Per conversation in issue #2507, IsotonicRegression appears to have regressed due to commit a9ea55f.
This IPython notebook demonstrates the failure on HEAD.
I tested the following two commits with the notebook:
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d255866: no difference, SUCCESS
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a9ea55f: difference, FAILURE
In other words, I think we can blame the switch for interp1d from "linear" to "slinear"; first thought is that 1-d spline "slinear" matrix formulation is ill-posed for x-ties, whereas the piecewise "linear" implementation is unaffected?
Small additional note: confirmed failure with test case where x-values are all non-zero, e.g., [1, 1, 2, 3, 4] instead of [0, 0, 1, 2, 3], so x=0 isn't part of the cause.