fix: pass marginal flag to all infer_ancestral_sequences calls#602
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Three call sites in TreeTime._run() pass **seq_kwargs to infer_ancestral_sequences without mapping marginal_sequences to the marginal parameter. The function defaults marginal=False, silently falling back to joint reconstruction in later iterations. - Add explicit marginal=seq_kwargs['marginal_sequences'] to the post-reroot call (input mode) and both iteration-loop calls, matching the pattern already used in the initial call - Add regression test that records every marginal argument and asserts none are False when branch_length_mode='marginal' Fixes #601
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this seems correct. |
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TreeTime._run()builds aseq_kwargsdict containingmarginal_sequences: Truewhenbranch_length_mode='marginal'. The first call toinfer_ancestral_sequencescorrectly maps this to themarginalparameter, but three later call sites pass only**seq_kwargs. Sinceinfer_ancestral_sequenceshasmarginal=Falseas default and does not consumemarginal_sequencesfrom**kwargs, those calls silently fall back to joint reconstruction in all iterations after the first.This PR adds
marginal=seq_kwargs['marginal_sequences']to the three affected call sites, matching the pattern already used in the initial call at line 238. A regression test monkeypatchesinfer_ancestral_sequencesto record everymarginalargument value and asserts that none areFalsewhen marginal mode is requested. Without the fix, the test fails at call #5; with the fix, all calls correctly use marginal reconstruction.Work items
marginal=argument to the post-rerootinfer_ancestral_sequencescall (input branch-length mode)marginal=argument to both iteration-loopinfer_ancestral_sequencescallstest_marginal_mode_used_in_all_iterations