test: add failing repro for skyline solver reporting non-convergence as success

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_nonconvergence;
 mod test_total_lh;

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

@@ -0,0 +1,56 @@
+#[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 "the solve is exact and cannot fail numerically".
+  //
+  // `solve_log_tc` returns `Ok(z)` unconditionally after its iteration loop. With
+  // `max_iter = 0` it performs no Newton step and returns the decoupled per-segment
+  // warm start, which for the default (positive) stiffness is not the regularized
+  // optimum. `optimize_skyline` still returns a successful `SkylineResult`, so a
+  // caller cannot distinguish an optimized skyline from an un-optimized one, and
+  // the pipeline's fail-loud contract cannot fire because no error is raised.
+  //
+  // Expected: a solve that ran no iterations (or that exhausts `max_iter` above the
+  // gradient tolerance) returns an error rather than reporting success.
+  #[test]
+  fn test_skyline_zero_iterations_reported_as_success() -> Result<(), Report> {
+    let params = SkylineParams {
+      n_points: 3,
+      max_iter: 0,
+      ..SkylineParams::default()
+    };
+
+    let result = optimize_skyline(&small_tree()?, &params);
+
+    assert!(
+      result.is_err(),
+      "optimize_skyline with max_iter=0 must not report success on a multi-segment regularized solve, but returned Ok"
+    );
+    Ok(())
+  }
+}