feat(analysis): per-step secondary multiplicity plots
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Replace the event-level n_sec confusion matrix with two step-resolved secondary-multiplicity comparisons: - sec_count_per_step: overlay histogram of how many secondaries a single step emits, rollout series vs reference. - sec_count_per_step_by_species: heatmap of per-step multiplicity of one species (zero row included) against species, drawn as one panel per rollout plus a reference panel, raw counts on a log color scale. Both are backed by a new sources.secondaries_by_step view, which tags each secondary with its emitting step — (event_id, parent_id, birth position) on the rollout side, the row index on the reference side — so neither plot needs a join against the step frame. Steps that emitted nothing are recovered by subtraction from the chunk's step count, keeping both specs sum-mergeable across condor chunks. The rollout multiplicity is derived from the actual secondary birth rows rather than the n_sec_pred column, which records the predicted count before the per-event max-tracks cap. _render_heatmap gained reference-panel and log-color support; marginal_distance_summary sets neither key and is unchanged. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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@@ -304,13 +304,15 @@ def test_render_one_of_each_kind(tmp_path: Path):
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"hm1",
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"secondaries",
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"heatmap",
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"Confusion (single rollout)",
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"Heatmap (single rollout)",
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"predicted",
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{
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"series": {"flow": [[1, 0], [0, 1]]},
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"reference": [[2, 0], [0, 1]],
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"row_labels": ["0", "1+"],
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"col_labels": ["0", "1+"],
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"cbar_label": "count",
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"log_color": True,
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},
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),
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]
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