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[WIP] Index.gather is not doing gather? #1263

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[WIP] Index.gather is not doing gather? #1263

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82a961f
make gather actually do gather
luizirber Dec 22, 2020
fe6152f
modify behavior of failing test
luizirber Dec 22, 2020
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4 changes: 3 additions & 1 deletion src/sourmash/index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,10 +108,12 @@ def gather(self, query, *args, **kwargs):

# actually do search!
results = []
query_mh = query.minhash
for ss in self.signatures():
cont = query.minhash.contained_by(ss.minhash, True)
cont = query_mh.contained_by(ss.minhash, True)
if cont and cont >= threshold:
results.append((cont, ss, self.filename))
query_mh.remove_many(ss.minhash.hashes)

results.sort(reverse=True, key=lambda x: (x[0], x[1].md5sum()))

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4 changes: 1 addition & 3 deletions tests/test_index.py
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Expand Up @@ -132,11 +132,9 @@ def test_linear_index_gather():
assert matches[0][1] == ss2

matches = lidx.gather(ss47)
assert len(matches) == 2
assert len(matches) == 1
assert matches[0][0] == 1.0
assert matches[0][1] == ss47
assert round(matches[1][0], 2) == 0.49
assert matches[1][1] == ss63
Comment on lines 134 to -139
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This test is a good example of the 'weird' behavior: if doing gather with ss47, it should match ss47 completely, and nothing will be left to match other sigs. But the test is asserting that there is a second match (ss63), at 0.49 containment. That's... not gather, that's a regular search using containment.



def test_linear_index_save():
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