled:
             raise ValueError(f"revindex scaled is {my_scaled}, not {scaled}")
-        if 0 and moltype is not None and moltype != my_moltype: #  @CTB
+        if 0 and moltype is not None and moltype != my_moltype:  #  @CTB
             raise ValueError(f"revindex moltype is {my_moltype}, not {moltype}")
 
         if picklist is not None:

tests/test_revindex.py

@@ -17,7 +17,7 @@
 ##
 
 
-class JaccardSearchBestOnly_ButIgnore(JaccardSearch): # @CTB remove?
+class JaccardSearchBestOnly_ButIgnore(JaccardSearch):  # @CTB remove?
     "A class that ignores certain results, but still does all the pruning."
 
     def __init__(self, ignore_list):
@@ -110,7 +110,7 @@ def test_revindex_best_containment():
 
 
 def test_revindex_gather_ignore():
-    raise pytest.skip('not implemented')
+    raise pytest.skip("not implemented")
     # check that RevIndex gather ignores things properly.
     sig2 = utils.get_test_data("2.fa.sig")
     sig47 = utils.get_test_data("47.fa.sig")
@@ -148,7 +148,7 @@ def test_revindex_insert_after_init():
 
     ss2 = load_one_signature_from_json(sig2, ksize=31)
     ss47 = load_one_signature_from_json(sig47)
-    ss63 = load_one_signature_from_json(sig63)
+    load_one_signature_from_json(sig63)
 
     lidx = RevIndex(template=ss2.minhash)
     lidx.insert(ss2)