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Non-sample nodes that are in no edge can't be dated. They now keep their input time, have NaN posterior mean/variance in node metadata and in variational_gamma's fit.node_posteriors(), and no longer affect the dating of other nodes (mutational_area ignores edgeless nodes when building epochs). Isolated samples still raise an error. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
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Sorry for delay here, I'll get to a review after the 13th |
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Thanks. I don't think there's anything controversial here, but it would be good to have an extra set of eyes on it. |
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Non-sample nodes that are in no edge can't be dated, but previously caused an error (
variational_gamma: "disconnected nodes";inside_outside/maximization: a misleading "not simplified" error).Now, for all methods:
mn/vrnode metadata is NaN, as are their rows invariational_gamma'sfit.node_posteriors()(inside_outsidealready gives NaN for fixed nodes).rescaling.mutational_area, which built time epochs from all nodes, so an isolated node with a large time distorted the rescaling.Tests:
TestIsolatedNodesintests/test_inference.py(all three methods, several isolated times; checks other node times are unchanged vs. the tree sequence without the node). Docs and changelog updated. Full suite passes; timing on 500 samples x 10 Mb is unchanged.