FIX: avoid EfficiencyWarning in OPTICS with metric='precomputed' - #34692
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DeaMariaLeon
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Aug 11, 2026
| # own neighbor | ||
| X.setdiag(X.diagonal()) | ||
| # Sorting could be undone by .setdiag(), make sure it's sorted | ||
| X = sort_graph_by_row_values(X, warn_when_not_sorted=False) |
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Note: The fix removes the EfficiencyWarning for every sparse precomputed input to OPTICS.fit. A user who passes an unsorted graph doesn't get a warning either.
This matches #34399 behaviour.
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Friendly ping @cakedev0 in case this was forgotten |
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Thank you! |
virchan
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Sep 4, 2026
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LGTM! Thank you everyone for your time!
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Thank you @virchan! |
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Reference Issues/PRs
Fixes #34647
What does this implement/fix? Explain your changes.
The issue and fix are the same as #34399:
OPTICSneeds each point to count as its own neighbour. So, for sparse input, the diagonal has to be made explicit.scikit-learn uses scipy's
setdiagto insert the point which un-sorts the sparse matrix that had already been sorted and emits a warning. To remove the warning (because points are not sorted), we need to callsort_graph_by_row_valuesafter the call tosetdiag.Note: The fix removes the
EfficiencyWarningfor every sparse precomputed input to OPTICS.fit. A user who passes an unsorted graph gets no warning either.This is matching #34399 behaviour.
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