test: add failing repro for non-monotone skyline segment boundaries

packages/treetime/src/coalescent/__tests__/mod.rs

@@ -7,4 +7,5 @@ mod test_integration;
 mod test_lineage_dynamics;
 mod test_optimize_tc;
 mod test_skyline;
+mod test_skyline_repro_boundaries;
 mod test_total_lh;

packages/treetime/src/coalescent/__tests__/test_skyline_repro_boundaries.rs

@@ -0,0 +1,58 @@
+#[cfg(test)]
+mod tests {
+  use crate::clock::date_constraints::load_date_constraints;
+  use crate::coalescent::skyline::{SkylineParams, optimize_skyline};
+  use crate::partition::timetree::GraphTimetree;
+  use eyre::Report;
+  use maplit::btreemap;
+  use treetime_io::dates_csv::{DateConstraint, DatesMap};
+  use treetime_io::nwk::nwk_read_str;
+
+  const SMALL_TREE_NWK: &str = "((leaf1:1.0,leaf2:1.0)internal1:1.0,leaf3:1.0)root:1.0;";
+
+  fn small_tree_dates() -> DatesMap {
+    btreemap! {
+      "root".to_owned() => Some(DateConstraint::exact(2000.0)),
+      "internal1".to_owned() => Some(DateConstraint::exact(2005.0)),
+      "leaf1".to_owned() => Some(DateConstraint::exact(2010.0)),
+      "leaf2".to_owned() => Some(DateConstraint::exact(2010.0)),
+      "leaf3".to_owned() => Some(DateConstraint::exact(2012.0)),
+    }
+  }
+
+  fn small_tree() -> Result<GraphTimetree, Report> {
+    let graph = nwk_read_str(SMALL_TREE_NWK)?;
+    load_date_constraints(&small_tree_dates(), &graph)?;
+    Ok(graph)
+  }
+
+  // Counterexample for "every segment owns mergers" / ascending boundaries.
+  //
+  // The small tree has only two distinct merger (internal-node) times, 2000 and
+  // 2005, but this requests 5 segments. `merger_quantile_boundaries` clamps each
+  // duplicate candidate against the previous boundary instead of coalescing merger
+  // events, so the returned grid is `[2000, 2000, 2000, 2002.5, 2005, 2012]`: two
+  // zero-width segments carrying no mergers. Zero-width segments are unreachable via
+  // `segment_index`, yet their `z_i` still participate in the smoothing penalty, so
+  // the fitted trajectory depends on phantom transitions.
+  //
+  // Expected: strictly increasing segment boundaries, or a rejected `n_points` when
+  // the tree cannot support that many merger-owning segments.
+  #[test]
+  fn test_skyline_segment_boundaries_strictly_increasing() -> Result<(), Report> {
+    let params = SkylineParams {
+      n_points: 5,
+      ..SkylineParams::default()
+    };
+
+    let result = optimize_skyline(&small_tree()?, &params)?;
+    let bounds = result.segment_boundaries.to_vec();
+    let strictly_increasing = bounds.windows(2).all(|w| w[1] > w[0]);
+
+    assert!(
+      strictly_increasing,
+      "segment boundaries must be strictly increasing (every segment spans a positive interval), got {bounds:?}"
+    );
+    Ok(())
+  }
+}