[MRG] fix pickle protocol to properly adjust ksize in __getstate__ (

#2265)

* add tests to reproduce bug #2262

* fix in __getstate__ rather than __setstate__

* add hp and dayhoff tests

* fix comment

src/sourmash/minhash.py

@@ -275,9 +275,13 @@ def __copy__(self):
 
     def __getstate__(self):
         "support pickling via __getstate__/__setstate__"
+
+        # note: we multiple ksize by 3 here so that
+        # pickle protocols that bypass __setstate__ <coff numpy coff>
+        # get a ksize that makes sense to the Rust layer. See #2262.
         return (
             self.num,
-            self.ksize,
+            self.ksize if self.is_dna else self.ksize*3,
             self.is_protein,
             self.dayhoff,
             self.hp,
@@ -1107,11 +1111,6 @@ def to_mutable(self):
         mut = MinHash.__new__(MinHash)
         state_tup = self.__getstate__()
 
-        # is protein/hp/dayhoff?
-        if state_tup[2] or state_tup[3] or state_tup[4]:
-            state_tup = list(state_tup)
-            # adjust ksize.
-            state_tup[1] = state_tup[1] * 3
         mut.__setstate__(state_tup)
         return mut
 

tests/test_minhash.py

@@ -1481,6 +1481,69 @@ def test_scaled_property(track_abundance):
     assert a.scaled == scaled
 
 
+def test_pickle_protein(track_abundance):
+    # check that protein/etc ksize is handled properly during serialization.
+    a = MinHash(0, 10, track_abundance=track_abundance, is_protein=True,
+                scaled=_get_scaled_for_max_hash(20))
+    for i in range(0, 40, 2):
+        a.add_hash(i)
+
+    b = pickle.loads(pickle.dumps(a))
+    assert a.ksize == b.ksize
+    assert b.num == a.num
+    assert b._max_hash == a._max_hash
+    assert b._max_hash == 20
+    assert b.is_protein
+    assert b.track_abundance == track_abundance
+    assert b.seed == a.seed
+    assert len(b.hashes) == len(a.hashes)
+    assert len(b.hashes) == 11
+    assert a.scaled == b.scaled
+    assert b.scaled != 0
+
+
+def test_pickle_dayhoff(track_abundance):
+    # check that dayhoff ksize is handled properly during serialization.
+    a = MinHash(0, 10, track_abundance=track_abundance, dayhoff=True,
+                scaled=_get_scaled_for_max_hash(20))
+    for i in range(0, 40, 2):
+        a.add_hash(i)
+
+    b = pickle.loads(pickle.dumps(a))
+    assert a.ksize == b.ksize
+    assert b.num == a.num
+    assert b._max_hash == a._max_hash
+    assert b._max_hash == 20
+    assert b.dayhoff
+    assert b.track_abundance == track_abundance
+    assert b.seed == a.seed
+    assert len(b.hashes) == len(a.hashes)
+    assert len(b.hashes) == 11
+    assert a.scaled == b.scaled
+    assert b.scaled != 0
+
+
+def test_pickle_hp(track_abundance):
+    # check that hp ksize is handled properly during serialization.
+    a = MinHash(0, 10, track_abundance=track_abundance, hp=True,
+                scaled=_get_scaled_for_max_hash(20))
+    for i in range(0, 40, 2):
+        a.add_hash(i)
+
+    b = pickle.loads(pickle.dumps(a))
+    assert a.ksize == b.ksize
+    assert b.num == a.num
+    assert b._max_hash == a._max_hash
+    assert b._max_hash == 20
+    assert b.hp
+    assert b.track_abundance == track_abundance
+    assert b.seed == a.seed
+    assert len(b.hashes) == len(a.hashes)
+    assert len(b.hashes) == 11
+    assert a.scaled == b.scaled
+    assert b.scaled != 0
+
+
 def test_pickle_max_hash(track_abundance):
     a = MinHash(0, 10, track_abundance=track_abundance,
                 scaled=_get_scaled_for_max_hash(20))

tests/test_sourmash.py

@@ -6317,6 +6317,20 @@ def test_compare_jaccard_ani(runtmp):
     print(c.last_result.out)
 
 
+def test_compare_jaccard_protein_parallel_ani_bug(runtmp):
+    # this checks a bug that occurred with serialization of protein minhash
+    # in parallel situations. See #2262.
+    c = runtmp
+
+    sigfile = utils.get_test_data("prot/protein.zip")
+
+    c.run_sourmash('compare', '--ani', '-p', '2', '--csv', 'output.csv',
+                   sigfile)
+
+    print(c.last_result.err)
+    print(c.last_result.out)
+
+
 def test_compare_containment_ani_asymmetry_distance(runtmp):
     # very specifically test asymmetry of ANI in containment matrices ;)
     # ...calculated with --distance