[MRG+1] Pass affinity to fix connectivity in linkage tree #9357
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jnothman
reviewed
Jul 14, 2017
| rng = np.random.RandomState(42) | ||
| X = rng.normal(size=(5, 5)) | ||
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| assert_raises(ValueError, linkage_tree, X, affinity='FakeAffinity') |
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I'm pretty sure this test will pass at master, i.e. an error will be raised by another part of linkage_tree.
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@jnothman I didn't notice there was a PR for that. I added a test that targets only the change right now, I'm not sure if that's an acceptable pattern, though. |
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This is okay. Not loving the test; would rather something that ensures correct functionality, but this is okay as a non-regression test. I'd prefer a fix which makes affinity a required arg of _fix_connectivity with no default value. Remove n_components (unused) at the same time. Thanks. |
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Fixed @jnothman |
jnothman
reviewed
Jul 17, 2017
| @@ -30,8 +30,7 @@ | |||
| # For non fully-connected graphs | |||
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| def _fix_connectivity(X, connectivity, n_components=None, | |||
| affinity="euclidean"): | |||
| def _fix_connectivity(X, connectivity, affinity): | |||
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Thanks @brenolf |
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Reference Issue
Resolves #9308.
What does this implement/fix? Explain your changes.
Pass the affinity value to be used by
pairwise_distancesin alinkage_treecall.Any other comments?
No.